@online{center_for_history_and_new_media_zotero_????, title = {Zotero Quick Start Guide}, url = {http://zotero.org/support/quick_start_guide}, author = {{Center for History and New Media}} } @article{adams_application_2015, title = {Application of Fragment-Based Screening to the Design of Inhibitors of Escherichia coli {DsbA}}, volume = {127}, issn = {1521-3757}, url = {http://onlinelibrary.wiley.com/doi/10.1002/ange.201410341/abstract}, doi = {10.1002/ange.201410341}, abstract = {The thiol-disulfide oxidoreductase enzyme {DsbA} catalyzes the formation of disulfide bonds in the periplasm of Gram-negative bacteria. {DsbA} substrates include proteins involved in bacterial virulence. In the absence of {DsbA}, many of these proteins do not fold correctly, which renders the bacteria avirulent. Thus {DsbA} is a critical mediator of virulence and inhibitors may act as antivirulence agents. Biophysical screening has been employed to identify fragments that bind to {DsbA} from Escherichia coli. Elaboration of one of these fragments produced compounds that inhibit {DsbA} activity in vitro. In cell-based assays, the compounds inhibit bacterial motility, but have no effect on growth in liquid culture, which is consistent with selective inhibition of {DsbA}. Crystal structures of inhibitors bound to {DsbA} indicate that they bind adjacent to the active site. Together, the data suggest that {DsbA} may be amenable to the development of novel antibacterial compounds that act by inhibiting bacterial virulence.}, pages = {2207--2212}, number = {7}, journaltitle = {Angewandte Chemie}, shortjournal = {Angew. Chem.}, author = {Adams, Luke A. and Sharma, Pooja and Mohanty, Biswaranjan and Ilyichova, Olga V. and Mulcair, Mark D. and Williams, Martin L. and Gleeson, Ellen C. and Totsika, Makrina and Doak, Bradley C. and Caria, Sofia and Rimmer, Kieran and Horne, James and Shouldice, Stephen R. and Vazirani, Mansha and Headey, Stephen J. and Plumb, Brent R. and Martin, Jennifer L. and Heras, Begoña and Simpson, Jamie S. and Scanlon, Martin J.}, urldate = {2017-05-01}, date = {2015-02-09}, langid = {english}, keywords = {bakterielle Ansteckungskraft, bakterielle Ansteckungskraft, Ecdsba, Ecdsba, Fragment-basierte Wirkstoff-Forschung, Fragment-basierte Wirkstoff-Forschung, Medizinische Chemie, Medizinische Chemie, Wirkstoff-Design, Wirkstoff-Design}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C92ME3DU\\Adams et al. - 2015 - Application of Fragment-Based Screening to the Des:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZRTWZVH4\\Adams et al. - 2015 - Application of Fragment-Based Screening to the Des.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C92ME3DU\\Adams et al. - 2015 - Application of Fragment-Based Screening to the Des:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TXBWX8CQ\\Adams et al. - 2015 - Application of Fragment-Based Screening to the Des.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HWZ7AFGS\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PFZ3W8P9\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HWZ7AFGS\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RNACBW9R\\abstract.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C92ME3DU\\Adams et al. - 2015 - Application of Fragment-Based Screening to the Des.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HWZ7AFGS\\abstract.html:text/html} } @article{liang_uptake_2015, title = {Uptake of the butyrate receptors, {GPR}41 and {GPR}43, in lipidic bicontinuous cubic phases suitable for in meso crystallization}, volume = {441}, issn = {0021-9797}, url = {http://www.sciencedirect.com/science/article/pii/S0021979714008534}, doi = {10.1016/j.jcis.2014.11.006}, abstract = {The butyrate G-protein coupled receptors ({GPCRs}), {GPR}41 and {GPR}43, have been implicated in colorectal cancer and leptin production. To date their function has not been elucidated as low levels of protein expression and difficulties in producing diffraction quality crystals have hindered their structural determination. In meso crystallization, which uses an artificial lipid membrane matrix to facilitate crystal growth, is becoming an increasingly successful crystallization technique, particularly for {GPCRs}. We report herein the lipid membrane matrix structural characterization for {GPR}41 and {GPR}43 within two lipid self-assembly systems (monoolein and phytantriol) commonly used for in meso crystallization and comment on their suitability for crystallizing these {GPCRs}. Synchrotron small angle X-ray scattering ({SAXS}) studies were used to determine the initial phase and uptake of these receptors within the lipid matrix and investigate the role of cholesterol in this process. The self-assembled lipid nanostructure was retained in the presence of {GPR}43 for both lipids but was destabilized for {GPR}41 in the phytantriol lipid system. The structural changes to the lipid matrix upon protein incorporation were greater for cholesterol-doped systems, potentially indicative of increased receptor uptake.}, pages = {78--84}, journaltitle = {Journal of Colloid and Interface Science}, shortjournal = {Journal of Colloid and Interface Science}, author = {Liang, Yi-Lynn and Conn, Charlotte E. and Drummond, Calum J. and Darmanin, Connie}, urldate = {2017-05-01}, date = {2015-03-01}, keywords = {Bicontinuous cubic phase, Bicontinuous cubic phase, Butyrate receptor, Butyrate receptor, {GPCR}, {GPCR}, {GPR}41, {GPR}41, {GPR}43, {GPR}43, In meso crystallization, In meso crystallization, Monoolein, Monoolein, Phytantriol, Phytantriol}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\55UTWWKR\\S0021979714008534:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6GHFW3PG\\S0021979714008534.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\55UTWWKR\\S0021979714008534:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NCBHNUXK\\S0021979714008534.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B9EUF96G\\Liang et al. - 2015 - Uptake of the butyrate receptors, GPR41 and GPR43,:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V2FV784A\\Liang et al. - 2015 - Uptake of the butyrate receptors, GPR41 and GPR43,.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B9EUF96G\\Liang et al. - 2015 - Uptake of the butyrate receptors, GPR41 and GPR43,:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SF2PQBSX\\Liang et al. - 2015 - Uptake of the butyrate receptors, GPR41 and GPR43,.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\F4X396E4\\S0021979714008534:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KSUI7GZQ\\S0021979714008534.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\F4X396E4\\S0021979714008534:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2N96GDT8\\S0021979714008534.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NU3ZXXXB\\Liang et al. - 2015 - Uptake of the butyrate receptors, GPR41 and GPR43,:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IH5PZ8GN\\Liang et al. - 2015 - Uptake of the butyrate receptors, GPR41 and GPR43,.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NU3ZXXXB\\Liang et al. - 2015 - Uptake of the butyrate receptors, GPR41 and GPR43,:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WT9XWF5S\\Liang et al. - 2015 - Uptake of the butyrate receptors, GPR41 and GPR43,.pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B9EUF96G\\Liang et al. - 2015 - Uptake of the butyrate receptors, GPR41 and GPR43,.pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NU3ZXXXB\\Liang et al. - 2015 - Uptake of the butyrate receptors, GPR41 and GPR43,.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\F4X396E4\\S0021979714008534.html:text/html;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\55UTWWKR\\S0021979714008534.html:text/html} } @article{xu_lrig1_2015, title = {{LRIG}1 Extracellular Domain: Structure and Function Analysis}, volume = {427}, issn = {0022-2836}, url = {http://www.sciencedirect.com/science/article/pii/S0022283615001734}, doi = {10.1016/j.jmb.2015.03.001}, shorttitle = {{LRIG}1 Extracellular Domain}, abstract = {We have expressed and purified three soluble fragments of the human {LRIG}1-{ECD} (extracellular domain): the {LRIG}1-{LRR} (leucine-rich repeat) domain, the {LRIG}1-3Ig (immunoglobulin-like) domain, and the {LRIG}1-{LRR}-1Ig fragment using baculovirus vectors in insect cells. The two {LRIG}1 domains crystallised so that we have been able to determine the three-dimensional structures at 2.3 Å resolution. We developed a three-dimensional structure for the {LRIG}1-{ECD} using homology modelling based on the {LINGO}-1 structure. The {LRIG}1-{LRR} domain and the {LRIG}1-{LRR}-1Ig fragment are monomers in solution, whereas the {LRIG}1-3Ig domain appears to be dimeric. We could not detect any binding of the {LRIG}1 domains or the {LRIG}1-{LRR}-1Ig fragment to the {EGF} receptor ({EGFR}), either in solution using biosensor analysis or when the {EGFR} was expressed on the cell surface. The {FLAG}-tagged {LRIG}1-{LRR}-1Ig fragment binds weakly to colon cancer cells regardless of the presence of {EGFRs}. Similarly, neither the soluble {LRIG}1-{LRR} nor the {LRIG}1-3Ig domains nor the full-length {LRIG}1 co-expressed in {HEK}293 cells inhibited ligand-stimulated activation of cell-surface {EGFR}.}, pages = {1934--1948}, number = {10}, journaltitle = {Journal of Molecular Biology}, shortjournal = {Journal of Molecular Biology}, author = {Xu, Yibin and Soo, Priscilla and Walker, Francesca and Zhang, Hui Hua and Redpath, Nicholas and Tan, Chin Wee and Nicola, Nicos A. and Adams, Timothy E. and Garrett, Thomas P. and Zhang, Jian-Guo and Burgess, Antony W.}, urldate = {2017-05-01}, date = {2015-05-22}, keywords = {{EGFR} inhibition, {EGFR} inhibition, leucine-rich repeat domain, leucine-rich repeat domain, {LINGO}-1, {LINGO}-1, stem cell marker, stem cell marker}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\G299MKKU\\Xu et al. - 2015 - LRIG1 Extracellular Domain Structure and Function:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\X4GZDDEV\\Xu et al. - 2015 - LRIG1 Extracellular Domain Structure and Function.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\G299MKKU\\Xu et al. - 2015 - LRIG1 Extracellular Domain Structure and Function:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\H5INGW88\\Xu et al. - 2015 - LRIG1 Extracellular Domain Structure and Function.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QTXIUMDG\\S0022283615001734:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HUJDFAKN\\S0022283615001734.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QTXIUMDG\\S0022283615001734:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I3HA8QSX\\S0022283615001734.html:text/html;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\G299MKKU\\Xu et al. - 2015 - LRIG1 Extracellular Domain Structure and Function.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QTXIUMDG\\S0022283615001734.html:text/html} } @article{kershaw_notch_2015, title = {Notch ligand delta-like1: X-ray crystal structure and binding affinity}, volume = {468}, rights = {© The Authors Journal compilation © 2015 Biochemical Society}, issn = {0264-6021, 1470-8728}, url = {http://www.biochemj.org/content/468/1/159}, doi = {10.1042/BJ20150010}, shorttitle = {Notch ligand delta-like1}, abstract = {The Notch pathway is a fundamental signalling system in most multicellular animals. We have determined the X-ray crystal structure of the extracellular domain of the Notch ligand delta-like ligand-1 (Dll-1). The structure incorporates the N-terminal C2 domain, receptor-binding {DSL} domain and the first six (of eight) {EGF} (epidermal growth factor)-like repeats, which form a highly extended conformation, confirmed by analytical ultracentrifugation. Comparison of our structure with a fragment of Jagged1 ligand allows us to dissect the similarities and differences between the ligand families. Differences in the C2 domains of Dll-1 and Jagged1 suggest their lipid-binding properties are likely to differ. A conserved hydrophobic patch on the surface of both Dll-1 and Jagged1 provides a likely receptor-interaction site that is common to both ligands. We also explore the binding affinity of Dll-1 for a fragment of Notch1 using different techniques. Apparent binding affinities vary when different techniques are used, explaining discrepancies in the literature. Using analytical ultracentrifugation, we perform for the first time binding analyses where both receptor and ligand are in solution, which confirms a Kd of 10 μM for this interaction.}, pages = {159--166}, number = {1}, journaltitle = {Biochemical Journal}, author = {Kershaw, Nadia J. and Church, Nicole L. and Griffin, Michael D. W. and Luo, Cindy S. and Adams, Timothy E. and Burgess, Antony W.}, urldate = {2017-05-01}, date = {2015-05-15}, langid = {english}, pmid = {25715738}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3R8NNB7B\\159:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IXM3EQRH\\159.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3R8NNB7B\\159:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2RKCSUEV\\159.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BC8DXAP2\\Kershaw et al. - 2015 - Notch ligand delta-like1 X-ray crystal structure:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HBK6R3BW\\Kershaw et al. - 2015 - Notch ligand delta-like1 X-ray crystal structure .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BC8DXAP2\\Kershaw et al. - 2015 - Notch ligand delta-like1 X-ray crystal structure:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\28XEWRU7\\Kershaw et al. - 2015 - Notch ligand delta-like1 X-ray crystal structure .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BZA25JQ3\\Kershaw et al. - 2015 - Notch ligand delta-like1 X-ray crystal structure:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4XUS3V7E\\Kershaw et al. - 2015 - Notch ligand delta-like1 X-ray crystal structure .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BZA25JQ3\\Kershaw et al. - 2015 - Notch ligand delta-like1 X-ray crystal structure:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5ET4XGHK\\Kershaw et al. - 2015 - Notch ligand delta-like1 X-ray crystal structure .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NNX3VQGC\\159:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5QGPFD47\\159.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NNX3VQGC\\159:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z2UZAKKG\\159.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BZA25JQ3\\Kershaw et al. - 2015 - Notch ligand delta-like1 X-ray crystal structure .pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BC8DXAP2\\Kershaw et al. - 2015 - Notch ligand delta-like1 X-ray crystal structure .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NNX3VQGC\\159.html:text/html;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3R8NNB7B\\159.html:text/html} } @article{robin_crystal_2015, title = {Crystal structure of Bax bound to the {BH}3 peptide of Bim identifies important contacts for interaction}, volume = {6}, rights = {© 2015 Nature Publishing Group}, url = {http://www.nature.com/cddis/journal/v6/n7/full/cddis2015141a.html}, doi = {10.1038/cddis.2015.141}, abstract = {The {BH}3-only protein Bim is a potent direct activator of the proapoptotic effector protein Bax, but the structural basis for its activity has remained poorly defined. Here we describe the crystal structure of the {BimBH}3 peptide bound to {BaxΔC}26 and structure-based mutagenesis studies. Similar to {BidBH}3, the {BimBH}3 peptide binds into the cognate surface groove of Bax using the conserved hydrophobic {BH}3 residues h1–h4. However, the structure and mutagenesis data show that Bim is less reliant compared with Bid on its ‘h0’ residues for activating Bax and that a single amino-acid difference between Bim and Bid encodes a fivefold difference in Bax-binding potency. Similar to the structures of {BidBH}3 and {BaxBH}3 bound to {BaxΔC}21, the structure of the {BimBH}3 complex with {BaxΔC} displays a cavity surrounded by Bax α1, α2, α5 and α8. Our results are consistent with a model in which binding of an activator {BH}3 domain to the Bax groove initiates separation of its core (α2–α5) and latch (α6–α8) domains, enabling its subsequent dimerisation and the permeabilisation of the mitochondrial outer membrane.}, pages = {e1809}, number = {7}, journaltitle = {Cell Death \& Disease}, shortjournal = {Cell Death Dis}, author = {Robin, A. Y. and Krishna Kumar, K. and Westphal, D. and Wardak, A. Z. and Thompson, G. V. and Dewson, G. and Colman, P. M. and Czabotar, P. E.}, urldate = {2017-05-01}, date = {2015-07-09}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5ZWPP79I\\cddis2015141a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TC8X4PWS\\cddis2015141a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5ZWPP79I\\cddis2015141a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J3MWEQ96\\cddis2015141a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NHIB35AH\\Robin et al. - 2015 - Crystal structure of Bax bound to the BH3 peptide:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P59SXF3B\\Robin et al. - 2015 - Crystal structure of Bax bound to the BH3 peptide .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NHIB35AH\\Robin et al. - 2015 - Crystal structure of Bax bound to the BH3 peptide:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2PH2GBPA\\Robin et al. - 2015 - Crystal structure of Bax bound to the BH3 peptide .pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NHIB35AH\\Robin et al. - 2015 - Crystal structure of Bax bound to the BH3 peptide .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5ZWPP79I\\cddis2015141a.html:text/html} } @article{warden_rational_2015, title = {Rational engineering of a mesohalophilic carbonic anhydrase to an extreme halotolerant biocatalyst}, volume = {6}, issn = {2041-1723}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4703901/}, doi = {10.1038/ncomms10278}, abstract = {Enzymes expressed by highly salt-tolerant organisms show many modifications compared with salt-affected counterparts including biased amino acid and lower α-helix content, lower solvent accessibility and negative surface charge. Here, we show that halotolerance can be generated in an enzyme solely by modifying surface residues. Rational design of carbonic anhydrase {II} is undertaken in three stages replacing 18 residues in total, crystal structures confirm changes are confined to surface residues. Catalytic activities and thermal unfolding temperatures of the designed enzymes increase at high salt concentrations demonstrating their shift to halotolerance, whereas the opposite response is found in the wild-type enzyme. Molecular dynamics calculations reveal a key role for sodium ions in increasing halotolerant enzyme stability largely through interactions with the highly ordered first Na+ hydration shell. For the first time, an approach to generate extreme halotolerance, a trait with broad application in industrial biocatalysis, in a wild-type enzyme is demonstrated., Halophilic organisms thrive in high salt conditions and express proteins that display desirable characteristics for industrial applications. Here, the authors use a rational design approach to transform wild-type carbonic anhydrase into a strongly halophilic enzyme.}, journaltitle = {Nature Communications}, shortjournal = {Nat Commun}, author = {Warden, Andrew C. and Williams, Michelle and Peat, Thomas S. and Seabrook, Shane A. and Newman, Janet and Dojchinov, Greg and Haritos, Victoria S.}, urldate = {2017-05-01}, date = {2015-12-21}, pmid = {26687908}, pmcid = {PMC4703901}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GECUPANU\\Warden et al. - 2015 - Rational engineering of a mesohalophilic carbonic:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\84EK3H3K\\Warden et al. - 2015 - Rational engineering of a mesohalophilic carbonic .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GECUPANU\\Warden et al. - 2015 - Rational engineering of a mesohalophilic carbonic:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KE7Z8PGQ\\Warden et al. - 2015 - Rational engineering of a mesohalophilic carbonic .pdf:application/pdf;PubMed Central Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GECUPANU\\Warden et al. - 2015 - Rational engineering of a mesohalophilic carbonic .pdf:application/pdf} } @article{baxter_tomato_2015, title = {The Tomato Defensin {TPP}3 Binds Phosphatidylinositol (4,5)-Bisphosphate via a Conserved Dimeric Cationic Grip Conformation To Mediate Cell Lysis}, volume = {35}, issn = {0270-7306, 1098-5549}, url = {http://mcb.asm.org/content/35/11/1964}, doi = {10.1128/MCB.00282-15}, abstract = {Defensins are a class of ubiquitously expressed cationic antimicrobial peptides ({CAPs}) that play an important role in innate defense. Plant defensins are active against a broad range of microbial pathogens and act via multiple mechanisms, including cell membrane permeabilization. The cytolytic activity of defensins has been proposed to involve interaction with specific lipid components in the target cell wall or membrane and defensin oligomerization. Indeed, the defensin Nicotiana alata defensin 1 ({NaD}1) binds to a broad range of membrane phosphatidylinositol phosphates and forms an oligomeric complex with phosphatidylinositol (4,5)-bisphosphate ({PIP}2) that facilitates membrane lysis of both mammalian tumor and fungal cells. Here, we report that the tomato defensin {TPP}3 has a unique lipid binding profile that is specific for {PIP}2 with which it forms an oligomeric complex that is critical for cytolytic activity. Structural characterization of {TPP}3 by X-ray crystallography and site-directed mutagenesis demonstrated that it forms a dimer in a “cationic grip” conformation that specifically accommodates the head group of {PIP}2 to mediate cooperative higher-order oligomerization and subsequent membrane permeabilization. These findings suggest that certain plant defensins are innate immune receptors for phospholipids and adopt conserved dimeric configurations to mediate {PIP}2 binding and membrane permeabilization. This mechanism of innate defense may be conserved across defensins from different species.}, pages = {1964--1978}, number = {11}, journaltitle = {Molecular and Cellular Biology}, shortjournal = {Mol. Cell. Biol.}, author = {Baxter, Amy A. and Richter, Viviane and Lay, Fung T. and Poon, Ivan K. H. and Adda, Christopher G. and Veneer, Prem K. and Phan, Thanh Kha and Bleackley, Mark R. and Anderson, Marilyn A. and Kvansakul, Marc and Hulett, Mark D.}, urldate = {2017-05-01}, date = {2015-06-01}, langid = {english}, pmid = {25802281}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6TBFADEX\\1964:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3HS2EZTB\\1964.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6TBFADEX\\1964:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FDVB4AZ7\\1964.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7RF7FK65\\Baxter et al. - 2015 - The Tomato Defensin TPP3 Binds Phosphatidylinosito:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CPECRC5A\\Baxter et al. - 2015 - The Tomato Defensin TPP3 Binds Phosphatidylinosito.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7RF7FK65\\Baxter et al. - 2015 - The Tomato Defensin TPP3 Binds Phosphatidylinosito:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GKVBR83D\\Baxter et al. - 2015 - The Tomato Defensin TPP3 Binds Phosphatidylinosito.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IC9PHTEE\\1964:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T5E8BZ7K\\1964.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IC9PHTEE\\1964:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QCB42GZJ\\1964.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SDJUAQNA\\Baxter et al. - 2015 - The Tomato Defensin TPP3 Binds Phosphatidylinosito:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N5XRDHCE\\Baxter et al. - 2015 - The Tomato Defensin TPP3 Binds Phosphatidylinosito.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SDJUAQNA\\Baxter et al. - 2015 - The Tomato Defensin TPP3 Binds Phosphatidylinosito:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RSMKNQHM\\Baxter et al. - 2015 - The Tomato Defensin TPP3 Binds Phosphatidylinosito.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7RF7FK65\\Baxter et al. - 2015 - The Tomato Defensin TPP3 Binds Phosphatidylinosito.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SDJUAQNA\\Baxter et al. - 2015 - The Tomato Defensin TPP3 Binds Phosphatidylinosito.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IC9PHTEE\\1964.html:text/html;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6TBFADEX\\1964.html:text/html} } @article{mobbs_determinants_2015, title = {Determinants of oligosaccharide specificity of the carbohydrate-binding modules of {AMP}-activated protein kinase}, volume = {468}, rights = {© The Authors Journal compilation © 2015 Biochemical Society}, issn = {0264-6021, 1470-8728}, url = {http://www.biochemj.org/content/468/2/245}, doi = {10.1042/BJ20150270}, abstract = {{AMP}-activated protein kinase ({AMPK}) is an αβγ heterotrimer that is important in regulating energy metabolism in all eukaryotes. The β-subunit exists in two isoforms (β1 and β2) and contains a carbohydrate-binding module ({CBM}) that interacts with glycogen. The two {CBM} isoforms (β1- and β2-{CBM}) are near identical in sequence and structure, yet show differences in carbohydrate-binding affinity. β2-{CBM} binds linear carbohydrates with 4-fold greater affinity than β1-{CBM} and binds single α1,6-branched carbohydrates up to 30-fold tighter. To understand these affinity differences, especially for branched carbohydrates, we determined the {NMR} solution structure of β2-{CBM} in complex with the single α1,6-branched carbohydrate glucosyl-β-cyclodextrin ({gBCD}) which supported the dynamic nature of the binding site, but resonance broadening prevented defining where the α1,6 branch bound. We therefore solved the X-ray crystal structures of β1- and β2-{CBM}, in complex with {gBCD}, to 1.7 and 2.0 Å (1 Å=0.1 nm) respectively. The additional threonine (Thr101) of β2-{CBM} expands the size of the surrounding loop, creating a pocket that accommodates the α1,6 branch. Hydrogen bonds are formed between the α1,6 branch and the backbone of Trp99 and Lys102 side chain of β2-{CBM}. In contrast, the α1,6 branch could not be observed in the β1-{CBM} structure, suggesting that it does not form a specific interaction. The orientation of {gBCD} bound to β1- and β2-{CBM} is supported by thermodynamic and kinetic data obtained through isothermal titration calorimetry ({ITC}) and {NMR}. These results suggest that {AMPK} containing the muscle-specific β2-isoform may have greater affinity for partially degraded glycogen.}, pages = {245--257}, number = {2}, journaltitle = {Biochemical Journal}, author = {Mobbs, Jesse I. and Koay, Ann and Paolo, Alex Di and Bieri, Michael and Petrie, Emma J. and Gorman, Michael A. and Doughty, Larissa and Parker, Michael W. and Stapleton, David I. and Griffin, Michael D. W. and Gooley, Paul R.}, urldate = {2017-05-01}, date = {2015-06-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A4T8R2NH\\Mobbs et al. - 2015 - Determinants of oligosaccharide specificity of the:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\63WM6FI4\\Mobbs et al. - 2015 - Determinants of oligosaccharide specificity of the.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A4T8R2NH\\Mobbs et al. - 2015 - Determinants of oligosaccharide specificity of the:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5EGWI96A\\Mobbs et al. - 2015 - Determinants of oligosaccharide specificity of the.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KWUUH277\\245:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TJ97M8HI\\245.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KWUUH277\\245:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8MDX7D5J\\245.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A4T8R2NH\\Mobbs et al. - 2015 - Determinants of oligosaccharide specificity of the.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KWUUH277\\245.html:text/html} } @article{marshall_variola_2015, title = {Variola virus F1L is a Bcl-2-like protein that unlike its vaccinia virus counterpart inhibits apoptosis independent of Bim}, volume = {6}, rights = {© 2015 Nature Publishing Group}, url = {http://www.nature.com/cddis/journal/v6/n3/abs/cddis201552a.html}, doi = {10.1038/cddis.2015.52}, abstract = {Subversion of host cell apoptosis is an important survival strategy for viruses to ensure their own proliferation and survival. Certain viruses express proteins homologous in sequence, structure and function to mammalian pro-survival B-cell lymphoma 2 (Bcl-2) proteins, which prevent rapid clearance of infected host cells. In vaccinia virus ({VV}), the virulence factor F1L was shown to be a potent inhibitor of apoptosis that functions primarily be engaging pro-apoptotic Bim. Variola virus ({VAR}), the causative agent of smallpox, harbors a homolog of F1L of unknown function. We show that {VAR} F1L is a potent inhibitor of apoptosis, and unlike all other characterized anti-apoptotic Bcl-2 family members lacks affinity for the Bim Bcl-2 homology 3 ({BH}3) domain. Instead, {VAR} F1L engages Bid {BH}3 as well as Bak and Bax {BH}3 domains. Unlike its {VV} homolog, variola F1L only protects against Bax-mediated apoptosis in cellular assays. Crystal structures of variola F1L bound to Bid and Bak {BH}3 domains reveal that variola F1L forms a domain-swapped Bcl-2 fold, which accommodates Bid and Bak {BH}3 in the canonical Bcl-2-binding groove, in a manner similar to {VV} F1L. Despite the observed conservation of structure and sequence, variola F1L inhibits apoptosis using a startlingly different mechanism compared with its {VV} counterpart. Our results suggest that unlike during {VV} infection, Bim neutralization may not be required during {VAR} infection. As molecular determinants for the human-specific tropism of {VAR} remain essentially unknown, identification of a different mechanism of action and utilization of host factors used by a {VAR} virulence factor compared with its {VV} homolog suggest that studying {VAR} directly may be essential to understand its unique tropism.}, pages = {e1680}, number = {3}, journaltitle = {Cell Death \& Disease}, shortjournal = {Cell Death Dis}, author = {Marshall, B. and Puthalakath, H. and Caria, S. and Chugh, S. and Doerflinger, M. and Colman, P. M. and Kvansakul, M.}, urldate = {2017-05-01}, date = {2015-03-12}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NCKEZJRJ\\cddis201552a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IPK77Z2J\\cddis201552a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NCKEZJRJ\\cddis201552a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IHD8XTPX\\cddis201552a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SZS8NXRP\\Marshall et al. - 2015 - Variola virus F1L is a Bcl-2-like protein that unl:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZUGXJ5BB\\Marshall et al. - 2015 - Variola virus F1L is a Bcl-2-like protein that unl.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SZS8NXRP\\Marshall et al. - 2015 - Variola virus F1L is a Bcl-2-like protein that unl:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BG9ABZGH\\Marshall et al. - 2015 - Variola virus F1L is a Bcl-2-like protein that unl.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XHB948P9\\cddis201552a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SVX2XHTV\\cddis201552a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XHB948P9\\cddis201552a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VC56U5RV\\cddis201552a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XXS8XE3J\\Marshall et al. - 2015 - Variola virus F1L is a Bcl-2-like protein that unl:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MS78RBZC\\Marshall et al. - 2015 - Variola virus F1L is a Bcl-2-like protein that unl.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XXS8XE3J\\Marshall et al. - 2015 - Variola virus F1L is a Bcl-2-like protein that unl:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BVPH6AHH\\Marshall et al. - 2015 - Variola virus F1L is a Bcl-2-like protein that unl.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SZS8NXRP\\Marshall et al. - 2015 - Variola virus F1L is a Bcl-2-like protein that unl.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XXS8XE3J\\Marshall et al. - 2015 - Variola virus F1L is a Bcl-2-like protein that unl.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XHB948P9\\cddis201552a.html:text/html;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NCKEZJRJ\\cddis201552a.html:text/html} } @article{burton_structural_2015, title = {Structural basis of Deerpox virus-mediated inhibition of apoptosis}, volume = {71}, rights = {Copyright (c) 2015 International Union of Crystallography}, issn = {1399-0047}, url = {http://scripts.iucr.org/cgi-bin/paper?cb5081}, doi = {10.1107/S1399004715009402}, abstract = {Apoptosis is a key innate defence mechanism to eliminate virally infected cells. To counteract premature host-cell apoptosis, poxviruses have evolved numerous molecular strategies, including the use of Bcl-2 proteins, to ensure their own survival. Here, it is reported that the Deerpox virus inhibitor of apoptosis, {DPV}022, only engages a highly restricted set of death-inducing Bcl-2 proteins, including Bim, Bax and Bak, with modest affinities. Structural analysis reveals that {DPV}022 adopts a Bcl-2 fold with a dimeric domain-swapped topology and binds pro-death Bcl-2 proteins via two conserved ligand-binding grooves found on opposite sides of the dimer. Structures of {DPV}022 bound to Bim, Bak and Bax {BH}3 domains reveal that a partial obstruction of the binding groove is likely to be responsible for the modest affinities of {DPV}022 for {BH}3 domains. These findings reveal that domain-swapped dimeric Bcl-2 folds are not unusual and may be found more widely in viruses. Furthermore, the modest affinities of {DPV}022 for pro-death Bcl-2 proteins suggest that two distinct classes of anti-apoptotic viral Bcl-2 proteins exist: those that are monomeric and tightly bind a range of death-inducing Bcl-2 proteins, and others such as {DPV}022 that are dimeric and only bind a very limited number of death-inducing Bcl-2 proteins with modest affinities.}, pages = {1593--1603}, number = {8}, journaltitle = {Acta Crystallographica Section D: Biological Crystallography}, shortjournal = {Acta Cryst D}, author = {Burton, D. R. and Caria, S. and Marshall, B. and Barry, M. and Kvansakul, M.}, urldate = {2017-05-01}, date = {2015-08-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5RB8V2AZ\\Burton et al. - 2015 - Structural basis of Deerpox virus-mediated inhibit:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QKHE55Z8\\Burton et al. - 2015 - Structural basis of Deerpox virus-mediated inhibit.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5RB8V2AZ\\Burton et al. - 2015 - Structural basis of Deerpox virus-mediated inhibit:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6B9NBI7X\\Burton et al. - 2015 - Structural basis of Deerpox virus-mediated inhibit.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GVNSHJMC\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WCKFEPC8\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GVNSHJMC\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9BMXS6M5\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5RB8V2AZ\\Burton et al. - 2015 - Structural basis of Deerpox virus-mediated inhibit.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GVNSHJMC\\paper.html:text/html} } @article{ren_structural_2016, title = {Structural and functional characterisation of ferret interleukin-2}, volume = {55}, issn = {0145-305X}, url = {http://www.sciencedirect.com/science/article/pii/S0145305X15300549}, doi = {10.1016/j.dci.2015.10.007}, abstract = {While the ferret is a valuable animal model for a number of human viral infections, such as influenza, Hendra and Nipah, evaluating the cellular immune response following infection has been hampered by the lack of a number of species-specific immunological reagents. Interleukin 2 ({IL}-2) is one such key cytokine. Ferret recombinant {IL}-2 incorporating a C-terminal histidine tag was expressed and purified and the three-dimensional structure solved and refined at 1.89 Å by X-ray crystallography, which represents the highest resolution and first non-human {IL}-2 structure. While ferret {IL}-2 displays the classic cytokine fold of the four-helix bundle structure, conformational flexibility was observed at the second helix and its neighbouring region in the bundle, which may result in the disruption of the spatial arrangement of residues involved in receptor binding interactions, implicating subtle differences between ferret and human {IL}-2 when initiating biological functions. Ferret recombinant {IL}-2 stimulated the proliferation of ferret lymph node cells and induced the expression of {mRNA} for {IFN}-γ and Granzyme A.}, pages = {32--38}, journaltitle = {Developmental \& Comparative Immunology}, shortjournal = {Developmental \& Comparative Immunology}, author = {Ren, Bin and {McKinstry}, William J. and Pham, Tam and Newman, Janet and Layton, Daniel S. and Bean, Andrew G. and Chen, Zhenjun and Laurie, Karen L. and Borg, Kathryn and Barr, Ian G. and Adams, Timothy E.}, urldate = {2017-05-01}, date = {2016-02}, keywords = {Ferret, Ferret, Lymphocyte proliferation, Lymphocyte proliferation, {mRNA} induction, {mRNA} induction, Recombinant interleukin-2, Recombinant interleukin-2, X-ray structure, X-ray structure}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TTE57X8F\\S0145305X15300549:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RFNZW2PI\\S0145305X15300549.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TTE57X8F\\S0145305X15300549:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NFDPSKKM\\S0145305X15300549.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XBB5AZNM\\Ren et al. - 2016 - Structural and functional characterisation of ferr:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PRGDVJKC\\Ren et al. - 2016 - Structural and functional characterisation of ferr.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XBB5AZNM\\Ren et al. - 2016 - Structural and functional characterisation of ferr:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RGVRPQMP\\Ren et al. - 2016 - Structural and functional characterisation of ferr.pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XBB5AZNM\\Ren et al. - 2016 - Structural and functional characterisation of ferr.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TTE57X8F\\S0145305X15300549.html:text/html} } @article{angeli_intramolecular_2016, title = {Intramolecular oxidative deselenization of acylselenoureas: a facile synthesis of benzoxazole amides and carbonic anhydrase inhibitors}, volume = {14}, url = {http://pubs.rsc.org/en/Content/ArticleLanding/2016/OB/C6OB02299E}, doi = {10.1039/C6OB02299E}, shorttitle = {Intramolecular oxidative deselenization of acylselenoureas}, pages = {11353--11356}, number = {48}, journaltitle = {Organic \& Biomolecular Chemistry}, author = {Angeli, A. and S. Peat, T. and Bartolucci, G. and Nocentini, A. and T. Supuran, C. and Carta, F.}, urldate = {2017-05-01}, date = {2016}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AT26VVHM\\c6ob02299e:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z6G67ZJS\\c6ob02299e.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AT26VVHM\\c6ob02299e:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GXE7EBQJ\\c6ob02299e.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NZI8BNUM\\Angeli et al. - 2016 - Intramolecular oxidative deselenization of acylsel:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E4X3SECG\\Angeli et al. - 2016 - Intramolecular oxidative deselenization of acylsel.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NZI8BNUM\\Angeli et al. - 2016 - Intramolecular oxidative deselenization of acylsel:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MTE8AF9D\\Angeli et al. - 2016 - Intramolecular oxidative deselenization of acylsel.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NZI8BNUM\\Angeli et al. - 2016 - Intramolecular oxidative deselenization of acylsel.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AT26VVHM\\c6ob02299e.html:text/html} } @article{christensen_structure_2016, title = {Structure and Function of Cyanobacterial {DHDPS} and {DHDPR}}, volume = {6}, issn = {2045-2322}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5109050/}, doi = {10.1038/srep37111}, abstract = {Lysine biosynthesis in bacteria and plants commences with a condensation reaction catalysed by dihydrodipicolinate synthase ({DHDPS}) followed by a reduction reaction catalysed by dihydrodipicolinate reductase ({DHDPR}). Interestingly, both {DHDPS} and {DHDPR} exist as different oligomeric forms in bacteria and plants. {DHDPS} is primarily a homotetramer in all species, but the architecture of the tetramer differs across kingdoms. {DHDPR} also exists as a tetramer in bacteria, but has recently been reported to be dimeric in plants. This study aimed to characterise for the first time the structure and function of {DHDPS} and {DHDPR} from cyanobacteria, which is an evolutionary important phylum that evolved at the divergence point between bacteria and plants. We cloned, expressed and purified {DHDPS} and {DHDPR} from the cyanobacterium Anabaena variabilis. The recombinant enzymes were shown to be folded by circular dichroism spectroscopy, enzymatically active employing the quantitative {DHDPS}-{DHDPR} coupled assay, and form tetramers in solution using analytical ultracentrifugation. Crystal structures of {DHDPS} and {DHDPR} from A. variabilis were determined at 1.92 Å and 2.83 Å, respectively, and show that both enzymes adopt the canonical bacterial tetrameric architecture. These studies indicate that the quaternary structure of bacterial and plant {DHDPS} and {DHDPR} diverged after cyanobacteria evolved.}, journaltitle = {Scientific Reports}, shortjournal = {Sci Rep}, author = {Christensen, Janni B. and Soares da Costa, T. P. and Faou, Pierre and Pearce, F. Grant and Panjikar, Santosh and Perugini, Matthew A.}, urldate = {2017-05-01}, date = {2016-11-15}, pmid = {27845445}, pmcid = {PMC5109050}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VG84VWJX\\Christensen et al. - 2016 - Structure and Function of Cyanobacterial DHDPS and:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GMZQSZHB\\Christensen et al. - 2016 - Structure and Function of Cyanobacterial DHDPS and.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VG84VWJX\\Christensen et al. - 2016 - Structure and Function of Cyanobacterial DHDPS and:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GI7584X6\\Christensen et al. - 2016 - Structure and Function of Cyanobacterial DHDPS and.pdf:application/pdf;PubMed Central Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VG84VWJX\\Christensen et al. - 2016 - Structure and Function of Cyanobacterial DHDPS and.pdf:application/pdf} } @article{brewster_structural_2016, title = {Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae}, volume = {6}, issn = {2045-2322}, url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062169/}, doi = {10.1038/srep35198}, abstract = {Chemoreceptors enable bacteria to detect chemical signals in the environment and navigate towards niches that are favourable for survival. The sensor domains of chemoreceptors function as the input modules for chemotaxis systems, and provide sensory specificity by binding specific ligands. Cache-like domains are the most common extracellular sensor module in prokaryotes, however only a handful have been functionally or structurally characterised. Here, we have characterised a chemoreceptor Cache-like sensor domain ({PscD}-{SD}) from the plant pathogen Pseudomonas syringae pv. actinidiae (Psa). High-throughput fluorescence thermal shift assays, combined with isothermal thermal titration calorimetry, revealed that {PscD}-{SD} binds specifically to C2 (glycolate and acetate) and C3 (propionate and pyruvate) carboxylates. We solved the structure of {PscD}-{SD} in complex with propionate using X-ray crystallography. The structure reveals the key residues that comprise the ligand binding pocket and dictate the specificity of this sensor domain for C2 and C3 carboxylates. We also demonstrate that all four carboxylate ligands are chemoattractants for Psa, but only two of these (acetate and pyruvate) are utilisable carbon sources. This result suggests that in addition to guiding the bacteria towards nutrients, another possible role for carboxylate sensing is in locating potential sites of entry into the host plant.}, journaltitle = {Scientific Reports}, shortjournal = {Sci Rep}, author = {Brewster, Jodi L. and {McKellar}, James L. O. and Finn, Thomas J. and Newman, Janet and Peat, Thomas S. and Gerth, Monica L.}, urldate = {2017-05-01}, date = {2016-10-13}, pmid = {27734909}, pmcid = {PMC5062169}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PD2VX6D8\\Brewster et al. - 2016 - Structural basis for ligand recognition by a Cache:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A3HVJFP8\\Brewster et al. - 2016 - Structural basis for ligand recognition by a Cache.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PD2VX6D8\\Brewster et al. - 2016 - Structural basis for ligand recognition by a Cache:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C37AK22I\\Brewster et al. - 2016 - Structural basis for ligand recognition by a Cache.pdf:application/pdf;PubMed Central Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PD2VX6D8\\Brewster et al. - 2016 - Structural basis for ligand recognition by a Cache.pdf:application/pdf} } @article{darmanin_effect_2016, title = {Effect of Lipidic Cubic Phase Structure on Functionality of the Dopamine 2L Receptor: Implications for in Meso Crystallization}, volume = {16}, issn = {1528-7483}, url = {http://dx.doi.org/10.1021/acs.cgd.6b00576}, doi = {10.1021/acs.cgd.6b00576}, shorttitle = {Effect of Lipidic Cubic Phase Structure on Functionality of the Dopamine 2L Receptor}, abstract = {The success of the lipidic cubic phase for crystallization, particularly of integral membrane proteins, is increasing. In the past two years, more than 25\% of membrane protein structures have been solved within the biomimetic environment of the lipidic cubic phase. However, the relationship between the lipid matrix and crystal growth still remains a mystery. Herein we show that the bilayer structure of the lipidic cubic phase is crucial to retention of the functionality of the dopamine D2 long receptor. Destruction of the cubic architecture at higher protein concentrations is associated with a significant drop in the amount of functional receptor. This has profound implications for in meso crystallization and suggests that preliminary experiments to determine the maximum protein loading within the lipidic cubic phase must be carried out prior to in meso crystallization experiments.}, pages = {5014--5022}, number = {9}, journaltitle = {Crystal Growth \& Design}, shortjournal = {Crystal Growth \& Design}, author = {Darmanin, Connie and Sarkar, Sampa and Castelli, Laura and Conn, Charlotte E.}, urldate = {2017-05-01}, date = {2016-09-07}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3TEJFP67\\Darmanin et al. - 2016 - Effect of Lipidic Cubic Phase Structure on Functio.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CP4V26VA\\acs.cgd.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3TEJFP67\\Darmanin et al. - 2016 - Effect of Lipidic Cubic Phase Structure on Functio:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HKWZNR2U\\Darmanin et al. - 2016 - Effect of Lipidic Cubic Phase Structure on Functio.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3TEJFP67\\Darmanin et al. - 2016 - Effect of Lipidic Cubic Phase Structure on Functio:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RVX9HA8T\\Darmanin et al. - 2016 - Effect of Lipidic Cubic Phase Structure on Functio.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CP4V26VA\\acs.cgd:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5BWTAJDX\\acs.cgd.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CP4V26VA\\acs.cgd:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2CDIGPJJ\\acs.cgd.html:text/html} } @article{hag_exploring_2016, title = {Exploring the in meso crystallization mechanism by characterizing the lipid mesophase microenvironment during the growth of single transmembrane α-helical peptide crystals}, volume = {374}, rights = {© 2016 The Author(s). http://royalsocietypublishing.org/{licencePublished} by the Royal Society. All rights reserved.}, issn = {1364-503X, 1471-2962}, url = {http://rsta.royalsocietypublishing.org/content/374/2072/20150125}, doi = {10.1098/rsta.2015.0125}, abstract = {The proposed mechanism for in meso crystallization of transmembrane proteins suggests that a protein or peptide is initially uniformly dispersed in the lipid self-assembly cubic phase but that crystals grow from a local lamellar phase, which acts as a conduit between the crystal and the bulk cubic phase. However, there is very limited experimental evidence for this theory. We have developed protocols to investigate the lipid mesophase microenvironment during crystal growth using standard procedures readily available in crystallography laboratories. This technique was used to characterize the microenvironment during crystal growth of the {DAP}12-{TM} peptide using synchrotron small angle X-ray scattering ({SAXS}) with a micro-sized X-ray beam. Crystal growth was found to occur from the gyroid cubic mesophase. For one in four crystals, a highly oriented local lamellar phase was observed, providing supporting evidence for the proposed mechanism for in meso crystallization. A new observation of this study was that we can differentiate diffraction peaks from crystals grown in meso, from peaks originating from the surrounding lipid matrix, potentially opening up the possibility of high-throughput {SAXS} analysis of in meso grown crystals. This article is part of the themed issue ‘Soft interfacial materials: from fundamentals to formulation’.}, pages = {20150125}, number = {2072}, journaltitle = {Phil. Trans. R. Soc. A}, shortjournal = {Phil. Trans. R. Soc. A}, author = {Hag, Leonie van 't and Knoblich, Konstantin and Seabrook, Shane A. and Kirby, Nigel M. and Mudie, Stephen T. and Lau, Deborah and Li, Xu and Gras, Sally L. and Mulet, Xavier and Call, Matthew E. and Call, Melissa J. and Drummond, Calum J. and Conn, Charlotte E.}, urldate = {2017-05-01}, date = {2016-07-28}, langid = {english}, pmid = {27298442}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CUSEKVS2\\20150125:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JNQKBTZ9\\20150125.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CUSEKVS2\\20150125:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IPWH5CPE\\20150125.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P68R4G43\\Hag et al. - 2016 - Exploring the in meso crystallization mechanism by:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7TT3ZPIF\\Hag et al. - 2016 - Exploring the in meso crystallization mechanism by.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P68R4G43\\Hag et al. - 2016 - Exploring the in meso crystallization mechanism by:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SUJJVZSM\\Hag et al. - 2016 - Exploring the in meso crystallization mechanism by.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P68R4G43\\Hag et al. - 2016 - Exploring the in meso crystallization mechanism by.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CUSEKVS2\\20150125.html:text/html} } @article{lee_physiological_2016, title = {Physiological restraint of Bak by Bcl-{xL} is essential for cell survival}, volume = {30}, issn = {0890-9369, 1549-5477}, url = {http://genesdev.cshlp.org/content/30/10/1240}, doi = {10.1101/gad.279414.116}, abstract = {Due to the myriad interactions between prosurvival and proapoptotic members of the Bcl-2 family of proteins, establishing the mechanisms that regulate the intrinsic apoptotic pathway has proven challenging. Mechanistic insights have primarily been gleaned from in vitro studies because genetic approaches in mammals that produce unambiguous data are difficult to design. Here we describe a mutation in mouse and human Bak that specifically disrupts its interaction with the prosurvival protein Bcl-{xL}. Substitution of Glu75 in {mBak} ({hBAK} Q77) for leucine does not affect the three-dimensional structure of Bak or killing activity but reduces its affinity for Bcl-{xL} via loss of a single hydrogen bond. Using this mutant, we investigated the requirement for physical restraint of Bak by Bcl-{xL} in apoptotic regulation. In vitro, {BakQ}75L cells were significantly more sensitive to various apoptotic stimuli. In vivo, loss of Bcl-{xL} binding to Bak led to significant defects in T-cell and blood platelet survival. Thus, we provide the first definitive in vivo evidence that prosurvival proteins maintain cellular viability by interacting with and inhibiting Bak.}, pages = {1240--1250}, number = {10}, journaltitle = {Genes \& Development}, shortjournal = {Genes Dev.}, author = {Lee, Erinna F. and Grabow, Stephanie and Chappaz, Stephane and Dewson, Grant and Hockings, Colin and Kluck, Ruth M. and Debrincat, Marlyse A. and Gray, Daniel H. and Witkowski, Matthew T. and Evangelista, Marco and Pettikiriarachchi, Anne and Bouillet, Philippe and Lane, Rachael M. and Czabotar, Peter E. and Colman, Peter M. and Smith, Brian J. and Kile, Benjamin T. and Fairlie, W. Douglas}, urldate = {2017-05-01}, date = {2016-05-15}, langid = {english}, pmid = {27198225}, keywords = {apoptosis, apoptosis, Bak, Bak, Bcl-2, Bcl-2, Bcl-{xL}, Bcl-{xL}, {BH}3, {BH}3}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\49IZVM6X\\1240:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FM4RXPID\\1240.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\49IZVM6X\\1240:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9EMAGG9B\\1240.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J3XM4SG4\\Lee et al. - 2016 - Physiological restraint of Bak by Bcl-xL is essent:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XFZTI2JE\\Lee et al. - 2016 - Physiological restraint of Bak by Bcl-xL is essent.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J3XM4SG4\\Lee et al. - 2016 - Physiological restraint of Bak by Bcl-xL is essent:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7I88J9KG\\Lee et al. - 2016 - Physiological restraint of Bak by Bcl-xL is essent.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J3XM4SG4\\Lee et al. - 2016 - Physiological restraint of Bak by Bcl-xL is essent.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\49IZVM6X\\1240.html:text/html} } @article{hunt_biochemical_2016, title = {Biochemical characterization of a halotolerant feruloyl esterase from Actinomyces spp.: refolding and activity following thermal deactivation}, volume = {100}, issn = {0175-7598, 1432-0614}, url = {https://link.springer.com/article/10.1007/s00253-015-7044-9}, doi = {10.1007/s00253-015-7044-9}, shorttitle = {Biochemical characterization of a halotolerant feruloyl esterase from Actinomyces spp.}, abstract = {Ferulic acid esterases ({FAE}, {EC}. 3.1.1.73) hydrolyse the linkage between hemicellulose and lignin and thus have potential for use in mild enzymatic pretreatment of biomass as an alternative to thermochemical approaches. Here, we report the characterization of a novel {FAE} ({ActOFaeI}) obtained from the bacterium, Actinomyces sp. oral which was recombinantly expressed in Escherichia coli {BL}21 in two forms: with and without its putative signal peptide. The truncated form was found to have {\textless}10 \% relative activity compared to the full length and was more prone to aggregation after purification. The enzyme with retained peptide demonstrated 2 to 4-fold higher activity against methyl caffeate and methyl p-coumarate, with specific activities of 477.6 and 174.4 U mg−1 respectively, than the equivalent activities of the benchmark {FAE} from Aspergillus niger A and B. {ActOFaeI} retained activity over a broad {pH} range with a maximum at 9 but {\textgreater}90 \% relative activity at {pH} 6.5 and an optimum reaction temperature of 30 °C. {ActOFaeI} increased activity by 15 \% in high salt conditions (1000 {mM} {NaCl}) and its thermal unfolding temperature improved from 41.5 °C in standard buffer to 74 °C in the presence of 2500 {mM} sodium malonate. {ActOFaeI} also released ferulic acid from destarched wheat bran when combined with a xylanase preparation. After treatment above the thermal denaturation temperature followed by cooling to room temperature, {ActOFaeI} demonstrated spontaneous refolding into an active state. {ActOFaeI} displays many useful characteristics for enzymatic pretreatment of lignocellulose and contributes to our understanding of this important family.}, pages = {1777--1787}, number = {4}, journaltitle = {Applied Microbiology and Biotechnology}, shortjournal = {Appl Microbiol Biotechnol}, author = {Hunt, Cameron J. and Tanksale, Akshat and Haritos, Victoria S.}, urldate = {2017-05-01}, date = {2016-02-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\98AXKID7\\Hunt et al. - 2016 - Biochemical characterization of a halotolerant fer:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\743EB2MV\\Hunt et al. - 2016 - Biochemical characterization of a halotolerant fer.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\98AXKID7\\Hunt et al. - 2016 - Biochemical characterization of a halotolerant fer:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\298DW4HQ\\Hunt et al. - 2016 - Biochemical characterization of a halotolerant fer.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZQF785FG\\s00253-015-7044-9:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3FCMKIV6\\s00253-015-7044-9.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZQF785FG\\s00253-015-7044-9:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ISDD3VR4\\s00253-015-7044-9.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\98AXKID7\\Hunt et al. - 2016 - Biochemical characterization of a halotolerant fer.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZQF785FG\\s00253-015-7044-9.html:text/html} } @article{dennis_structural_2016, title = {Structural Basis for the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase from Staphylococcus aureus and Escherichia coli}, volume = {59}, issn = {0022-2623}, url = {http://dx.doi.org/10.1021/acs.jmedchem.6b00002}, doi = {10.1021/acs.jmedchem.6b00002}, abstract = {6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase ({HPPK}) is a member of the folate biosynthesis pathway found in prokaryotes and lower eukaryotes that catalyzes the pyrophosphoryl transfer from the {ATP} cofactor to a 6-hydroxymethyl-7,8-dihydropterin substrate. We report the chemical synthesis of a series of S-functionalized 8-mercaptoguanine (8MG) analogues as substrate site inhibitors of {HPPK} and quantify binding against the E. coli and S. aureus enzymes ({EcHPPK} and {SaHPPK}). The results demonstrate that analogues incorporating acetophenone-based substituents have comparable affinities for both enzymes. Preferential binding of benzyl-substituted 8MG derivatives to {SaHPPK} was reconciled when a cryptic pocket unique to {SaHPPK} was revealed by X-ray crystallography. Differential chemical shift perturbation analysis confirmed this to be a common mode of binding for this series to {SaHPPK}. One compound (41) displayed binding affinities of 120 {nM} and 1.76 μM for {SaHPPK} and {EcHPPK}, respectively, and represents a lead for the development of more potent and selective inhibitors of {SaHPPK}.}, pages = {5248--5263}, number = {11}, journaltitle = {Journal of Medicinal Chemistry}, shortjournal = {J. Med. Chem.}, author = {Dennis, Matthew L. and Pitcher, Noel P. and Lee, Michael D. and {DeBono}, Aaron J. and Wang, Zhong-Chang and Harjani, Jitendra R. and Rahmani, Raphaël and Cleary, Ben and Peat, Thomas S. and Baell, Jonathan B. and Swarbrick, James D.}, urldate = {2017-05-01}, date = {2016-06-09}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KE97VH9W\\Dennis et al. - 2016 - Structural Basis for the Selective Binding of Inhi.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N6GCQ26F\\acs.jmedchem.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KE97VH9W\\Dennis et al. - 2016 - Structural Basis for the Selective Binding of Inhi:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5DV72BBV\\Dennis et al. - 2016 - Structural Basis for the Selective Binding of Inhi.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KE97VH9W\\Dennis et al. - 2016 - Structural Basis for the Selective Binding of Inhi:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A2PI2GXZ\\Dennis et al. - 2016 - Structural Basis for the Selective Binding of Inhi.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N6GCQ26F\\acs.jmedchem:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2RVTHEAD\\acs.jmedchem.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N6GCQ26F\\acs.jmedchem:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WAPAQCE4\\acs.jmedchem.html:text/html} } @article{broughton_conformational_2016, title = {Conformational Changes in the {GM}-{CSF} Receptor Suggest a Molecular Mechanism for Affinity Conversion and Receptor Signaling}, volume = {24}, issn = {0969-2126}, url = {http://www.sciencedirect.com/science/article/pii/S0969212616301241}, doi = {10.1016/j.str.2016.05.017}, abstract = {Summary The {GM}-{CSF}, {IL}-3, and {IL}-5 receptors constitute the βc family, playing important roles in inflammation, autoimmunity, and cancer. Typical of heterodimeric type I cytokine receptors, signaling requires recruitment of the shared subunit to the initial cytokine:α subunit binary complex through an affinity conversion mechanism. This critical process is poorly understood due to the paucity of crystal structures of both binary and ternary receptor complexes for the same cytokine. We have now solved the structure of the binary {GM}-{CSF}:{GMRα} complex at 2.8-Å resolution and compared it with the structure of the ternary complex, revealing distinct conformational changes. Guided by these differences we performed mutational and functional studies that, importantly, show {GMRα} interactions playing a major role in receptor signaling while βc interactions control high-affinity binding. These results support the notion that conformational changes underlie the mechanism of {GM}-{CSF} receptor activation and also suggest how related type I cytokine receptors signal.}, pages = {1271--1281}, number = {8}, journaltitle = {Structure}, shortjournal = {Structure}, author = {Broughton, Sophie E. and Hercus, Timothy R. and Nero, Tracy L. and Dottore, Mara and {McClure}, Barbara J. and Dhagat, Urmi and Taing, Houng and Gorman, Michael A. and King-Scott, Jack and Lopez, Angel F. and Parker, Michael W.}, urldate = {2017-05-01}, date = {2016-08-02}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3SK5IDE2\\S0969212616301241:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TNKDIHGB\\S0969212616301241.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3SK5IDE2\\S0969212616301241:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZEP9A5MR\\S0969212616301241.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FM96X5CD\\Broughton et al. - 2016 - Conformational Changes in the GM-CSF Receptor Sugg:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JEKUEZJ2\\Broughton et al. - 2016 - Conformational Changes in the GM-CSF Receptor Sugg.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FM96X5CD\\Broughton et al. - 2016 - Conformational Changes in the GM-CSF Receptor Sugg:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ABFDVWWU\\Broughton et al. - 2016 - Conformational Changes in the GM-CSF Receptor Sugg.pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FM96X5CD\\Broughton et al. - 2016 - Conformational Changes in the GM-CSF Receptor Sugg.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3SK5IDE2\\S0969212616301241.html:text/html} } @article{mujumdar_unusual_2016, title = {An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition, and Protein X-ray Structures of Psammaplin C}, volume = {59}, issn = {0022-2623}, url = {http://dx.doi.org/10.1021/acs.jmedchem.6b00443}, doi = {10.1021/acs.jmedchem.6b00443}, shorttitle = {An Unusual Natural Product Primary Sulfonamide}, abstract = {Psammaplin C is one of only two described natural product primary sulfonamides. Here we report the synthesis of psammaplin C and evaluate the inhibition profile against therapeutically relevant carbonic anhydrase ({CA}) zinc metalloenzymes. The compound exhibited unprecedented inhibition of an important cancer-associated isozyme, {hCA} {XII}, with a Ki of 0.79 {nM}. The compound also displayed good isoform selectivity for {hCA} {XII} over other {CAs}. We present the first reported protein X-ray crystal structures of psammaplin C in complex with human {CAs}. We engineered the easily crystallized {hCA} {II} enzyme to mimic both the {hCA} {IX} and {hCA} {XII} binding sites and then utilized protein X-ray crystallography to determine the binding pose of psammaplin C within the {hCA} {II}, {hCA} {IX}, and {hCA} {XII} mimic active sites, all to high resolution. This is the first time a natural product primary sulfonamide inhibitor has been assessed for inhibition and binding to {CAs}.}, pages = {5462--5470}, number = {11}, journaltitle = {Journal of Medicinal Chemistry}, shortjournal = {J. Med. Chem.}, author = {Mujumdar, Prashant and Teruya, Kanae and Tonissen, Kathryn F. and Vullo, Daniela and Supuran, Claudiu T. and Peat, Thomas S. and Poulsen, Sally-Ann}, urldate = {2017-05-01}, date = {2016-06-09}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GC8R6CRM\\Mujumdar et al. - 2016 - An Unusual Natural Product Primary Sulfonamide Sy.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AEHUJW8F\\acs.jmedchem.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AEHUJW8F\\acs.jmedchem:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SZTF6I4G\\acs.jmedchem.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AEHUJW8F\\acs.jmedchem:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BFAFG3VX\\acs.jmedchem.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GC8R6CRM\\Mujumdar et al. - 2016 - An Unusual Natural Product Primary Sulfonamide Sy:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8J3JAC73\\Mujumdar et al. - 2016 - An Unusual Natural Product Primary Sulfonamide Sy.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GC8R6CRM\\Mujumdar et al. - 2016 - An Unusual Natural Product Primary Sulfonamide Sy:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XJ4ATI3N\\Mujumdar et al. - 2016 - An Unusual Natural Product Primary Sulfonamide Sy.pdf:application/pdf} } @article{anasir_structural_2017, title = {Structural Basis of Apoptosis Inhibition by the Fowlpox Virus Protein {FPV}039}, issn = {0021-9258, 1083-351X}, url = {http://www.jbc.org/content/early/2017/04/14/jbc.M116.768879}, doi = {10.1074/jbc.M116.768879}, abstract = {Programmed cell death or apoptosis of infected host cells is an important defense mechanism in response to viral infections. This process is regulated by pro-apoptotic and pro-survival members of the B-cell lymphoma 2 (Bcl-2) protein family. To counter premature death of a virus-infected cell, poxviruses use a range of different molecular strategies, including the mimicry of pro-survival Bcl-2 proteins. One such viral pro-survival protein is the fowlpox virus protein {FPV}039, which is a potent apoptosis inhibitor, but the precise molecular mechanism by which {FPV}039 inhibits apoptosis is unknown. To understand how fowlpox virus inhibits apoptosis we examined {FPV}039 using isothermal titration calorimetry, small-angle X-ray scattering and X-ray crystallography. Here, we report that the fowlpox virus pro-survival protein {FPV}039 promiscuously binds to cellular pro-apoptotic Bcl-2, and engages all major pro-apoptotic Bcl-2 proteins. Unlike other identified viral Bcl-2 proteins to date, {FPV}039 engaged with cellular pro-apoptotic Bcl-2 with affinities comparable to those of Bcl-2's endogenous cellular counterparts. Structural studies revealed that {FPV}039 adopts the conserved Bcl-2 fold observed in cellular pro-survival Bcl-2 proteins, and closely mimics the structure of the pro-survival Bcl-2 family protein Mcl-1. Our findings suggest that {FPV}039 is a pan Bcl-2 protein inhibitor that can engage all host {BH}3-only proteins as well as Bcl-2 associated X, apoptosis regulator (Bax) and Bcl-2 antagonist/killer (Bak) proteins to inhibit premature apoptosis of an infected host cell. This work therefore provides a mechanistic platform to better understand {FPV}039-mediated apoptosis inhibition.}, pages = {jbc.M116.768879}, journaltitle = {Journal of Biological Chemistry}, shortjournal = {J. Biol. Chem.}, author = {Anasir, Mohd Ishtiaq and Caria, Sofia and Skinner, Michael A. and Kvansakul, Marc}, urldate = {2017-05-01}, date = {2017-04-14}, langid = {english}, pmid = {28411240}, keywords = {apoptosis, apoptosis, B-cell lymphoma 2 (Bcl-2) family, B-cell lymphoma 2 (Bcl-2) family, isothermal titration calorimetry ({ITC}), isothermal titration calorimetry ({ITC}), poxvirus, poxvirus, small-angle X-ray scattering ({SAXS}), small-angle X-ray scattering ({SAXS}), X-ray crystallography, X-ray crystallography}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4BZ4PCI9\\Anasir et al. - 2017 - Structural Basis of Apoptosis Inhibition by the Fo:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HEJVF3T3\\Anasir et al. - 2017 - Structural Basis of Apoptosis Inhibition by the Fo.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4BZ4PCI9\\Anasir et al. - 2017 - Structural Basis of Apoptosis Inhibition by the Fo:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FRBTQ4X5\\Anasir et al. - 2017 - Structural Basis of Apoptosis Inhibition by the Fo.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HJVPVD69\\jbc.M116.768879:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VD794VSI\\jbc.M116.768879.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HJVPVD69\\jbc.M116.768879:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PWU36S8H\\jbc.M116.768879.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4BZ4PCI9\\Anasir et al. - 2017 - Structural Basis of Apoptosis Inhibition by the Fo.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HJVPVD69\\jbc.M116.768879.html:text/html} } @article{peat_high-resolution_2017, title = {High-Resolution X-Ray Structures of Two Functionally Distinct Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes}, volume = {83}, issn = {0099-2240, 1098-5336}, url = {http://aem.asm.org/content/83/9/e03365-16}, doi = {10.1128/AEM.03365-16}, abstract = {The Toblerone fold was discovered recently when the first structure of the cyclic amide hydrolase, {AtzD} (a cyanuric acid hydrolase), was elucidated. We surveyed the cyclic amide hydrolase family, finding a strong correlation between phylogenetic distribution and specificity for either cyanuric acid or barbituric acid. One of six classes ({IV}) could not be tested due to a lack of expression of the proteins from it, and another class (V) had neither cyanuric acid nor barbituric acid hydrolase activity. High-resolution X-ray structures were obtained for a class {VI} barbituric acid hydrolase (1.7 Å) from a Rhodococcus species and a class V cyclic amide hydrolase (2.4 Å) from a Frankia species for which we were unable to identify a substrate. Both structures were homologous with the tetrameric Toblerone fold enzyme {AtzD}, demonstrating a high degree of structural conservation within the cyclic amide hydrolase family. The barbituric acid hydrolase structure did not contain zinc, in contrast with early reports of zinc-dependent activity for this enzyme. Instead, each barbituric acid hydrolase monomer contained either Na+ or Mg2+, analogous to the structural metal found in cyanuric acid hydrolase. The Frankia cyclic amide hydrolase contained no metal but instead formed unusual, reversible, intermolecular vicinal disulfide bonds that contributed to the thermal stability of the protein. The active sites were largely conserved between the three enzymes, differing at six positions, which likely determine substrate specificity. {IMPORTANCE} The Toblerone fold enzymes catalyze an unusual ring-opening hydrolysis with cyclic amide substrates. A survey of these enzymes shows that there is a good correlation between physiological function and phylogenetic distribution within this family of enzymes and provide insights into the evolutionary relationships between the cyanuric acid and barbituric acid hydrolases. This family of enzymes is structurally and mechanistically distinct from other enzyme families; however, to date the structure of just two, physiologically identical, enzymes from this family has been described. We present two new structures: a barbituric acid hydrolase and an enzyme of unknown function. These structures confirm that members of the {CyAH} family have the unusual Toblerone fold, albeit with some significant differences.}, pages = {e03365--16}, number = {9}, journaltitle = {Applied and Environmental Microbiology}, shortjournal = {Appl. Environ. Microbiol.}, author = {Peat, Thomas S. and Balotra, Sahil and Wilding, Matthew and Hartley, Carol J. and Newman, Janet and Scott, Colin}, urldate = {2017-05-01}, date = {2017-05-01}, langid = {english}, pmid = {28235873}, keywords = {atrazine, atrazine, evolution, evolution, hydrolase, hydrolase, phylogenetic analysis, phylogenetic analysis, structure-activity relationships, structure-activity relationships, triazine, triazine}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I8XD8VRB\\Peat et al. - 2017 - High-Resolution X-Ray Structures of Two Functional:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E89XDTN4\\Peat et al. - 2017 - High-Resolution X-Ray Structures of Two Functional.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I8XD8VRB\\Peat et al. - 2017 - High-Resolution X-Ray Structures of Two Functional:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6U6IZ3E6\\Peat et al. - 2017 - High-Resolution X-Ray Structures of Two Functional.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\M6J6WP2A\\e03365-16:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N73ATI6V\\e03365-16.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\M6J6WP2A\\e03365-16:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\X7QFVDQX\\e03365-16.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I8XD8VRB\\Peat et al. - 2017 - High-Resolution X-Ray Structures of Two Functional.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\M6J6WP2A\\e03365-16.html:text/html} } @article{banjara_structural_2017, title = {Structural insight into African Swine Fever virus A179L mediated inhibition of apoptosis}, issn = {0022-538X, 1098-5514}, url = {http://jvi.asm.org/content/early/2017/01/04/JVI.02228-16}, doi = {10.1128/JVI.02228-16}, abstract = {Programmed cell death is a tightly controlled process critical for the removal of damaged or infected cells. Pro- and anti-apoptotic proteins of the Bcl-2 family are pivotal mediators of this process. African Swine Fever virus ({ASFV}) is a large {DNA} virus, the only member of the Asfarviridae family, and harbors A179L, a putative Bcl-2 like protein. A179L has been shown to bind to several pro-apoptotic Bcl-2 proteins, however the hierarchy of binding and the structural basis for apoptosis inhibition are currently not understood. We systematically evaluated the ability of A179L to bind pro-apoptotic Bcl-2 family members, and show that A179L is the first anti-apoptotic Bcl-2 protein to bind to all major death inducing mammalian Bcl-2 proteins. We then defined the structural basis for apoptosis inhibition of A179L by determining crystal structures of A179L bound to both Bid and Bax {BH}3 motifs. Our findings provide a mechanistic understanding for the potent anti-apoptotic activity of A179L by identifying it as the first pan pro-death Bcl-2 binder, and serve as a platform for more detailed investigations into the role of A179L during {ASFV} infection. {IMPORTANCE} Numerous viruses have acquired strategies to subvert apoptosis by encoding proteins capable of sequestering pro-apoptotic host proteins. African Swine Fever virus ({ASFV}), a large {DNA} virus and the only member of the Asfarviridae family, encodes the protein A179L that functions to prevent apoptosis. We show that A179L is unusual amongst anti-apoptotic Bcl-2 proteins in being able to physically bind to all core death inducing mammalian Bcl-2 proteins. Currently, little is known regarding the molecular interactions between A179L and the pro-apoptotic Bcl-2 members. Using crystal structures of A179L bound to two of the identified pro-apoptotic Bcl-2 proteins, Bid and Bax, we now provide a 3D view of how A179L sequesters host pro-apoptotic proteins, which is crucial for subverting premature host cell apoptosis.}, pages = {JVI.02228--16}, journaltitle = {Journal of Virology}, shortjournal = {J. Virol.}, author = {Banjara, Suresh and Caria, Sofia and Dixon, Linda K. and Hinds, Mark G. and Kvansakul, Marc}, urldate = {2017-05-01}, date = {2017-01-04}, langid = {english}, pmid = {28053104}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\28Q77HGK\\JVI.02228-16:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GQIUJSBT\\JVI.02228-16.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\28Q77HGK\\JVI.02228-16:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\26M9ERGQ\\JVI.02228-16.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IZW5XUGN\\Banjara et al. - 2017 - Structural insight into African Swine Fever virus:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V2R5ZWPP\\Banjara et al. - 2017 - Structural insight into African Swine Fever virus .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IZW5XUGN\\Banjara et al. - 2017 - Structural insight into African Swine Fever virus:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MHPC5RCK\\Banjara et al. - 2017 - Structural insight into African Swine Fever virus .pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IZW5XUGN\\Banjara et al. - 2017 - Structural insight into African Swine Fever virus .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\28Q77HGK\\JVI.02228-16.html:text/html} } @article{caria_structural_2017, title = {Structural insight into an evolutionarily ancient programmed cell death regulator – the crystal structure of marine sponge {BHP}2 bound to {LB}-Bak-2}, volume = {8}, rights = {© 2017 Nature Publishing Group}, url = {http://www.nature.com/cddis/journal/v8/n1/abs/cddis2016469a.html}, doi = {10.1038/cddis.2016.469}, abstract = {Sponges of the porifera family harbor some of the evolutionary most ancient orthologs of the B-cell lymphoma-2 (Bcl-2) family, a protein family critical to regulation of apoptosis. The genome of the sponge Geodia cydonium contains the putative pro-survival Bcl-2 homolog {BHP}2, which protects sponge tissue as well as mammalian Hek-293 and {NIH}-3T3 cells against diverse apoptotic stimuli. The Lake Baikal demosponge Lubomirskia baicalensis has been shown to encode both putative pro-survival Bcl-2 ({LB}-Bcl-2) and pro-apoptotic Bcl-2 members ({LB}-Bak-2), which have been implied in axis formation (branches) in L. baicalensis. However, the molecular mechanism of action of sponge-encoded orthologs of Bcl-2 remains to be clarified. Here, we report that the pro-survival Bcl-2 ortholog {BHP}2 from G. cydonium is able to bind the {BH}3 motif of a pro-apoptotic Bcl-2 protein, {LB}-Bak-2 of the sponge L. baicalensis. Furthermore, we determined the crystal structure of {BHP}2 bound to {LB}-Bak-2, which revealed that using a binding groove conserved across all pro-survival Bcl-2 proteins, {BHP}2 binds multi-motif Bax-like proteins through their {BH}3-binding regions. However, {BHP}2 discriminates against {BH}3-only bearing proteins by blocking access to a hydrophobic pocket that is critical for {BH}3 motif binding in pro-survival Bcl-2 proteins from higher organisms. This differential binding mode is reflected in a structure-based phylogenetic comparison of {BHP}2 with other Bcl-2 family members, which revealed that {BHP}2 does not cluster with either Bcl-2 members of higher organisms or pathogen-encoded homologs, and assumes a discrete position. Our findings suggest that the molecular machinery and mechanisms for executing Bcl-2-mediated apoptosis as observed in mammals are evolutionary ancient, with early regulation of apoptotic machineries closely resembling their modern counterparts in mammals rather than Caenorhabditis elegans or drosophila.}, pages = {e2543}, number = {1}, journaltitle = {Cell Death \& Disease}, shortjournal = {Cell Death Dis}, author = {Caria, Sofia and Hinds, Mark G. and Kvansakul, Marc}, urldate = {2017-05-01}, date = {2017-01-12}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ETKGAECN\\cddis2016469a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5ACNNRPR\\cddis2016469a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ETKGAECN\\cddis2016469a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\M4QZ39JD\\cddis2016469a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GE75A6VK\\Caria et al. - 2017 - Structural insight into an evolutionarily ancient:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I5XEGPK6\\Caria et al. - 2017 - Structural insight into an evolutionarily ancient .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GE75A6VK\\Caria et al. - 2017 - Structural insight into an evolutionarily ancient:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WUISCB6P\\Caria et al. - 2017 - Structural insight into an evolutionarily ancient .pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GE75A6VK\\Caria et al. - 2017 - Structural insight into an evolutionarily ancient .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ETKGAECN\\cddis2016469a.html:text/html} } @article{rosa_meltdown:_2015, title = {Meltdown: A Tool to Help in the Interpretation of Thermal Melt Curves Acquired by Differential Scanning Fluorimetry}, volume = {20}, issn = {1087-0571}, url = {http://dx.doi.org/10.1177/1087057115584059}, doi = {10.1177/1087057115584059}, shorttitle = {Meltdown}, abstract = {The output of a differential scanning fluorimetry ({DSF}) assay is a series of melt curves, which need to be interpreted to get value from the assay. An application that translates raw thermal melt curve data into more easily assimilated knowledge is described. This program, called “Meltdown,” conducts four main activities—control checks, curve normalization, outlier rejection, and melt temperature (Tm) estimation—and performs optimally in the presence of triplicate (or higher) sample data. The final output is a report that summarizes the results of a {DSF} experiment. The goal of Meltdown is not to replace human analysis of the raw fluorescence data but to provide a meaningful and comprehensive interpretation of the data to make this useful experimental technique accessible to inexperienced users, as well as providing a starting point for detailed analyses by more experienced users.}, pages = {898--905}, number = {7}, journaltitle = {Journal of Biomolecular Screening}, shortjournal = {J Biomol Screen}, author = {Rosa, Nicholas and Ristic, Marko and Seabrook, Shane A. and Lovell, David and Lucent, Del and Newman, Janet}, urldate = {2017-05-01}, date = {2015-08-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\862DHAU6\\Rosa et al. - 2015 - Meltdown A Tool to Help in the Interpretation of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AN45BVBQ\\Rosa et al. - 2015 - Meltdown A Tool to Help in the Interpretation of .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\862DHAU6\\Rosa et al. - 2015 - Meltdown A Tool to Help in the Interpretation of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8RU8UAAR\\Rosa et al. - 2015 - Meltdown A Tool to Help in the Interpretation of .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V4PNK2HQ\\Rosa et al. - 2015 - Meltdown A Tool to Help in the Interpretation of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NPMRNQWG\\Rosa et al. - 2015 - Meltdown A Tool to Help in the Interpretation of .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V4PNK2HQ\\Rosa et al. - 2015 - Meltdown A Tool to Help in the Interpretation of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JW75G23R\\Rosa et al. - 2015 - Meltdown A Tool to Help in the Interpretation of .pdf:application/pdf;SAGE PDF Full Text:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V4PNK2HQ\\Rosa et al. - 2015 - Meltdown A Tool to Help in the Interpretation of .pdf:application/pdf;SAGE PDF Full Text:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\862DHAU6\\Rosa et al. - 2015 - Meltdown A Tool to Help in the Interpretation of .pdf:application/pdf} } @article{knoblich_transmembrane_2015, title = {Transmembrane Complexes of {DAP}12 Crystallized in Lipid Membranes Provide Insights into Control of Oligomerization in Immunoreceptor Assembly}, volume = {11}, issn = {2211-1247}, url = {http://www.sciencedirect.com/science/article/pii/S2211124715004623}, doi = {10.1016/j.celrep.2015.04.045}, abstract = {Summary The membrane-spanning α helices of single-pass receptors play crucial roles in stabilizing oligomeric structures and transducing biochemical signals across the membrane. Probing intermolecular transmembrane interactions in single-pass receptors presents unique challenges, reflected in a gross underrepresentation of their membrane-embedded domains in structural databases. Here, we present two high-resolution structures of transmembrane assemblies from a eukaryotic single-pass protein crystallized in a lipidic membrane environment. Trimeric and tetrameric structures of the immunoreceptor signaling module {DAP}12, determined to 1.77-Å and 2.14-Å resolution, respectively, are organized by the same polar surfaces that govern intramembrane assembly with client receptors. We demonstrate that, in addition to the well-studied dimeric form, these trimeric and tetrameric structures are made in cells, and their formation is competitive with receptor association in the {ER}. The polar transmembrane sequences therefore act as primary determinants of oligomerization specificity through interplay between charge shielding and sequestration of polar surfaces within helix interfaces.}, pages = {1184--1192}, number = {8}, journaltitle = {Cell Reports}, shortjournal = {Cell Reports}, author = {Knoblich, Konstantin and Park, Soohyung and Lutfi, Mariam and van ’t Hag, Leonie and Conn, Charlotte E. and Seabrook, Shane A. and Newman, Janet and Czabotar, Peter E. and Im, Wonpil and Call, Matthew E. and Call, Melissa J.}, urldate = {2017-05-01}, date = {2015-05-26}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\72DGTS24\\Knoblich et al. - 2015 - Transmembrane Complexes of DAP12 Crystallized in L:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ETIS9SC7\\Knoblich et al. - 2015 - Transmembrane Complexes of DAP12 Crystallized in L.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\72DGTS24\\Knoblich et al. - 2015 - Transmembrane Complexes of DAP12 Crystallized in L:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S4SRST3J\\Knoblich et al. - 2015 - Transmembrane Complexes of DAP12 Crystallized in L.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IWJ8AVKU\\S2211124715004623:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9RJU73PV\\S2211124715004623.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IWJ8AVKU\\S2211124715004623:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I43GTFFA\\S2211124715004623.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KFBNSQMR\\S2211124715004623:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8E7IV4V5\\S2211124715004623.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KFBNSQMR\\S2211124715004623:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TQMWUZTD\\S2211124715004623.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QVVVB3XD\\Knoblich et al. - 2015 - Transmembrane Complexes of DAP12 Crystallized in L:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6WJNKJPR\\Knoblich et al. - 2015 - Transmembrane Complexes of DAP12 Crystallized in L.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QVVVB3XD\\Knoblich et al. - 2015 - Transmembrane Complexes of DAP12 Crystallized in L:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ITV8BRE4\\Knoblich et al. - 2015 - Transmembrane Complexes of DAP12 Crystallized in L.pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QVVVB3XD\\Knoblich et al. - 2015 - Transmembrane Complexes of DAP12 Crystallized in L.pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\72DGTS24\\Knoblich et al. - 2015 - Transmembrane Complexes of DAP12 Crystallized in L.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KFBNSQMR\\S2211124715004623.html:text/html;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IWJ8AVKU\\S2211124715004623.html:text/html} } @article{newman_x-ray_2015, title = {X-Ray Structure of the Amidase Domain of {AtzF}, the Allophanate Hydrolase from the Cyanuric Acid-Mineralizing Multienzyme Complex}, volume = {81}, issn = {0099-2240, 1098-5336}, url = {http://aem.asm.org/content/81/2/470}, doi = {10.1128/AEM.02783-14}, abstract = {The activity of the allophanate hydrolase from Pseudomonas sp. strain {ADP}, {AtzF}, provides the final hydrolytic step for the mineralization of s-triazines, such as atrazine and cyanuric acid. Indeed, the action of {AtzF} provides metabolic access to two of the three nitrogens in each triazine ring. The X-ray structure of the N-terminal amidase domain of {AtzF} reveals that it is highly homologous to allophanate hydrolases involved in a different catabolic process in other organisms (i.e., the mineralization of urea). The smaller C-terminal domain does not appear to have a physiologically relevant catalytic function, as reported for the allophanate hydrolase of Kluyveromyces lactis, when purified enzyme was tested in vitro. However, the C-terminal domain does have a function in coordinating the quaternary structure of {AtzF}. Interestingly, we also show that {AtzF} forms a large, ca. 660-{kDa}, multienzyme complex with {AtzD} and {AtzE} that is capable of mineralizing cyanuric acid. The function of this complex may be to channel substrates from one active site to the next, effectively protecting unstable metabolites, such as allophanate, from solvent-mediated decarboxylation to a dead-end metabolic product.}, pages = {470--480}, number = {2}, journaltitle = {Applied and Environmental Microbiology}, shortjournal = {Appl. Environ. Microbiol.}, author = {Newman, Janet and Cowieson, Nathan P. and French, Nigel G. and Campbell, Peter M. and Briggs, Lyndall J. and Warden, Andrew C. and Easton, Christopher J. and Peat, Thomas S. and Scott, Colin}, urldate = {2017-05-01}, date = {2015-01-15}, langid = {english}, pmid = {25362066}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CXMPF4GU\\Balotra et al. - 2015 - X-Ray Structure of the Amidase Domain of AtzF, the:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\U68A2VWT\\Balotra et al. - 2015 - X-Ray Structure of the Amidase Domain of AtzF, the.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CXMPF4GU\\Balotra et al. - 2015 - X-Ray Structure of the Amidase Domain of AtzF, the:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DIAZX3KI\\Balotra et al. - 2015 - X-Ray Structure of the Amidase Domain of AtzF, the.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DA3F2E5Z\\470:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\83CMER55\\470.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DA3F2E5Z\\470:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MU2QANHM\\470.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NDHG33DW\\Balotra et al. - 2015 - X-Ray Structure of the Amidase Domain of AtzF, the:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\92X4J5Q3\\Balotra et al. - 2015 - X-Ray Structure of the Amidase Domain of AtzF, the.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NDHG33DW\\Balotra et al. - 2015 - X-Ray Structure of the Amidase Domain of AtzF, the:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N6QJHH43\\Balotra et al. - 2015 - X-Ray Structure of the Amidase Domain of AtzF, the.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SDNZFKDN\\470:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8NCS5F8H\\470.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SDNZFKDN\\470:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IHPEK6C2\\470.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CXMPF4GU\\Balotra et al. - 2015 - X-Ray Structure of the Amidase Domain of AtzF, the.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NDHG33DW\\Balotra et al. - 2015 - X-Ray Structure of the Amidase Domain of AtzF, the.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DA3F2E5Z\\470.html:text/html;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SDNZFKDN\\470.html:text/html} } @article{ristic_formulation_2015, title = {Formulation screening by differential scanning fluorimetry: how often does it work?}, volume = {71}, rights = {Copyright (c) 2015 International Union of Crystallography}, issn = {2053-230X}, url = {http://scripts.iucr.org/cgi-bin/paper?rl5104}, doi = {10.1107/S2053230X15012662}, shorttitle = {Formulation screening by differential scanning fluorimetry}, abstract = {There is strong evidence to suggest that a protein sample needs to be well folded and uniform in order to form protein crystals, and it is accepted knowledge that the formulation can have profound effects on the behaviour of the protein sample. The technique of differential scanning fluorimetry ({DSF}) is a very accessible method to determine protein stability as a function of the formulation chemistry and the temperature. A diverse set of 252 soluble protein samples was subjected to a standard formulation-screening protocol using {DSF}. Automated analysis of the {DSF} results suggest that in over 35\% of cases buffer screening significantly increases the stability of the protein sample. Of the 28 standard formulations tested, three stood out as being statistically better than the others: these included a formulation containing the buffer citrate, long known to be `protein friendly'; bis-tris and {ADA} were also identified as being very useful buffers in protein formulations.}, pages = {1359--1364}, number = {10}, journaltitle = {Acta Crystallographica Section F: Structural Biology Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Ristic, M. and Rosa, N. and Seabrook, S. A. and Newman, J.}, urldate = {2017-05-01}, date = {2015-10-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5ZJRVXVB\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VRPIEFX9\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5ZJRVXVB\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z64EVGIU\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T2TKJDIE\\Ristic et al. - 2015 - Formulation screening by differential scanning flu:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KBEH5PED\\Ristic et al. - 2015 - Formulation screening by differential scanning flu.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T2TKJDIE\\Ristic et al. - 2015 - Formulation screening by differential scanning flu:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IAV2BRE9\\Ristic et al. - 2015 - Formulation screening by differential scanning flu.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T2TKJDIE\\Ristic et al. - 2015 - Formulation screening by differential scanning flu.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5ZJRVXVB\\paper.html:text/html} } @article{wilding_-alanine_2016, title = {A β-Alanine Catabolism Pathway Containing a Highly Promiscuous ω-Transaminase in the 12-Aminododecanate-Degrading Pseudomonas sp. Strain {AAC}}, volume = {82}, issn = {0099-2240, 1098-5336}, url = {http://aem.asm.org/content/82/13/3846}, doi = {10.1128/AEM.00665-16}, abstract = {We previously isolated the transaminase {KES}23458 from Pseudomonas sp. strain {AAC} as a promising biocatalyst for the production of 12-aminododecanoic acid, a constituent building block of nylon-12. Here, we report the subsequent characterization of this transaminase. It exhibits activity with a broad substrate range which includes α-, β-, and ω-amino acids, as well as α,ω-diamines and a number of other industrially relevant compounds. It is therefore a prospective candidate for the biosynthesis of a range of polyamide monomers. The crystal structure of {KES}23458 revealed that the protein forms a dimer containing a large active site pocket and unusual phosphorylated histidine residues. To infer the physiological role of the transaminase, we expressed, purified, and characterized a dehydrogenase from the same operon, {KES}23460. Unlike the transaminase, the dehydrogenase was shown to be quite selective, catalyzing the oxidation of malonic acid semialdehyde, formed from β-alanine transamination via {KES}23458. In keeping with previous reports, the dehydrogenase was shown to catalyze both a coenzyme A ({CoA})-dependent reaction to form acetyl-{CoA} and a significantly slower {CoA}-independent reaction to form acetate. These findings support the original functional assignment of {KES}23458 as a β-alanine transaminase. However, a seemingly well-adapted active site and promiscuity toward unnatural compounds, such as 12-aminododecanoic acid, suggest that this enzyme could perform multiple functions for Pseudomonas sp. strain {AAC}. {IMPORTANCE} We describe the characterization of an industrially relevant transaminase able to metabolize 12-aminododecanoic acid, a constituent building block of the widely used polymer nylon-12, and we report the biochemical and structural characterization of the transaminase protein. A physiological role for this highly promiscuous enzyme is proposed based on the characterization of a related gene from the host organism. Molecular dynamics simulations were carried out to compare the conformational changes in the transaminase protein to better understand the determinants of specificity in the protein. This study makes a substantial contribution that is of interest to the broad biotechnology and enzymology communities, providing insights into the catalytic activity of an industrially relevant biocatalyst as well as the biological function of this operon.}, pages = {3846--3856}, number = {13}, journaltitle = {Applied and Environmental Microbiology}, shortjournal = {Appl. Environ. Microbiol.}, author = {Wilding, Matthew and Peat, Thomas S. and Newman, Janet and Scott, Colin}, urldate = {2017-05-01}, date = {2016-07-01}, langid = {english}, pmid = {27107110}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9MIDDEB5\\3846:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\M9UGXT57\\3846.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9MIDDEB5\\3846:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IHSFZT32\\3846.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KHQ2KNVC\\Wilding et al. - 2016 - A β-Alanine Catabolism Pathway Containing a Highly:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z8IZQ8WI\\Wilding et al. - 2016 - A β-Alanine Catabolism Pathway Containing a Highly.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KHQ2KNVC\\Wilding et al. - 2016 - A β-Alanine Catabolism Pathway Containing a Highly:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\57SSDJSC\\Wilding et al. - 2016 - A β-Alanine Catabolism Pathway Containing a Highly.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KHQ2KNVC\\Wilding et al. - 2016 - A β-Alanine Catabolism Pathway Containing a Highly.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9MIDDEB5\\3846.html:text/html} } @article{zabara_nanoscience_2017, title = {The nanoscience behind the art of in-meso crystallization of membrane proteins}, volume = {9}, url = {http://pubs.rsc.org/en/Content/ArticleLanding/2017/NR/C6NR07634C}, doi = {10.1039/C6NR07634C}, pages = {754--763}, number = {2}, journaltitle = {Nanoscale}, author = {Zabara, Alexandru and G. Meikle, Thomas and Newman, Janet and S. Peat, Thomas and E. Conn, Charlotte and J. Drummond, Calum}, urldate = {2017-05-01}, date = {2017}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IN7W3IKB\\Zabara et al. - 2017 - The nanoscience behind the art of in-meso crystall:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2CD97ZNS\\Zabara et al. - 2017 - The nanoscience behind the art of in-meso crystall.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IN7W3IKB\\Zabara et al. - 2017 - The nanoscience behind the art of in-meso crystall:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EMQD9B8X\\Zabara et al. - 2017 - The nanoscience behind the art of in-meso crystall.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SVVVSM2E\\c6nr07634c:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QS48TWAN\\c6nr07634c.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SVVVSM2E\\c6nr07634c:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3ET8MQT7\\c6nr07634c.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IN7W3IKB\\Zabara et al. - 2017 - The nanoscience behind the art of in-meso crystall.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SVVVSM2E\\c6nr07634c.html:text/html} } @article{balotra_crystallization_2014, title = {Crystallization and preliminary X-ray diffraction analysis of the amidase domain of allophanate hydrolase from Pseudomonas sp. strain {ADP}}, volume = {70}, rights = {http://creativecommons.org/licenses/by/2.0/uk}, issn = {2053-230X}, url = {http://scripts.iucr.org/cgi-bin/paper?no5038}, doi = {10.1107/S2053230X13034705}, abstract = {The allophanate hydrolase from Pseudomonas sp. strain {ADP} was expressed and purified, and a tryptic digest fragment was subsequently identified, expressed and purified. This 50 {kDa} construct retained amidase activity and was crystallized. The crystals diffracted to 2.5 Å resolution and adopted space group P21, with unit-cell parameters a = 82.4, b = 179.2, c = 112.6 Å, β = 106.6°.}, pages = {310--315}, number = {3}, journaltitle = {Acta Crystallographica Section F: Structural Biology Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Balotra, S. and Newman, J. and French, N. G. and Briggs, L. J. and Peat, T. S. and Scott, C.}, urldate = {2017-05-15}, date = {2014-03-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C9ZUIM9M\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CPBR2RUX\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C9ZUIM9M\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BCGMV9K7\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KS26RN58\\Balotra et al. - 2014 - Crystallization and preliminary X-ray diffraction:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4H4NISXU\\Balotra et al. - 2014 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KS26RN58\\Balotra et al. - 2014 - Crystallization and preliminary X-ray diffraction:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KHM6HPC4\\Balotra et al. - 2014 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KS26RN58\\Balotra et al. - 2014 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C9ZUIM9M\\paper.html:text/html} } @article{kenny_nitrate_2014, title = {Nitrate in the active site of protein tyrosine phosphatase 1B is a putative mimetic of the transition state}, volume = {70}, rights = {Copyright (c) 2014 International Union of Crystallography}, issn = {1399-0047}, url = {http://scripts.iucr.org/cgi-bin/paper?kw5081}, doi = {10.1107/S1399004713031052}, abstract = {The X-ray crystal structure of the complex of protein tyrosine phosphatase 1B with nitrate anion has been determined and modelled quantum-mechanically. Two protomers were present in the structure, one with the mechanistically important {WPD} loop closed and the other with this loop open. Nitrate was observed bound to each protomer, making close contacts with the S atom of the catalytic cysteine and a tyrosine residue from a crystallographically related protomer.}, pages = {565--571}, number = {2}, journaltitle = {Acta Crystallographica Section D: Biological Crystallography}, shortjournal = {Acta Cryst D, Acta Cryst Sect D, Acta Crystallogr D, Acta Crystallogr Sect D, Acta Crystallogr D Biol Crystallogr, Acta Crystallogr Sect D Biol Crystallogr}, author = {Kenny, P. W. and Newman, J. and Peat, T. S.}, urldate = {2017-05-15}, date = {2014-02-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GKCE7GZ2\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KEFEM9PP\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GKCE7GZ2\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZPU232PH\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SBUZNRDH\\Kenny et al. - 2014 - Nitrate in the active site of protein tyrosine pho:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QXUQS78A\\Kenny et al. - 2014 - Nitrate in the active site of protein tyrosine pho.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SBUZNRDH\\Kenny et al. - 2014 - Nitrate in the active site of protein tyrosine pho:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AN2HZATM\\Kenny et al. - 2014 - Nitrate in the active site of protein tyrosine pho.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SBUZNRDH\\Kenny et al. - 2014 - Nitrate in the active site of protein tyrosine pho.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GKCE7GZ2\\paper.html:text/html} } @article{van_t_hag_meso_2014, title = {In Meso Crystallization: Compatibility of Different Lipid Bicontinuous Cubic Mesophases with the Cubic Crystallization Screen in Aqueous Solution}, volume = {14}, issn = {1528-7483}, url = {http://dx.doi.org/10.1021/cg4018954}, doi = {10.1021/cg4018954}, shorttitle = {In Meso Crystallization}, abstract = {In meso crystallization uses bicontinuous cubic lipidic mesophases as matrices for the crystallization of membrane proteins. In this work, we look at the impact of a screen specifically marketed as compatible with the cubic mesophase, the Cubic crystallization screen (Emerald {BioSystems}), on the cubic mesophases formed by three different lipids: monoolein, monopalmitolein, and phytantriol. The Cubic screen was found to be compatible with cubic mesophase retention under most crystallization conditions for all three lipids studied. The effect of the individual components comprising the multicomponent screen was deconvoluted in two ways. Initially, the effect of specific poly(ethylene glycol) ({PEG}) and salt components on the cubic mesophase was determined using small-angle X-ray scattering ({SAXS}). The effect of high-molecular-weight (Mw) {PEG} was shown to dominate the phase behavior within the screen. The effect of additional salts present within the screen becomes important for low Mw {PEG} molecules. Finally, a recently developed multiple linear-regression modeling method was shown to deconvolute the effect of individual components within the screen effectively.}, pages = {1771--1781}, number = {4}, journaltitle = {Crystal Growth \& Design}, shortjournal = {Crystal Growth \& Design}, author = {van ’t Hag, Leonie and Darmanin, Connie and Le, Tu C. and Mudie, Stephen and Conn, Charlotte E. and Drummond, Calum J.}, urldate = {2017-05-15}, date = {2014-04-02}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ST52Z9AE\\van ’t Hag et al. - 2014 - In Meso Crystallization Compatibility of Differen.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N5XHZP28\\cg4018954.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N5XHZP28\\cg4018954:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TDZXTFE8\\cg4018954.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N5XHZP28\\cg4018954:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FHFH7AXT\\cg4018954.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ST52Z9AE\\van ’t Hag et al. - 2014 - In Meso Crystallization Compatibility of Differen:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PWK46FU9\\van ’t Hag et al. - 2014 - In Meso Crystallization Compatibility of Differen.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ST52Z9AE\\van ’t Hag et al. - 2014 - In Meso Crystallization Compatibility of Differen:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JGS5AB9B\\van ’t Hag et al. - 2014 - In Meso Crystallization Compatibility of Differen.pdf:application/pdf} } @article{peat_interrogating_2014, title = {Interrogating {HIV} integrase for compounds that bind- a {SAMPL} challenge}, volume = {28}, issn = {0920-654X, 1573-4951}, url = {https://link.springer.com/article/10.1007/s10822-014-9721-7}, doi = {10.1007/s10822-014-9721-7}, abstract = {Tremendous gains and novel methods are often developed when people are challenged to do something new or difficult. This process is enhanced when people compete against each other-this can be seen in sport as well as in science and technology (e.g. the space race). The {SAMPL} challenges, like the {CASP} challenges, aim to challenge modellers and software developers to develop new ways of looking at molecular interactions so the community as a whole can progress in the accurate prediction of these interactions. In order for this challenge to occur, data must be supplied so the prospective test can be done. We have supplied unpublished data related to a drug discovery program run several years ago on {HIV} integrase for the {SAMPL}4 challenge. This paper describes the methods used to obtain these data and the chemistry involved.}, pages = {347--362}, number = {4}, journaltitle = {Journal of Computer-Aided Molecular Design}, shortjournal = {J Comput Aided Mol Des}, author = {Peat, Thomas S. and Dolezal, Olan and Newman, Janet and Mobley, David and Deadman, John J.}, urldate = {2017-05-15}, date = {2014-04-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\96RE8ZG4\\s10822-014-9721-7:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZB6VEHMA\\s10822-014-9721-7.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\96RE8ZG4\\s10822-014-9721-7:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DSDZGG8H\\s10822-014-9721-7.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KF3JMBSJ\\Peat et al. - 2014 - Interrogating HIV integrase for compounds that bin:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JHV3HAHJ\\Peat et al. - 2014 - Interrogating HIV integrase for compounds that bin.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KF3JMBSJ\\Peat et al. - 2014 - Interrogating HIV integrase for compounds that bin:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S7T3AM9D\\Peat et al. - 2014 - Interrogating HIV integrase for compounds that bin.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KF3JMBSJ\\Peat et al. - 2014 - Interrogating HIV integrase for compounds that bin.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\96RE8ZG4\\s10822-014-9721-7.html:text/html} } @article{atkinson_identification_2014, title = {Identification of the bona fide {DHDPS} from a common plant pathogen}, volume = {82}, issn = {1097-0134}, url = {http://onlinelibrary.wiley.com/doi/10.1002/prot.24539/abstract}, doi = {10.1002/prot.24539}, abstract = {Agrobacterium tumefaciens is a Gram-negative soil-borne bacterium that causes Crown Gall disease in many economically important crops. The absence of a suitable chemical treatment means there is a need to discover new anti-Crown Gall agents and also characterize bona fide drug targets. One such target is dihydrodipicolinate synthase ({DHDPS}), a homo-tetrameric enzyme that catalyzes the committed step in the metabolic pathway yielding meso-diaminopimelate and lysine. Interestingly, there are 10 putative {DHDPS} genes annotated in the A. tumefaciens genome, including three whose structures have recently been determined ({PDB} {IDs}: 3B4U, 2HMC, and 2R8W). However, we show using quantitative enzyme kinetic assays that nine of the 10 {dapA} gene products, including 3B4U, 2HMC, and 2R8W, lack {DHDPS} function in vitro. A sequence alignment showed that the product of the {dapA}7 gene contains all of the conserved residues known to be important for {DHDPS} catalysis and allostery. This gene was cloned and the recombinant product expressed and purified. Our studies show that the purified enzyme (i) possesses {DHDPS} enzyme activity, (ii) is allosterically inhibited by lysine, and (iii) adopts the canonical homo-tetrameric structure in both solution and the crystal state. This study describes for the first time the structure, function and allostery of the bona fide {DHDPS} from A. tumefaciens, which offers insight into the rational design of pesticide agents for combating Crown Gall disease. Proteins 2014; 82:1869–1883. © 2014 Wiley Periodicals, Inc.}, pages = {1869--1883}, number = {9}, journaltitle = {Proteins: Structure, Function, and Bioinformatics}, shortjournal = {Proteins}, author = {Atkinson, Sarah C. and Hor, Lilian and Dogovski, Con and Dobson, Renwick C. J. and Perugini, Matthew A.}, urldate = {2017-05-15}, date = {2014-09-01}, langid = {english}, keywords = {allostery, allostery, analytical ultracentrifugation, analytical ultracentrifugation, Crown Gall disease, Crown Gall disease, dihydrodipicolinate synthase, dihydrodipicolinate synthase, enzyme kinetics, enzyme kinetics, enzyme structure, enzyme structure, lysine biosynthesis, lysine biosynthesis, X-ray crystallography, X-ray crystallography}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WWC5WRHJ\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FMDDWAZT\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WWC5WRHJ\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\G5FWX9U3\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z23JVJVD\\Atkinson et al. - 2014 - Identification of the bona fide DHDPS from a commo:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KKAK4CV2\\Atkinson et al. - 2014 - Identification of the bona fide DHDPS from a commo.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z23JVJVD\\Atkinson et al. - 2014 - Identification of the bona fide DHDPS from a commo:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I476MS8A\\Atkinson et al. - 2014 - Identification of the bona fide DHDPS from a commo.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z23JVJVD\\Atkinson et al. - 2014 - Identification of the bona fide DHDPS from a commo.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WWC5WRHJ\\abstract.html:text/html} } @article{moeker_cyclic_2014, title = {Cyclic Secondary Sulfonamides: Unusually Good Inhibitors of Cancer-Related Carbonic Anhydrase Enzymes}, volume = {57}, issn = {0022-2623}, url = {http://dx.doi.org/10.1021/jm500255y}, doi = {10.1021/jm500255y}, shorttitle = {Cyclic Secondary Sulfonamides}, abstract = {Carbonic anhydrase {IX} ({CA} {IX}) is a target for hypoxic cancer therapies, and the discovery of {CA} {IX} selective ligands is imperative for the development of these agents. Primary sulfonamides are broad specificity inhibitors of {CA} enzymes, while secondary sulfonamides are generally poor {CA} inhibitors. However, saccharin, a cyclic secondary sulfonamide, has unusually good inhibition of {CA} {IX} (Ki = 103 {nM}). In this study, we demonstrate that the affinity and selectivity of saccharin for {CA} {IX} can be further modulated when linked to hydrophobic or hydrophilic substituents. The hydrophilic glycoconjugate derivative (12) showed improved inhibition of {CA} {IX} (Ki = 49.5 {nM}) and extremely poor inhibition of the predominant off-target {CAs} (Ki {\textgreater} 50 000 {nM}) compared to saccharin. This {\textgreater}1000-fold selectivity for {CA} {IX} over off-target {CAs} is unprecedented for classical primary sulfonamide {CA} inhibitors. Our study highlights the potential of cyclic secondary sulfonamides to be exploited for the discovery of potent, cancer-selective {CA} inhibitors.}, pages = {3522--3531}, number = {8}, journaltitle = {Journal of Medicinal Chemistry}, shortjournal = {J. Med. Chem.}, author = {Moeker, Janina and Peat, Thomas S. and Bornaghi, Laurent F. and Vullo, Daniela and Supuran, Claudiu T. and Poulsen, Sally-Ann}, urldate = {2017-05-15}, date = {2014-04-24}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JCBQBX5V\\Moeker et al. - 2014 - Cyclic Secondary Sulfonamides Unusually Good Inhi.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2NJ3U3C9\\jm500255y.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2NJ3U3C9\\jm500255y:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7PRU5ZX3\\jm500255y.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2NJ3U3C9\\jm500255y:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HH67VR2C\\jm500255y.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JCBQBX5V\\Moeker et al. - 2014 - Cyclic Secondary Sulfonamides Unusually Good Inhi:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9UG456V6\\Moeker et al. - 2014 - Cyclic Secondary Sulfonamides Unusually Good Inhi.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JCBQBX5V\\Moeker et al. - 2014 - Cyclic Secondary Sulfonamides Unusually Good Inhi:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NIQ5J67I\\Moeker et al. - 2014 - Cyclic Secondary Sulfonamides Unusually Good Inhi.pdf:application/pdf} } @article{north_cloning_2014, title = {Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of N-acetylmannosamine kinase from methicillin-resistant Staphylococcus aureus}, volume = {70}, rights = {Copyright (c) 2014 International Union of Crystallography}, issn = {2053-230X}, url = {http://scripts.iucr.org/cgi-bin/paper?no5047}, doi = {10.1107/S2053230X14007250}, abstract = {N-Acetylmannosamine kinase ({EC} 2.7.1.60) is involved in the catabolism of sialic acid for many bacterial pathogens implicated in human disease such as Escherichia coli, Staphylococcus aureus, Vibrio cholerae and V. vulnificus. Interestingly, some human commensals and bacterial pathogens can scavenge sialic acids from their surrounding environment and degrade them as a source of carbon, nitrogen and energy. This process requires a cluster of genes known as the `Nan-Nag cluster', which have proven to be essential for S. aureus growth on sialic acids, suggesting that the pathway is a viable antimicrobial drug target. The enzyme N-acetylmannosamine kinase is involved in the catabolism of sialic acid, transferring a phosphate group from adenosine-5′-triphosphate to the C6 position of N-acetylmannosamine to generate N-acetylmannosamine-6-phosphate. The gene was cloned into an appropriate expression vector; recombinant protein was expressed in E. coli {BL}21 ({DE}3) cells and purified via anion-exchange chromatography, hydrophobic interaction chromatography and size-exclusion chromatography. Purified N-acetylmannosamine kinase was screened for crystallization. The best crystal diffracted to a resolution of beyond 2.6 Å in space group P2. Understanding the structural nature of this enzyme from methicillin-resistant S. aureus will provide insights necessary for the development of future antimicrobials.}, pages = {643--649}, number = {5}, journaltitle = {Acta Crystallographica Section F: Structural Biology Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {North, R. A. and Seizova, S. and Stampfli, A. and Kessans, S. A. and Suzuki, H. and Griffin, M. D. W. and Kvansakul, M. and Dobson, R. C. J.}, urldate = {2017-05-15}, date = {2014-05-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TEWVFQSA\\North et al. - 2014 - Cloning, expression, purification, crystallization:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5ZVS35UG\\North et al. - 2014 - Cloning, expression, purification, crystallization.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TEWVFQSA\\North et al. - 2014 - Cloning, expression, purification, crystallization:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RE8N7A8B\\North et al. - 2014 - Cloning, expression, purification, crystallization.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VMAVBCPI\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T2TTJMK7\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VMAVBCPI\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HZATW2HB\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TEWVFQSA\\North et al. - 2014 - Cloning, expression, purification, crystallization.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VMAVBCPI\\paper.html:text/html} } @article{oliver_purification_2014, title = {The purification, crystallization and preliminary X-ray diffraction analysis of two isoforms of meso-diaminopimelate decarboxylase from Arabidopsis thaliana}, volume = {70}, rights = {Copyright (c) 2014 International Union of Crystallography}, issn = {2053-230X}, url = {http://scripts.iucr.org/cgi-bin/paper?hc5170}, doi = {10.1107/S2053230X14007699}, abstract = {Diaminopimelate decarboxylase catalyses the last step in the diaminopimelate-biosynthetic pathway leading to S-lysine: the decarboxylation of meso-diaminopimelate to form S-lysine. Lysine biosynthesis occurs only in microorganisms and plants, and lysine is essential for the growth and development of animals. Thus, the diaminopimelate pathway represents an attractive target for antimicrobial and herbicide treatments and has received considerable attention from both a mechanistic and a structural viewpoint. Diaminopimelate decarboxylase has only been characterized in prokaryotic species. This communication describes the first structural studies of two diaminopimelate decarboxylase isoforms from a plant. The Arabidopsis thaliana diaminopimelate decarboxylase {cDNAs} At3g14390 (encoding {DapDc}1) and At5g11880 (encoding {DapDc}2) were cloned from genomic {DNA} and the recombinant proteins were expressed and purified from Escherichia coli Rosetta ({DE}3) cells. The crystals of {DapDc}1 and {DapDc}2 diffracted to beyond 2.00 and 2.27 Å resolution, respectively. Understanding the structural biology of diaminopimelate decarboxylase from a eukaryotic species will provide insights for the development of future herbicide treatments, in particular.}, pages = {663--668}, number = {5}, journaltitle = {Acta Crystallographica Section F: Structural Biology Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Oliver, M. R. and Crowther, J. M. and Leeman, M. M. and Kessans, S. A. and North, R. A. and Donovan, K. A. and Griffin, M. D. W. and Suzuki, H. and Hudson, A. O. and Kasanmascheff, M. and Dobson, R. C. J.}, urldate = {2017-05-15}, date = {2014-05-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E39CZ4RQ\\Oliver et al. - 2014 - The purification, crystallization and preliminary:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WVF7T97D\\Oliver et al. - 2014 - The purification, crystallization and preliminary .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E39CZ4RQ\\Oliver et al. - 2014 - The purification, crystallization and preliminary:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EHFWWWBB\\Oliver et al. - 2014 - The purification, crystallization and preliminary .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WSWZX7XZ\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J6CX5M7E\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WSWZX7XZ\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\948M9QUZ\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E39CZ4RQ\\Oliver et al. - 2014 - The purification, crystallization and preliminary .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WSWZX7XZ\\paper.html:text/html} } @article{murphy_insights_2014, title = {Insights into the evolution of divergent nucleotide-binding mechanisms among pseudokinases revealed by crystal structures of human and mouse {MLKL}}, volume = {457}, rights = {© The Authors Journal compilation © 2014 Biochemical Society}, issn = {0264-6021, 1470-8728}, url = {http://www.biochemj.org/content/457/3/369}, doi = {10.1042/BJ20131270}, abstract = {The pseudokinase {MLKL} (mixed lineage kinase domain-like) was identified recently as an essential checkpoint in the programmed necrosis or ‘necroptosis’ cell death pathway. In the present study, we report the crystal structure of the human {MLKL} pseudokinase domain at 1.7 Å (1 Å=0.1 nm) resolution and probe its nucleotide-binding mechanism by performing structure-based mutagenesis. By comparing the structures and nucleotide-binding determinants of human and mouse {MLKL} orthologues, the present study provides insights into the evolution of nucleotide-binding mechanisms among pseudokinases and their mechanistic divergence from conventional catalytically active protein kinases.}, pages = {369--377}, number = {3}, journaltitle = {Biochemical Journal}, author = {Murphy, James M. and Lucet, Isabelle S. and Hildebrand, Joanne M. and Tanzer, Maria C. and Young, Samuel N. and Sharma, Pooja and Lessene, Guillaume and Alexander, Warren S. and Babon, Jeffrey J. and Silke, John and Czabotar, Peter E.}, urldate = {2017-05-15}, date = {2014-02-01}, langid = {english}, pmid = {24219132}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AFSGUDW8\\Murphy et al. - 2014 - Insights into the evolution of divergent nucleotid:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AB92BE69\\Murphy et al. - 2014 - Insights into the evolution of divergent nucleotid.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AFSGUDW8\\Murphy et al. - 2014 - Insights into the evolution of divergent nucleotid:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GPHQEKRR\\Murphy et al. - 2014 - Insights into the evolution of divergent nucleotid.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HQ5KBBWA\\369:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BGWDFPDM\\369.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HQ5KBBWA\\369:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KNKEAM27\\369.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J72P5743\\Murphy et al. - 2014 - Insights into the evolution of divergent nucleotid:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KNT3Z2VT\\Murphy et al. - 2014 - Insights into the evolution of divergent nucleotid.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J72P5743\\Murphy et al. - 2014 - Insights into the evolution of divergent nucleotid:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P9XPZTE5\\Murphy et al. - 2014 - Insights into the evolution of divergent nucleotid.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TR286XZH\\369:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MGXKXFBQ\\369.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TR286XZH\\369:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZM2GNTHI\\369.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AFSGUDW8\\Murphy et al. - 2014 - Insights into the evolution of divergent nucleotid.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J72P5743\\Murphy et al. - 2014 - Insights into the evolution of divergent nucleotid.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HQ5KBBWA\\369.html:text/html;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TR286XZH\\369.html:text/html} } @article{richter_structural_2014, title = {Structural and functional analysis of {MiD}51, a dynamin receptor required for mitochondrial fission}, volume = {204}, rights = {© 2014 Richter et al.. This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 3.0 Unported license, as described at http://creativecommons.org/licenses/by-nc-sa/3.0/).}, issn = {0021-9525, 1540-8140}, url = {http://jcb.rupress.org/content/204/4/477}, doi = {10.1083/jcb.201311014}, abstract = {Mitochondrial fission is important for organelle transport, inheritance, and turnover, and alterations in fission are seen in neurological disease. In mammals, mitochondrial fission is executed by dynamin-related protein 1 (Drp1), a cytosolic guanosine triphosphatase that polymerizes and constricts the organelle. Recruitment of Drp1 to mitochondria involves receptors including Mff, {MiD}49, and {MiD}51. {MiD}49/51 form foci at mitochondrial constriction sites and coassemble with Drp1 to drive fission. Here, we solved the crystal structure of the cytosolic domain of human {MiD}51, which adopts a nucleotidyltransferase fold. Although {MiD}51 lacks catalytic residues for transferase activity, it specifically binds guanosine diphosphate and adenosine diphosphate. {MiD}51 mutants unable to bind nucleotides were still able to recruit Drp1. Disruption of an additional region in {MiD}51 that is not part of the nucleotidyltransferase fold blocked Drp1 recruitment and assembly of {MiD}51 into foci. {MiD}51 foci are also dependent on the presence of Drp1, and after scission they are distributed to daughter organelles, supporting the involvement of {MiD}51 in the fission apparatus.}, pages = {477--486}, number = {4}, journaltitle = {J Cell Biol}, shortjournal = {J Cell Biol}, author = {Richter, Viviane and Palmer, Catherine S. and Osellame, Laura D. and Singh, Abeer P. and Elgass, Kirstin and Stroud, David A. and Sesaki, Hiromi and Kvansakul, Marc and Ryan, Michael T.}, urldate = {2017-05-15}, date = {2014-02-17}, langid = {english}, pmid = {24515348}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T8FRT7AX\\Richter et al. - 2014 - Structural and functional analysis of MiD51, a dyn:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FKWBGBD9\\Richter et al. - 2014 - Structural and functional analysis of MiD51, a dyn.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T8FRT7AX\\Richter et al. - 2014 - Structural and functional analysis of MiD51, a dyn:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KMKWKTHP\\Richter et al. - 2014 - Structural and functional analysis of MiD51, a dyn.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XT3ZTT86\\477:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\F6636XZI\\477.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XT3ZTT86\\477:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MVSK26NK\\477.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T8FRT7AX\\Richter et al. - 2014 - Structural and functional analysis of MiD51, a dyn.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XT3ZTT86\\477.html:text/html} } @article{luft_crystallization_2014, title = {Crystallization screening: the influence of history on current practice}, volume = {70}, rights = {http://creativecommons.org/licenses/by/2.0/uk}, issn = {2053-230X}, url = {http://scripts.iucr.org/cgi-bin/paper?en5551}, doi = {10.1107/S2053230X1401262X}, shorttitle = {Crystallization screening}, abstract = {While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed.}, pages = {835--853}, number = {7}, journaltitle = {Acta Crystallographica Section F: Structural Biology Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Luft, J. R. and Newman, J. and Snell, E. H.}, urldate = {2017-05-15}, date = {2014-07-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EM2W7PQT\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8HZSBMBJ\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EM2W7PQT\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\H8UQGDP8\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZZ44JCJH\\Luft et al. - 2014 - Crystallization screening the influence of histor:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3QR7QFGH\\Luft et al. - 2014 - Crystallization screening the influence of histor.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZZ44JCJH\\Luft et al. - 2014 - Crystallization screening the influence of histor:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WUTASXND\\Luft et al. - 2014 - Crystallization screening the influence of histor.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZZ44JCJH\\Luft et al. - 2014 - Crystallization screening the influence of histor.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EM2W7PQT\\paper.html:text/html} } @article{ren_unprecedented_2014, title = {Unprecedented conformational flexibility revealed in the ligand-binding domains of the Bovicola ovis ecdysone receptor ({EcR}) and ultraspiracle ({USP}) subunits}, volume = {70}, rights = {Copyright (c) 2014 International Union of Crystallography}, issn = {1399-0047}, url = {http://scripts.iucr.org/cgi-bin/paper?mn5062}, doi = {10.1107/S1399004714009626}, abstract = {The heterodimeric ligand-binding region of the Bovicola ovis ecdysone receptor has been crystallized either in the presence of an ecdysteroid or a synthetic methylene lactam insecticide. Two X-ray crystallographic structures, determined at 2.7 Å resolution, show that the ligand-binding domains of both subunits of this receptor, like those of other nuclear receptors, can display significant conformational flexibility. Thermal melt experiments show that while ponasterone A stabilizes the higher order structure of the heterodimer in solution, the methylene lactam destabilizes it. The conformations of the {EcR} and {USP} subunits observed in the structure crystallized in the presence of the methylene lactam have not been seen previously in any ecdysone receptor structure and represent a new level of conformational flexibility for these important receptors. Interestingly, the new {USP} conformation presents an open, unoccupied ligand-binding pocket.}, pages = {1954--1964}, number = {7}, journaltitle = {Acta Crystallographica Section D: Biological Crystallography}, shortjournal = {Acta Cryst D, Acta Cryst Sect D, Acta Crystallogr D, Acta Crystallogr Sect D, Acta Crystallogr D Biol Crystallogr, Acta Crystallogr Sect D Biol Crystallogr}, author = {Ren, B. and Peat, T. S. and Streltsov, V. A. and Pollard, M. and Fernley, R. and Grusovin, J. and Seabrook, S. and Pilling, P. and Phan, T. and Lu, L. and Lovrecz, G. O. and Graham, L. D. and Hill, R. J.}, urldate = {2017-05-15}, date = {2014-07-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2CZEQEXD\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RVXSXXPB\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2CZEQEXD\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T82KZDGZ\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\728CIBE2\\Ren et al. - 2014 - Unprecedented conformational flexibility revealed:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TRMCTABH\\Ren et al. - 2014 - Unprecedented conformational flexibility revealed .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\728CIBE2\\Ren et al. - 2014 - Unprecedented conformational flexibility revealed:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KX4RHDRD\\Ren et al. - 2014 - Unprecedented conformational flexibility revealed .pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\728CIBE2\\Ren et al. - 2014 - Unprecedented conformational flexibility revealed .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2CZEQEXD\\paper.html:text/html} } @article{brouwer_bak_2014, title = {Bak Core and Latch Domains Separate during Activation, and Freed Core Domains Form Symmetric Homodimers}, volume = {55}, issn = {1097-2765}, url = {http://www.sciencedirect.com/science/article/pii/S1097276514006091}, doi = {10.1016/j.molcel.2014.07.016}, abstract = {Summary Apoptotic stimuli activate and oligomerize the proapoptotic proteins Bak and Bax, resulting in mitochondrial outer-membrane permeabilization and subsequent cell death. This activation can occur when certain {BH}3-only proteins interact directly with Bak and Bax. Recently published crystal structures reveal that Bax separates into core and latch domains in response to {BH}3 peptides. The distinguishing characteristics of {BH}3 peptides capable of directly activating Bax were also elucidated. Here we identify specific {BH}3 peptides capable of “unlatching” Bak and describe structural insights into Bak activation and oligomerization. Crystal structures and crosslinking experiments demonstrate that Bak undergoes a conformational change similar to that of Bax upon activation. A structure of the Bak core domain dimer provides a high-resolution image of this key intermediate in the pore-forming oligomer. Our results confirm an analogous mechanism for activation and dimerization of Bak and Bax in response to certain {BH}3 peptides.}, pages = {938--946}, number = {6}, journaltitle = {Molecular Cell}, shortjournal = {Molecular Cell}, author = {Brouwer, Jason M. and Westphal, Dana and Dewson, Grant and Robin, Adeline Y. and Uren, Rachel T. and Bartolo, Ray and Thompson, Geoff V. and Colman, Peter M. and Kluck, Ruth M. and Czabotar, Peter E.}, urldate = {2017-05-15}, date = {2014-09-18}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\48NG844G\\Brouwer et al. - 2014 - Bak Core and Latch Domains Separate during Activat:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6GJ2QVBX\\Brouwer et al. - 2014 - Bak Core and Latch Domains Separate during Activat.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\48NG844G\\Brouwer et al. - 2014 - Bak Core and Latch Domains Separate during Activat:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\D23KNZTV\\Brouwer et al. - 2014 - Bak Core and Latch Domains Separate during Activat.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BP624Q9E\\S1097276514006091:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DI578UGQ\\S1097276514006091.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BP624Q9E\\S1097276514006091:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\55FHBKR2\\S1097276514006091.html:text/html;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\48NG844G\\Brouwer et al. - 2014 - Bak Core and Latch Domains Separate during Activat.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BP624Q9E\\S1097276514006091.html:text/html} } @article{calero_identifying_2014, title = {Identifying, studying and making good use of macromolecular crystals}, volume = {70}, rights = {http://creativecommons.org/licenses/by/2.0/uk}, issn = {2053-230X}, url = {http://scripts.iucr.org/cgi-bin/paper?en5553}, doi = {10.1107/S2053230X14016574}, abstract = {Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed.}, pages = {993--1008}, number = {8}, journaltitle = {Acta Crystallographica Section F: Structural Biology Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Calero, G. and Cohen, A. E. and Luft, J. R. and Newman, J. and Snell, E. H.}, urldate = {2017-05-15}, date = {2014-08-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GNSVWXMP\\Calero et al. - 2014 - Identifying, studying and making good use of macro:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JQ4H67FG\\Calero et al. - 2014 - Identifying, studying and making good use of macro.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GNSVWXMP\\Calero et al. - 2014 - Identifying, studying and making good use of macro:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P93PD4U9\\Calero et al. - 2014 - Identifying, studying and making good use of macro.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\STU6JU44\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JFHFCR56\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\STU6JU44\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JS66N8JC\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GNSVWXMP\\Calero et al. - 2014 - Identifying, studying and making good use of macro.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\STU6JU44\\paper.html:text/html} } @article{chen_contrasting_2014, title = {Contrasting Effects of Nanoparticle Binding on Protein Denaturation}, volume = {118}, issn = {1932-7447}, url = {http://dx.doi.org/10.1021/jp506135m}, doi = {10.1021/jp506135m}, abstract = {Understanding the interactions between nanoparticles ({NPs}) and proteins is essential for the design of bionanotechnology and biomedicine and for delineating the biological implications of nanomaterials for safe nanotechnology. In the present study we have examined protein denaturation in the presence of {NPs}, using the high-throughput technique of differential scanning fluorometry. Specifically, the melting temperature of human immunoglobulin ({IgG}) rose from 59.5 to 68.5 °C while that of lysozyme dropped from 74.0 to 68.8 °C for increasing {NP}:protein molar ratios. This contrast in protein stability was further examined by circular dichroism spectroscopy and Thioflavin T measurements, where a marked increase in β-sheets as well as amyloid fibrillation occurred in lysozyme while small changes were seen in the secondary structure of {IgG}. Our immunoassays further revealed a greatly elevated cytokine production in the cells treated with fullerol-lysozyme and a mostly unchanged {TNF}-α secretion in {THP}-1 cells exposed to fullerol-{IgG}, suggesting a connection between changes in protein secondary structure induced by fullerol binding and their triggered immune responses. These contrasting effects imply that, due to their finite solubility and size {NPs} display the duality of both a particle and a chemical and, therefore, do not conform to the conventional role of a ligand in protein stabilization.}, pages = {22069--22078}, number = {38}, journaltitle = {The Journal of Physical Chemistry C}, shortjournal = {J. Phys. Chem. C}, author = {Chen, Pengyu and Seabrook, Shane A. and Epa, V. Chandana and Kurabayashi, Katsuo and Barnard, Amanda S. and Winkler, David A. and Kirby, Jason K. and Ke, Pu Chun}, urldate = {2017-05-15}, date = {2014-09-25}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7U3PJWNX\\Chen et al. - 2014 - Contrasting Effects of Nanoparticle Binding on Pro.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BZURFFZD\\jp506135m.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7U3PJWNX\\Chen et al. - 2014 - Contrasting Effects of Nanoparticle Binding on Pro:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UD8PKECK\\Chen et al. - 2014 - Contrasting Effects of Nanoparticle Binding on Pro.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7U3PJWNX\\Chen et al. - 2014 - Contrasting Effects of Nanoparticle Binding on Pro:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WUDMTMQU\\Chen et al. - 2014 - Contrasting Effects of Nanoparticle Binding on Pro.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BZURFFZD\\jp506135m:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UDCRPUP4\\jp506135m.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BZURFFZD\\jp506135m:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A6J9Q8GZ\\jp506135m.html:text/html} } @article{jackson_300-fold_2014, title = {300-Fold Increase in Production of the Zn2+-Dependent Dechlorinase {TrzN} in Soluble Form via Apoenzyme Stabilization}, volume = {80}, issn = {0099-2240, 1098-5336}, url = {http://aem.asm.org/content/80/13/4003}, doi = {10.1128/AEM.00916-14}, abstract = {Microbial metalloenzymes constitute a large library of biocatalysts, a number of which have already been shown to catalyze the breakdown of toxic chemicals or industrially relevant chemical transformations. However, while there is considerable interest in harnessing these catalysts for biotechnology, for many of the enzymes, their large-scale production in active, soluble form in recombinant systems is a significant barrier to their use. In this work, we demonstrate that as few as three mutations can result in a 300-fold increase in the expression of soluble {TrzN}, an enzyme from Arthrobacter aurescens with environmental applications that catalyzes the hydrolysis of triazine herbicides, in Escherichia coli. Using a combination of X-ray crystallography, kinetic analysis, and computational simulation, we show that the majority of the improvement in expression is due to stabilization of the apoenzyme rather than the metal ion-bound holoenzyme. This provides a structural and mechanistic explanation for the observation that many compensatory mutations can increase levels of soluble-protein production without increasing the stability of the final, active form of the enzyme. This study provides a molecular understanding of the importance of the stability of metal ion free states to the accumulation of soluble protein and shows that differences between apoenzyme and holoenzyme structures can result in mutations affecting the stability of either state differently.}, pages = {4003--4011}, number = {13}, journaltitle = {Applied and Environmental Microbiology}, shortjournal = {Appl. Environ. Microbiol.}, author = {Jackson, Colin J. and Coppin, Christopher W. and Carr, Paul D. and Aleksandrov, Alexey and Wilding, Matthew and Sugrue, Elena and Ubels, Joanna and Paks, Michael and Newman, Janet and Peat, Thomas S. and Russell, Robyn J. and Field, Martin and Weik, Martin and Oakeshott, John G. and Scott, Colin}, urldate = {2017-05-15}, date = {2014-07-01}, langid = {english}, pmid = {24771025}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\94BTI3C9\\4003:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FIKAAGAB\\4003.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\94BTI3C9\\4003:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6NZ6N6XV\\4003.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QRZMTK7U\\Jackson et al. - 2014 - 300-Fold Increase in Production of the Zn2+-Depend:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7AAURWEF\\Jackson et al. - 2014 - 300-Fold Increase in Production of the Zn2+-Depend.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QRZMTK7U\\Jackson et al. - 2014 - 300-Fold Increase in Production of the Zn2+-Depend:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9E4I5PAI\\Jackson et al. - 2014 - 300-Fold Increase in Production of the Zn2+-Depend.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QRZMTK7U\\Jackson et al. - 2014 - 300-Fold Increase in Production of the Zn2+-Depend.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\94BTI3C9\\4003.html:text/html} } @article{mele_quantifying_2014, title = {Quantifying the quality of the experiments used to grow protein crystals: the {iQC} suite}, volume = {47}, rights = {Copyright (c) 2014 International Union of Crystallography}, issn = {1600-5767}, url = {http://scripts.iucr.org/cgi-bin/paper?aj5232}, doi = {10.1107/S1600576714009728}, shorttitle = {Quantifying the quality of the experiments used to grow protein crystals}, abstract = {Millions of crystallization trials are set up each year, with no clear metrics for determining if the experiments were correctly dispensed. This article reports the development of a software tool ({iQC} – image Quality Control) that recognizes factors associated with suboptimal experimental control during the setting up of protein crystallization trials. In its simplest form, {iQC} returns a report that gives an overall rating to the quality of an experimental setup. The {iQC} software is able to identify many common problems observed in setting up crystallization trials – droplets that have associated splatter; droplets with air bubbles; the positional accuracy of droplet placement; elongated or otherwise `non-circular' drops – as well as detecting small and large droplets. An obvious use of this application is to track the status of the instrumentation used to set up crystallization trials in a multi-user laboratory.}, pages = {1097--1106}, number = {3}, journaltitle = {Journal of Applied Crystallography}, shortjournal = {J Appl Cryst, J Appl Crystallogr}, author = {Mele, K. and Li, R. and Fazio, V. J. and Newman, J.}, urldate = {2017-05-15}, date = {2014-06-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CDXSPAFN\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7B8IG3ZM\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CDXSPAFN\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HIMDRKQ8\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SGWFRTUF\\Mele et al. - 2014 - Quantifying the quality of the experiments used to:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AA97J37B\\Mele et al. - 2014 - Quantifying the quality of the experiments used to.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SGWFRTUF\\Mele et al. - 2014 - Quantifying the quality of the experiments used to:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\D6VV68KN\\Mele et al. - 2014 - Quantifying the quality of the experiments used to.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SGWFRTUF\\Mele et al. - 2014 - Quantifying the quality of the experiments used to.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CDXSPAFN\\paper.html:text/html} } @article{newman_whats_2014, title = {What’s in a Name? Moving Towards a Limited Vocabulary for Macromolecular Crystallisation}, volume = {67}, issn = {1445-0038}, url = {http://www.publish.csiro.au/CH/CH14199}, doi = {10.1071/CH14199}, shorttitle = {What’s in a Name?}, abstract = {Australian Journal of Chemistry - an International Journal for Chemical Science publishes research papers from all fields of chemical science.}, pages = {1813--1817}, number = {12}, journaltitle = {Australian Journal of Chemistry}, shortjournal = {Aust. J. Chem.}, author = {Newman, Janet and Peat, Thomas S. and Savage, G. Paul}, urldate = {2017-05-15}, date = {2014-12-24}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\D9QKC8I8\\CH14199:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MQ9A7XC5\\CH14199.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\D9QKC8I8\\CH14199:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TNNCSXM3\\CH14199.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VBPK4W56\\Newman et al. - 2014 - What’s in a Name Moving Towards a Limited Vocabul:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4XKAA9FD\\Newman et al. - 2014 - What’s in a Name Moving Towards a Limited Vocabul.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VBPK4W56\\Newman et al. - 2014 - What’s in a Name Moving Towards a Limited Vocabul:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VE22ZKK2\\Newman et al. - 2014 - What’s in a Name Moving Towards a Limited Vocabul.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VBPK4W56\\Newman et al. - 2014 - What’s in a Name Moving Towards a Limited Vocabul.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\D9QKC8I8\\CH14199.html:text/html} } @article{lee_functional_2014, title = {The Functional Differences between Pro-survival and Pro-apoptotic B Cell Lymphoma 2 (Bcl-2) Proteins Depend on Structural Differences in Their Bcl-2 Homology 3 ({BH}3) Domains}, volume = {289}, issn = {0021-9258, 1083-351X}, url = {http://www.jbc.org/content/289/52/36001}, doi = {10.1074/jbc.M114.610758}, abstract = {Bcl-2 homology 3 ({BH}3) domains are short sequence motifs that mediate nearly all protein-protein interactions between B cell lymphoma 2 (Bcl-2) family proteins in the intrinsic apoptotic cell death pathway. These sequences are found on both pro-survival and pro-apoptotic members, although their primary function is believed to be associated with induction of cell death. Here, we identify critical features of the {BH}3 domains of pro-survival proteins that distinguish them functionally from their pro-apoptotic counterparts. Biochemical and x-ray crystallographic studies demonstrate that these differences reduce the capacity of most pro-survival proteins to form high affinity “{BH}3-in-groove” complexes that are critical for cell death induction. Switching these residues for the corresponding residues in Bcl-2 homologous antagonist/killer (Bak) increases the binding affinity of isolated {BH}3 domains for pro-survival proteins; however, their exchange in the context of the parental protein causes rapid proteasomal degradation due to protein destabilization. This is supported by further x-ray crystallographic studies that capture elements of this destabilization in one pro-survival protein, Bcl-w. In pro-apoptotic Bak, we demonstrate that the corresponding distinguishing residues are important for its cell-killing capacity and antagonism by pro-survival proteins.}, pages = {36001--36017}, number = {52}, journaltitle = {Journal of Biological Chemistry}, shortjournal = {J. Biol. Chem.}, author = {Lee, Erinna F. and Dewson, Grant and Evangelista, Marco and Pettikiriarachchi, Anne and Gold, Grace J. and Zhu, Haoran and Colman, Peter M. and Fairlie, W. Douglas}, urldate = {2017-05-15}, date = {2014-12-26}, langid = {english}, pmid = {25371206}, keywords = {apoptosis, apoptosis, B cell Lymphoma 2 (Bcl-2) Family, B cell Lymphoma 2 (Bcl-2) Family, Cell Death, Cell Death, Peptides, Peptides, Protein Structure, Protein Structure}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ASTRRM8R\\Lee et al. - 2014 - The Functional Differences between Pro-survival an:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AFK5VTZS\\Lee et al. - 2014 - The Functional Differences between Pro-survival an.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ASTRRM8R\\Lee et al. - 2014 - The Functional Differences between Pro-survival an:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QSB9CKA5\\Lee et al. - 2014 - The Functional Differences between Pro-survival an.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\URVBC4HG\\36001:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FIPV4U32\\36001.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\URVBC4HG\\36001:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8P3HG9HR\\36001.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ASTRRM8R\\Lee et al. - 2014 - The Functional Differences between Pro-survival an.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\URVBC4HG\\36001.html:text/html} } @article{fazio_drunken_2014, title = {A drunken search in crystallization space}, volume = {70}, rights = {Copyright (c) 2014 International Union of Crystallography}, issn = {2053-230X}, url = {http://scripts.iucr.org/cgi-bin/paper?en5555}, doi = {10.1107/S2053230X1401841X}, abstract = {The {REMARK}280 field of the Protein Data Bank is the richest open source of successful crystallization information. The {REMARK}280 field is optional and currently uncurated, so significant effort needs to be applied to extract reliable data. There are well over 15 000 crystallization conditions available commercially from 12 different vendors. After putting the {PDB} crystallization information and the commercial cocktail data into a consistent format, these data are used to extract information about the overlap between the two sets of crystallization conditions. An estimation is made as to which commercially available conditions are most appropriate for producing well diffracting crystals by looking at which commercial conditions are found unchanged (or almost unchanged) in the {PDB}. Further analyses include which commercial kits are the most appropriate for shotgun or more traditional approaches to crystallization screening. This analysis suggests that almost 40\% of the crystallization conditions found currently in the {PDB} are identical or very similar to a commercial condition.}, pages = {1303--1311}, number = {10}, journaltitle = {Acta Crystallographica Section F: Structural Biology Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Fazio, V. J. and Peat, T. S. and Newman, J.}, urldate = {2017-05-15}, date = {2014-10-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N4AQU26C\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UC7H6AQ7\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N4AQU26C\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WAUIZVFH\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XE5NP5U5\\Fazio et al. - 2014 - A drunken search in crystallization space:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FXZPRUJ4\\Fazio et al. - 2014 - A drunken search in crystallization space.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XE5NP5U5\\Fazio et al. - 2014 - A drunken search in crystallization space:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NC9EZMAJ\\Fazio et al. - 2014 - A drunken search in crystallization space.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XE5NP5U5\\Fazio et al. - 2014 - A drunken search in crystallization space.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N4AQU26C\\paper.html:text/html} } @article{dennis_structure-based_2014, title = {Structure-Based Design and Development of Functionalized Mercaptoguanine Derivatives as Inhibitors of the Folate Biosynthesis Pathway Enzyme 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase from Staphylococcus aureus}, volume = {57}, issn = {0022-2623}, url = {http://dx.doi.org/10.1021/jm501417f}, doi = {10.1021/jm501417f}, abstract = {6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase ({HPPK}), an enzyme from the folate biosynthesis pathway, catalyzes the pyrophosphoryl transfer from {ATP} to 6-hydroxymethyl-7,8-dihydropterin and is a yet-to-be-drugged antimicrobial target. Building on our previous discovery that 8-mercaptoguanine (8MG) is an inhibitor of Staphylococcus aureus {HPPK} ({SaHPPK}), we have identified and characterized the binding of an S8-functionalized derivative (3). X-ray structures of both the {SaHPPK}/3/cofactor analogue ternary and the {SaHPPK}/cofactor analogue binary complexes have provided insight into cofactor recognition and key residues that move over 30 Å upon binding of 3, whereas {NMR} measurements reveal a partially plastic ternary complex active site. Synthesis and binding analysis of a set of analogues of 3 have identified an advanced new lead compound (11) displaying {\textgreater}20-fold higher affinity for {SaHPPK} than 8MG. A number of these exhibited low micromolar affinity for dihydropteroate synthase ({DHPS}), the adjacent, downstream enzyme to {HPPK}, and may thus represent promising new leads to bienzyme inhibitors.}, pages = {9612--9626}, number = {22}, journaltitle = {Journal of Medicinal Chemistry}, shortjournal = {J. Med. Chem.}, author = {Dennis, Matthew L. and Chhabra, Sandeep and Wang, Zhong-Chang and Debono, Aaron and Dolezal, Olan and Newman, Janet and Pitcher, Noel P. and Rahmani, Raphael and Cleary, Ben and Barlow, Nicholas and Hattarki, Meghan and Graham, Bim and Peat, Thomas S. and Baell, Jonathan B. and Swarbrick, James D.}, urldate = {2017-05-15}, date = {2014-11-26}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GUTWQGCR\\Dennis et al. - 2014 - Structure-Based Design and Development of Function.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TP3IF2EW\\jm501417f.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GUTWQGCR\\Dennis et al. - 2014 - Structure-Based Design and Development of Function:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4XXNXVIV\\Dennis et al. - 2014 - Structure-Based Design and Development of Function.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GUTWQGCR\\Dennis et al. - 2014 - Structure-Based Design and Development of Function:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\356DBFZT\\Dennis et al. - 2014 - Structure-Based Design and Development of Function.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TP3IF2EW\\jm501417f:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\52IGVISF\\jm501417f.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TP3IF2EW\\jm501417f:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MHSIZRMQ\\jm501417f.html:text/html} } @incollection{owens_crystallization:_2015, title = {Crystallization: Digging into the Past to Learn Lessons for the Future}, rights = {©2015 Springer Science+Business Media New York}, isbn = {978-1-4939-2229-1}, url = {http://dx.doi.org/10.1007/978-1-4939-2230-7_8}, series = {Methods in Molecular Biology}, shorttitle = {Crystallization}, abstract = {Crystals of biological macromolecules have been observed and grown for well over a century. More effort has been put into biological crystallization in the last few decades due to the importance of X-ray crystal structures, the advent of synchrotron radiation sources, improved computational speed, better software, and the availability of recombinant protein. Here we focus on two important areas of crystal growth: firstly, on techniques for stabilizing the protein sample, and secondly, on strategies and approaches for selecting the crystallization cocktails most suitable for different strategies.}, pages = {141--156}, number = {1261}, booktitle = {Structural Proteomics}, publisher = {Springer New York}, author = {Fazio, {VincentJ}. and Peat, {ThomasS}. and Newman, Janet}, editor = {Owens, Raymond J.}, urldate = {2017-05-15}, date = {2015-01-01}, note = {{DOI}: 10.1007/978-1-4939-2230-7\_8}, keywords = {Crystallization screening, Crystallization screening, Differential scanning fluorimetry, Differential scanning fluorimetry, Proteins, Proteins}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TKB26E96\\Fazio et al. - 2015 - Crystallization Digging into the Past to Learn Le:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A8ZS6THQ\\Fazio et al. - 2015 - Crystallization Digging into the Past to Learn Le.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TKB26E96\\Fazio et al. - 2015 - Crystallization Digging into the Past to Learn Le:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9S6ATVMX\\Fazio et al. - 2015 - Crystallization Digging into the Past to Learn Le.pdf:application/pdf;Springer Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TKB26E96\\Fazio et al. - 2015 - Crystallization Digging into the Past to Learn Le.pdf:application/pdf} } @article{ivask_dna_2015, title = {{DNA} Melting and Genotoxicity Induced by Silver Nanoparticles and Graphene}, volume = {28}, issn = {0893-228X}, url = {http://dx.doi.org/10.1021/acs.chemrestox.5b00052}, doi = {10.1021/acs.chemrestox.5b00052}, abstract = {We have revealed a connection between {DNA}-nanoparticle ({NP}) binding and in vitro {DNA} damage induced by citrate- and branched polyethylenimine-coated silver nanoparticles (c-{AgNPs} and b-{AgNPs}) as well as graphene oxide ({GO}) nanosheets. All three types of nanostructures triggered an early onset of {DNA} melting, where the extent of the melting point shift depends upon both the type and concentration of the {NPs}. Specifically, at a {DNA}/{NP} weight ratio of 1.1/1, the melting temperature of lambda {DNA} dropped from 94 °C down to 76 °C, 60 °C, and room temperature for {GO}, c-{AgNPs} and b-{AgNPs}, respectively. Consistently, dynamic light scattering revealed that the largest changes in {DNA} hydrodynamic size were also associated with the binding of b-{AgNPs}. Upon introduction to cells, b-{AgNPs} also exhibited the highest cytotoxicity, at the half-maximal inhibitory ({IC}50) concentrations of 3.2, 2.9, and 5.2 mg/L for B and T-lymphocyte cell lines and primary lymphocytes, compared to the values of 13.4, 12.2, and 12.5 mg/L for c-{AgNPs} and 331, 251, and 120 mg/L for {GO} nanosheets, respectively. At cytotoxic concentrations, all {NPs} elicited elevated genotoxicities via the increased number of micronuclei in the lymphocyte cells. However, b-{AgNPs} also induced micronuclei at subtoxic concentrations starting from 0.1 mg/L, likely due to their stronger cellular adhesion and internalization, as well as their subsequent interference with normal {DNA} synthesis or chromosome segregation during the cell cycle. This study facilitates our understanding of the effects of {NP} chemical composition, surface charge, and morphology on {DNA} stability and genotoxicity, with implications ranging from nanotoxicology to nanobiotechnology and nanomedicine.}, pages = {1023--1035}, number = {5}, journaltitle = {Chemical Research in Toxicology}, shortjournal = {Chem. Res. Toxicol.}, author = {Ivask, Angela and Voelcker, Nicolas H. and Seabrook, Shane A. and Hor, Maryam and Kirby, Jason K. and Fenech, Michael and Davis, Thomas P. and Ke, Pu Chun}, urldate = {2017-05-15}, date = {2015-05-18}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NMAIITTM\\Ivask et al. - 2015 - DNA Melting and Genotoxicity Induced by Silver Nan.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\49RBGVVQ\\acs.chemrestox.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\49RBGVVQ\\acs.chemrestox:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XUA7M78C\\acs.chemrestox.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\49RBGVVQ\\acs.chemrestox:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2C8FPBPS\\acs.chemrestox.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NMAIITTM\\Ivask et al. - 2015 - DNA Melting and Genotoxicity Induced by Silver Nan:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CZTR4JN7\\Ivask et al. - 2015 - DNA Melting and Genotoxicity Induced by Silver Nan.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NMAIITTM\\Ivask et al. - 2015 - DNA Melting and Genotoxicity Induced by Silver Nan:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8VABQV7E\\Ivask et al. - 2015 - DNA Melting and Genotoxicity Induced by Silver Nan.pdf:application/pdf} } @article{srivastava_roquin_2015, title = {Roquin binds {microRNA}-146a and Argonaute2 to regulate {microRNA} homeostasis}, volume = {6}, rights = {© 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.}, issn = {2041-1723}, url = {http://www.nature.com/ncomms/2015/150220/ncomms7253/full/ncomms7253.html}, doi = {10.1038/ncomms7253}, abstract = {Roquin is an {RNA}-binding protein that promotes the degradation of specific {mRNAs} and is crucial for the maintenance of peripheral immune tolerance. Here the authors show that, in addition to its target {mRNAs}, Roquin can bind {miR}-146a and the {RISC} component Ago2 to control homeostasis of both {RNA} species.}, pages = {6253}, journaltitle = {Nature Communications}, author = {Srivastava, Monika and Duan, Guowen and Kershaw, Nadia J. and Athanasopoulos, Vicki and Yeo, Janet H. C. and Ose, Toyoyuki and Hu, Desheng and Brown, Simon H. J. and Jergic, Slobodan and Patel, Hardip R. and Pratama, Alvin and Richards, Sashika and Verma, Anil and Jones, E. Yvonne and Heissmeyer, Vigo and Preiss, Thomas and Dixon, Nicholas E. and Chong, Mark M. W. and Babon, Jeffrey J. and Vinuesa, Carola G.}, urldate = {2017-05-15}, date = {2015-02-20}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9KDPF7VX\\ncomms7253:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HFWFIX9E\\ncomms7253.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9KDPF7VX\\ncomms7253:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\359MU3I5\\ncomms7253.html:text/html;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9KDPF7VX\\ncomms7253.html:text/html} } @article{tanpure_carbonic_2015, title = {Carbonic Anhydrase Inhibitors with Dual-Tail Moieties To Match the Hydrophobic and Hydrophilic Halves of the Carbonic Anhydrase Active Site}, volume = {58}, issn = {0022-2623}, url = {http://dx.doi.org/10.1021/jm501798g}, doi = {10.1021/jm501798g}, abstract = {We present a new approach to carbonic anhydrase {II} ({CA} {II}) inhibitor design that enables close interrogation of the regions of the {CA} active site where there is the greatest variability in amino acid residues among the different {CA} isozymes. By appending dual tail groups onto the par excellence {CA} inhibitor acetazolamide, compounds that may interact with the distinct hydrophobic and hydrophilic halves of the {CA} {II} active site were prepared. The dual-tail combinations selected included (i) two hydrophobic moieties, (ii) two hydrophilic moieties, and (iii) one hydrophobic and one hydrophilic moiety. The {CA} enzyme inhibition profile as well as the protein X-ray crystal structure of compound 3, comprising one hydrophobic and one hydrophilic tail moiety, in complex with {CA} {II} is described. This novel dual-tail approach has provided an enhanced opportunity to more fully exploit interactions with the {CA} active site by enabling these molecules to interact with the distinct halves of the active site. In addition to the dual-tail compounds, a corresponding set of single-tail derivatives was synthesized, enabling a comparative analysis of the single-tail versus dual-tail compound {CA} inhibition profile.}, pages = {1494--1501}, number = {3}, journaltitle = {Journal of Medicinal Chemistry}, shortjournal = {J. Med. Chem.}, author = {Tanpure, Rajendra P. and Ren, Bin and Peat, Thomas S. and Bornaghi, Laurent F. and Vullo, Daniela and Supuran, Claudiu T. and Poulsen, Sally-Ann}, urldate = {2017-05-15}, date = {2015-02-12}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2RJ4TDJ3\\Tanpure et al. - 2015 - Carbonic Anhydrase Inhibitors with Dual-Tail Moiet.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NQ2X7SMX\\jm501798g.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2RJ4TDJ3\\Tanpure et al. - 2015 - Carbonic Anhydrase Inhibitors with Dual-Tail Moiet:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9H9K5U6V\\Tanpure et al. - 2015 - Carbonic Anhydrase Inhibitors with Dual-Tail Moiet.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2RJ4TDJ3\\Tanpure et al. - 2015 - Carbonic Anhydrase Inhibitors with Dual-Tail Moiet:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XBU49TAZ\\Tanpure et al. - 2015 - Carbonic Anhydrase Inhibitors with Dual-Tail Moiet.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NQ2X7SMX\\jm501798g:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RQCPSENQ\\jm501798g.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NQ2X7SMX\\jm501798g:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A5VMPX3A\\jm501798g.html:text/html} } @article{wang_thermostability_2015, title = {Thermostability and reversibility of silver nanoparticle–protein binding}, volume = {17}, url = {http://pubs.rsc.org/en/Content/ArticleLanding/2015/CP/C4CP04996A}, doi = {10.1039/C4CP04996A}, pages = {1728--1739}, number = {3}, journaltitle = {Physical Chemistry Chemical Physics}, author = {Wang, Bo and A. Seabrook, Shane and Nedumpully-Govindan, Praveen and Chen, Pengyu and Yin, Hong and Waddington, Lynne and Chandana Epa, V. and A. Winkler, David and K. Kirby, Jason and Ding, Feng and Chun Ke, Pu}, urldate = {2017-05-15}, date = {2015}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9F8Z67P3\\Wang et al. - 2015 - Thermostability and reversibility of silver nanopa:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZJE6XR95\\Wang et al. - 2015 - Thermostability and reversibility of silver nanopa.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9F8Z67P3\\Wang et al. - 2015 - Thermostability and reversibility of silver nanopa:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S9H878G8\\Wang et al. - 2015 - Thermostability and reversibility of silver nanopa.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\75IQBMV6\\c4cp04996a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3MMQUNX3\\c4cp04996a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\75IQBMV6\\c4cp04996a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NF659FV2\\c4cp04996a.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9F8Z67P3\\Wang et al. - 2015 - Thermostability and reversibility of silver nanopa.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\75IQBMV6\\c4cp04996a.html:text/html} } @article{menting_structural_2015, title = {Structural Congruency of Ligand Binding to the Insulin and Insulin/Type 1 Insulin-like Growth Factor Hybrid Receptors}, volume = {23}, issn = {0969-2126}, url = {http://www.sciencedirect.com/science/article/pii/S0969212615001744}, doi = {10.1016/j.str.2015.04.016}, abstract = {Summary The homodimeric insulin and type 1 insulin-like growth factor receptors ({IR} and {IGF}-1R) share a common architecture and each can bind all three ligands within the family: insulin and insulin-like growth factors I and {II} ({IGF}-I and {IFG}-{II}). The receptor monomers also assemble as heterodimers, the primary ligand-binding sites of which each comprise the first leucine-rich repeat domain (L1) of one receptor type and an α-chain C-terminal segment (α{CT}) of the second receptor type. We present here crystal structures of {IGF}-I bound to such a hybrid primary binding site and of a ligand-free version of an {IR} α{CT} peptide bound to an {IR} L1 plus cysteine-rich domain construct ({IR}310.T). These structures, refined at 3.0-Å resolution, prove congruent to respective existing structures of insulin-complexed {IR}310.T and the intact apo-{IR} ectodomain. As such, they provide key missing links in the emerging, but sparse, repertoire of structures defining the receptor family.}, pages = {1271--1282}, number = {7}, journaltitle = {Structure}, shortjournal = {Structure}, author = {Menting, John G. and Lawrence, Callum F. and Kong, Geoffrey K. -W. and Margetts, Mai B. and Ward, Colin W. and Lawrence, Michael C.}, urldate = {2017-05-15}, date = {2015-07-07}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\32MX8URA\\Menting et al. - 2015 - Structural Congruency of Ligand Binding to the Ins:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4FBPSE49\\Menting et al. - 2015 - Structural Congruency of Ligand Binding to the Ins.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\32MX8URA\\Menting et al. - 2015 - Structural Congruency of Ligand Binding to the Ins:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JVV748RG\\Menting et al. - 2015 - Structural Congruency of Ligand Binding to the Ins.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AMNP7N7X\\S0969212615001744:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\G24S5PVD\\S0969212615001744.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AMNP7N7X\\S0969212615001744:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\F4FFWR22\\S0969212615001744.html:text/html;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\32MX8URA\\Menting et al. - 2015 - Structural Congruency of Ligand Binding to the Ins.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AMNP7N7X\\S0969212615001744.html:text/html} } @article{chan_using_2013, title = {Using Graphs to Represent Crystallization Conditions}, volume = {13}, issn = {1528-7483}, url = {http://dx.doi.org/10.1021/cg301755a}, doi = {10.1021/cg301755a}, abstract = {We describe a novel graphical representation of a crystallization condition that provides an intuitive guide to setting the upper and lower concentration boundaries in a fine screen based around that condition.}, pages = {1290--1294}, number = {3}, journaltitle = {Crystal Growth \& Design}, shortjournal = {Crystal Growth \& Design}, author = {Chan, Michelle and Fazio, Vincent J. and Newman, Janet}, urldate = {2017-05-15}, date = {2013-03-06}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RPF9X8CP\\Chan et al. - 2013 - Using Graphs to Represent Crystallization Conditio.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KZ9SDICF\\cg301755a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KZ9SDICF\\cg301755a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TZZ2NKEF\\cg301755a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KZ9SDICF\\cg301755a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C33F6VAU\\cg301755a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RPF9X8CP\\Chan et al. - 2013 - Using Graphs to Represent Crystallization Conditio:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E8KA763X\\Chan et al. - 2013 - Using Graphs to Represent Crystallization Conditio.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RPF9X8CP\\Chan et al. - 2013 - Using Graphs to Represent Crystallization Conditio:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5QVR5N6M\\Chan et al. - 2013 - Using Graphs to Represent Crystallization Conditio.pdf:application/pdf} } @article{chhabra_exploring_2013, title = {Exploring the Chemical Space around 8-Mercaptoguanine as a Route to New Inhibitors of the Folate Biosynthesis Enzyme {HPPK}}, volume = {8}, issn = {1932-6203}, url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0059535}, doi = {10.1371/journal.pone.0059535}, abstract = {As the second essential enzyme of the folate biosynthetic pathway, the potential antimicrobial target, {HPPK} (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase), catalyzes the Mg2+-dependant transfer of pyrophosphate from the cofactor ({ATP}) to the substrate, 6-hydroxymethyl-7,8-dihydropterin. Recently, we showed that 8-mercaptoguanine (8-{MG}) bound at the substrate site ({KD} ∼13 µM), inhibited the S. aureus enzyme ({SaHPPK}) ({IC}50 ∼ 41 µM), and determined the structure of the {SaHPPK}/8-{MG} complex. Here we present the synthesis of a series of guanine derivatives, together with their {HPPK} binding affinities, as determined by {SPR} and {ITC} analysis. The binding mode of the most potent was investigated using 2D {NMR} spectroscopy and X-ray crystallography. The results indicate, firstly, that the {SH} group of 8-{MG} makes a significant contribution to the free energy of binding. Secondly, direct N9 substitution, or tautomerization arising from N7 substitution in some cases, leads to a dramatic reduction in affinity due to loss of a critical N9-H···Val46 hydrogen bond, combined with the limited space available around the N9 position. The water-filled pocket under the N7 position is significantly more tolerant of substitution, with a hydroxyl ethyl 8-{MG} derivative attached to N7 (compound 21a) exhibiting an affinity for the apo enzyme comparable to the parent compound ({KD} ∼ 12 µM). In contrast to 8-{MG}, however, 21a displays competitive binding with the {ATP} cofactor, as judged by {NMR} and {SPR} analysis. The 1.85 Å X-ray structure of the {SaHPPK}/21a complex confirms that extension from the N7 position towards the Mg2+-binding site, which affords the only tractable route out from the pterin-binding pocket. Promising strategies for the creation of more potent binders might therefore include the introduction of groups capable of interacting with the Mg2+ centres or Mg2+ -binding residues, as well as the development of bitopic inhibitors featuring 8-{MG} linked to a moiety targeting the {ATP} cofactor binding site.}, pages = {e59535}, number = {4}, journaltitle = {{PLOS} {ONE}}, shortjournal = {{PLOS} {ONE}}, author = {Chhabra, Sandeep and Barlow, Nicholas and Dolezal, Olan and Hattarki, Meghan K. and Newman, Janet and Peat, Thomas S. and Graham, Bim and Swarbrick, James D.}, urldate = {2017-05-15}, date = {2013-04-02}, keywords = {Binding analysis, Binding analysis, Cofactors (biochemistry), Cofactors (biochemistry), Crystal structure, Crystal structure, enzyme structure, enzyme structure, Hydrogen bonding, Hydrogen bonding, Reversed phase chromatography, Reversed phase chromatography, Solid-phase extraction, Solid-phase extraction, Two-dimensional {NMR} spectroscopy, Two-dimensional {NMR} spectroscopy}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B2R3Z2IP\\Chhabra et al. - 2013 - Exploring the Chemical Space around 8-Mercaptoguan:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I855HGZ4\\Chhabra et al. - 2013 - Exploring the Chemical Space around 8-Mercaptoguan.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B2R3Z2IP\\Chhabra et al. - 2013 - Exploring the Chemical Space around 8-Mercaptoguan:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5MA5ST3X\\Chhabra et al. - 2013 - Exploring the Chemical Space around 8-Mercaptoguan.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FFXFGPIH\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XIBQZ63C\\article.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FFXFGPIH\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CR5BVE6J\\article.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B2R3Z2IP\\Chhabra et al. - 2013 - Exploring the Chemical Space around 8-Mercaptoguan.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FFXFGPIH\\article.html:text/html} } @article{czabotar_bax_2013, title = {Bax Crystal Structures Reveal How {BH}3 Domains Activate Bax and Nucleate Its Oligomerization to Induce Apoptosis}, volume = {152}, issn = {0092-8674}, url = {http://www.sciencedirect.com/science/article/pii/S009286741201553X}, doi = {10.1016/j.cell.2012.12.031}, abstract = {Summary In stressed cells, apoptosis ensues when Bcl-2 family members Bax or Bak oligomerize and permeabilize the mitochondrial outer membrane. Certain {BH}3-only relatives can directly activate them to mediate this pivotal, poorly understood step. To clarify the conformational changes that induce Bax oligomerization, we determined crystal structures of {BaxΔC}21 treated with detergents and {BH}3 peptides. The peptides bound the Bax canonical surface groove but, unlike their complexes with prosurvival relatives, dissociated Bax into two domains. The structures define the sequence signature of activator {BH}3 domains and reveal how they can activate Bax via its groove by favoring release of its {BH}3 domain. Furthermore, Bax helices α2–α5 alone adopted a symmetric homodimer structure, supporting the proposal that two Bax molecules insert their {BH}3 domain into each other’s surface groove to nucleate oligomerization. A planar lipophilic surface on this homodimer may engage the membrane. Our results thus define critical Bax transitions toward apoptosis.}, pages = {519--531}, number = {3}, journaltitle = {Cell}, shortjournal = {Cell}, author = {Czabotar, Peter E. and Westphal, Dana and Dewson, Grant and Ma, Stephen and Hockings, Colin and Fairlie, W. Douglas and Lee, Erinna F. and Yao, Shenggen and Robin, Adeline Y. and Smith, Brian J. and Huang, David C. S. and Kluck, Ruth M. and Adams, Jerry M. and Colman, Peter M.}, urldate = {2017-05-15}, date = {2013-01-31}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B8Z5FMTG\\Czabotar et al. - 2013 - Bax Crystal Structures Reveal How BH3 Domains Acti:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IV6U8HZA\\Czabotar et al. - 2013 - Bax Crystal Structures Reveal How BH3 Domains Acti.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B8Z5FMTG\\Czabotar et al. - 2013 - Bax Crystal Structures Reveal How BH3 Domains Acti:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V9JBZ45T\\Czabotar et al. - 2013 - Bax Crystal Structures Reveal How BH3 Domains Acti.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\STK2EDT3\\S009286741201553X:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TGES5BJS\\S009286741201553X.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\STK2EDT3\\S009286741201553X:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6CQPMUSK\\S009286741201553X.html:text/html;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B8Z5FMTG\\Czabotar et al. - 2013 - Bax Crystal Structures Reveal How BH3 Domains Acti.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\STK2EDT3\\S009286741201553X.html:text/html} } @article{dcruz_crystal_2013, title = {Crystal structure of the {TRIM}25 B30.2 ({PRYSPRY}) domain: a key component of antiviral signalling}, volume = {456}, rights = {© The Authors Journal compilation © 2013 Biochemical Society}, issn = {0264-6021, 1470-8728}, url = {http://www.biochemj.org/content/456/2/231}, doi = {10.1042/BJ20121425}, shorttitle = {Crystal structure of the {TRIM}25 B30.2 ({PRYSPRY}) domain}, abstract = {{TRIM} (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. {TRIM}25 [also known as Efp (oestrogen-responsive finger protein)] has been implicated in the regulation of oestrogen receptor α signalling and in the regulation of innate immune signalling via {RIG}-I (retinoic acid-inducible gene-I). {RIG}-I senses cytosolic viral {RNA} and is subsequently ubiquitinated by {TRIM}25 at its N-terminal {CARDs} (caspase recruitment domains), leading to type I interferon production. The interaction with {RIG}-I is dependent on the {TRIM}25 B30.2 domain, a protein-interaction domain composed of the {PRY} and {SPRY} tandem sequence motifs. In the present study we describe the 1.8 Å crystal structure of the {TRIM}25 B30.2 domain, which exhibits a typical B30.2/{SPRY} domain fold comprising two N-terminal α-helices, thirteen β-strands arranged into two β-sheets and loop regions of varying lengths. A comparison with other B30.2/{SPRY} structures and an analysis of the loop regions identified a putative binding pocket, which is likely to be involved in binding target proteins. This was supported by mutagenesis and functional analyses, which identified two key residues (Asp488 and Trp621) in the {TRIM}25 B30.2 domain as being critical for binding to the {RIG}-I {CARDs}.}, pages = {231--240}, number = {2}, journaltitle = {Biochemical Journal}, author = {D’Cruz, Akshay A. and Kershaw, Nadia J. and Chiang, Jessica J. and Wang, May K. and Nicola, Nicos A. and Babon, Jeffrey J. and Gack, Michaela U. and Nicholson, Sandra E.}, urldate = {2017-05-15}, date = {2013-12-01}, langid = {english}, pmid = {24015671}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\45QI8HND\\231:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4XHVBGA9\\231.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\45QI8HND\\231:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\F4AF8F94\\231.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XSWB3SDZ\\D’Cruz et al. - 2013 - Crystal structure of the TRIM25 B30.2 (PRYSPRY) do:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I97MCVGP\\D’Cruz et al. - 2013 - Crystal structure of the TRIM25 B30.2 (PRYSPRY) do.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XSWB3SDZ\\D’Cruz et al. - 2013 - Crystal structure of the TRIM25 B30.2 (PRYSPRY) do:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N5HBEWA6\\D’Cruz et al. - 2013 - Crystal structure of the TRIM25 B30.2 (PRYSPRY) do.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XSWB3SDZ\\D’Cruz et al. - 2013 - Crystal structure of the TRIM25 B30.2 (PRYSPRY) do.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\45QI8HND\\231.html:text/html} } @article{desbois_practical_2013, title = {Some practical guidelines for {UV} imaging in the protein crystallization laboratory}, volume = {69}, rights = {http://creativecommons.org/licenses/by/2.0/uk}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?dp5039}, doi = {10.1107/S1744309112048634}, abstract = {High-throughput imaging of protein crystallization experiments with ultraviolet ({UV}) light has recently become commercially available and can enable crystallographers to differentiate between crystals of protein and those of salt, as the visualization of protein crystals is based on intrinsic tryptophan fluorescence. Unfortunately, {UV} imaging is not a panacea, as some protein crystals will not fluoresce under {UV} excitation and some salt crystals are {UV}-fluorescently active. As a new technology, there is little experience within the general community on how to use this technology effectively and what caveats to look out for. Here, an attempt is made to identify some of the common problems that may arise using {UV}-imaging technology by examining test proteins, common crystallization reagents and a range of proteins by assessing their {UV}–Vis absorbance spectra. Some pointers are offered as to which systems may not be appropriate for this methodology.}, pages = {201--208}, number = {2}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Desbois, S. and Seabrook, S. A. and Newman, J.}, urldate = {2017-05-15}, date = {2013-02-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3MQW8QIH\\Desbois et al. - 2013 - Some practical guidelines for UV imaging in the pr:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NNN2B7HA\\Desbois et al. - 2013 - Some practical guidelines for UV imaging in the pr.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3MQW8QIH\\Desbois et al. - 2013 - Some practical guidelines for UV imaging in the pr:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VZJ8AJ37\\Desbois et al. - 2013 - Some practical guidelines for UV imaging in the pr.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UJNT35IF\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8W53S9QK\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UJNT35IF\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VWAM3A4R\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3MQW8QIH\\Desbois et al. - 2013 - Some practical guidelines for UV imaging in the pr.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UJNT35IF\\paper.html:text/html} } @article{dolezal_fragment_2014, title = {Fragment Screening for the Modelling Community: {SPR}, {ITC}, and Crystallography}, volume = {66}, issn = {1445-0038}, url = {http://www.publish.csiro.au/ch/ch13302}, doi = {10.1071/CH13302}, shorttitle = {Fragment Screening for the Modelling Community}, abstract = {Australian Journal of Chemistry - an International Journal for Chemical Science publishes research papers from all fields of chemical science.}, pages = {1507--1517}, number = {12}, journaltitle = {Australian Journal of Chemistry}, shortjournal = {Aust. J. Chem.}, author = {Dolezal, Olan and Doughty, Larissa and Hattarki, Meghan K. and Fazio, Vincent J. and Caradoc-Davies, Tom T. and Newman, Janet and Peat, Thomas S.}, urldate = {2017-05-15}, date = {2014-01-10}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\92TEFD9W\\ch13302:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QKE59AVE\\ch13302.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\92TEFD9W\\ch13302:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GM5MT2UA\\ch13302.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P62HZVMS\\Dolezal et al. - 2014 - Fragment Screening for the Modelling Community SP:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UNSBR49I\\Dolezal et al. - 2014 - Fragment Screening for the Modelling Community SP.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P62HZVMS\\Dolezal et al. - 2014 - Fragment Screening for the Modelling Community SP:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KGZH9XVJ\\Dolezal et al. - 2014 - Fragment Screening for the Modelling Community SP.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P62HZVMS\\Dolezal et al. - 2014 - Fragment Screening for the Modelling Community SP.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\92TEFD9W\\ch13302.html:text/html} } @article{kershaw_socs3_2013, title = {{SOCS}3 binds specific receptor–{JAK} complexes to control cytokine signaling by direct kinase inhibition}, volume = {20}, rights = {© 2013 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.}, issn = {1545-9993}, url = {http://www.nature.com/nsmb/journal/v20/n4/abs/nsmb.2519.html}, doi = {10.1038/nsmb.2519}, abstract = {The inhibitory protein {SOCS}3 plays a key part in the immune and hematopoietic systems by regulating signaling induced by specific cytokines. {SOCS}3 functions by inhibiting the catalytic activity of Janus kinases ({JAKs}) that initiate signaling within the cell. We determined the crystal structure of a ternary complex between mouse {SOCS}3, {JAK}2 (kinase domain) and a fragment of the interleukin-6 receptor β-chain. The structure shows that {SOCS}3 binds {JAK}2 and receptor simultaneously, using two opposing surfaces. While the phosphotyrosine-binding groove on the {SOCS}3 {SH}2 domain is occupied by receptor, {JAK}2 binds in a phosphoindependent manner to a noncanonical surface. The kinase-inhibitory region of {SOCS}3 occludes the substrate-binding groove on {JAK}2, and biochemical studies show that it blocks substrate association. These studies reveal that {SOCS}3 targets specific {JAK}–cytokine receptor pairs and explains the mechanism and specificity of {SOCS} action. View full text}, pages = {469--476}, number = {4}, journaltitle = {Nature Structural \& Molecular Biology}, shortjournal = {Nat Struct Mol Biol}, author = {Kershaw, Nadia J. and Murphy, James M. and Liau, Nicholas P. D. and Varghese, Leila N. and Laktyushin, Artem and Whitlock, Eden L. and Lucet, Isabelle S. and Nicola, Nicos A. and Babon, Jeffrey J.}, urldate = {2017-05-15}, date = {2013-04}, langid = {english}, keywords = {Cell signalling, Cell signalling, Cytokines, Cytokines, Structural biology, Structural biology, X-ray crystallography, X-ray crystallography}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6T9GDX4H\\Kershaw et al. - 2013 - SOCS3 binds specific receptor–JAK complexes to con:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IXF56VAZ\\Kershaw et al. - 2013 - SOCS3 binds specific receptor–JAK complexes to con.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6T9GDX4H\\Kershaw et al. - 2013 - SOCS3 binds specific receptor–JAK complexes to con:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2EE5VXKZ\\Kershaw et al. - 2013 - SOCS3 binds specific receptor–JAK complexes to con.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8ZJXN4SX\\nsmb.2519:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7VPSCUP4\\nsmb.2519.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8ZJXN4SX\\nsmb.2519:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KBZCFKZB\\nsmb.2519.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6T9GDX4H\\Kershaw et al. - 2013 - SOCS3 binds specific receptor–JAK complexes to con.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8ZJXN4SX\\nsmb.2519.html:text/html} } @article{le_computational_2013, title = {Computational Modeling and Prediction of the Complex Time-Dependent Phase Behavior of Lyotropic Liquid Crystals under in Meso Crystallization Conditions}, volume = {13}, issn = {1528-7483}, url = {http://dx.doi.org/10.1021/cg301730z}, doi = {10.1021/cg301730z}, abstract = {Membrane-bound proteins comprise a very important class of drug targets. Solution of their structures by X-ray crystallography has been hampered by difficulties in crystallizing them in biologically relevant conformations. Novel amphiphilic materials that form bicontinuous cubic phases are being used to support the growth of crystals. However the cubic phase may transit to other lipidic mesophase structures under the influence of the different components within the crystallization screen. Furthermore the mesophases may evolve with time, a process that is poorly understood but potentially critical for controlled crystal growth. Recent advances in high-throughput screening of lipid systems have allowed us to generate a large body of data on the influence of screen components on the cubic phase. However it has been difficult to deconvolute individual effects in the multicomponent system present during a crystallization trial. We have therefore developed robust and predictive computational models that predict how the phase behavior of lyotropic liquid crystals changes over time and under the influence of crystallization additives. Our work demonstrates that the complex phase behavior of amphiphilic nanostructured nanoparticles can be captured with high accuracy using modern, robust machine learning methods. We predicted the existence of individual nanophases with accuracies of 98–99\% and the complex coexistence of multiple phases to a similar accuracy using nonlinear models: linear models were not as effective and robust. This approach also allowed us to determine which crystallization screen components were most relevant to the temporal evolution of individual mesophases.}, pages = {1267--1276}, number = {3}, journaltitle = {Crystal Growth \& Design}, shortjournal = {Crystal Growth \& Design}, author = {Le, Tu C. and Conn, Charlotte E. and Burden, Frank R. and Winkler, David A.}, urldate = {2017-05-15}, date = {2013-03-06}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\369FD77S\\Le et al. - 2013 - Computational Modeling and Prediction of the Compl.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\G5EHEAFJ\\cg301730z.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\369FD77S\\Le et al. - 2013 - Computational Modeling and Prediction of the Compl:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TGNTJ9EI\\Le et al. - 2013 - Computational Modeling and Prediction of the Compl.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\369FD77S\\Le et al. - 2013 - Computational Modeling and Prediction of the Compl:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8NJVINWH\\Le et al. - 2013 - Computational Modeling and Prediction of the Compl.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\G5EHEAFJ\\cg301730z:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FH7ITERR\\cg301730z.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\G5EHEAFJ\\cg301730z:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QGHTJ65U\\cg301730z.html:text/html} } @article{le_predicting_2013, title = {Predicting the Effect of Lipid Structure on Mesophase Formation during in Meso Crystallization}, volume = {13}, issn = {1528-7483}, url = {http://dx.doi.org/10.1021/cg400513y}, doi = {10.1021/cg400513y}, abstract = {Bicontinuous cubic lipidic materials are increasingly used as crystallization media for in meso crystallization of membrane proteins ({MPs}). Varying the lipid architecture may assist with encapsulation of larger proteins and promote crystal growth. However, not all lipids are compatible with the components of typical crystallization screens, and compatibility must therefore be checked prior to crystallization trials. The method currently used, high-throughput small-angle X-ray scattering ({HT} {SAXS}), may be time-consuming and is costly in valuable {MP}. We have therefore employed a modeling approach using Bayesian regularized neural networks to accurately predict the complex phase behavior of lipid materials under the influence of the {PACT} crystallization screen and determine the lipid characteristics that allow a lipid to retain a cubic phase under the multiple components required during an in meso crystallization trial. This information will be used to select robust lipids for use in crystallization trials and may allow for the rational design of new lipids, specifically for in meso crystallization.}, pages = {3126--3137}, number = {7}, journaltitle = {Crystal Growth \& Design}, shortjournal = {Crystal Growth \& Design}, author = {Le, Tu C. and Conn, Charlotte E. and Burden, Frank R. and Winkler, David A.}, urldate = {2017-05-15}, date = {2013-07-03}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MA66S632\\Le et al. - 2013 - Predicting the Effect of Lipid Structure on Mesoph.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FQCCFVBP\\cg400513y.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FQCCFVBP\\cg400513y:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\H2S4EK68\\cg400513y.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FQCCFVBP\\cg400513y:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SIX8HBNC\\cg400513y.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MA66S632\\Le et al. - 2013 - Predicting the Effect of Lipid Structure on Mesoph:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\R9BRVQN2\\Le et al. - 2013 - Predicting the Effect of Lipid Structure on Mesoph.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MA66S632\\Le et al. - 2013 - Predicting the Effect of Lipid Structure on Mesoph:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FJ8FPCRB\\Le et al. - 2013 - Predicting the Effect of Lipid Structure on Mesoph.pdf:application/pdf} } @article{menting_how_2013, title = {How insulin engages its primary binding site on the insulin receptor}, volume = {493}, rights = {© 2013 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.}, issn = {0028-0836}, url = {http://www.nature.com/nature/journal/v493/n7431/abs/nature11781.html}, doi = {10.1038/nature11781}, abstract = {Insulin receptor signalling has a central role in mammalian biology, regulating cellular metabolism, growth, division, differentiation and survival. Insulin resistance contributes to the pathogenesis of type 2 diabetes mellitus and the onset of Alzheimer/'s disease; aberrant signalling occurs in diverse cancers, exacerbated by cross-talk with the homologous type 1 insulin-like growth factor receptor ({IGF}1R). Despite more than three decades of investigation, the three-dimensional structure of the insulin-insulin receptor complex has proved elusive, confounded by the complexity of producing the receptor protein. Here we present the first view, to our knowledge, of the interaction of insulin with its primary binding site on the insulin receptor, on the basis of four crystal structures of insulin bound to truncated insulin receptor constructs. The direct interaction of insulin with the first leucine-rich-repeat domain (L1) of insulin receptor is seen to be sparse, the hormone instead engaging the insulin receptor carboxy-terminal α-chain (α{CT}) segment, which is itself remodelled on the face of L1 upon insulin binding. Contact between insulin and L1 is restricted to insulin B-chain residues. The α{CT} segment displaces the B-chain C-terminal β-strand away from the hormone core, revealing the mechanism of a long-proposed conformational switch in insulin upon receptor engagement. This mode of hormone-receptor recognition is novel within the broader family of receptor tyrosine kinases. We support these findings by photo-crosslinking data that place the suggested interactions into the context of the holoreceptor and by isothermal titration calorimetry data that dissect the hormone-insulin receptor interface. Together, our findings provide an explanation for a wealth of biochemical data from the insulin receptor and {IGF}1R systems relevant to the design of therapeutic insulin analogues.}, pages = {241--245}, number = {7431}, journaltitle = {Nature}, shortjournal = {Nature}, author = {Menting, John G. and Whittaker, Jonathan and Margetts, Mai B. and Whittaker, Linda J. and Kong, Geoffrey K.-W. and Smith, Brian J. and Watson, Christopher J. and Žáková, Lenka and Kletvíková, Emília and Jiráček, Jiří and Chan, Shu Jin and Steiner, Donald F. and Dodson, Guy G. and Brzozowski, Andrzej M. and Weiss, Michael A. and Ward, Colin W. and Lawrence, Michael C.}, urldate = {2017-05-15}, date = {2013-01-10}, langid = {english}, keywords = {Diabetes, Diabetes, X-ray crystallography, X-ray crystallography}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\53SAU3XT\\nature11781:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NMKSFXQQ\\nature11781.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\53SAU3XT\\nature11781:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MZ2QGXFP\\nature11781.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NJE45EBX\\Menting et al. - 2013 - How insulin engages its primary binding site on th:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XK56KU72\\Menting et al. - 2013 - How insulin engages its primary binding site on th.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NJE45EBX\\Menting et al. - 2013 - How insulin engages its primary binding site on th:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DFR8S49Z\\Menting et al. - 2013 - How insulin engages its primary binding site on th.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NJE45EBX\\Menting et al. - 2013 - How insulin engages its primary binding site on th.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\53SAU3XT\\nature11781.html:text/html} } @article{mulet_high-throughput_2013, title = {High-Throughput Development of Amphiphile Self-Assembly Materials: Fast-Tracking Synthesis, Characterization, Formulation, Application, and Understanding}, volume = {46}, issn = {0001-4842}, url = {http://dx.doi.org/10.1021/ar300285u}, doi = {10.1021/ar300285u}, shorttitle = {High-Throughput Development of Amphiphile Self-Assembly Materials}, abstract = {Amphiphile self-assembly materials, which contain both a hydrophilic and a hydrophobic domain, have great potential in high-throughput and combinatorial approaches to discovery and development. However, the materials chemistry community has not embraced these ideas to anywhere near the extent that the medicinal chemistry community has. While this situation is beginning to change, extracting the full potential of high-throughput approaches in the development of self-assembling materials will require further development in the synthesis, characterization, formulation, and application domains.One of the key factors that make small molecule amphiphiles prospective building blocks for next generation multifunctional materials is their ability to self-assemble into complex nanostructures through low-energy transformations. Scientists can potentially tune, control, and functionalize these structures, but only after establishing their inherent properties. Because both robotic materials handling and customized rapid characterization equipment are increasingly available, high-throughput solutions are now attainable. These address traditional development bottlenecks associated with self-assembling amphiphile materials, such as their structural characterization and the assessment of end-use functional performance.A high-throughput methodology can help streamline materials development workflows, in accord with existing high-throughput discovery pipelines such as those used by the pharmaceutical industry in drug discovery. Chemists have identified several areas that are amenable to a high-throughput approach for amphiphile self-assembly materials development. These allow an exploration of not only a large potential chemical, compositional, and structural space, but also material properties, formulation, and application variables. These areas of development include materials synthesis and preparation, formulation, characterization, and screening performance for the desired end application. High-throughput data analysis is crucial at all stages to keep pace with data collection.In this Account, we describe high-throughput advances in the field of amphiphile self-assembly, focusing on nanostructured lyotropic liquid crystalline materials, which form when amphiphiles are added to a polar solvent. We outline recent progress in the automated preparation of amphiphile molecules and their nanostructured self-assembly systems both in the bulk phase and in dispersed colloidal particulate systems. Once prepared, we can structurally characterize these systems by establishing phase behavior in a high-throughput manner with both laboratory (infrared and light polarization microscopy) and synchrotron facilities (small-angle X-ray scattering).Additionally, we provide three case studies to demonstrate how chemists can use high-throughput approaches to evaluate the functional performance of amphiphile self-assembly materials. The high-throughput methodology for the set-up and characterization of large matrix in meso membrane protein crystallization trials can illustrate an application of bulk phase self-assembling amphiphiles. For dispersed colloidal systems, two nanomedicine examples highlight advances in high-throughput preparation, characterization, and evaluation: drug delivery and magnetic resonance imaging agents.}, pages = {1497--1505}, number = {7}, journaltitle = {Accounts of Chemical Research}, shortjournal = {Acc. Chem. Res.}, author = {Mulet, Xavier and Conn, Charlotte E. and Fong, Celesta and Kennedy, Danielle F. and Moghaddam, Minoo J. and Drummond, Calum J.}, urldate = {2017-05-15}, date = {2013-07-16}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HPX6H43A\\Mulet et al. - 2013 - High-Throughput Development of Amphiphile Self-Ass.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C96B9SUA\\ar300285u.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C96B9SUA\\ar300285u:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Q4E69IZ8\\ar300285u.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C96B9SUA\\ar300285u:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UA4IR2W3\\ar300285u.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HPX6H43A\\Mulet et al. - 2013 - High-Throughput Development of Amphiphile Self-Ass:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QDE8MTA6\\Mulet et al. - 2013 - High-Throughput Development of Amphiphile Self-Ass.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HPX6H43A\\Mulet et al. - 2013 - High-Throughput Development of Amphiphile Self-Ass:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N4XPXEGR\\Mulet et al. - 2013 - High-Throughput Development of Amphiphile Self-Ass.pdf:application/pdf} } @article{murphy_pseudokinase_2013, title = {The Pseudokinase {MLKL} Mediates Necroptosis via a Molecular Switch Mechanism}, volume = {39}, issn = {1074-7613}, url = {http://www.sciencedirect.com/science/article/pii/S1074761313003488}, doi = {10.1016/j.immuni.2013.06.018}, abstract = {Summary Mixed lineage kinase domain-like ({MLKL}) is a component of the “necrosome,” the multiprotein complex that triggers tumor necrosis factor ({TNF})-induced cell death by necroptosis. To define the specific role and molecular mechanism of {MLKL} action, we generated {MLKL}-deficient mice and solved the crystal structure of {MLKL}. Although {MLKL}-deficient mice were viable and displayed no hematopoietic anomalies or other obvious pathology, cells derived from these animals were resistant to {TNF}-induced necroptosis unless {MLKL} expression was restored. Structurally, {MLKL} comprises a four-helical bundle tethered to the pseudokinase domain, which contains an unusual pseudoactive site. Although the pseudokinase domain binds {ATP}, it is catalytically inactive and its essential nonenzymatic role in necroptotic signaling is induced by receptor-interacting serine-threonine kinase 3 ({RIPK}3)-mediated phosphorylation. Structure-guided mutation of the {MLKL} pseudoactive site resulted in constitutive, {RIPK}3-independent necroptosis, demonstrating that modification of {MLKL} is essential for propagation of the necroptosis pathway downstream of {RIPK}3.}, pages = {443--453}, number = {3}, journaltitle = {Immunity}, shortjournal = {Immunity}, author = {Murphy, James M. and Czabotar, Peter E. and Hildebrand, Joanne M. and Lucet, Isabelle S. and Zhang, Jian-Guo and Alvarez-Diaz, Silvia and Lewis, Rowena and Lalaoui, Najoua and Metcalf, Donald and Webb, Andrew I. and Young, Samuel N. and Varghese, Leila N. and Tannahill, Gillian M. and Hatchell, Esme C. and Majewski, Ian J. and Okamoto, Toru and Dobson, Renwick C. J. and Hilton, Douglas J. and Babon, Jeffrey J. and Nicola, Nicos A. and Strasser, Andreas and Silke, John and Alexander, Warren S.}, urldate = {2017-05-15}, date = {2013-09-19}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5FESGPGP\\S1074761313003488:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MAF5GT4R\\S1074761313003488.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5FESGPGP\\S1074761313003488:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MS489N9C\\S1074761313003488.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S6HGNSIU\\Murphy et al. - 2013 - The Pseudokinase MLKL Mediates Necroptosis via a M:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WD5QJUMB\\Murphy et al. - 2013 - The Pseudokinase MLKL Mediates Necroptosis via a M.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S6HGNSIU\\Murphy et al. - 2013 - The Pseudokinase MLKL Mediates Necroptosis via a M:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HTWP2VED\\Murphy et al. - 2013 - The Pseudokinase MLKL Mediates Necroptosis via a M.pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S6HGNSIU\\Murphy et al. - 2013 - The Pseudokinase MLKL Mediates Necroptosis via a M.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5FESGPGP\\S1074761313003488.html:text/html} } @article{newman_crystallization_2013, title = {Crystallization reports are the backbone of Acta Cryst. F, but do they have any spine?}, volume = {69}, rights = {Copyright (c) 2013 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?wd5209}, doi = {10.1107/S1744309113014152}, abstract = {Crystallization of macromolecules is famously difficult. By knowing what has worked for others, researchers can ease the process, both in the case where the protein has already been crystallized and in the situation where more general guidelines are needed. The 264 crystallization communications published in Acta Crystallographica Section F in 2012 have been reviewed, and from this analysis some information about trends in crystallization has been gleaned. More importantly, it was found that there are several ways in which the utility of these communications could be increased: to make each individual paper a more complete crystallization record; and to provide a means for taking a snapshot of what the current `best practices' are in the field.}, pages = {712--718}, number = {7}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Newman, J. and Burton, D. R. and Caria, S. and Desbois, S. and Gee, C. L. and Fazio, V. J. and Kvansakul, M. and Marshall, B. and Mills, G. and Richter, V. and Seabrook, S. A. and Wu, M. and Peat, T. S.}, urldate = {2017-05-15}, date = {2013-07-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NG22X634\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VHXGX9NG\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NG22X634\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\H9ZBSTQ6\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QR34FWKG\\Newman et al. - 2013 - Crystallization reports are the backbone of Acta C:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CSCXZBVF\\Newman et al. - 2013 - Crystallization reports are the backbone of Acta C.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QR34FWKG\\Newman et al. - 2013 - Crystallization reports are the backbone of Acta C:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TZVBM8WS\\Newman et al. - 2013 - Crystallization reports are the backbone of Acta C.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QR34FWKG\\Newman et al. - 2013 - Crystallization reports are the backbone of Acta C.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NG22X634\\paper.html:text/html} } @article{newman_determination_2013, title = {Determination of the Structure of the Catabolic N-Succinylornithine Transaminase ({AstC}) from Escherichia coli}, volume = {8}, issn = {1932-6203}, url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058298}, doi = {10.1371/journal.pone.0058298}, abstract = {Escherichia coli possesses two acyl ornithine aminotransferases, one catabolic ({AstC}) and the other anabolic ({ArgD}), that participate in L-arginine metabolism. Although only 58\% identical, the enzymes have been shown to be functionally interchangeable. Here we have purified {AstC} and have obtained X-ray crystal structures of apo and holo-{AstC} and of the enzyme complexed with its physiological substrate, succinylornithine. We compare the structures obtained in this study with those of {ArgD} from Salmonella typhimurium obtained elsewhere, finding several notable differences. Docking studies were used to explore the docking modes of several substrates (ornithine, succinylornithine and acetylornithine) and the co-substrate glutamate/α-ketogluterate. The docking studies support our observations that {AstC} has a strong preference for acylated ornithine species over ornithine itself, and suggest that the increase in specificity associated with acylation is caused by steric and desolvation effects rather than specific interactions between the substrate and enzyme.}, pages = {e58298}, number = {3}, journaltitle = {{PLOS} {ONE}}, shortjournal = {{PLOS} {ONE}}, author = {Newman, Janet and Seabrook, Shane and Surjadi, Regina and Williams, Charlotte C. and Lucent, Del and Wilding, Matthew and Scott, Colin and Peat, Thomas S.}, urldate = {2017-05-15}, date = {2013-03-06}, keywords = {Arginine, Arginine, Cofactors (biochemistry), Cofactors (biochemistry), Crystal growth, Crystal growth, Crystals, Crystals, Crystal structure, Crystal structure, Electron density, Electron density, Hydrogen bonding, Hydrogen bonding, Phosphates, Phosphates}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AWHKUKZF\\Newman et al. - 2013 - Determination of the Structure of the Catabolic N-:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3TA2SRS8\\Newman et al. - 2013 - Determination of the Structure of the Catabolic N-.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AWHKUKZF\\Newman et al. - 2013 - Determination of the Structure of the Catabolic N-:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\D9RJVJ8E\\Newman et al. - 2013 - Determination of the Structure of the Catabolic N-.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WPBHIDQM\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VBZ93P83\\article.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WPBHIDQM\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RIKPHXV9\\article.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AWHKUKZF\\Newman et al. - 2013 - Determination of the Structure of the Catabolic N-.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WPBHIDQM\\article.html:text/html} } @article{nisbet_structural_2013, title = {Structural studies of the tethered N-terminus of the Alzheimer's disease amyloid-β peptide}, volume = {81}, issn = {1097-0134}, url = {http://onlinelibrary.wiley.com/doi/10.1002/prot.24312/abstract}, doi = {10.1002/prot.24312}, abstract = {Alzheimer's disease is the most common form of dementia in humans and is related to the accumulation of the amyloid-β (Aβ) peptide and its interaction with metals (Cu, Fe, and Zn) in the brain. Crystallographic structural information about Aβ peptide deposits and the details of the metal-binding site is limited owing to the heterogeneous nature of aggregation states formed by the peptide. Here, we present a crystal structure of Aβ residues 1–16 fused to the N-terminus of the Escherichia coli immunity protein Im7, and stabilized with the fragment antigen binding fragment of the anti-Aβ N-terminal antibody {WO}2. The structure demonstrates that Aβ residues 10–16, which are not in complex with the antibody, adopt a mixture of local polyproline {II}-helix and turn type conformations, enhancing cooperativity between the two adjacent histidine residues His13 and His14. Furthermore, this relatively rigid region of Aβ (residues, 10–16) appear as an almost independent unit available for trapping metal ions and provides a rationale for the His13-metal-His14 coordination in the Aβ1–16 fragment implicated in Aβ metal binding. This novel structure, therefore, has the potential to provide a foundation for investigating the effect of metal ion binding to Aβ and illustrates a potential target for the development of future Alzheimer's disease therapeutics aimed at stabilizing the N-terminal monomer structure, in particular residues His13 and His14, and preventing Aβ metal-binding-induced neurotoxicity.Proteins 2013; 81:1748–1758. © 2013 Wiley Periodicals, Inc.}, pages = {1748--1758}, number = {10}, journaltitle = {Proteins: Structure, Function, and Bioinformatics}, shortjournal = {Proteins}, author = {Nisbet, Rebecca M. and Nuttall, Stewart D. and Robert, Remy and Caine, Joanne M. and Dolezal, Olan and Hattarki, Meghan and Pearce, Lesley A. and Davydova, Natalia and Masters, Colin L. and Varghese, Jose N. and Streltsov, Victor A.}, urldate = {2017-05-15}, date = {2013-10-01}, langid = {english}, keywords = {Alzheimer's disease, Alzheimer's disease, amyloid-β, amyloid-β, Aβ crystal structure, Aβ crystal structure, Im7, Im7, {WO}-2 Fab, {WO}-2 Fab}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5G5R9B6P\\Nisbet et al. - 2013 - Structural studies of the tethered N-terminus of t:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S8PE5DEF\\Nisbet et al. - 2013 - Structural studies of the tethered N-terminus of t.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5G5R9B6P\\Nisbet et al. - 2013 - Structural studies of the tethered N-terminus of t:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XCJ3P47X\\Nisbet et al. - 2013 - Structural studies of the tethered N-terminus of t.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GT8MFIGE\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AQBCBSQS\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GT8MFIGE\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JCHBDMR6\\abstract.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5G5R9B6P\\Nisbet et al. - 2013 - Structural studies of the tethered N-terminus of t.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GT8MFIGE\\abstract.html:text/html} } @article{north_cloning_2013, title = {Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus}, volume = {69}, rights = {Copyright (c) 2013 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?nj5146}, doi = {10.1107/S1744309113003060}, abstract = {The enzyme N-acetylneuraminate lyase ({EC} 4.1.3.3) is involved in the metabolism of sialic acids. Specifically, the enzyme catalyzes the retro-aldol cleavage of N-acetylneuraminic acid to form N-acetyl-d-mannosamine and pyruvate. Sialic acids comprise a large family of nine-carbon amino sugars, all of which are derived from the parent compound N-acetylneuraminic acid. In recent years, N-acetylneuraminate lyase has received considerable attention from both mechanistic and structural viewpoints and has been recognized as a potential antimicrobial drug target. The N-acetylneuraminate lyase gene was cloned from methicillin-resistant Staphylococcus aureus genomic {DNA}, and recombinant protein was expressed and purified from Escherichia coli {BL}21 ({DE}3). The enzyme crystallized in a number of crystal forms, predominantly from {PEG} precipitants, with the best crystal diffracting to beyond 1.70 Å resolution in space group P21. Molecular replacement indicates the presence of eight monomers per asymmetric unit. Understanding the structural biology of N-acetylneuraminate lyase in pathogenic bacteria, such as methicillin-resistant S. aureus, will provide insights for the development of future antimicrobials.}, pages = {306--312}, number = {3}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {North, R. A. and Kessans, S. A. and Atkinson, S. C. and Suzuki, H. and Watson, A. J. A. and Burgess, B. R. and Angley, L. M. and Hudson, A. O. and Varsani, A. and Griffin, M. D. W. and Fairbanks, A. J. and Dobson, R. C. J.}, urldate = {2017-05-15}, date = {2013-03-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5QXNBKU9\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\W438C825\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5QXNBKU9\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XGKKWMRX\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FZW65RIF\\North et al. - 2013 - Cloning, expression, purification, crystallization:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WT27EURA\\North et al. - 2013 - Cloning, expression, purification, crystallization.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FZW65RIF\\North et al. - 2013 - Cloning, expression, purification, crystallization:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FB8SF55S\\North et al. - 2013 - Cloning, expression, purification, crystallization.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FZW65RIF\\North et al. - 2013 - Cloning, expression, purification, crystallization.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5QXNBKU9\\paper.html:text/html} } @article{peat_cyanuric_2013, title = {Cyanuric acid hydrolase: evolutionary innovation by structural concatenation}, volume = {88}, issn = {1365-2958}, url = {http://onlinelibrary.wiley.com/doi/10.1111/mmi.12249/abstract}, doi = {10.1111/mmi.12249}, shorttitle = {Cyanuric acid hydrolase}, abstract = {The cyanuric acid hydrolase, {AtzD}, is the founding member of a newly identified family of ring-opening amidases. We report the first X-ray structure for this family, which is a novel fold (termed the ‘Toblerone’ fold) that likely evolved via the concatenation of monomers of the trimeric {YjgF} superfamily and the acquisition of a metal binding site. Structures of {AtzD} with bound substrate (cyanuric acid) and inhibitors (phosphate, barbituric acid and melamine), along with mutagenesis studies, allowed the identification of the active site. The {AtzD} monomer, active site and substrate all possess threefold rotational symmetry, to the extent that the active site possesses three potential Ser–Lys catalytic dyads. A single catalytic dyad (Ser85–Lys42) is hypothesized, based on biochemical evidence and crystallographic data. A plausible catalytic mechanism based on these observations is also presented. A comparison with a homology model of the related barbiturase, Bar, was used to infer the active-site residues responsible for substrate specificity, and the phylogeny of the 68 {AtzD}-like enzymes in the database were analysed in light of this structure–function relationship.}, pages = {1149--1163}, number = {6}, journaltitle = {Molecular Microbiology}, shortjournal = {Molecular Microbiology}, author = {Peat, Thomas S. and Balotra, Sahil and Wilding, Matthew and French, Nigel G. and Briggs, Lyndall J. and Panjikar, Santosh and Cowieson, Nathan and Newman, Janet and Scott, Colin}, urldate = {2017-05-15}, date = {2013-06-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EJKF5RFQ\\Peat et al. - 2013 - Cyanuric acid hydrolase evolutionary innovation b:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A6Z5AJPQ\\Peat et al. - 2013 - Cyanuric acid hydrolase evolutionary innovation b.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EJKF5RFQ\\Peat et al. - 2013 - Cyanuric acid hydrolase evolutionary innovation b:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UEHCZPE9\\Peat et al. - 2013 - Cyanuric acid hydrolase evolutionary innovation b.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HFEMX8EP\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AH6GV8UD\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HFEMX8EP\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VC69UN34\\abstract.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EJKF5RFQ\\Peat et al. - 2013 - Cyanuric acid hydrolase evolutionary innovation b.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HFEMX8EP\\abstract.html:text/html} } @article{polekhina_structure_2013, title = {Structure of the N-terminal domain of human thioredoxin-interacting protein}, volume = {69}, rights = {Copyright (c) 2013 International Union of Crystallography}, issn = {0907-4449}, url = {http://scripts.iucr.org/cgi-bin/paper?lv5025}, doi = {10.1107/S0907444912047099}, abstract = {Thioredoxin-interacting protein ({TXNIP}) is one of the six known α-arrestins and has recently received considerable attention owing to its involvement in redox signalling and metabolism. Various stress stimuli such as high glucose, heat shock, {UV}, H2O2 and mechanical stress among others robustly induce the expression of {TXNIP}, resulting in the sequestration and inactivation of thioredoxin, which in turn leads to cellular oxidative stress. While {TXNIP} is the only α-arrestin known to bind thioredoxin, {TXNIP} and two other α-arrestins, Arrdc4 and Arrdc3, have been implicated in metabolism. Furthermore, owing to its roles in the pathologies of diabetes and cardiovascular disease, {TXNIP} is considered to be a promising drug target. Based on their amino-acid sequences, {TXNIP} and the other α-arrestins are remotely related to β-arrestins. Here, the crystal structure of the N-terminal domain of {TXNIP} is reported. It provides the first structural information on any of the α-arrestins and reveals that although {TXNIP} adopts a β-­arrestin fold as predicted, it is structurally more similar to Vps26 proteins than to β-arrestins, while sharing below 15\% pairwise sequence identity with either.}, pages = {333--344}, number = {3}, journaltitle = {Acta Crystallographica Section D: Biological Crystallography}, shortjournal = {Acta Cryst D, Acta Cryst Sect D, Acta Crystallogr D, Acta Crystallogr Sect D, Acta Crystallogr D Biol Crystallogr, Acta Crystallogr Sect D Biol Crystallogr}, author = {Polekhina, G. and Ascher, D. B. and Kok, S. F. and Beckham, S. and Wilce, M. and Waltham, M.}, urldate = {2017-05-15}, date = {2013-03-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8KQ2P788\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JVE9GGBR\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8KQ2P788\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\URXPG4DM\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P969DCBQ\\Polekhina et al. - 2013 - Structure of the N-terminal domain of human thiore:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HXG3QJ7H\\Polekhina et al. - 2013 - Structure of the N-terminal domain of human thiore.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P969DCBQ\\Polekhina et al. - 2013 - Structure of the N-terminal domain of human thiore:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QH8WTNRB\\Polekhina et al. - 2013 - Structure of the N-terminal domain of human thiore.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P969DCBQ\\Polekhina et al. - 2013 - Structure of the N-terminal domain of human thiore.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8KQ2P788\\paper.html:text/html} } @article{redpath_production_2013, title = {Production of a human neutralizing monoclonal antibody and its crystal structure in complex with ectodomain 3 of the interleukin-13 receptor α1}, volume = {451}, issn = {0264-6021, 1470-8728}, url = {http://biochemj.org/lookup/doi/10.1042/BJ20121819}, doi = {10.1042/BJ20121819}, pages = {165--175}, number = {2}, journaltitle = {Biochemical Journal}, author = {Redpath, Nicholas T. and Xu, Yibin and Wilson, Nicholas J. and Fabri, Louis J. and Baca, Manuel and Andrews, Arna E. and Braley, Hal and Lu, Ping and Ireland, Cheryl and Ernst, Robin E. and Woods, Andrea and Forrest, Gail and An, Zhiqiang and Zaller, Dennis M. and Strohl, William R. and Luo, Cindy S. and Czabotar, Peter E. and Garrett, Thomas P. J. and Hilton, Douglas J. and Nash, Andrew D. and Zhang, Jian-Guo and Nicola, Nicos A.}, urldate = {2017-05-15}, date = {2013-04-15}, langid = {english} } @article{ren_expression_2013, title = {Expression, purification, crystallization and preliminary X-ray diffraction analysis of a lactococcal bacteriophage small terminase subunit}, volume = {69}, rights = {Copyright (c) 2013 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?wd5200}, doi = {10.1107/S174430911300184X}, abstract = {Terminases are enzymes that are required for the insertion of a single viral genome into the interior of a viral procapsid by a process referred to as `encapsulation or packaging'. Many double-stranded {DNA} viruses such as bacteriophages T3, T4, T7, λ and {SPP}1, as well as herpes viruses, utilize terminase enzymes for this purpose. All the terminase enzymes described to date require two subunits, a small subunit referred to as {TerS} and a large subunit referred to as {TerL}, for in vivo activity. The {TerS} and {TerL} subunits interact with each other to form a functional hetero-oligomeric enzyme complex; however the stoichiometry and oligomeric state have not been determined. We have cloned, expressed and purified recombinant small terminase {TerS} from a 936 lactococcal bacteriophage strain {ASCC}454, initially isolated from a dairy factory. The terminase was crystallized using a combination of nanolitre sitting drops and vapour diffusion using sodium malonate as the precipitant, and crystallization optimized using standard vapour-diffusion hanging drops set up in the presence of a nitrogen atmosphere. The crystals belong to the P2 space group, with unit-cell parameters a = 73.93, b = 158.48, c = 74.23 Å, and diffract to 2.42 Å resolution using synchrotron radiation. A self-rotation function calculation revealed that the terminase oligomerizes into an octamer in the asymmetric unit, although size-exclusion chromatography suggests that it is possible for it to form an oligomer of up to 13 subunits.}, pages = {275--279}, number = {3}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Ren, B. and Pham, T. M. and Surjadi, R. and Robinson, C. P. and Le, T. and Chandry, P. S. and Peat, T. S. and {McKinstry}, W. J.}, urldate = {2017-05-15}, date = {2013-03-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B84BDZWD\\Ren et al. - 2013 - Expression, purification, crystallization and prel:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2DVPAQ3R\\Ren et al. - 2013 - Expression, purification, crystallization and prel.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B84BDZWD\\Ren et al. - 2013 - Expression, purification, crystallization and prel:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V6PUZQ73\\Ren et al. - 2013 - Expression, purification, crystallization and prel.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JW5AGNPU\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4SADWUBP\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JW5AGNPU\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GM6Z6B7P\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B84BDZWD\\Ren et al. - 2013 - Expression, purification, crystallization and prel.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JW5AGNPU\\paper.html:text/html} } @article{ryan_ammonium_2013, title = {Ammonium hydroxide treatment of Aβ produces an aggregate free solution suitable for biophysical and cell culture characterization}, volume = {1}, issn = {2167-8359}, url = {https://peerj.com/articles/73}, doi = {10.7717/peerj.73}, abstract = {Alzheimer’s disease is the leading cause of dementia in the elderly. Pathologically it is characterized by the presence of amyloid plaques and neuronal loss within the brain tissue of affected individuals. It is now widely hypothesised that fibrillar structures represent an inert structure. Biophysical and toxicity assays attempting to characterize the formation of both the fibrillar and the intermediate oligomeric structures of Aβ typically involves preparing samples which are largely monomeric; the most common method by which this is achieved is to use the fluorinated organic solvent 1,1,1,3,3,3-hexafluoro-2-propanol ({HFIP}). Recent evidence has suggested that this method is not 100\% effective in producing an aggregate free solution. We show, using dynamic light scattering, size exclusion chromatography and small angle X-ray scattering that this is indeed the case, with {HFIP} pretreated Aβ peptide solutions displaying an increased proportion of oligomeric and aggregated material and an increased propensity to aggregate. Furthermore we show that an alternative technique, involving treatment with strong alkali results in a much more homogenous solution that is largely monomeric. These techniques for solubilising and controlling the oligomeric state of Aβ are valuable starting points for future biophysical and toxicity assays.}, pages = {e73}, journaltitle = {{PeerJ}}, shortjournal = {{PeerJ}}, author = {Ryan, Timothy M. and Caine, Joanne and Mertens, Haydyn D. T. and Kirby, Nigel and Nigro, Julie and Breheney, Kerry and Waddington, Lynne J. and Streltsov, Victor A. and Curtain, Cyril and Masters, Colin L. and Roberts, Blaine R.}, urldate = {2017-05-15}, date = {2013-05-07}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GKGSTZ6A\\Ryan et al. - 2013 - Ammonium hydroxide treatment of Aβ produces an agg:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3NFURJ7J\\Ryan et al. - 2013 - Ammonium hydroxide treatment of Aβ produces an agg.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GKGSTZ6A\\Ryan et al. - 2013 - Ammonium hydroxide treatment of Aβ produces an agg:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S8BWNGPC\\Ryan et al. - 2013 - Ammonium hydroxide treatment of Aβ produces an agg.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IN7AMCZ6\\73:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VPCR5BWV\\73.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IN7AMCZ6\\73:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2WMESBI2\\73.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GKGSTZ6A\\Ryan et al. - 2013 - Ammonium hydroxide treatment of Aβ produces an agg.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IN7AMCZ6\\73.html:text/html} } @article{schulze_disruption_2013, title = {Disruption of Hydrogen Bonds between Major Histocompatibility Complex Class {II} and the Peptide N-Terminus Is Not Sufficient to Form a Human Leukocyte Antigen-{DM} Receptive State of Major Histocompatibility Complex Class {II}}, volume = {8}, issn = {1932-6203}, url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069228}, doi = {10.1371/journal.pone.0069228}, abstract = {Peptide presentation by {MHC} class {II} is of critical importance to the function of {CD}4+ T cells. {HLA}-{DM} resides in the endosomal pathway and edits the peptide repertoire of newly synthesized {MHC} class {II} molecules before they are exported to the cell surface. {HLA}-{DM} ensures {MHC} class {II} molecules bind high affinity peptides by targeting unstable {MHC} class {II}:peptide complexes for peptide exchange. Research over the past decade has implicated the peptide N-terminus in modulating the ability of {HLA}-{DM} to target a given {MHC} class {II}:peptide combination. In particular, attention has been focused on both the hydrogen bonds between {MHC} class {II} and peptide, and the occupancy of the P1 anchor pocket. We sought to solve the crystal structure of a {HLA}-{DR}1 molecule containing a truncated hemagglutinin peptide missing three N-terminal residues compared to the full-length sequence (residues 306–318) to determine the nature of the {MHC} class {II}:peptide species that binds {HLA}-{DM}. Here we present structural evidence that {HLA}-{DR}1 that is loaded with a peptide truncated to the P1 anchor residue such that it cannot make select hydrogen bonds with the peptide N-terminus, adopts the same conformation as molecules loaded with full-length peptide. {HLA}-{DR}1:peptide combinations that were unable to engage up to four key hydrogen bonds were also unable to bind {HLA}-{DM}, while those truncated to the P2 residue bound well. These results indicate that the conformational changes in {MHC} class {II} molecules that are recognized by {HLA}-{DM} occur after disengagement of the P1 anchor residue.}, pages = {e69228}, number = {7}, journaltitle = {{PLOS} {ONE}}, shortjournal = {{PLOS} {ONE}}, author = {Schulze, Monika-Sarah E. D. and Anders, Anne-Kathrin and Sethi, Dhruv K. and Call, Melissa J.}, urldate = {2017-05-15}, date = {2013-07-25}, keywords = {Crystallization, Crystallization, Crystal structure, Crystal structure, Hydrogen bonding, Hydrogen bonding, Major histocompatibility complex, Major histocompatibility complex, Molecular structure, Molecular structure, Peptides, Peptides, Peptide synthesis, Peptide synthesis, Valine, Valine}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EN9HB8RC\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\92U2DWKJ\\article.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EN9HB8RC\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VIKJB9Z8\\article.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MVT3TWJK\\Schulze et al. - 2013 - Disruption of Hydrogen Bonds between Major Histoco:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SWMZ8I82\\Schulze et al. - 2013 - Disruption of Hydrogen Bonds between Major Histoco.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MVT3TWJK\\Schulze et al. - 2013 - Disruption of Hydrogen Bonds between Major Histoco:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TTXJKSZ4\\Schulze et al. - 2013 - Disruption of Hydrogen Bonds between Major Histoco.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MVT3TWJK\\Schulze et al. - 2013 - Disruption of Hydrogen Bonds between Major Histoco.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EN9HB8RC\\article.html:text/html} } @article{seabrook_high-throughput_2013, title = {High-Throughput Thermal Scanning for Protein Stability: Making a Good Technique More Robust}, volume = {15}, issn = {2156-8952}, url = {http://dx.doi.org/10.1021/co400013v}, doi = {10.1021/co400013v}, shorttitle = {High-Throughput Thermal Scanning for Protein Stability}, abstract = {We present a high-throughput approach to help define experimental formulations that enhance protein stability, which is based on differential scanning fluorimetry ({DSF}). The method involves defining the thermal stability of a protein against a screen of 13 buffer systems, systematically sampling {pH} from 5.0 to 9.0 at high and low salt concentrations, using both redundancy and extensive controls to make the method robust. The screen allows rapid determination of a suitable base formulation for protein samples, and is particularly useful for difficult samples: those that are rapidly degraded or cannot be sufficiently concentrated for downstream analyses. Data obtained from three samples in this assay illustrate the vastly different values for thermal stability that can be obtained from different formulations. This approach is simple to interpret and reliable enough that it has been implemented as a service through the Collaborative Crystallisation Centre (C3).}, pages = {387--392}, number = {8}, journaltitle = {{ACS} Combinatorial Science}, shortjournal = {{ACS} Comb. Sci.}, author = {Seabrook, Shane A. and Newman, Janet}, urldate = {2017-05-15}, date = {2013-08-12}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7AWUT5HH\\Seabrook and Newman - 2013 - High-Throughput Thermal Scanning for Protein Stabi.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HQKKT2EE\\co400013v.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7AWUT5HH\\Seabrook and Newman - 2013 - High-Throughput Thermal Scanning for Protein Stabi:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KE92MTX7\\Seabrook and Newman - 2013 - High-Throughput Thermal Scanning for Protein Stabi.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7AWUT5HH\\Seabrook and Newman - 2013 - High-Throughput Thermal Scanning for Protein Stabi:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\72F9DZ69\\Seabrook and Newman - 2013 - High-Throughput Thermal Scanning for Protein Stabi.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HQKKT2EE\\co400013v:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\U3IB7Z6K\\co400013v.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HQKKT2EE\\co400013v:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EJIGRMSH\\co400013v.html:text/html} } @article{wu_expression_2013, title = {Expression, purification, crystallization and preliminary X-ray analysis of tannase from Lactobacillus plantarum}, volume = {69}, rights = {Copyright (c) 2013 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?bo5119}, doi = {10.1107/S1744309113006143}, abstract = {Tannase catalyses the hydrolysis of the galloyl ester bond of tannins to release gallic acid. It belongs to the serine esterases and has wide applications in the food, feed, beverage, pharmaceutical and chemical industries. The tannase from Lactobacillus plantarum was cloned, expressed and purified. The protein was crystallized by the sitting-drop vapour-diffusion method with microseeding. The crystals belonged to space group P1, with unit-cell paramters a = 46.5, b = 62.8, c = 83.8 Å, α = 70.4, β = 86.0, γ = 79.4°. Although the enzyme exists mainly as a monomer in solution, it forms a dimer in the asymmetric unit of the crystal. The crystals diffracted to beyond 1.60 Å resolution using synchrotron radiation and a complete data set was collected to 1.65 Å resolution.}, pages = {456--459}, number = {4}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Wu, M. and Peng, X. and Wen, H. and Wang, Q. and Chen, Q. and {McKinstry}, W. J. and Ren, B.}, urldate = {2017-05-15}, date = {2013-04-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DHGMW4KM\\Wu et al. - 2013 - Expression, purification, crystallization and prel:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HNZSKRCF\\Wu et al. - 2013 - Expression, purification, crystallization and prel.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DHGMW4KM\\Wu et al. - 2013 - Expression, purification, crystallization and prel:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S5RZ3CQ2\\Wu et al. - 2013 - Expression, purification, crystallization and prel.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DIU23Z56\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7ZUTQ6VI\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DIU23Z56\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2C8THW6A\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DHGMW4KM\\Wu et al. - 2013 - Expression, purification, crystallization and prel.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DIU23Z56\\paper.html:text/html} } @article{siddiqui_cloning_2013, title = {Cloning to crystallization of dihydrodipicolinate synthase from the intracellular pathogen Legionella pneumophila}, volume = {69}, rights = {Copyright (c) 2013 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?dp5053}, doi = {10.1107/S1744309113024639}, abstract = {Dihydrodipicolinate synthase ({DHDPS}) catalyses the rate-limiting step in the biosynthesis of meso-diaminopimelate and lysine. Here, the cloning, expression, purification and crystallization of {DHDPS} from the intracellular pathogen Legionella pneumophila are described. Crystals grown in the presence of high-molecular-weight {PEG} precipitant and magnesium chloride were found to diffract beyond 1.65 Å resolution. The crystal lattice belonged to the hexagonal space group P6122, with unit-cell parameters a = b = 89.31, c = 290.18 Å, and contained two molecules in the asymmetric unit. The crystal structure was determined by molecular replacement using a single chain of Pseudomonas aeruginosa {DHDPS} as the search model.}, pages = {1177--1181}, number = {10}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Siddiqui, T. and Paxman, J. J. and Dogovski, C. and Panjikar, S. and Perugini, M. A.}, urldate = {2017-05-15}, date = {2013-10-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\M3GH8NTD\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5ASIZJKH\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\M3GH8NTD\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZPBIPSVV\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QJJRVK9Q\\Siddiqui et al. - 2013 - Cloning to crystallization of dihydrodipicolinate:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5I3HC6GK\\Siddiqui et al. - 2013 - Cloning to crystallization of dihydrodipicolinate .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QJJRVK9Q\\Siddiqui et al. - 2013 - Cloning to crystallization of dihydrodipicolinate:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UWEUBTRQ\\Siddiqui et al. - 2013 - Cloning to crystallization of dihydrodipicolinate .pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QJJRVK9Q\\Siddiqui et al. - 2013 - Cloning to crystallization of dihydrodipicolinate .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\M3GH8NTD\\paper.html:text/html} } @article{mele_using_2014, title = {Using Time Courses To Enrich the Information Obtained from Images of Crystallization Trials}, volume = {14}, issn = {1528-7483}, url = {http://pubs.acs.org/doi/abs/10.1021/cg4014569}, doi = {10.1021/cg4014569}, abstract = {Visual identification of crystals from experimental setups (droplets) underpins the field of structural biology, and there is an increasing use of automation to capture records of crystallization trials — snapshots of the experiments over time — which are then used to identify crystals for subsequent analysis. Here we describe an algorithm that locates differences between images within an image time-course of a crystallization experiment. A user-accessible “front end” to this functionality is provided by tagging images, which have been identified as changed, and using an existing (commercial) viewing software package to display the tagged images. The existence of change appears to be a powerful tool to filter out images that do not need further human examination, as the rate of false negatives is low and the method is general. We identify significant change in a time sequence of crystallization images by using a process of image alignment, drop recognition, masking, filtering, and comparison. We propose that this process might be a powerful way of picking up changes in crystallization experiments which happen after weeks or months.}, pages = {261--269}, number = {1}, journaltitle = {Crystal Growth \& Design}, shortjournal = {Crystal Growth \& Design}, author = {Mele, Katarina and Lekamge, B. M. Thamali and Fazio, Vincent J. and Newman, Janet}, urldate = {2017-05-15}, date = {2014-01-02}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z3JJR7K5\\Mele et al. - 2014 - Using Time Courses To Enrich the Information Obtai.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZXHPTSCM\\cg4014569.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z3JJR7K5\\Mele et al. - 2014 - Using Time Courses To Enrich the Information Obtai:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4358R65T\\Mele et al. - 2014 - Using Time Courses To Enrich the Information Obtai.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z3JJR7K5\\Mele et al. - 2014 - Using Time Courses To Enrich the Information Obtai:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9K68SJAG\\Mele et al. - 2014 - Using Time Courses To Enrich the Information Obtai.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZXHPTSCM\\cg4014569:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RXEGATCR\\cg4014569.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZXHPTSCM\\cg4014569:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S8X75UCD\\cg4014569.html:text/html} } @article{ascher_crystallization_2012, title = {Crystallization and preliminary X-ray diffraction analysis of human endoplasmic reticulum aminopeptidase 2}, volume = {68}, rights = {Copyright (c) 2012 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?dp5019}, doi = {10.1107/S1744309112006963}, abstract = {Endoplasmic reticulum aminopeptidase 2 ({ERAP}2) is a critical enzyme involved in the final processing of {MHC} class I antigens. Peptide trimming by {ERAP}2 and the other members of the oxytocinase subfamily is essential to customize longer precursor peptides in order to fit them to the correct length required for presentation on major histocompatibility complex class I molecules. While recent structures of {ERAP}1 have provided an understanding of the `molecular-ruler' mechanism of substrate selection, little is known about the complementary activities of its homologue {ERAP}2 despite their sharing 49\% sequence identity. In order to gain insights into the structure–function relationship of the oxytocinase subfamily, and in particular {ERAP}2, the luminal region of human {ERAP}2 has been crystallized in the presence of the inhibitor bestatin. The crystals belonged to an orthorhombic space group and diffracted anisotropically to 3.3 Å resolution in the best direction on an in-house X-ray source. A molecular-replacement solution suggested that the enzyme has adopted the closed state as has been observed in other inhibitor-bound aminopeptidase structures.}, pages = {468--471}, number = {4}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Ascher, D. B. and Polekhina, G. and Parker, M. W.}, urldate = {2017-05-15}, date = {2012-04-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ENXVERTJ\\Ascher et al. - 2012 - Crystallization and preliminary X-ray diffraction:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3RJTBSR3\\Ascher et al. - 2012 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ENXVERTJ\\Ascher et al. - 2012 - Crystallization and preliminary X-ray diffraction:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EXNEPGR5\\Ascher et al. - 2012 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TZPAM7CB\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GBNVHHAD\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TZPAM7CB\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UB8TNUAJ\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ENXVERTJ\\Ascher et al. - 2012 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TZPAM7CB\\paper.html:text/html} } @article{atkinson_cloning_2012, title = {Cloning, expression, purification and crystallization of dihydrodipicolinate synthase from Agrobacterium tumefaciens}, volume = {68}, rights = {Copyright (c) 2012 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?en5504}, doi = {10.1107/S1744309112033052}, abstract = {Dihydrodipicolinate synthase ({DHDPS}) catalyzes the first committed step of the lysine-biosynthesis pathway in bacteria, plants and some fungi. This study describes the cloning, expression, purification and crystallization of {DHDPS} ({NP}\_354047.1) from the plant pathogen Agrobacterium tumefaciens ({AgT}-{DHDPS}). Enzyme-kinetics studies demonstrate that {AgT}-{DHDPS} possesses {DHDPS} activity in vitro. Crystals of {AgT}-{DHDPS} were grown in the unliganded form and in forms with substrate bound and with substrate plus allosteric inhibitor (lysine) bound. X-ray diffraction data sets were subsequently collected to a maximum resolution of 1.40 Å. Determination of the structure with and without substrate and inhibitor will offer insight into the design of novel pesticide agents.}, pages = {1040--1047}, number = {9}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Atkinson, S. C. and Dogovski, C. and Dobson, R. C. J. and Perugini, M. A.}, urldate = {2017-05-15}, date = {2012-09-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\344SC6IW\\Atkinson et al. - 2012 - Cloning, expression, purification and crystallizat:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RQU3Z59C\\Atkinson et al. - 2012 - Cloning, expression, purification and crystallizat.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\344SC6IW\\Atkinson et al. - 2012 - Cloning, expression, purification and crystallizat:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MRHHUGUH\\Atkinson et al. - 2012 - Cloning, expression, purification and crystallizat.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IV4GQT5Q\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZHQ7QUR8\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IV4GQT5Q\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NJKG9DM5\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\344SC6IW\\Atkinson et al. - 2012 - Cloning, expression, purification and crystallizat.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IV4GQT5Q\\paper.html:text/html} } @article{atkinson_crystal_2012, title = {Crystal, Solution and In silico Structural Studies of Dihydrodipicolinate Synthase from the Common Grapevine}, volume = {7}, issn = {1932-6203}, url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038318}, doi = {10.1371/journal.pone.0038318}, abstract = {Dihydrodipicolinate synthase ({DHDPS}) catalyzes the rate limiting step in lysine biosynthesis in bacteria and plants. The structure of {DHDPS} has been determined from several bacterial species and shown in most cases to form a homotetramer or dimer of dimers. However, only one plant {DHDPS} structure has been determined to date from the wild tobacco species, Nicotiana sylvestris (Blickling et al. (1997) J. Mol. Biol. 274, 608–621). Whilst N. sylvestris {DHDPS} also forms a homotetramer, the plant enzyme adopts a ‘back-to-back’ dimer of dimers compared to the ‘head-to-head’ architecture observed for bacterial {DHDPS} tetramers. This raises the question of whether the alternative quaternary architecture observed for N. sylvestris {DHDPS} is common to all plant {DHDPS} enzymes. Here, we describe the structure of {DHDPS} from the grapevine plant, Vitis vinifera, and show using analytical ultracentrifugation, small-angle X-ray scattering and X-ray crystallography that V. vinifera {DHDPS} forms a ‘back-to-back’ homotetramer, consistent with N. sylvestris {DHDPS}. This study is the first to demonstrate using both crystal and solution state measurements that {DHDPS} from the grapevine plant adopts an alternative tetrameric architecture to the bacterial form, which is important for optimizing protein dynamics as suggested by molecular dynamics simulations reported in this study.}, pages = {e38318}, number = {6}, journaltitle = {{PLOS} {ONE}}, shortjournal = {{PLOS} {ONE}}, author = {Atkinson, Sarah C. and Dogovski, Con and Downton, Matthew T. and Pearce, F. Grant and Reboul, Cyril F. and Buckle, Ashley M. and Gerrard, Juliet A. and Dobson, Renwick C. J. and Wagner, John and Perugini, Matthew A.}, urldate = {2017-05-15}, date = {2012-06-25}, keywords = {Crystals, Crystals, Crystal structure, Crystal structure, Dimers (Chemical physics), Dimers (Chemical physics), enzyme structure, enzyme structure, Molecular dynamics, Molecular dynamics, Nicotiana, Nicotiana, Pyruvate, Pyruvate, Small-angle scattering, Small-angle scattering}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ADZRV88J\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P4EAZWPX\\article.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ADZRV88J\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4VCVI7P2\\article.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\X7FC5RUH\\Atkinson et al. - 2012 - Crystal, Solution and In silico Structural Studies:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8EK83FKU\\Atkinson et al. - 2012 - Crystal, Solution and In silico Structural Studies.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\X7FC5RUH\\Atkinson et al. - 2012 - Crystal, Solution and In silico Structural Studies:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NC4JFZ32\\Atkinson et al. - 2012 - Crystal, Solution and In silico Structural Studies.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\X7FC5RUH\\Atkinson et al. - 2012 - Crystal, Solution and In silico Structural Studies.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ADZRV88J\\article.html:text/html} } @article{caria_crystallization_2012, title = {Crystallization and preliminary X-ray characterization of Epstein–Barr virus {BHRF}1 in complex with a benzoylurea peptidomimetic}, volume = {68}, rights = {Copyright (c) 2012 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?nj5138}, doi = {10.1107/S1744309112043333}, abstract = {{BHRF}1 is a pro-survival Bcl-2 homologue encoded by Epstein–Barr virus ({EBV}) that plays a key role in preventing premature host cell death during viral infection and may contribute to the development of malignancies associated with chronic {EBV} infections. The anti-apoptotic action of {BHRF}1 is based on its ability to sequester pro-apoptotic Bcl-2 family proteins, in particular Bim and Bak. These interactions have been previously studied in three dimensions by determining crystal structures of {BHRF}1 in complex with both Bim and Bak {BH}3 domains. Screening of a library of peptidomimetic compounds based on the benzoylurea scaffold that mimics critical Bim {BH}3 domain side chains against {BHRF}1 led to the identification of an inhibitor of {BHRF}1 that displays micromolar affinity. Single crystals were obtained from the co-crystallization of recombinant {BHRF}1 protein with this peptidomimetic compound. The crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 66.8, b = 91.1, c = 151.9 Å. Diffraction data were collected to 2.11 Å resolution on the {MX}2 beamline at the Australian Synchrotron.}, pages = {1521--1524}, number = {12}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Caria, S. and Chugh, S. and Nhu, D. and Lessene, G. and Kvansakul, M.}, urldate = {2017-05-15}, date = {2012-12-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6BKQ3GAR\\Caria et al. - 2012 - Crystallization and preliminary X-ray characteriza:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VFNT6ARR\\Caria et al. - 2012 - Crystallization and preliminary X-ray characteriza.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6BKQ3GAR\\Caria et al. - 2012 - Crystallization and preliminary X-ray characteriza:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KXUIVH6C\\Caria et al. - 2012 - Crystallization and preliminary X-ray characteriza.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NIXVRJQX\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\H5KEMFKC\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NIXVRJQX\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4M7PMTVD\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6BKQ3GAR\\Caria et al. - 2012 - Crystallization and preliminary X-ray characteriza.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NIXVRJQX\\paper.html:text/html} } @article{chhabra_structure_2012, title = {Structure of S. aureus {HPPK} and the Discovery of a New Substrate Site Inhibitor}, volume = {7}, issn = {1932-6203}, url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029444}, doi = {10.1371/journal.pone.0029444}, abstract = {The first structural and biophysical data on the folate biosynthesis pathway enzyme and drug target, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase ({SaHPPK}), from the pathogen Staphylococcus aureus is presented. {HPPK} is the second essential enzyme in the pathway catalysing the pyrophosphoryl transfer from cofactor ({ATP}) to the substrate (6-hydroxymethyl-7,8-dihydropterin, {HMDP}). In-silico screening identified 8-mercaptoguanine which was shown to bind with an equilibrium dissociation constant, Kd, of ∼13 µM as measured by isothermal titration calorimetry ({ITC}) and surface plasmon resonance ({SPR}). An {IC}50 of ∼41 µM was determined by means of a luminescent kinase assay. In contrast to the biological substrate, the inhibitor has no requirement for magnesium or the {ATP} cofactor for competitive binding to the substrate site. The 1.65 Å resolution crystal structure of the inhibited complex showed that it binds in the pterin site and shares many of the key intermolecular interactions of the substrate. Chemical shift and 15N heteronuclear {NMR} measurements reveal that the fast motion of the pterin-binding loop (L2) is partially dampened in the {SaHPPK}/{HMDP}/α,β-methylene adenosine 5′-triphosphate ({AMPCPP}) ternary complex, but the {ATP} loop (L3) remains mobile on the µs-ms timescale. In contrast, for the {SaHPPK}/8-mercaptoguanine/{AMPCPP} ternary complex, the loop L2 becomes rigid on the fast timescale and the L3 loop also becomes more ordered – an observation that correlates with the large entropic penalty associated with inhibitor binding as revealed by {ITC}. {NMR} data, including 15N-1H residual dipolar coupling measurements, indicate that the sulfur atom in the inhibitor is important for stabilizing and restricting important motions of the L2 and L3 catalytic loops in the inhibited ternary complex. This work describes a comprehensive analysis of a new {HPPK} inhibitor, and may provide a foundation for the development of novel antimicrobials targeting the folate biosynthetic pathway.}, pages = {e29444}, number = {1}, journaltitle = {{PLOS} {ONE}}, shortjournal = {{PLOS} {ONE}}, author = {Chhabra, Sandeep and Dolezal, Olan and Collins, Brett M. and Newman, Janet and Simpson, Jamie S. and Macreadie, Ian G. and Fernley, Ross and Peat, Thomas S. and Swarbrick, James D.}, urldate = {2017-05-15}, date = {2012-01-19}, keywords = {Amides, Amides, Cofactors (biochemistry), Cofactors (biochemistry), Crystal structure, Crystal structure, Enzyme inhibitors, Enzyme inhibitors, enzyme structure, enzyme structure, Hydrogen bonding, Hydrogen bonding, {NMR} relaxation, {NMR} relaxation, {NMR} spectroscopy, {NMR} spectroscopy}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6UE7QR56\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SFV968ZC\\article.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6UE7QR56\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DTBMXMUH\\article.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JIVZ83ZZ\\Chhabra et al. - 2012 - Structure of S. aureus HPPK and the Discovery of a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\277A8WKQ\\Chhabra et al. - 2012 - Structure of S. aureus HPPK and the Discovery of a.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JIVZ83ZZ\\Chhabra et al. - 2012 - Structure of S. aureus HPPK and the Discovery of a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\95NMIG54\\Chhabra et al. - 2012 - Structure of S. aureus HPPK and the Discovery of a.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JIVZ83ZZ\\Chhabra et al. - 2012 - Structure of S. aureus HPPK and the Discovery of a.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6UE7QR56\\article.html:text/html} } @article{conn_effect_2012, title = {Effect of lipid architecture on cubic phase susceptibility to crystallisation screens}, volume = {8}, issn = {1744-6848}, url = {http://pubs.rsc.org/en/content/articlelanding/2012/sm/c2sm25705j}, doi = {10.1039/C2SM25705J}, abstract = {The proposed mechanism for in meso crystallisation depends, at least initially, on retention of the underlying cubic phase. However, a crystallisation trial requires screening across a wide range of crystallisation conditions, containing polymers, salts, buffers and at varying {pH}, all of which are known to drive structural changes in lipid phases. We have previously shown that the lipid monoolein ({MO}) is relatively robust to the components of the {PACT} crystallization screen. Here we extend our research to determine the susceptibility of the 3-D ordered cubic phase formed by four different lipids; monoolein, phytantriol, phytanoyl monoethanolamide and H-farnesoyl monoethanolamide, to two different crystallisation screens (the {PACT} and {PEG}-ion screens) in situ, within a 96-well crystallisation plate. Addition of screen is shown to result in rich and varied phase behaviour with the transformation to 1-D ordered lamellar, 2-D ordered hexagonal and disordered micellar phases in many wells. We have rationalized the structural changes for each lipid by a consideration of the osmotic stress exerted by the {PEG} components, and the position of various anions and cations present in the Hofmeister series. The nanostructure of the cubic phase is shown to be the most important parameter affecting the susceptibility of the cubic phase structure to the components of the screen. In particular, a reduction in lipid bilayer thickness and water channel diameter increases the susceptibility.}, pages = {6884--6896}, number = {26}, journaltitle = {Soft Matter}, shortjournal = {Soft Matter}, author = {Conn, Charlotte E. and Darmanin, Connie and Mulet, Xavier and Hawley, Adrian and Drummond, Calum J.}, urldate = {2017-05-15}, date = {2012-06-13}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2IJW6FTX\\c2sm25705j:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CTIDKIUF\\c2sm25705j.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2IJW6FTX\\c2sm25705j:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WBRSG8DC\\c2sm25705j.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QFGUK3BJ\\Conn et al. - 2012 - Effect of lipid architecture on cubic phase suscep:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PW4AHRWD\\Conn et al. - 2012 - Effect of lipid architecture on cubic phase suscep.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QFGUK3BJ\\Conn et al. - 2012 - Effect of lipid architecture on cubic phase suscep:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XU7K6QTP\\Conn et al. - 2012 - Effect of lipid architecture on cubic phase suscep.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QFGUK3BJ\\Conn et al. - 2012 - Effect of lipid architecture on cubic phase suscep.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2IJW6FTX\\c2sm25705j.html:text/html} } @article{conn_high-throughput_2012, title = {High-throughput analysis of the structural evolution of the monoolein cubic phase in situ under crystallogenesis conditions}, volume = {8}, issn = {1744-6848}, url = {http://pubs.rsc.org/en/content/articlelanding/2012/sm/c2sm07232g}, doi = {10.1039/C2SM07232G}, abstract = {We have tracked the structural evolution of the monoolein bicontinuous cubic phase under in meso crystallogenesis conditions. Significantly, all measurements have been carried out in situ within a crystallisation plate reproducing the exact conditions during a crystallisation trial. The structure of the {MO} cubic phase, doped with a small concentration of amyloid-beta peptide, was measured 1 day, 5 days, 7 days and 21 days after addition of {PACT} crystallisation screen, which systematically varies cation, anion, {pH} and polyethylene glycol ({PEG}). The components of the screen had a significant impact on the structure of the cubic phase. We have rationalised the structural variation with respect to the effect of the individual screen components. Specifically addition of higher Mw {PEG} effected a transition from a diamond cubic phase ({QIID}) to a gyroid cubic phase ({QIIG}) across the majority of the plate and the {QIIG} phase became more prevalent with time. The effect of individual salts was correlated with their position in the Hofmeister series. Changes in {pH} and buffer system had a more minor effect on mesophase structure. We have discussed the implications of the observed structural changes with respect to the putative mechanism of protein crystal growth within a lipidic cubic phase.}, pages = {2310--2321}, number = {7}, journaltitle = {Soft Matter}, shortjournal = {Soft Matter}, author = {Conn, Charlotte E. and Darmanin, Connie and Mulet, Xavier and Cann, Sophie Le and Kirby, Nigel and Drummond, Calum J.}, urldate = {2017-05-15}, date = {2012-01-25}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JPNXP3QK\\Conn et al. - 2012 - High-throughput analysis of the structural evoluti:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ACFZGSDH\\Conn et al. - 2012 - High-throughput analysis of the structural evoluti.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JPNXP3QK\\Conn et al. - 2012 - High-throughput analysis of the structural evoluti:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3E4GMTVB\\Conn et al. - 2012 - High-throughput analysis of the structural evoluti.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T3Z3U6EZ\\c2sm07232g:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AUIARTWM\\c2sm07232g.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T3Z3U6EZ\\c2sm07232g:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\M5H86HRB\\c2sm07232g.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JPNXP3QK\\Conn et al. - 2012 - High-throughput analysis of the structural evoluti.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T3Z3U6EZ\\c2sm07232g.html:text/html} } @article{darmanin_high-throughput_2012, title = {High-Throughput Production and Structural Characterization of Libraries of Self-Assembly Lipidic Cubic Phase Materials}, volume = {14}, issn = {2156-8952}, url = {http://dx.doi.org/10.1021/co2001718}, doi = {10.1021/co2001718}, abstract = {A protocol is presented for the high-throughput ({HT}) production of lyotropic liquid crystalline phases from libraries of lipids and lipid mixtures using standard liquid dispensing robotics, implementing methods that circumvent the problems traditionally associated with handling the highly viscous cubic phase. In addition, the ability to structurally characterize lipidic phases and assess functionality for membrane proteins contained within cubic phases, in a {HT} manner, is demonstrated. The techniques are combined and exemplified using the application of membrane protein crystallization within lipidic cubic phases.}, pages = {247--252}, number = {4}, journaltitle = {{ACS} Combinatorial Science}, shortjournal = {{ACS} Comb. Sci.}, author = {Darmanin, Connie and Conn, Charlotte E. and Newman, Janet and Mulet, Xavier and Seabrook, Shane A. and Liang, Yi-Lynn and Hawley, Adrian and Kirby, Nigel and Varghese, Joseph N. and Drummond, Calum J.}, urldate = {2017-05-15}, date = {2012-04-09}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WC3KV4MM\\Darmanin et al. - 2012 - High-Throughput Production and Structural Characte.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C7I5VUTS\\co2001718.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C7I5VUTS\\co2001718:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RJ5RDKKW\\co2001718.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C7I5VUTS\\co2001718:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GKR6SP7P\\co2001718.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WC3KV4MM\\Darmanin et al. - 2012 - High-Throughput Production and Structural Characte:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EGXG33EE\\Darmanin et al. - 2012 - High-Throughput Production and Structural Characte.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WC3KV4MM\\Darmanin et al. - 2012 - High-Throughput Production and Structural Characte:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N8V6GF33\\Darmanin et al. - 2012 - High-Throughput Production and Structural Characte.pdf:application/pdf} } @article{davydova_preparation_2012, title = {Preparation of human vascular endothelial growth factor-D for structural and preclinical therapeutic studies}, volume = {82}, issn = {1046-5928}, url = {http://www.sciencedirect.com/science/article/pii/S1046592812000022}, doi = {10.1016/j.pep.2012.01.001}, abstract = {Vascular endothelial growth factor-D ({VEGF}-D), a secreted angiogenic and lymphangiogenic glycoprotein, enhances tumor growth and metastasis in animal models, and its expression correlates with metastasis and poor patient outcome in some cancers – it is therefore considered a target for novel anti-cancer therapeutics. The definition of the structure of the complex of {VEGF}-D bound to its receptors would be beneficial for design of inhibitors of {VEGF}-D signaling aimed at restricting the growth and spread of cancer. In addition, there is interest in using {VEGF}-D protein for therapeutic angiogenesis and lymphangiogenesis in the settings of cardiovascular diseases and lymphedema, respectively. However, {VEGF}-D has proven difficult to express and purify in a highly bioactive form due to a tendency to exist as monomers rather than bioactive dimers. Here we describe a protocol for expression and purification of mature human {VEGF}-D, and a mutant thereof with reduced glycosylation, potentially suitable for preclinical therapeutic and structural studies, respectively. The degree of glycosylation in mature {VEGF}-D was reduced by eliminating one of the two N-glycosylation sites, and expressing the protein in Lec3.2.8.1 cells which had reduced glycosylation capacity. Mature {VEGF}-D and the glycosylation mutant were each enriched for the biologically active dimeric form by optimizing the separation of dimer from monomer via gel filtration, followed by conversion of remaining monomers to dimers via treatment with cysteine. The glycosylation mutant of {VEGF}-D intended for structural studies preserved all the cysteine residues of mature {VEGF}-D, in contrast to previous structural studies, exhibited comparable receptor binding to mature {VEGF}-D and might facilitate structural studies of the {VEGF}-D/{VEGFR}-3 complex.}, pages = {232--239}, number = {1}, journaltitle = {Protein Expression and Purification}, shortjournal = {Protein Expression and Purification}, author = {Davydova, Natalia and Streltsov, Victor A. and Roufail, Sally and Lovrecz, George O. and Stacker, Steven A. and Adams, Timothy E. and Achen, Marc G.}, urldate = {2017-05-15}, date = {2012-03}, keywords = {Deglycosylation, Deglycosylation, Human mature {VEGF}-D, Human mature {VEGF}-D, Lymphangiogenesis, Lymphangiogenesis, Protein expression and purification, Protein expression and purification}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7TTDEPTA\\Davydova et al. - 2012 - Preparation of human vascular endothelial growth f:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QRWENBBN\\Davydova et al. - 2012 - Preparation of human vascular endothelial growth f.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7TTDEPTA\\Davydova et al. - 2012 - Preparation of human vascular endothelial growth f:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DB9MRWJE\\Davydova et al. - 2012 - Preparation of human vascular endothelial growth f.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HFEWQFS2\\S1046592812000022:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EXS9KBXN\\S1046592812000022.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HFEWQFS2\\S1046592812000022:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CNBF4T75\\S1046592812000022.html:text/html;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7TTDEPTA\\Davydova et al. - 2012 - Preparation of human vascular endothelial growth f.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HFEWQFS2\\S1046592812000022.html:text/html} } @article{lay_crystallization_2012, title = {Crystallization and preliminary X-ray crystallographic analysis of the plant defensin {NaD}1}, volume = {68}, rights = {Copyright (c) 2012 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?pu5355}, doi = {10.1107/S1744309111049530}, abstract = {Plant defensins are small (∼5 {kDa}) basic cysteine-rich proteins that are being explored in important agricultural crops for their ability to confer enhanced disease resistance against fungal pathogens. {NaD}1, isolated from the flowers of the ornamental tobacco (Nicotiana alata), is a particularly well characterized antifungal defensin. Here, the crystallization and preliminary X-ray crystallo­graphic analysis of {NaD}1 is reported. Crystals of {NaD}1 were crystallized using the sitting-drop vapour-diffusion method at 291 K. Data were collected from two crystal forms to 1.4 and 1.6 Å resolution, respectively. The crystals of form A belonged to the monoclinic space group P21, with unit-cell parameters a = 32.697, b = 32.685, c = 41.977 Å, α = 90, β = 100.828, γ = 90°, whereas crystals of form B belonged to the trigonal space group P3221, with unit-cell parameters a = b = 33.091, c = 128.77 Å, α = β = 90, γ = 120°.}, pages = {85--88}, number = {1}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Lay, F. T. and Mills, G. D. and Hulett, M. D. and Kvansakul, M.}, urldate = {2017-05-15}, date = {2012-01-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CTVZ3QCX\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5SXENUXG\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CTVZ3QCX\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\H34D6799\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WTMQQARK\\Lay et al. - 2012 - Crystallization and preliminary X-ray crystallogra:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9K6DDR4F\\Lay et al. - 2012 - Crystallization and preliminary X-ray crystallogra.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WTMQQARK\\Lay et al. - 2012 - Crystallization and preliminary X-ray crystallogra:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PW2GBK45\\Lay et al. - 2012 - Crystallization and preliminary X-ray crystallogra.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WTMQQARK\\Lay et al. - 2012 - Crystallization and preliminary X-ray crystallogra.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CTVZ3QCX\\paper.html:text/html} } @article{lay_recombinant_2012, title = {Recombinant expression and purification of the tomato defensin {TPP}3 and its preliminary X-ray crystallographic analysis}, volume = {68}, rights = {Copyright (c) 2012 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?nj5113}, doi = {10.1107/S1744309112001510}, abstract = {Class {II} defensins have been shown to have potent antifungal activity and are being exploited to protect agricultural crops against fungal pathogens. {TPP}3 is a poorly characterized member of the class {II} plant defensin family from tomato. To gain structural insight into the function of {TPP}3, soluble recombinant {TPP}3 was expressed and purified using the Pichia pastoris expression system, and the crystallization and preliminary X-ray crystallographic analysis of the protein are reported. Crystals of {rTPP}3 were obtained using the sitting-drop vapour-diffusion method at 293 K. Diffraction data were collected to 1.7 Å resolution. The crystals belonged to the hexagonal space group P6122, with unit-cell parameters a = 64.97, b = 64.97, c = 82.40 Å, α = 90, β = 90, γ = 120°.}, pages = {314--316}, number = {3}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Lay, F. T. and Veneer, P. K. and Hulett, M. D. and Kvansakul, M.}, urldate = {2017-05-15}, date = {2012-03-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6NVPZZDJ\\Lay et al. - 2012 - Recombinant expression and purification of the tom:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JI4S2EGX\\Lay et al. - 2012 - Recombinant expression and purification of the tom.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6NVPZZDJ\\Lay et al. - 2012 - Recombinant expression and purification of the tom:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\M652A6QS\\Lay et al. - 2012 - Recombinant expression and purification of the tom.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UFDG4TKZ\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KJH4EVW3\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UFDG4TKZ\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9WSISGMU\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6NVPZZDJ\\Lay et al. - 2012 - Recombinant expression and purification of the tom.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UFDG4TKZ\\paper.html:text/html} } @article{newman_need_2012, title = {On the need for an international effort to capture, share and use crystallization screening data}, volume = {68}, rights = {http://creativecommons.org/licenses/by/2.0/uk}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?en5482}, doi = {10.1107/S1744309112002618}, abstract = {When crystallization screening is conducted many outcomes are observed but typically the only trial recorded in the literature is the condition that yielded the crystal(s) used for subsequent diffraction studies. The initial hit that was optimized and the results of all the other trials are lost. These missing results contain information that would be useful for an improved general understanding of crystallization. This paper provides a report of a crystallization data exchange ({XDX}) workshop organized by several international large-scale crystallization screening laboratories to discuss how this information may be captured and utilized. A group that administers a significant fraction of the world's crystallization screening results was convened, together with chemical and structural data informaticians and computational scientists who specialize in creating and analysing large disparate data sets. The development of a crystallization ontology for the crystallization community was proposed. This paper (by the attendees of the workshop) provides the thoughts and rationale leading to this conclusion. This is brought to the attention of the wider audience of crystallographers so that they are aware of these early efforts and can contribute to the process going forward.}, pages = {253--258}, number = {3}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Newman, J. and Bolton, E. E. and Müller-Dieckmann, J. and Fazio, V. J. and Gallagher, D. T. and Lovell, D. and Luft, J. R. and Peat, T. S. and Ratcliffe, D. and Sayle, R. A. and Snell, E. H. and Taylor, K. and Vallotton, P. and Velanker, S. and von Delft, F.}, urldate = {2017-05-15}, date = {2012-03-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9JW5XBCE\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TXI72JE5\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9JW5XBCE\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2ZFWKS9J\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JP4CX55J\\Newman et al. - 2012 - On the need for an international effort to capture:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZFEVQ8NE\\Newman et al. - 2012 - On the need for an international effort to capture.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JP4CX55J\\Newman et al. - 2012 - On the need for an international effort to capture:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KNVVD49E\\Newman et al. - 2012 - On the need for an international effort to capture.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JP4CX55J\\Newman et al. - 2012 - On the need for an international effort to capture.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9JW5XBCE\\paper.html:text/html} } @article{newman_dingo_2012, title = {The {DINGO} dataset: a comprehensive set of data for the {SAMPL} challenge}, volume = {26}, issn = {0920-654X, 1573-4951}, url = {https://link.springer.com/article/10.1007/s10822-011-9521-2}, doi = {10.1007/s10822-011-9521-2}, shorttitle = {The {DINGO} dataset}, abstract = {Part of the latest {SAMPL} challenge was to predict how a small fragment library of 500 commercially available compounds would bind to a protein target. In order to assess the modellers’ work, a reasonably comprehensive set of data was collected using a number of techniques. These included surface plasmon resonance, isothermal titration calorimetry, protein crystallization and protein crystallography. Using these techniques we could determine the kinetics of fragment binding, the energy of binding, how this affects the ability of the target to crystallize, and when the fragment did bind, the pose or orientation of binding. Both the final data set and all of the raw images have been made available to the community for scrutiny and further work. This overview sets out to give the parameters of the experiments done and what might be done differently for future studies.}, pages = {497--503}, number = {5}, journaltitle = {Journal of Computer-Aided Molecular Design}, shortjournal = {J Comput Aided Mol Des}, author = {Newman, Janet and Dolezal, Olan and Fazio, Vincent and Caradoc-Davies, Tom and Peat, Thomas S.}, urldate = {2017-05-15}, date = {2012-05-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7M9PHCNG\\s10822-011-9521-2:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9CZX4RGI\\s10822-011-9521-2.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7M9PHCNG\\s10822-011-9521-2:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TQBERBBZ\\s10822-011-9521-2.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E2TVAE5P\\Newman et al. - 2012 - The DINGO dataset a comprehensive set of data for:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JAUNPWK7\\Newman et al. - 2012 - The DINGO dataset a comprehensive set of data for.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E2TVAE5P\\Newman et al. - 2012 - The DINGO dataset a comprehensive set of data for:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CXWT4QHW\\Newman et al. - 2012 - The DINGO dataset a comprehensive set of data for.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E2TVAE5P\\Newman et al. - 2012 - The DINGO dataset a comprehensive set of data for.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7M9PHCNG\\s10822-011-9521-2.html:text/html} } @article{newman_universal_2012, title = {A universal indicator dye {pH} assay for crystallization solutions and other high-throughput applications}, volume = {68}, rights = {Copyright (c) 2012 International Union of Crystallography}, issn = {0907-4449}, url = {http://scripts.iucr.org/cgi-bin/paper?be5201}, doi = {10.1107/S0907444912018768}, abstract = {In protein crystallization, as well as in many other fields, it is known that the {pH} at which experiments are performed is often the key factor in the success or failure of the trials. With the trend towards plate-based high-throughput experimental techniques, measuring the {pH} values of solutions one by one becomes prohibitively time- and reagent-expensive. As part of an {HT} crystallization facility, a colour-based {pH} assay that is rapid, uses very little reagent and is suitable for 96-well or higher density plates has been developed.}, pages = {1003--1009}, number = {8}, journaltitle = {Acta Crystallographica Section D: Biological Crystallography}, shortjournal = {Acta Cryst D, Acta Cryst Sect D, Acta Crystallogr D, Acta Crystallogr Sect D, Acta Crystallogr D Biol Crystallogr, Acta Crystallogr Sect D Biol Crystallogr}, author = {Newman, J. and Sayle, R. A. and Fazio, V. J.}, urldate = {2017-05-15}, date = {2012-08-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8Q8PTP47\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\65P7M356\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8Q8PTP47\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CUB6ZT7S\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WXJBH6V8\\Newman et al. - 2012 - A universal indicator dye pH assay for crystalliza:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CXTWM3UH\\Newman et al. - 2012 - A universal indicator dye pH assay for crystalliza.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WXJBH6V8\\Newman et al. - 2012 - A universal indicator dye pH assay for crystalliza:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KMKZIWPX\\Newman et al. - 2012 - A universal indicator dye pH assay for crystalliza.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WXJBH6V8\\Newman et al. - 2012 - A universal indicator dye pH assay for crystalliza.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8Q8PTP47\\paper.html:text/html} } @article{peat_crystal_2012, title = {Crystal Structure of an Indole-3-Acetic Acid Amido Synthetase from Grapevine Involved in Auxin Homeostasis}, volume = {24}, issn = {, 1532-298X}, url = {http://www.plantcell.org/content/24/11/4525}, doi = {10.1105/tpc.112.102921}, abstract = {Auxins are important for plant growth and development, including the control of fruit ripening. Conjugation to amino acids by indole-3-acetic acid ({IAA})-amido synthetases is an important part of auxin homeostasis. The structure of the auxin-conjugating Gretchen Hagen3-1 ({GH}3-1) enzyme from grapevine (Vitis vinifera), in complex with an inhibitor (adenosine-5′-[2-(1H-indol-3-yl)ethyl]phosphate), is presented. Comparison with a previously published benzoate-conjugating enzyme from Arabidopsis thaliana indicates that grapevine {GH}3-1 has a highly similar domain structure and also undergoes a large conformational change during catalysis. Mutational analyses and structural comparisons with other proteins have identified residues likely to be involved in acyl group, amino acid, and {ATP} substrate binding. Vv {GH}3-1 is a monomer in solution and requires magnesium ions solely for the adenlyation reaction. Modeling of {IAA} and two synthetic auxins, benzothiazole-2-oxyacetic acid ({BTOA}) and 1-naphthaleneacetic acid ({NAA}), into the active site indicates that {NAA} and {BTOA} are likely to be poor substrates for this enzyme, confirming previous enzyme kinetic studies. This suggests a reason for the increased effectiveness of {NAA} and {BTOA} as auxins in planta and provides a tool for designing new and effective auxins.}, pages = {4525--4538}, number = {11}, journaltitle = {The Plant Cell}, shortjournal = {Plant Cell}, author = {Peat, Thomas S. and Böttcher, Christine and Newman, Janet and Lucent, Del and Cowieson, Nathan and Davies, Christopher}, urldate = {2017-05-15}, date = {2012-11-01}, langid = {english}, pmid = {23136372}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I3C49ICF\\Peat et al. - 2012 - Crystal Structure of an Indole-3-Acetic Acid Amido:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DTFP68ZA\\Peat et al. - 2012 - Crystal Structure of an Indole-3-Acetic Acid Amido.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I3C49ICF\\Peat et al. - 2012 - Crystal Structure of an Indole-3-Acetic Acid Amido:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UXB7AJEJ\\Peat et al. - 2012 - Crystal Structure of an Indole-3-Acetic Acid Amido.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SAUHVSB6\\4525:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PGN6KVWJ\\4525.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SAUHVSB6\\4525:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DXMG3U9G\\4525.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I3C49ICF\\Peat et al. - 2012 - Crystal Structure of an Indole-3-Acetic Acid Amido.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SAUHVSB6\\4525.html:text/html} } @article{peat_small_2012, title = {Small Molecule Inhibitors of the {LEDGF} Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design}, volume = {7}, issn = {1932-6203}, url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040147}, doi = {10.1371/journal.pone.0040147}, abstract = {A fragment-based screen against human immunodeficiency virus type 1 ({HIV}) integrase led to a number of compounds that bound to the lens epithelium derived growth factor ({LEDGF}) binding site of the integrase catalytic core domain. We determined the crystallographic structures of complexes of the {HIV} integrase catalytic core domain for 10 of these compounds and quantitated the binding by surface plasmon resonance. We demonstrate that the compounds inhibit the interaction of {LEDGF} with {HIV} integrase in a proximity {AlphaScreen} assay, an assay for the {LEDGF} enhancement of {HIV} integrase strand transfer and in a cell based assay. The compounds identified represent a potential framework for the development of a new series of {HIV} integrase inhibitors that do not bind to the catalytic site of the enzyme.}, pages = {e40147}, number = {7}, journaltitle = {{PLOS} {ONE}}, shortjournal = {{PLOS} {ONE}}, author = {Peat, Thomas S. and Rhodes, David I. and Vandegraaff, Nick and Le, Giang and Smith, Jessica A. and Clark, Lisa J. and Jones, Eric D. and Coates, Jonathan A. V. and Thienthong, Neeranat and Newman, Janet and Dolezal, Olan and Mulder, Roger and Ryan, John H. and Savage, G. Paul and Francis, Craig L. and Deadman, John J.}, urldate = {2017-05-15}, date = {2012-07-10}, keywords = {Crystallography, Crystallography, Crystals, Crystals, Crystal structure, Crystal structure, {HIV}, {HIV}, Hydrogen bonding, Hydrogen bonding, Library screening, Library screening, Protein structure comparison, Protein structure comparison, Small molecules, Small molecules}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2475SCNX\\Peat et al. - 2012 - Small Molecule Inhibitors of the LEDGF Site of Hum:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\D5N2WHEM\\Peat et al. - 2012 - Small Molecule Inhibitors of the LEDGF Site of Hum.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2475SCNX\\Peat et al. - 2012 - Small Molecule Inhibitors of the LEDGF Site of Hum:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EW7HFRZ7\\Peat et al. - 2012 - Small Molecule Inhibitors of the LEDGF Site of Hum.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DR3U23SR\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5R4HBTZ3\\article.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DR3U23SR\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RFNG786G\\article.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2475SCNX\\Peat et al. - 2012 - Small Molecule Inhibitors of the LEDGF Site of Hum.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DR3U23SR\\article.html:text/html} } @article{wielens_parallel_2013, title = {Parallel Screening of Low Molecular Weight Fragment Libraries: Do Differences in Methodology Affect Hit Identification?}, volume = {18}, issn = {1087-0571}, url = {http://dx.doi.org/10.1177/1087057112465979}, doi = {10.1177/1087057112465979}, shorttitle = {Parallel Screening of Low Molecular Weight Fragment Libraries}, abstract = {Fragment screening is becoming widely accepted as a technique to identify hit compounds for the development of novel lead compounds. In neighboring laboratories, we have recently, and independently, performed a fragment screening campaign on the {HIV}-1 integrase core domain ({IN}) using similar commercially purchased fragment libraries. The two campaigns used different screening methods for the preliminary identification of fragment hits; one used saturation transfer difference nuclear magnetic resonance spectroscopy ({STD}-{NMR}), and the other used surface plasmon resonance ({SPR}) spectroscopy. Both initial screens were followed by X-ray crystallography. Using the {STD}-{NMR}/X-ray approach, 15 {IN}/fragment complexes were identified, whereas the {SPR}/X-ray approach found 6 complexes. In this article, we compare the approaches that were taken by each group and the results obtained, and we look at what factors could potentially influence the final results. We find that despite using different approaches with little overlap of initial hits, both approaches identified binding sites on {IN} that provided a basis for fragment-based lead discovery and further lead development. Comparison of hits identified in the two studies highlights a key role for both the conditions under which fragment binding is measured and the criteria selected to classify hits.}, pages = {147--159}, number = {2}, journaltitle = {Journal of Biomolecular Screening}, shortjournal = {J Biomol Screen}, author = {Wielens, Jerome and Headey, Stephen J. and Rhodes, David I. and Mulder, Roger J. and Dolezal, Olan and Deadman, John J. and Newman, Janet and Chalmers, David K. and Parker, Michael W. and Peat, Thomas S. and Scanlon, Martin J.}, urldate = {2017-05-15}, date = {2013-02-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KDUETCWD\\Wielens et al. - 2013 - Parallel Screening of Low Molecular Weight Fragmen:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DI54MMUR\\Wielens et al. - 2013 - Parallel Screening of Low Molecular Weight Fragmen.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KDUETCWD\\Wielens et al. - 2013 - Parallel Screening of Low Molecular Weight Fragmen:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\42FH5JI6\\Wielens et al. - 2013 - Parallel Screening of Low Molecular Weight Fragmen.pdf:application/pdf;SAGE PDF Full Text:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KDUETCWD\\Wielens et al. - 2013 - Parallel Screening of Low Molecular Weight Fragmen.pdf:application/pdf} } @article{atkinson_cloning_2011, title = {Cloning, expression, purification and crystallization of dihydrodipicolinate synthase from the grapevine Vitis vinifera}, volume = {67}, rights = {Copyright (c) 2011 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?pu5341}, doi = {10.1107/S1744309111038395}, abstract = {Dihydrodipicolinate synthase ({DHDPS}) catalyses the first committed step of the lysine-biosynthesis pathway in bacteria, plants and some fungi. This study describes the cloning, expression, purification and crystallization of {DHDPS} from the grapevine Vitis vinifera (Vv-{DHDPS}). Following in-drop cleavage of the hexahistidine tag, cocrystals of Vv-{DHDPS} with the substrate pyruvate were grown in 0.1 M Bis-Tris propane {pH} 8.2, 0.2 M sodium bromide, 20\%(w/v) {PEG} 3350. X-ray diffraction data in space group P1 at a resolution of 2.2 Å are presented. Preliminary diffraction data analysis indicated the presence of eight molecules per asymmetric unit ({VM} = 2.55 Å3 Da−1, 52\% solvent content). The pending crystal structure of Vv-{DHDPS} will provide insight into the molecular evolution in quaternary structure of {DHDPS} enzymes.}, pages = {1537--1541}, number = {12}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Atkinson, S. C. and Dogovski, C. and Newman, J. and Dobson, R. C. J. and Perugini, M. A.}, urldate = {2017-05-15}, date = {2011-12-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PZVCSWGA\\Atkinson et al. - 2011 - Cloning, expression, purification and crystallizat:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RBWZPFMH\\Atkinson et al. - 2011 - Cloning, expression, purification and crystallizat.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PZVCSWGA\\Atkinson et al. - 2011 - Cloning, expression, purification and crystallizat:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RS6PFV8F\\Atkinson et al. - 2011 - Cloning, expression, purification and crystallizat.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VDBU6HJC\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8X3222CF\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VDBU6HJC\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XG778G5T\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PZVCSWGA\\Atkinson et al. - 2011 - Cloning, expression, purification and crystallizat.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VDBU6HJC\\paper.html:text/html} } @article{cross_tyrosine_2011, title = {Tyrosine Latching of a Regulatory Gate Affords Allosteric Control of Aromatic Amino Acid Biosynthesis}, volume = {286}, issn = {0021-9258, 1083-351X}, url = {http://www.jbc.org/content/286/12/10216}, doi = {10.1074/jbc.M110.209924}, abstract = {The first step of the shikimate pathway for aromatic amino acid biosynthesis is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase ({DAH}7PS). Thermotoga maritima {DAH}7PS ({TmaDAH}7PS) is tetrameric, with monomer units comprised of a core catalytic (β/α)8 barrel and an N-terminal domain. This enzyme is inhibited strongly by tyrosine and to a lesser extent by the presence of phenylalanine. A truncated mutant of {TmaDAH}7PS lacking the N-terminal domain was catalytically more active and completely insensitive to tyrosine and phenylalanine, consistent with a role for this domain in allosteric inhibition. The structure of this protein was determined to 2.0 Å. In contrast to the wild-type enzyme, this enzyme is dimeric. Wild-type {TmaDAH}7PS was co-crystallized with tyrosine, and the structure of this complex was determined to a resolution of 2.35 Å. Tyrosine was found to bind at the interface between two regulatory N-terminal domains, formed from diagonally located monomers of the tetramer, revealing a major reorganization of the regulatory domain with respect to the barrel relative to unliganded enzyme. This significant conformational rearrangement observed in the crystal structures was also clearly evident from small angle X-ray scattering measurements recorded in the presence and absence of tyrosine. The closed conformation adopted by the protein on tyrosine binding impedes substrate entry into the neighboring barrel, revealing an unusual tyrosine-controlled gating mechanism for allosteric control of this enzyme.}, pages = {10216--10224}, number = {12}, journaltitle = {Journal of Biological Chemistry}, shortjournal = {J. Biol. Chem.}, author = {Cross, Penelope J. and Dobson, Renwick C. J. and Patchett, Mark L. and Parker, Emily J.}, urldate = {2017-05-15}, date = {2011-03-25}, langid = {english}, pmid = {21282100}, keywords = {Allosteric Regulation, Allosteric Regulation, Aromatic Amino Acid Biosynthesis, Aromatic Amino Acid Biosynthesis, Enzyme Catalysis, Enzyme Catalysis, Enzyme inhibitors, Enzyme inhibitors, Enzyme Mechanisms, Enzyme Mechanisms, enzyme structure, enzyme structure, Tyrosine, Tyrosine}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HBX68BXJ\\10216:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QTMS5WM3\\10216.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HBX68BXJ\\10216:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UXZEZ2VP\\10216.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZW764T9A\\Cross et al. - 2011 - Tyrosine Latching of a Regulatory Gate Affords All:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UIF6ZE5K\\Cross et al. - 2011 - Tyrosine Latching of a Regulatory Gate Affords All.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZW764T9A\\Cross et al. - 2011 - Tyrosine Latching of a Regulatory Gate Affords All:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4GBAA6H4\\Cross et al. - 2011 - Tyrosine Latching of a Regulatory Gate Affords All.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZW764T9A\\Cross et al. - 2011 - Tyrosine Latching of a Regulatory Gate Affords All.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HBX68BXJ\\10216.html:text/html} } @article{czabotar_mutation_2011, title = {Mutation to Bax beyond the {BH}3 Domain Disrupts Interactions with Pro-survival Proteins and Promotes Apoptosis}, volume = {286}, issn = {0021-9258, 1083-351X}, url = {http://www.jbc.org/content/286/9/7123}, doi = {10.1074/jbc.M110.161281}, abstract = {Pro-survival members of the Bcl-2 family of proteins restrain the pro-apoptotic activity of Bax, either directly through interactions with Bax or indirectly by sequestration of activator {BH}3-only proteins, or both. Mutations in Bax that promote apoptosis can provide insight into how Bax is regulated. Here, we describe crystal structures of the pro-survival proteins Mcl-1 and Bcl-{xL} in complex with a 34-mer peptide from Bax that encompasses its {BH}3 domain. These structures reveal canonical interactions between four signature hydrophobic amino acids from the {BaxBH}3 domain and the {BH}3-binding groove of the pro-survival proteins. In both structures, Met-74 from the Bax peptide engages with the {BH}3-binding groove in a fifth hydrophobic interaction. Various Bax Met-74 mutants disrupt interactions between Bax and all pro-survival proteins, but these Bax mutants retain pro-apoptotic activity. Bax/Bak-deficient mouse embryonic fibroblast cells reconstituted with several Bax Met-74 mutants are more sensitive to the {BH}3 mimetic compound {ABT}-737 as compared with cells expressing wild-type Bax. Furthermore, the cells expressing Bax Met-74 mutants are less viable in colony assays even in the absence of an external apoptotic stimulus. These results support a model in which direct restraint of Bax by pro-survival Bcl-2 proteins is a barrier to apoptosis.}, pages = {7123--7131}, number = {9}, journaltitle = {Journal of Biological Chemistry}, shortjournal = {J. Biol. Chem.}, author = {Czabotar, Peter E. and Lee, Erinna F. and Thompson, Geoff V. and Wardak, Ahmad Z. and Fairlie, W. Douglas and Colman, Peter M.}, urldate = {2017-05-15}, date = {2011-03-04}, langid = {english}, pmid = {21199865}, keywords = {apoptosis, apoptosis, Cell Death, Cell Death, Crystal structure, Crystal structure, Mitochondrial Apoptosis, Mitochondrial Apoptosis, Protein Structure, Protein Structure}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BGNHBWFU\\Czabotar et al. - 2011 - Mutation to Bax beyond the BH3 Domain Disrupts Int:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KQ5QW578\\Czabotar et al. - 2011 - Mutation to Bax beyond the BH3 Domain Disrupts Int.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BGNHBWFU\\Czabotar et al. - 2011 - Mutation to Bax beyond the BH3 Domain Disrupts Int:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\35J7VR6A\\Czabotar et al. - 2011 - Mutation to Bax beyond the BH3 Domain Disrupts Int.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DREXZ7MM\\7123:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DBNAIEKB\\7123.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DREXZ7MM\\7123:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\R53TFZHP\\7123.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BGNHBWFU\\Czabotar et al. - 2011 - Mutation to Bax beyond the BH3 Domain Disrupts Int.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DREXZ7MM\\7123.html:text/html} } @article{dobson_ll-diaminopimelate_2011, title = {L,L-Diaminopimelate Aminotransferase from Chlamydomonas reinhardtii: A Target for Algaecide Development}, volume = {6}, issn = {1932-6203}, url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020439}, doi = {10.1371/journal.pone.0020439}, shorttitle = {L,L-Diaminopimelate Aminotransferase from Chlamydomonas reinhardtii}, abstract = {In some bacterial species and photosynthetic cohorts, including algae, the enzyme l,l-diaminopimelate aminotransferase ({DapL}) (E.C. 2.6.1.83) is involved in the anabolism of the essential amino acid L-lysine. {DapL} catalyzes the conversion of tetrahydrodipicolinate ({THDPA}) to l,l-diaminopimelate (l,l-{DAP}), in one step bypassing the {DapD}, {DapC} and {DapE} enzymatic reactions present in the acyl {DAP} pathways. Here we present an in vivo and in vitro characterization of the {DapL} ortholog from the alga Chlamydomonas reinhardtii (Cr-{DapL}). The in vivo analysis illustrated that the enzyme is able to functionally complement the E. coli dap auxotrophs and was essential for plant development in Arabidopsis. In vitro, the enzyme was able to inter-convert {THDPA} and l,l-{DAP}, showing strong substrate specificity. Cr-{DapL} was dimeric in both solution and when crystallized. The structure of Cr-{DapL} was solved in its apo form, showing an overall architecture of a α/β protein with each monomer in the dimer adopting a pyridoxal phosphate-dependent transferase-like fold in a V-shaped conformation. The active site comprises residues from both monomers in the dimer and shows some rearrangement when compared to the apo-{DapL} structure from Arabidopsis. Since animals do not possess the enzymatic machinery necessary for the de novo synthesis of the amino acid l-lysine, enzymes involved in this pathway are attractive targets for the development of antibiotics, herbicides and algaecides.}, pages = {e20439}, number = {5}, journaltitle = {{PLOS} {ONE}}, shortjournal = {{PLOS} {ONE}}, author = {Dobson, Renwick C. J. and Girón, Irma and Hudson, André O.}, urldate = {2017-05-15}, date = {2011-05-25}, keywords = {Aminotransferases, Aminotransferases, Arabidopsis thaliana, Arabidopsis thaliana, Chlamydomonas reinhardtii, Chlamydomonas reinhardtii, Crystal structure, Crystal structure, Dimers (Chemical physics), Dimers (Chemical physics), Enzyme assays, Enzyme assays, enzyme structure, enzyme structure, Protein structure comparison, Protein structure comparison}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IIEPTMXB\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7WRHZDA9\\article.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IIEPTMXB\\article:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RNURBUM5\\article.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PHC6J7HS\\Dobson et al. - 2011 - L,L-Diaminopimelate Aminotransferase from Chlamydo:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\U8WFZCCP\\Dobson et al. - 2011 - L,L-Diaminopimelate Aminotransferase from Chlamydo.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PHC6J7HS\\Dobson et al. - 2011 - L,L-Diaminopimelate Aminotransferase from Chlamydo:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Q25XNAWU\\Dobson et al. - 2011 - L,L-Diaminopimelate Aminotransferase from Chlamydo.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PHC6J7HS\\Dobson et al. - 2011 - L,L-Diaminopimelate Aminotransferase from Chlamydo.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IIEPTMXB\\article.html:text/html} } @article{gorman_crystal_2011, title = {Crystal structure of the Leishmania major {MIX} protein: A scaffold protein that mediates protein–protein interactions}, volume = {20}, issn = {1469-896X}, url = {http://onlinelibrary.wiley.com/doi/10.1002/pro.631/abstract}, doi = {10.1002/pro.631}, shorttitle = {Crystal structure of the Leishmania major {MIX} protein}, abstract = {Infection by Leishmania and Trypanosoma causes severe disease and can be fatal. The reduced effectiveness of current treatments is largely due to drug resistance, hence the urgent need to develop new drugs, preferably against novel targets. We have recently identified a mitochondrial membrane-anchored protein, designated {MIX}, which occurs exclusively in these parasites and is essential for virulence. We have determined the crystal structure of Leishmania major {MIX} to a resolution of 2.4 Å. {MIX} forms an all α-helical fold comprising seven α-helices that fold into a single domain. The distribution of helices is similar to a number of scaffold proteins, namely {HEAT} repeats, 14-3-3, and tetratricopeptide repeat proteins, suggesting that {MIX} mediates protein–protein interactions. Accordingly, using copurification and mass spectroscopy we were able to identify several proteins that may interact with {MIX} in vivo. Being parasite specific, {MIX} is a promising new drug target and, thus, the structure and potential interacting partners provide a basis for structure-guided drug discovery.}, pages = {1060--1068}, number = {6}, journaltitle = {Protein Science}, shortjournal = {Protein Science}, author = {Gorman, Michael A. and Uboldi, Alex D. and Walsh, Peter J. and Tan, Kher Shing and Hansen, Guido and Huyton, Trevor and Ji, Hong and Curtis, Joan and Kedzierski, Lukasz and Papenfuss, Anthony T. and Dogovski, Con and Perugini, Matthew A. and Simpson, Richard J. and Handman, Emanuela and Parker, Michael W.}, urldate = {2017-05-15}, date = {2011-06-01}, langid = {english}, keywords = {14-3-3, 14-3-3, Crystal structure, Crystal structure, {HEAT}, {HEAT}, Leishmania, Leishmania, {TPR} motif, {TPR} motif}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7T7MAHS7\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I3V3VBIZ\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7T7MAHS7\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QJWACXIN\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B5CHDFMJ\\Gorman et al. - 2011 - Crystal structure of the Leishmania major MIX prot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TUAUFP3R\\Gorman et al. - 2011 - Crystal structure of the Leishmania major MIX prot.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B5CHDFMJ\\Gorman et al. - 2011 - Crystal structure of the Leishmania major MIX prot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BMGFMC4C\\Gorman et al. - 2011 - Crystal structure of the Leishmania major MIX prot.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B5CHDFMJ\\Gorman et al. - 2011 - Crystal structure of the Leishmania major MIX prot.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7T7MAHS7\\abstract.html:text/html} } @article{griffin_crystallization_2011, title = {Crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase 2 from Arabidopsis thaliana}, volume = {67}, rights = {Copyright (c) 2011 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?us5036}, doi = {10.1107/S1744309111033276}, abstract = {Dihydrodipicolinate synthase ({DHDPS}; {EC} 4.2.1.52) catalyzes the first committed step of the lysine-biosynthetic pathway in plants and bacteria. Since (S)-lysine biosynthesis does not occur in animals, {DHDPS} is an attractive target for rational antibiotic and herbicide design. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of {DHDPS}2 from Arabidopsis thaliana are reported. Diffraction-quality protein crystals belonged to space group P21212.}, pages = {1386--1390}, number = {11}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Griffin, M. D. W. and Billakanti, J. M. and Gerrard, J. A. and Dobson, R. C. J. and Pearce, F. G.}, urldate = {2017-05-15}, date = {2011-11-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TS9XA7DI\\Griffin et al. - 2011 - Crystallization and preliminary X-ray diffraction:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3WDF2SNG\\Griffin et al. - 2011 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TS9XA7DI\\Griffin et al. - 2011 - Crystallization and preliminary X-ray diffraction:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TF7TPGB6\\Griffin et al. - 2011 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V7Q622QC\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DFZ7K8KQ\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V7Q622QC\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DEK4KJ2S\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TS9XA7DI\\Griffin et al. - 2011 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V7Q622QC\\paper.html:text/html} } @article{gunn_purification_2011, title = {Purification, crystallization, small-angle X-ray scattering and preliminary X-ray diffraction analysis of the {SH}2 domain of the Csk-homologous kinase}, volume = {67}, rights = {Copyright (c) 2011 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?dp5002}, doi = {10.1107/S1744309110053728}, abstract = {The C-terminal Src kinase (Csk) and Csk-homologous kinase ({CHK}) are endogenous inhibitors of the proto-oncogenic Src family of protein tyrosine kinases ({SFKs}). Phosphotyrosyl peptide binding to their Src-homology 2 ({SH}2) domains activates Csk and {CHK}, enhancing their ability to suppress {SFK} signalling; however, the detailed mechanistic basis of this activation event is unclear. The {CHK} {SH}2 was expressed in Escherichia coli and the purified protein was characterized as monomeric by synchrotron small-angle X-ray scattering in-line with size-exclusion chromatography. The {CHK} {SH}2 crystallized in 0.2 M sodium bromide, 0.1 M bis-Tris propane {pH} 6.5 and 20\% polyethylene glycol 3350 and the best crystals diffracted to ∼1.6 Å resolution. The crystals belonged to space group P2, with unit-cell parameters a = 25.8, b = 34.6, c = 63.2 Å, β = 99.4°.}, pages = {336--339}, number = {3}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Gunn, N. J. and Gorman, M. A. and Dobson, R. C. J. and Parker, M. W. and Mulhern, T. D.}, urldate = {2017-05-15}, date = {2011-03-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6RPPQUXV\\Gunn et al. - 2011 - Purification, crystallization, small-angle X-ray s:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CUXER49M\\Gunn et al. - 2011 - Purification, crystallization, small-angle X-ray s.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6RPPQUXV\\Gunn et al. - 2011 - Purification, crystallization, small-angle X-ray s:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GFTMTGSM\\Gunn et al. - 2011 - Purification, crystallization, small-angle X-ray s.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XBWS9XS4\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4RNBXAMU\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XBWS9XS4\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2K3PTIWE\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6RPPQUXV\\Gunn et al. - 2011 - Purification, crystallization, small-angle X-ray s.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XBWS9XS4\\paper.html:text/html} } @article{hudson_crystallization_2011, title = {Crystallization and preliminary X-ray diffraction analysis of l,l-diaminopimelate aminotransferase ({DapL}) from Chlamydomonas reinhardtii}, volume = {67}, rights = {Copyright (c) 2011 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?pu5311}, doi = {10.1107/S174430911004844X}, abstract = {In the anabolic synthesis of diaminopimelate and lysine in plants and in some bacteria, the enzyme l,l-diaminopimelate aminotransferase ({DapL}; {EC} 2.6.1.83) catalyzes the conversion of tetrahydrodipicolinic acid ({THDPA}) to l,l-diaminopimelate, bypassing the {DapD}, {DapC} and {DapE} enzymatic steps in the bacterial acyl pathways. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of {DapL} from the alga Chlamydomonas reinhardtii are presented. Protein crystals were grown in conditions containing 25\%(w/v) {PEG} 3350 and 200 {mM} lithium sulfate and initially diffracted to ∼1.35 Å resolution. They belonged to space group P212121, with unit-cell parameters a = 58.9, b = 91.8, c = 162.9 Å. The data were processed to 1.55 Å resolution with an Rmerge of 0.081, an Rp.i.m. of 0.044, an Rr.i.m of 0.093 and a {VM} of 2.28 Å3 Da−1.}, pages = {140--143}, number = {1}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Hudson, A. O. and Girón, I. and Dobson, R. C. J.}, urldate = {2017-05-15}, date = {2011-01-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9E6NEJQC\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A22837Z3\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9E6NEJQC\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4PV6VMU9\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XSP9D4RT\\Hudson et al. - 2011 - Crystallization and preliminary X-ray diffraction:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MXWTF5HZ\\Hudson et al. - 2011 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XSP9D4RT\\Hudson et al. - 2011 - Crystallization and preliminary X-ray diffraction:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MR2E3S22\\Hudson et al. - 2011 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XSP9D4RT\\Hudson et al. - 2011 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9E6NEJQC\\paper.html:text/html} } @article{keegan_evaluating_2011, title = {Evaluating the solution from {MrBUMP} and {BALBES}}, volume = {67}, rights = {http://creativecommons.org/licenses/by/2.0/uk}, issn = {0907-4449}, url = {http://scripts.iucr.org/cgi-bin/paper?ba5167}, doi = {10.1107/S0907444911007530}, abstract = {Molecular replacement is one of the key methods used to solve the problem of determining the phases of structure factors in protein structure solution from X-ray image diffraction data. Its success rate has been steadily improving with the development of improved software methods and the increasing number of structures available in the {PDB} for use as search models. Despite this, in cases where there is low sequence identity between the target-structure sequence and that of its set of possible homologues it can be a difficult and time-consuming chore to isolate and prepare the best search model for molecular replacement. {MrBUMP} and {BALBES} are two recent developments from {CCP}4 that have been designed to automate and speed up the process of determining and preparing the best search models and putting them through molecular replacement. Their intention is to provide the user with a broad set of results using many search models and to highlight the best of these for further processing. An overview of both programs is presented along with a description of how best to use them, citing case studies and the results of large-scale testing of the software.}, pages = {313--323}, number = {4}, journaltitle = {Acta Crystallographica Section D: Biological Crystallography}, shortjournal = {Acta Cryst D, Acta Cryst Sect D, Acta Crystallogr D, Acta Crystallogr Sect D, Acta Crystallogr D Biol Crystallogr, Acta Crystallogr Sect D Biol Crystallogr}, author = {Keegan, R. M. and Long, F. and Fazio, V. J. and Winn, M. D. and Murshudov, G. N. and Vagin, A. A.}, urldate = {2017-05-15}, date = {2011-04-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\55ZE2JDP\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZWJKBQPE\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\55ZE2JDP\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KUVGE3J3\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AE7XQVQ6\\Keegan et al. - 2011 - Evaluating the solution from MrBUMP and BALBES:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9K6RDHZP\\Keegan et al. - 2011 - Evaluating the solution from MrBUMP and BALBES.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AE7XQVQ6\\Keegan et al. - 2011 - Evaluating the solution from MrBUMP and BALBES:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FTHN77TS\\Keegan et al. - 2011 - Evaluating the solution from MrBUMP and BALBES.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AE7XQVQ6\\Keegan et al. - 2011 - Evaluating the solution from MrBUMP and BALBES.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\55ZE2JDP\\paper.html:text/html} } @article{kennedy_evaluating_2011, title = {Evaluating Protic Ionic Liquids as Protein Crystallization Additives}, volume = {11}, issn = {1528-7483}, url = {http://dx.doi.org/10.1021/cg1017104}, doi = {10.1021/cg1017104}, abstract = {Protic ionic liquids ({PILs}) have been evaluated as additives in protein crystallization trials. Ten ionic liquids were incorporated as additives along with the {JCSG}+ sparse matrix screen for the crystallization of lysozyme, glucose isomerase, and trypsin. When used as additives, the {PILs} were identified to influence the crystallization of these globular proteins. Crystal structures obtained for lysozyme with each of the 10 {PILs} under identical conditions showed no change in the crystal structure of the protein; however, in three of the ten cases fragments of the ionic liquids were observed to be incorporated within the protein.}, pages = {1777--1785}, number = {5}, journaltitle = {Crystal Growth \& Design}, shortjournal = {Crystal Growth \& Design}, author = {Kennedy, Danielle F. and Drummond, Calum J. and Peat, Thomas S. and Newman, Janet}, urldate = {2017-05-15}, date = {2011-05-04}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SK8TR7J8\\Kennedy et al. - 2011 - Evaluating Protic Ionic Liquids as Protein Crystal.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AGZ435JC\\cg1017104.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AGZ435JC\\cg1017104:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RF2GAW3R\\cg1017104.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AGZ435JC\\cg1017104:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\H4SGN58I\\cg1017104.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SK8TR7J8\\Kennedy et al. - 2011 - Evaluating Protic Ionic Liquids as Protein Crystal:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EI9VHXIQ\\Kennedy et al. - 2011 - Evaluating Protic Ionic Liquids as Protein Crystal.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SK8TR7J8\\Kennedy et al. - 2011 - Evaluating Protic Ionic Liquids as Protein Crystal:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AEUPHKXB\\Kennedy et al. - 2011 - Evaluating Protic Ionic Liquids as Protein Crystal.pdf:application/pdf} } @article{laguerre_preparation_2011, title = {Preparation, crystallization and preliminary X-ray diffraction analysis of two intestinal fatty-acid binding proteins in the presence of 11-(dansylamino)undecanoic acid}, volume = {67}, rights = {Copyright (c) 2011 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?en5442}, doi = {10.1107/S1744309110051481}, abstract = {Fatty-acid binding proteins ({FABPs}) are abundantly expressed proteins that bind a range of lipophilic molecules. They have been implicated in the import and intracellular distribution of their ligands and have been linked with metabolic and inflammatory responses in the cells in which they are expressed. Despite their high sequence identity, human intestinal {FABP} ({hIFABP}) and rat intestinal {FABP} ({rIFABP}) bind some ligands with different affinities. In order to address the structural basis of this differential binding, diffraction-quality crystals have been obtained of {hIFABP} and {rIFABP} in complex with the fluorescent fatty-acid analogue 11-(dansylamino)undecanoic acid.}, pages = {291--295}, number = {2}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Laguerre, A. and Wielens, J. and Parker, M. W. and Porter, C. J. H. and Scanlon, M. J.}, urldate = {2017-05-15}, date = {2011-02-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5KBDQTG9\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AC29HFWC\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5KBDQTG9\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KFJID7PD\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SP75H6MM\\Laguerre et al. - 2011 - Preparation, crystallization and preliminary X-ray:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2UFUEG3Q\\Laguerre et al. - 2011 - Preparation, crystallization and preliminary X-ray.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SP75H6MM\\Laguerre et al. - 2011 - Preparation, crystallization and preliminary X-ray:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XWTTGKVE\\Laguerre et al. - 2011 - Preparation, crystallization and preliminary X-ray.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SP75H6MM\\Laguerre et al. - 2011 - Preparation, crystallization and preliminary X-ray.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5KBDQTG9\\paper.html:text/html} } @article{lee_discovery_2011, title = {Discovery and molecular characterization of a Bcl-2–regulated cell death pathway in schistosomes}, volume = {108}, issn = {0027-8424, 1091-6490}, url = {http://www.pnas.org/content/108/17/6999}, doi = {10.1073/pnas.1100652108}, abstract = {Schistosomiasis is an infectious disease caused by parasites of the phylum platyhelminthe. Here, we describe the identification and characterization of a Bcl-2–regulated apoptosis pathway in Schistosoma japonicum and S. mansoni. Genomic, biochemical, and cell-based mechanistic studies provide evidence for a tripartite pathway, similar to that in humans including {BH}3-only proteins that are inhibited by prosurvival Bcl-2–like molecules, and Bax/Bak-like proteins that facilitate mitochondrial outer-membrane permeabilization. Because Bcl-2 proteins have been successfully targeted with “{BH}3 mimetic” drugs, particularly in the treatment of cancer, we investigated whether schistosome apoptosis pathways could provide targets for future antischistosomal drug discovery efforts. Accordingly, we showed that a schistosome prosurvival protein, {sjA}, binds {ABT}-737, a well-characterized {BH}3 mimetic. A crystal structure of {sjA} bound to a {BH}3 peptide provides direct evidence for the feasibility of developing {BH}3 mimetics to target Bcl-2 prosurvival proteins in schistosomes, suggesting an alternative application for this class of drugs beyond cancer treatment.}, pages = {6999--7003}, number = {17}, journaltitle = {Proceedings of the National Academy of Sciences}, shortjournal = {{PNAS}}, author = {Lee, Erinna F. and Clarke, Oliver B. and Evangelista, Marco and Feng, Zhiping and Speed, Terence P. and Tchoubrieva, Elissaveta B. and Strasser, Andreas and Kalinna, Bernd H. and Colman, Peter M. and Fairlie, W. Douglas}, urldate = {2017-05-15}, date = {2011-04-26}, langid = {english}, pmid = {21444803}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NCHI7I8I\\6999:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NRKENDMB\\6999.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NCHI7I8I\\6999:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TGFC2TT5\\6999.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P4UNDSQ8\\Lee et al. - 2011 - Discovery and molecular characterization of a Bcl-:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J9SEAI6F\\Lee et al. - 2011 - Discovery and molecular characterization of a Bcl-.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P4UNDSQ8\\Lee et al. - 2011 - Discovery and molecular characterization of a Bcl-:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B66TCQ4Q\\Lee et al. - 2011 - Discovery and molecular characterization of a Bcl-.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P4UNDSQ8\\Lee et al. - 2011 - Discovery and molecular characterization of a Bcl-.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NCHI7I8I\\6999.html:text/html} } @article{lee_crystal_2011, title = {Crystal Structure of a {BCL}-W Domain-Swapped Dimer: Implications for the Function of {BCL}-2 Family Proteins}, volume = {19}, issn = {0969-2126}, url = {http://www.sciencedirect.com/science/article/pii/S0969212611002577}, doi = {10.1016/j.str.2011.07.015}, shorttitle = {Crystal Structure of a {BCL}-W Domain-Swapped Dimer}, abstract = {Summary The prosurvival and proapoptotic proteins of the {BCL}-2 family share a similar three-dimensional fold despite their opposing functions. However, many biochemical studies highlight the requirement for conformational changes for the functioning of both types of proteins, although structural data to support such changes remain elusive. Here, we describe the X-ray structure of dimeric {BCL}-W that reveals a major conformational change involving helices α3 and α4 hinging away from the core of the protein. Biochemical and functional studies reveal that the α4-α5 hinge region is required for dimerization of {BCL}-W, and functioning of both pro- and antiapoptotic {BCL}-2 proteins. Hence, this structure reveals a conformational flexibility not seen in previous {BCL}-2 protein structures and provides insights into how these regulators of apoptosis can change conformation to exert their function.}, pages = {1467--1476}, number = {10}, journaltitle = {Structure}, shortjournal = {Structure}, author = {Lee, Erinna F. and Dewson, Grant and Smith, Brian J. and Evangelista, Marco and Pettikiriarachchi, Anne and Dogovski, Con and Perugini, Matthew A. and Colman, Peter M. and Fairlie, W. Douglas}, urldate = {2017-05-15}, date = {2011-10-12}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6XBQK353\\S0969212611002577:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9CEW5VC7\\S0969212611002577.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6XBQK353\\S0969212611002577:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\68MJIZKR\\S0969212611002577.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UXMAGFBP\\Lee et al. - 2011 - Crystal Structure of a BCL-W Domain-Swapped Dimer:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z8G9K5HV\\Lee et al. - 2011 - Crystal Structure of a BCL-W Domain-Swapped Dimer.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UXMAGFBP\\Lee et al. - 2011 - Crystal Structure of a BCL-W Domain-Swapped Dimer:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TR78EVTV\\Lee et al. - 2011 - Crystal Structure of a BCL-W Domain-Swapped Dimer.pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UXMAGFBP\\Lee et al. - 2011 - Crystal Structure of a BCL-W Domain-Swapped Dimer.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6XBQK353\\S0969212611002577.html:text/html} } @article{lee_structural_2011, title = {Structural Basis of Bcl-{xL} Recognition by a {BH}3-Mimetic α/β-Peptide Generated by Sequence-Based Design}, volume = {12}, issn = {1439-7633}, url = {http://onlinelibrary.wiley.com/doi/10.1002/cbic.201100314/abstract}, doi = {10.1002/cbic.201100314}, abstract = {The crystal structure of a complex between the prosurvival protein Bcl-{xL} and an α/β-peptide 21-mer is described. The α/β-peptide contains six β-amino acid residues distributed periodically throughout the sequence and adopts an α-helix-like conformation that mimics the bioactive shape of the Puma {BH}3 domain. The α/β-peptide forms all of the noncovalent contacts that have previously been identified as necessary for recognition of the prosurvival protein by an authentic {BH}3 domain. Comparison of our α/β-peptide:Bcl-{xL} structure with structures of complexes between native {BH}3 domains and Bcl-2 family proteins reveals how subtle adjustments, including variations in helix radius and helix bowing, allow the α/β-peptide to engage Bcl-{xL} with high affinity. Geometric comparisons of the {BH}3-mimetic α/β-peptide with α/β-peptides in helix-bundle assemblies provide insight on the conformational plasticity of backbones that contain combinations of α- and β-amino acid residues. The {BH}3-mimetic α/β-peptide displays prosurvival protein-binding preferences distinct from those of Puma {BH}3 itself, even though these two oligomers have identical side-chain sequences. Our results suggest origins for this backbone-dependent change in selectivity.}, pages = {2025--2032}, number = {13}, journaltitle = {{ChemBioChem}}, shortjournal = {{ChemBioChem}}, author = {Lee, Erinna F. and Smith, Brian J. and Horne, W. Seth and Mayer, Kelsey N. and Evangelista, Marco and Colman, Peter M. and Gellman, Samuel H. and Fairlie, W. Douglas}, urldate = {2017-05-15}, date = {2011-09-05}, langid = {english}, keywords = {apoptosis, apoptosis, {BH}3 domain, {BH}3 domain, foldamers, foldamers, Peptides, Peptides, peptidomimetics, peptidomimetics}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MK3J6XBR\\Lee et al. - 2011 - Structural Basis of Bcl-xL Recognition by a BH3-Mi:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4EUC4JHT\\Lee et al. - 2011 - Structural Basis of Bcl-xL Recognition by a BH3-Mi.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MK3J6XBR\\Lee et al. - 2011 - Structural Basis of Bcl-xL Recognition by a BH3-Mi:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2RH8VP26\\Lee et al. - 2011 - Structural Basis of Bcl-xL Recognition by a BH3-Mi.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SWJKRI7W\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E9BM7XVV\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SWJKRI7W\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WI3J4CVG\\abstract.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MK3J6XBR\\Lee et al. - 2011 - Structural Basis of Bcl-xL Recognition by a BH3-Mi.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SWJKRI7W\\abstract.html:text/html} } @article{newman_one_2011, title = {One plate, two plates, a thousand plates. How crystallisation changes with large numbers of samples}, volume = {55}, issn = {1046-2023}, url = {http://www.sciencedirect.com/science/article/pii/S1046202311000922}, doi = {10.1016/j.ymeth.2011.04.004}, series = {Methods in Structural Proteomics}, abstract = {Turning commercial lab automation into a high-throughput centre requires an underlying process, and implementing checks to ensure that the process is working as it should. At the Collaborative Crystallisation Centre (C3), protein samples from local, national and international groups are set up in crystallisation screening and optimisation experiments with two thousand 96 well plates being set up each year. During its five years of operation, the C3 has implemented a series of enabling protocols – from simple ‘reality checks’ to determine if a screen has evaporated during storage to more sophisticated systems such as a sample labelling and tracking system. The most important – and perhaps surprising – lesson has been how much effort is required to effectively communicate between the centre and its clients, as well as between the centre’s staff members. It is easy to confuse the concept of ‘high throughput’ in any field with the idea of setting up an experiment quickly. Although automation can be used to set up a single experiment more rapidly than can be done by hand, the distinguishing feature of a high throughput technology is the sustainability of the increased rate.}, pages = {73--80}, number = {1}, journaltitle = {Methods}, shortjournal = {Methods}, author = {Newman, Janet}, urldate = {2017-05-15}, date = {2011-09}, keywords = {Automation, Automation, High throughput, High throughput, Protein crystallisation, Protein crystallisation}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\42NNPUZX\\Newman - 2011 - One plate, two plates, a thousand plates. How crys:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8NNCZMHE\\Newman - 2011 - One plate, two plates, a thousand plates. How crys.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\42NNPUZX\\Newman - 2011 - One plate, two plates, a thousand plates. How crys:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I8XNUDHN\\Newman - 2011 - One plate, two plates, a thousand plates. How crys.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P9ZGZ4GU\\S1046202311000922:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S2DH8QDW\\S1046202311000922.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P9ZGZ4GU\\S1046202311000922:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7UZMXQKP\\S1046202311000922.html:text/html;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\42NNPUZX\\Newman - 2011 - One plate, two plates, a thousand plates. How crys.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\P9ZGZ4GU\\S1046202311000922.html:text/html} } @article{newman_crystallization_2011, title = {Crystallization of an apo form of human arginase: using all the tools in the toolbox simultaneously}, volume = {67}, rights = {Copyright (c) 2011 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?rp5058}, doi = {10.1107/S1744309110046208}, shorttitle = {Crystallization of an apo form of human arginase}, abstract = {Arginase ({EC} 3.5.3.1) is an aminohydrolase that acts on l-arginine to produce urea and ornithine. Two isotypes of the enzyme are found in humans. Type I is predominantly produced in the liver and is a homotrimer of 35 {kDa} subunits. Human arginase ({hArginase}) I is seen to be up-regulated in many diseases and is a potential therapeutic target for many diverse indications. Previous reports of crystallization and structure determination of {hArginase} have always included inhibitors of the enzyme: here, the first case of a true apo crystal form of the enzyme which is suitable for small-molecule soaking is reported. The crystals belonged to space group P212121 and have approximate unit-cell parameters a = 53, b = 67.5, c = 250 Å. The crystals showed slightly anisotropic diffraction to beyond 2.0 Å resolution.}, pages = {90--93}, number = {1}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Newman, J. and Pearce, L. and Lesburg, C. A. and Strickland, C. and Peat, T. S.}, urldate = {2017-05-15}, date = {2011-01-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GCQPH63K\\Newman et al. - 2011 - Crystallization of an apo form of human arginase:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9VIPZMMG\\Newman et al. - 2011 - Crystallization of an apo form of human arginase .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GCQPH63K\\Newman et al. - 2011 - Crystallization of an apo form of human arginase:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MU68D4U8\\Newman et al. - 2011 - Crystallization of an apo form of human arginase .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZKGNQZNN\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IB4V78HD\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZKGNQZNN\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FMGPN6UV\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GCQPH63K\\Newman et al. - 2011 - Crystallization of an apo form of human arginase .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZKGNQZNN\\paper.html:text/html} } @article{nuttall_isolation_2011, title = {Isolation, kinetic analysis, and structural characterization of an antibody targeting the Bacillus anthracis major spore surface protein {BclA}}, volume = {79}, issn = {1097-0134}, url = {http://onlinelibrary.wiley.com/doi/10.1002/prot.22971/abstract}, doi = {10.1002/prot.22971}, abstract = {One method of laboratory- or field-based testing for anthrax is detection of Bacillus anthracis spores by high-affinity, high specificity binding reagents. From a pool of monoclonal antibodies, we selected one such candidate (A4D11) with high affinity for {tBclA}, a truncated version of the B. anthracis exosporium protein {BclA}. Kinetic analysis utilising both standard and kinetic titration on a Biacore biosensor indicated antibody affinities in the 300 {pM} range for recombinant {tBclA}, and the A4D11 antibody was also re-formatted into {scFv} configuration with no loss of affinity. However, assays against B. anthracis and related Bacilli species showed limited binding of intact spores as well as significant cross-reactivity between species. These results were rationalized by determination of the three-dimensional crystallographic structure of the {scFv}-{tBclA} complex. A4D11 binds the side of the {tBclA} trimer, contacting a face of the antigen normally packed against adjacent trimers within the exosporium structure; this inter-spore interface is highly conserved between Bacilli species. Our results indicate the difficulty of generating a high-affinity antibody to differentiate between the highly conserved spore structures of closely related species, but suggest the possibility of future structure-based antibody design for this difficult target. Proteins 2011. © 2011 Wiley-Liss, Inc.}, pages = {1306--1317}, number = {4}, journaltitle = {Proteins: Structure, Function, and Bioinformatics}, shortjournal = {Proteins}, author = {Nuttall, Stewart D. and Wilkins, Michelle L. and Streltsov, Victor A. and Pontes-Braz, Luisa and Dolezal, Olan and Tran, Hung and Liu, Chun-Qiang}, urldate = {2017-05-15}, date = {2011-04-01}, langid = {english}, keywords = {anthrax, anthrax, biosensor, biosensor, exosporium, exosporium, infectious disease, infectious disease, merohedral twinning, merohedral twinning, {scFv} complex, {scFv} complex}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4PNJPEW5\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WUK4SNW3\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4PNJPEW5\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C74V88BB\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZMTNS6KN\\Nuttall et al. - 2011 - Isolation, kinetic analysis, and structural charac:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UII5SGVH\\Nuttall et al. - 2011 - Isolation, kinetic analysis, and structural charac.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZMTNS6KN\\Nuttall et al. - 2011 - Isolation, kinetic analysis, and structural charac:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\R3UBC29R\\Nuttall et al. - 2011 - Isolation, kinetic analysis, and structural charac.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZMTNS6KN\\Nuttall et al. - 2011 - Isolation, kinetic analysis, and structural charac.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4PNJPEW5\\abstract.html:text/html} } @article{pearce_characterization_2011, title = {Characterization of monomeric dihydrodipicolinate synthase variant reveals the importance of substrate binding in optimizing oligomerization}, volume = {1814}, issn = {1570-9639}, url = {http://www.sciencedirect.com/science/article/pii/S1570963911002111}, doi = {10.1016/j.bbapap.2011.07.016}, abstract = {To gain insights into the role of quaternary structure in the {TIM}-barrel family of enzymes, we introduced mutations to the {DHDPS} enzyme of Thermotoga maritima, which we have previously shown to be a stable tetramer in solution. These mutations were aimed at reducing the number of salt bridges at one of the two tetramerization interface of the enzyme, which contains many more interactions than the well characterized equivalent interface of the mesophilic Escherichia coli {DHDPS} enzyme. The resulting variants had altered quaternary structure, as shown by analytical ultracentrifugation, gel filtration liquid chromatography, and small angle X-ray scattering, and X-ray crystallographic studies confirmed that one variant existed as an independent monomer, but with few changes to the secondary and tertiary structure. Reduction of higher order assembly resulted in a loss of thermal stability, as measured by a variety of methods, and impaired catalytic function. Binding of pyruvate increased the oligomeric status of the variants, with a concomitant increase in thermal stability, suggesting a role for substrate binding in optimizing stable, higher order structures. The results of this work show that the salt bridges located at the tetramerization interface of {DHDPS} play a significant role in maintaining higher order structures, and demonstrate the importance of quaternary structure in determining protein stability and in the optimization of enzyme catalysis.}, pages = {1900--1909}, number = {12}, journaltitle = {Biochimica et Biophysica Acta ({BBA}) - Proteins and Proteomics}, shortjournal = {Biochimica et Biophysica Acta ({BBA}) - Proteins and Proteomics}, author = {Pearce, F. Grant and Dobson, Renwick C. J. and Jameson, Geoffrey B. and Perugini, Matthew A. and Gerrard, Juliet A.}, urldate = {2017-05-15}, date = {2011-12}, keywords = {Cooperative assembly, Cooperative assembly, dihydrodipicolinate synthase, dihydrodipicolinate synthase, Quaternary structure, Quaternary structure, (S)-lysine biosynthesis, (S)-lysine biosynthesis, Thermal stability, Thermal stability, Thermotoga maritima, Thermotoga maritima}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5ABABRPX\\Pearce et al. - 2011 - Characterization of monomeric dihydrodipicolinate:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Q9SFD299\\Pearce et al. - 2011 - Characterization of monomeric dihydrodipicolinate .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5ABABRPX\\Pearce et al. - 2011 - Characterization of monomeric dihydrodipicolinate:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7VTHQ4RC\\Pearce et al. - 2011 - Characterization of monomeric dihydrodipicolinate .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Q39XS3IU\\S1570963911002111:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RVDS6S9F\\S1570963911002111.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Q39XS3IU\\S1570963911002111:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EWNJBBP7\\S1570963911002111.html:text/html;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5ABABRPX\\Pearce et al. - 2011 - Characterization of monomeric dihydrodipicolinate .pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Q39XS3IU\\S1570963911002111.html:text/html} } @article{polekhina_crystallization_2011, title = {Crystallization and preliminary X-ray analysis of the N-terminal domain of human thioredoxin-interacting protein}, volume = {67}, rights = {Copyright (c) 2011 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?rl5005}, doi = {10.1107/S1744309111010347}, abstract = {Thioredoxin-interacting protein ({TXNIP}) is a negative regulator of thioredoxin and its roles in the pathologies of diabetes and cardiovascular diseases have marked it out as a potential drug target. Expression of {TXNIP} is robustly induced under various stress conditions such as high glucose, heat shock, {UV}, H2O2 and mechanical stress amongst others. Elevated levels of {TXNIP} result in the sequestration and inactivation of thioredoxin, leading to cellular oxidative stress. For some time, this was the only known function of {TXNIP}; however, more recently the protein has been shown to play a role in regulation of glucose uptake and activation of the inflammasome. Based on the primary sequence, {TXNIP} is remotely related to β-arrestins, which include the visual arrestins. {TXNIP} has thus been classified as a member of the α-arrestin family, which to date includes five other members. None of the other α-arrestins are known to interact with thioredoxin, although curiously one has been implicated in glucose uptake. In order to gain insight into the structure–function relationships of the α-arrestin protein family, and particularly that of {TXNIP}, the N-­terminal domain of {TXNIP} has been crystallized. The crystals belonged to a monoclinic space group and diffracted to 3 Å resolution using synchrotron radiation.}, pages = {613--617}, number = {5}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Polekhina, G. and Ascher, D. B. and Kok, S. F. and Waltham, M.}, urldate = {2017-05-15}, date = {2011-05-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3E7HX9F9\\Polekhina et al. - 2011 - Crystallization and preliminary X-ray analysis of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IFCFG92U\\Polekhina et al. - 2011 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3E7HX9F9\\Polekhina et al. - 2011 - Crystallization and preliminary X-ray analysis of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3S6ZGKTD\\Polekhina et al. - 2011 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3SMWBUX5\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\F5UZETI3\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3SMWBUX5\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5HJK6CTX\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3E7HX9F9\\Polekhina et al. - 2011 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3SMWBUX5\\paper.html:text/html} } @article{rhodes_structural_2011, title = {Structural Basis for a New Mechanism of Inhibition of H I V-1 Integrase Identified by Fragment Screening and Structure-Based Design}, volume = {21}, issn = {0956-3202}, url = {http://journals.sagepub.com/doi/abs/10.3851/IMP1716}, doi = {10.3851/IMP1716}, abstract = {Background:{HIV}-1 integrase is a clinically validated therapeutic target for the treatment of {HIV}-1 infection, with one approved therapeutic currently on the market. This enzyme represents an attractive target for the development of new inhibitors to {HIV}-1 that are effective against the current resistance mutations.Methods:A fragment-based screening method employing surface plasmon resonance and {NMR} was initially used to detect interactions between integrase and fragments. The binding sites of the fragments were elucidated by crystallography and the structural information used to design and synthesize improved ligands.Results:The location of binding of fragments to the catalytic core of integrase was found to be in a previously undescribed binding site, adjacent to the mobile loop. Enzyme assays confirmed that formation of enzyme?fragment complexes inhibits the catalytic activity of integrase and the structural data was utilized to further develop these fragments into more potent novel enzyme inhibitors.Conclusions:We have defined a new site in integrase as a valid region for the structure-based design of allosteric integrase inhibitors. Using a structure-based design process we have improved the activity of the initial fragments 45-fold.}, pages = {155--168}, number = {4}, journaltitle = {Antiviral Chemistry and Chemotherapy}, shortjournal = {Antivir Chem Chemother}, author = {Rhodes, David I and Peat, Thomas S and Vandegraaff, Nick and Jeevarajah, Dharshini and Le, Giang and Jones, Eric D and Smith, Jessica A and Coates, Jonathan {AV} and Winfeld, Lisa J and Thienthong, Neeranat and Newman, Janet and Lucent, Del and Ryan, John H and Savage, G Paul and Francis, Craig L and Deadman, John J}, urldate = {2017-05-15}, date = {2011-04-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N3V83ARQ\\Rhodes et al. - 2011 - Structural Basis for a New Mechanism of Inhibition:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C9IM9ZIU\\Rhodes et al. - 2011 - Structural Basis for a New Mechanism of Inhibition.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N3V83ARQ\\Rhodes et al. - 2011 - Structural Basis for a New Mechanism of Inhibition:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\U9WUXBFM\\Rhodes et al. - 2011 - Structural Basis for a New Mechanism of Inhibition.pdf:application/pdf;SAGE PDF Full Text:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N3V83ARQ\\Rhodes et al. - 2011 - Structural Basis for a New Mechanism of Inhibition.pdf:application/pdf} } @article{rhodes_crystal_2011, title = {Crystal Structures of Novel Allosteric Peptide Inhibitors of {HIV} Integrase Identify New Interactions at the {LEDGF} Binding Site}, volume = {12}, issn = {1439-7633}, url = {http://onlinelibrary.wiley.com/doi/10.1002/cbic.201100350/abstract}, doi = {10.1002/cbic.201100350}, abstract = {An optimised method of solution cyclisation gave us access to a series of peptides including {SLKIDNLD} (2). We investigated the crystallographic complexes of the {HIV} integrase ({HIV}-{IN}) catalytic core domain with 13 of the peptides and identified multiple interactions at the binding site, including hydrogen bonds with residues Thr125 and Gln95, that have not previously been described as being accessible within the binding site. We show that the peptides inhibit the interaction of lens epithelium-derived growth factor ({LEDGF}) with {HIV}-{IN} in a proximity {AlphaScreen} assay and in an assay for the {LEDGF} enhancement of {HIV}-{IN} strand transfer. The interactions identified represent a potential framework for the development of new {HIV}-{IN} inhibitors.}, pages = {2311--2315}, number = {15}, journaltitle = {{ChemBioChem}}, shortjournal = {{ChemBioChem}}, author = {Rhodes, David I. and Peat, Thomas S. and Vandegraaff, Nick and Jeevarajah, Dharshini and Newman, Janet and Martyn, John and Coates, Jonathan A. V. and Ede, Nicholas J. and Rea, Philip and Deadman, John J.}, urldate = {2017-05-15}, date = {2011-10-17}, langid = {english}, keywords = {co-crystal structures, co-crystal structures, cyclic peptides, cyclic peptides, {HIV}-1 integrase, {HIV}-1 integrase, inhibitors, inhibitors, {LEDGF}, {LEDGF}}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7RS73RX7\\Rhodes et al. - 2011 - Crystal Structures of Novel Allosteric Peptide Inh:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZPUBT5PK\\Rhodes et al. - 2011 - Crystal Structures of Novel Allosteric Peptide Inh.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7RS73RX7\\Rhodes et al. - 2011 - Crystal Structures of Novel Allosteric Peptide Inh:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z675ZNUN\\Rhodes et al. - 2011 - Crystal Structures of Novel Allosteric Peptide Inh.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GA4FZBEB\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KR2FKIEC\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GA4FZBEB\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8B44FMM9\\abstract.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7RS73RX7\\Rhodes et al. - 2011 - Crystal Structures of Novel Allosteric Peptide Inh.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GA4FZBEB\\abstract.html:text/html} } @article{streltsov_crystal_2011, title = {Crystal Structure of the Amyloid-β p3 Fragment Provides a Model for Oligomer Formation in Alzheimer's Disease}, volume = {31}, rights = {Copyright © 2011 the authors 0270-6474/11/311419-08\$15.00/0}, issn = {0270-6474, 1529-2401}, url = {http://www.jneurosci.org/content/31/4/1419}, doi = {10.1523/JNEUROSCI.4259-10.2011}, abstract = {Alzheimer's disease is a progressive neurodegenerative disorder associated with the presence of amyloid-β (Aβ) peptide fibrillar plaques in the brain. However, current evidence suggests that soluble nonfibrillar Aβ oligomers may be the major drivers of Aβ-mediated synaptic dysfunction. Structural information on these Aβ species has been very limited because of their noncrystalline and unstable nature. Here, we describe a crystal structure of amylogenic residues 18–41 of the Aβ peptide (equivalent to the p3 α/γ-secretase fragment of amyloid precursor protein) presented within the {CDR}3 loop region of a shark Ig new antigen receptor ({IgNAR}) single variable domain antibody. The predominant oligomeric species is a tightly associated Aβ dimer, with paired dimers forming a tetramer in the crystal caged within four {IgNAR} domains, preventing uncontrolled amyloid formation. Our structure correlates with independently observed features of small nonfibrillar Aβ oligomers and reveals conserved elements consistent with residues and motifs predicted as critical in Aβ folding and oligomerization, thus potentially providing a model system for nonfibrillar oligomer formation in Alzheimer's disease.}, pages = {1419--1426}, number = {4}, journaltitle = {Journal of Neuroscience}, shortjournal = {J. Neurosci.}, author = {Streltsov, Victor A. and Varghese, Joseph N. and Masters, Colin L. and Nuttall, Stewart D.}, urldate = {2017-05-15}, date = {2011-01-26}, langid = {english}, pmid = {21273426}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A9AQ9IFP\\Streltsov et al. - 2011 - Crystal Structure of the Amyloid-β p3 Fragment Pro:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J4HSQZPX\\Streltsov et al. - 2011 - Crystal Structure of the Amyloid-β p3 Fragment Pro.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A9AQ9IFP\\Streltsov et al. - 2011 - Crystal Structure of the Amyloid-β p3 Fragment Pro:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5WNKCQ7E\\Streltsov et al. - 2011 - Crystal Structure of the Amyloid-β p3 Fragment Pro.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PE9U76NG\\1419:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NFMWV3CH\\1419.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PE9U76NG\\1419:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WU698MV7\\1419.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A9AQ9IFP\\Streltsov et al. - 2011 - Crystal Structure of the Amyloid-β p3 Fragment Pro.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PE9U76NG\\1419.html:text/html} } @inproceedings{vallotton_observation_2011, title = {An Observation about Circular Shortest Paths: Dealing with Additional Constraints Using Branch and Bound}, doi = {10.1109/DICTA.2011.92}, shorttitle = {An Observation about Circular Shortest Paths}, abstract = {Circular shortest paths represent a powerful methodology for image segmentation. The circularity condition ensures that the contour found by the algorithm is closed, a natural requirement for regular objects. Several implementations have been proposed in the past that either promise closure with high probability or ensure closure strictly, but with a mild computational efficiency handicap. Circularity can be viewed as a priori information that helps recover the correct object contour. Our "observation" is that circularity is only one among many possible constraints that can be imposed on shortest paths to guide them to a desirable solution. In this contribution, we illustrate this opportunity under a volume constraint but the concept is generally applicable. We also describe several adornments to the circular shortest path algorithm that proved useful in applications.}, eventtitle = {2011 International Conference on Digital Image Computing: Techniques and Applications}, pages = {513--517}, booktitle = {2011 International Conference on Digital Image Computing: Techniques and Applications}, author = {Vallotton, P. and Lovell, D. and Newman, J.}, date = {2011-12}, keywords = {Algorithm design and analysis, Algorithm design and analysis, Binary trees, Binary trees, branch and bound, branch and bound, circularity condition, circularity condition, Circular shortest path, Circular shortest path, circular shortest paths, circular shortest paths, computational efficiency handicap, computational efficiency handicap, contour tracing, contour tracing, Crystals, Crystals, droplet detection, droplet detection, graph algorithms, graph algorithms, Hessiann matrix, Hessiann matrix, image analysis, image analysis, image constraints, image constraints, Image edge detection, Image edge detection, image segmentation, image segmentation, Joining processes, Joining processes, Pattern recognition, Pattern recognition, Sun, Sun, tree searching, tree searching}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9V4PQ3FP\\Vallotton et al. - 2011 - An Observation about Circular Shortest Paths Deal:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4D7KU94Q\\Vallotton et al. - 2011 - An Observation about Circular Shortest Paths Deal.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9V4PQ3FP\\Vallotton et al. - 2011 - An Observation about Circular Shortest Paths Deal:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TAJ765CJ\\Vallotton et al. - 2011 - An Observation about Circular Shortest Paths Deal.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DUP4H2D4\\6128712:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TG4K68KU\\6128712.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DUP4H2D4\\6128712:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DTNGQMTB\\6128712.html:text/html;IEEE Xplore Abstract Record:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DUP4H2D4\\6128712.html:text/html;IEEE Xplore Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9V4PQ3FP\\Vallotton et al. - 2011 - An Observation about Circular Shortest Paths Deal.pdf:application/pdf} } @article{ve_crystallization_2011, title = {Crystallization, X-ray diffraction analysis and preliminary structure determination of the {TIR} domain from the flax resistance protein L6}, volume = {67}, rights = {Copyright (c) 2011 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?uo5017}, doi = {10.1107/S1744309110051006}, abstract = {The Toll/interleukin-1 receptor ({TIR}) domain is a protein–protein interaction domain that is found in both animal and plant immune receptors. In animal Toll-like receptor signalling, both homotypic {TIR}-domain interactions between two receptor molecules and heterotypic interactions between receptors and {TIR}-domain-containing adaptors are required for initiation of an innate immune response. The {TIR} domains in cytoplasmic nucleotide-binding/leucine-rich repeat ({NB}-{LRR}) plant disease-resistance proteins are not as well characterized, but recent studies have suggested a role in defence signalling. In this study, the crystallization, X-ray diffraction analysis and preliminary structure determination of the {TIR} domain from the flax resistance protein L6 (L6TIR) are reported. Plate-like crystals of L6TIR were obtained using {PEG} 200 as a precipitant and diffracted X-rays to 2.3 Å resolution. Pseudo-translation complicated the initial assignment of the crystal symmetry, which was ultimately found to correspond to space group P21212 with two molecules per asymmetric unit. The structure of L6TIR was solved by molecular replacement using the structure of the {TIR}-domain-containing protein {AT}1G72930 from Arabidopsis as a template.}, pages = {237--240}, number = {2}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Ve, T. and Williams, S. and Valkov, E. and Ellis, J. G. and Dodds, P. N. and Kobe, B.}, urldate = {2017-05-15}, date = {2011-02-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8EE6ESWZ\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XVGXNDVF\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8EE6ESWZ\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RZFW4XUX\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XQEHJK2S\\Ve et al. - 2011 - Crystallization, X-ray diffraction analysis and pr:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\23DDTJ9R\\Ve et al. - 2011 - Crystallization, X-ray diffraction analysis and pr.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XQEHJK2S\\Ve et al. - 2011 - Crystallization, X-ray diffraction analysis and pr:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B3CP9WIP\\Ve et al. - 2011 - Crystallization, X-ray diffraction analysis and pr.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XQEHJK2S\\Ve et al. - 2011 - Crystallization, X-ray diffraction analysis and pr.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8EE6ESWZ\\paper.html:text/html} } @article{wong_minimal_2011, title = {Minimal requirements for actin filament disassembly revealed by structural analysis of malaria parasite actin-depolymerizing factor 1}, volume = {108}, issn = {0027-8424, 1091-6490}, url = {http://www.pnas.org/content/108/24/9869}, doi = {10.1073/pnas.1018927108}, abstract = {Malaria parasite cell motility is a process that is dependent on the dynamic turnover of parasite-derived actin filaments. Despite its central role, actin's polymerization state is controlled by a set of identifiable regulators that is markedly reduced compared with those of other eukaryotic cells. In Plasmodium falciparum, the most virulent species that affects humans, this minimal repertoire includes two members of the actin-depolymerizing factor/cofilin ({AC}) family of proteins, P. falciparum actin-depolymerizing factor 1 ({PfADF}1) and P. falciparum actin-depolymerizing factor 2. This essential class of actin regulator is involved in the control of filament dynamics at multiple levels, from monomer binding through to filament depolymerization and severing. Previous biochemical analyses have suggested that {PfADF}1 sequesters monomeric actin but, unlike most eukaryotic counterparts, has limited potential to bind or depolymerize filaments. The molecular basis for these unusual properties and implications for parasite cell motility have not been established. Here we present the crystal structure of an apicomplexan {AC} protein, {PfADF}1. We show that {PfADF}1 lacks critical residues previously implicated as essential for {AC}-mediated actin filament binding and disassembly, having a substantially reduced filament-binding loop and C-terminal α4 helix. Despite this divergence in structure, we demonstrate that {PfADF}1 is capable of efficient actin filament severing. Furthermore, this severing occurs despite {PfADF}1’s low binding affinity for filaments. Comparative structural analysis along with biochemical and microscopy evidence establishes that severing is reliant on the availability of an exposed basic residue in the filament-binding loop, a conserved minimal requirement that defines {AC}-mediated filament disassembly across eukaryotic cells.}, pages = {9869--9874}, number = {24}, journaltitle = {Proceedings of the National Academy of Sciences}, shortjournal = {{PNAS}}, author = {Wong, Wilson and Skau, Colleen T. and Marapana, Danushka S. and Hanssen, Eric and Taylor, Nicole L. and Riglar, David T. and Zuccala, Elizabeth S. and Angrisano, Fiona and Lewis, Heather and Catimel, Bruno and Clarke, Oliver B. and Kershaw, Nadia J. and Perugini, Matthew A. and Kovar, David R. and Gulbis, Jacqueline M. and Baum, Jake}, urldate = {2017-05-15}, date = {2011-06-14}, langid = {english}, pmid = {21628589}, keywords = {circular dichroism spectroscopy, circular dichroism spectroscopy, Crystallography, Crystallography, gliding motility, gliding motility, tight junction, tight junction, total internal reflection fluorescence microscopy, total internal reflection fluorescence microscopy}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N8WVF6MZ\\Wong et al. - 2011 - Minimal requirements for actin filament disassembl:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JVXTZEWC\\Wong et al. - 2011 - Minimal requirements for actin filament disassembl.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N8WVF6MZ\\Wong et al. - 2011 - Minimal requirements for actin filament disassembl:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IBDBE3VE\\Wong et al. - 2011 - Minimal requirements for actin filament disassembl.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WND9XG6V\\9869:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MFN25AGW\\9869.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WND9XG6V\\9869:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JDD5A4C9\\9869.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N8WVF6MZ\\Wong et al. - 2011 - Minimal requirements for actin filament disassembl.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WND9XG6V\\9869.html:text/html} } @article{chhabra_crystallization_2010, title = {Crystallization and preliminary X-ray analysis of 6-­hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Staphylococcus aureus}, volume = {66}, rights = {Copyright (c) 2010 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?bo5075}, doi = {10.1107/S1744309110010857}, abstract = {6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase ({HPPK}) catalyzes the Mg2+-dependent transfer of pyrophosphate from {ATP} to 6-hydroxymethyl-7,8-­dihydropterin ({HMDP}), forming 6-hydroxymethyl-7,8-dihydropterin pyro­phosphate, which is a critical step in the de novo folic acid-biosynthesis pathway. Diffraction-quality crystals of {HPPK} from the medically relevant species Staphylococcus aureus were grown in the presence of ammonium sulfate or sodium malonate and diffracted to better than 1.65 Å resolution. The crystals belonged to space group P21, with unit-cell parameters a = 36.8, b = 76.6, c = 51.5 Å, α = γ = 90.0, β = 100.2°. The crystals contained two molecules per asymmetric unit, with a volume per protein weight ({VM}) of 2.04 Å3 Da−1 and an estimated solvent content of 39.6\%.}, pages = {575--578}, number = {5}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Chhabra, S. and Newman, J. and Peat, T. S. and Fernley, R. T. and Caine, J. and Simpson, J. S. and Swarbrick, J. D.}, urldate = {2017-05-15}, date = {2010-05-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GUIPAQ3X\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A65ZHM3V\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GUIPAQ3X\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EMQTTBZG\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KEBJF8Z4\\Chhabra et al. - 2010 - Crystallization and preliminary X-ray analysis of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NAH8M5CS\\Chhabra et al. - 2010 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KEBJF8Z4\\Chhabra et al. - 2010 - Crystallization and preliminary X-ray analysis of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VMHGM9Q8\\Chhabra et al. - 2010 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KEBJF8Z4\\Chhabra et al. - 2010 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GUIPAQ3X\\paper.html:text/html} } @article{clarke_domain_2010, title = {Domain Reorientation and Rotation of an Intracellular Assembly Regulate Conduction in Kir Potassium Channels}, volume = {141}, issn = {0092-8674}, url = {http://www.sciencedirect.com/science/article/pii/S0092867410005015}, doi = {10.1016/j.cell.2010.05.003}, abstract = {Summary Potassium channels embedded in cell membranes employ gates to regulate K+ current. While a specific constriction in the permeation pathway has historically been implicated in gating, recent reports suggest that the signature ion selectivity filter located in the outer membrane leaflet may be equally important. Inwardly rectifying K+ channels also control the directionality of flow, using intracellular polyamines to stem ion efflux by a valve-like action. This study presents crystallographic evidence of interdependent gates in the conduction pathway and reveals the mechanism of polyamine block. Reorientation of the intracellular domains, concomitant with activation, instigates polyamine release from intracellular binding sites to block the permeation pathway. Conformational adjustments of the slide helices, achieved by rotation of the cytoplasmic assembly relative to the pore, are directly correlated to the ion configuration in the selectivity filter. Ion redistribution occurs irrespective of the constriction, suggesting a more expansive role of the selectivity filter in gating than previously appreciated. {PaperFlick}}, pages = {1018--1029}, number = {6}, journaltitle = {Cell}, shortjournal = {Cell}, author = {Clarke, Oliver B. and Caputo, Alessandro T. and Hill, Adam P. and Vandenberg, Jamie I. and Smith, Brian J. and Gulbis, Jacqueline M.}, urldate = {2017-05-15}, date = {2010-06-11}, keywords = {{CELLBIO}, {CELLBIO}, {MOLNEURO}, {MOLNEURO}, {SIGNALING}, {SIGNALING}}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4HJR248V\\Clarke et al. - 2010 - Domain Reorientation and Rotation of an Intracellu:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UCZN76FJ\\Clarke et al. - 2010 - Domain Reorientation and Rotation of an Intracellu.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4HJR248V\\Clarke et al. - 2010 - Domain Reorientation and Rotation of an Intracellu:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\H53AW3BB\\Clarke et al. - 2010 - Domain Reorientation and Rotation of an Intracellu.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VPS7INPD\\S0092867410005015:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RGNC9FW7\\S0092867410005015.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VPS7INPD\\S0092867410005015:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\G7DW6KQU\\S0092867410005015.html:text/html;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4HJR248V\\Clarke et al. - 2010 - Domain Reorientation and Rotation of an Intracellu.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VPS7INPD\\S0092867410005015.html:text/html} } @article{dommaraju_cloning_2010, title = {Cloning, expression and crystallization of dihydrodipicolinate reductase from methicillin-resistant Staphylococcus aureus}, volume = {66}, rights = {Copyright (c) 2010 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?gj5072}, doi = {10.1107/S1744309109047964}, abstract = {Dihydrodipicolinate reductase ({DHDPR}; {EC} 1.3.1.26) catalyzes the nucleotide ({NADH}/{NADPH}) dependent second step of the lysine-biosynthesis pathway in bacteria and plants. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of {DHDPR} from methicillin-resistant Staphylococcus aureus ({MRSA}-{DHDPR}) are presented. The enzyme was crystallized in a number of forms, predominantly with ammonium sulfate as a precipitant, with the best crystal form diffracting to beyond 3.65 Å resolution. Crystal structures of the apo form as well as of cofactor ({NADPH}) bound and inhibitor (2,6-pyridinedicarboxylate) bound forms of {MRSA}-{DHDPR} will provide insight into the structure and function of this essential enzyme and valid drug target.}, pages = {57--60}, number = {1}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Dommaraju, S. and Gorman, M. A. and Dogovski, C. and Pearce, F. G. and Gerrard, J. A. and Dobson, R. C. J. and Parker, M. W. and Perugini, M. A.}, urldate = {2017-05-15}, date = {2010-01-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E68PX6CD\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NCJPTVDS\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E68PX6CD\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3W66MMF2\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VGCKCGXI\\Dommaraju et al. - 2010 - Cloning, expression and crystallization of dihydro:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PHQBQVPG\\Dommaraju et al. - 2010 - Cloning, expression and crystallization of dihydro.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VGCKCGXI\\Dommaraju et al. - 2010 - Cloning, expression and crystallization of dihydro:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S2HR6W3M\\Dommaraju et al. - 2010 - Cloning, expression and crystallization of dihydro.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VGCKCGXI\\Dommaraju et al. - 2010 - Cloning, expression and crystallization of dihydro.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E68PX6CD\\paper.html:text/html} } @article{dransfield_human_2010, title = {A Human Monoclonal Antibody against Insulin-Like Growth Factor-{II} Blocks the Growth of Human Hepatocellular Carcinoma Cell Lines In vitro and In vivo}, volume = {9}, rights = {©2010 American Association for Cancer Research.}, issn = {1535-7163, 1538-8514}, url = {http://mct.aacrjournals.org/content/9/6/1809}, doi = {10.1158/1535-7163.MCT-09-1134}, abstract = {Elevated expression of insulin-like growth factor-{II} ({IGF}-{II}) is frequently observed in a variety of human malignancies, including breast, colon, and liver cancer. As {IGF}-{II} can deliver a mitogenic signal through both {IGF}-{IR} and an alternately spliced form of the insulin receptor ({IR}-A), neutralizing the biological activity of this growth factor directly is a potential alternative option to {IGF}-{IR}–directed agents. Using a Fab-displaying phage library and a biotinylated precursor form of {IGF}-{II} (1–104 amino acids) as a target, we isolated Fabs specific for the E-domain {COOH}-terminal extension form of {IGF}-{II} and for mature {IGF}-{II}. One of these Fabs that bound to both forms of {IGF}-{II} was reformatted into a full-length {IgG}, expressed, purified, and subjected to further analysis. This antibody ({DX}-2647) displayed a very high affinity for {IGF}-{II}/{IGF}-{IIE} ({KD} value of 49 and 10 pmol/L, respectively) compared with {IGF}-I (∼10 nmol/L) and blocked binding of {IGF}-{II} to {IGF}-{IR}, {IR}-A, a panel of insulin-like growth factor–binding proteins, and the mannose-6-phosphate receptor. A crystal complex of the parental Fab of {DX}-2647 bound to {IGF}-{II} was resolved to 2.2 Å. {DX}-2647 inhibited {IGF}-{II} and, to a lesser extent, {IGF}-I–induced receptor tyrosine phosphorylation, cellular proliferation, and both anchorage-dependent and anchorage-independent colony formation in various cell lines. In addition, {DX}-2647 slowed tumor progression in the Hep3B xenograft model, causing decreased tumoral {CD}31 staining as well as reduced {IGF}-{IIE} and {IGF}-{IR} phosphorylation levels. Therefore, {DX}-2647 offers an alternative approach to targeting {IGF}-{IR}, blocking {IGF}-{II} signaling through both {IGF}-{IR} and {IR}-A. Mol Cancer Ther; 9(6); 1809–19. ©2010 {AACR}.}, pages = {1809--1819}, number = {6}, journaltitle = {Molecular Cancer Therapeutics}, shortjournal = {Mol Cancer Ther}, author = {Dransfield, Daniel T. and Cohen, Edward H. and Chang, Qing and Sparrow, Lindsay G. and Bentley, John D. and Dolezal, Olan and Xiao, Xiaowen and Peat, Thomas S. and Newman, Janet and Pilling, Patricia A. and Phan, Tram and Priebe, Ilka and Brierley, Gemma V. and Kastrapeli, Niksa and Kopacz, Kris and Martik, Diana and Wassaf, Dina and Rank, Douglas and Conley, Greg and Huang, Yan and Adams, Timothy E. and Cosgrove, Leah}, urldate = {2017-05-15}, date = {2010-06-01}, langid = {english}, pmid = {20515953}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8WUXN7I8\\Dransfield et al. - 2010 - A Human Monoclonal Antibody against Insulin-Like G:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z8JC5BA3\\Dransfield et al. - 2010 - A Human Monoclonal Antibody against Insulin-Like G.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8WUXN7I8\\Dransfield et al. - 2010 - A Human Monoclonal Antibody against Insulin-Like G:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\R55BU7MM\\Dransfield et al. - 2010 - A Human Monoclonal Antibody against Insulin-Like G.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\F79JSIJE\\1809:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\25SIGVHZ\\1809.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\F79JSIJE\\1809:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RNN6JEMA\\1809.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8WUXN7I8\\Dransfield et al. - 2010 - A Human Monoclonal Antibody against Insulin-Like G.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\F79JSIJE\\1809.html:text/html} } @article{ernberg_new_2010, title = {A new crystal form of human vascular adhesion protein 1}, volume = {66}, rights = {Copyright (c) 2010 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?tb5032}, doi = {10.1107/S1744309110041515}, abstract = {Human vascular adhesion protein 1 ({VAP}-1) is involved in lymphocyte–endothelial cell adhesion and has been implicated in many human inflammatory diseases. {VAP}-1 is a member of the copper amine oxidase family of enzymes with a trihydroxyphenylalanine quinone ({TPQ}) cofactor. Previously characterized crystals of {VAP}-1 suffered from anisotropy and contained disordered regions; in addition, one form was consistently twinned. In an effort to grow crystals that diffracted to higher resolution for inhibitor-binding studies, a construct with an N-terminal deletion was made and expressed in the Chinese hamster ovary ({CHO}) glycosylation mutant cell line Lec8. Screening produced crystals that displayed some anisotropy and contained seven molecules per asymmetric unit. These crystals belonged to space group C2, with unit-cell parameters a = 394.5, b = 115.8, c = 179.3 Å, β = 112.3°. The structure was refined to a resolution of 2.9 Å, with Rcryst and Rfree values of 0.250 and 0.286, respectively.}, pages = {1572--1578}, number = {12}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Ernberg, K. and {McGrath}, A. P. and Peat, T. S. and Adams, T. E. and Xiao, X. and Pham, T. and Newman, J. and {McDonald}, I. A. and Collyer, C. A. and Guss, J. M.}, urldate = {2017-05-15}, date = {2010-12-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\52QHDXZR\\Ernberg et al. - 2010 - A new crystal form of human vascular adhesion prot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9ASRTGQT\\Ernberg et al. - 2010 - A new crystal form of human vascular adhesion prot.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\52QHDXZR\\Ernberg et al. - 2010 - A new crystal form of human vascular adhesion prot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8T5P3E3Q\\Ernberg et al. - 2010 - A new crystal form of human vascular adhesion prot.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\93FDRIXP\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\92GXM2JS\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\93FDRIXP\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EIS64ACF\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\52QHDXZR\\Ernberg et al. - 2010 - A new crystal form of human vascular adhesion prot.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\93FDRIXP\\paper.html:text/html} } @article{hor_crystallization_2010, title = {Crystallization and preliminary X-ray diffraction analysis of diaminopimelate epimerase from Escherichia coli}, volume = {66}, rights = {Copyright (c) 2010 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?nj5045}, doi = {10.1107/S1744309109047708}, abstract = {Diaminopimelate ({DAP}) epimerase ({EC} 5.1.1.7) catalyzes the penultimate step of lysine biosynthesis in bacteria and plants, converting l,l-diaminopimelate to meso-diaminopimelate. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of {DAP} epimerase from Escherichia coli are presented. Crystals were obtained in space group P41212 and diffracted to 2.0 Å resolution, with unit-cell parameters a = b = 89.4, c = 179.6 Å. Molecular replacement was conducted using Bacillus anthracis {DAP} epimerase as a search model and showed the presence of two molecules in the asymmetric unit, with an initial Rfree of 0.456 and Rwork of 0.416.}, pages = {37--40}, number = {1}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Hor, L. and Dobson, R. C. J. and Dogovski, C. and Hutton, C. A. and Perugini, M. A.}, urldate = {2017-05-15}, date = {2010-01-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IIU4GHKQ\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S4EK7HPM\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IIU4GHKQ\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HGPNTXQF\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XQBSNPDW\\Hor et al. - 2010 - Crystallization and preliminary X-ray diffraction:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WT8U73PW\\Hor et al. - 2010 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XQBSNPDW\\Hor et al. - 2010 - Crystallization and preliminary X-ray diffraction:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S83JRCFK\\Hor et al. - 2010 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XQBSNPDW\\Hor et al. - 2010 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IIU4GHKQ\\paper.html:text/html} } @article{kvansakul_structural_2010, title = {Structural Basis for Apoptosis Inhibition by Epstein-Barr Virus {BHRF}1}, volume = {6}, issn = {1553-7374}, url = {http://dx.plos.org/10.1371/journal.ppat.1001236}, doi = {10.1371/journal.ppat.1001236}, pages = {e1001236}, number = {12}, journaltitle = {{PLoS} Pathogens}, author = {Kvansakul, Marc and Wei, Andrew H. and Fletcher, Jamie I. and Willis, Simon N. and Chen, Lin and Roberts, Andrew W. and Huang, David C. S. and Colman, Peter M.}, editor = {Jung, Jae U.}, urldate = {2017-05-15}, date = {2010-12-23}, langid = {english} } @article{luang_crystallisation_2010, title = {Crystallisation of Wild-Type and Variant Forms of a Recombinant Plant Enzyme β-D-Glucan Glucohydrolase from Barley (Hordeum vulgare L.) and Preliminary X-ray Analysis}, volume = {11}, rights = {http://creativecommons.org/licenses/by/3.0/}, url = {http://www.mdpi.com/1422-0067/11/7/2759}, doi = {10.3390/ijms11072759}, abstract = {Wild-type and variant crystals of a recombinant enzyme β-d-glucan glucohydrolase from barley (Hordeum vulgare L.) were obtained by macroseeding and cross-seeding with microcrystals obtained from native plant protein. Crystals grew to dimensions of up to 500 x 250 x 375 µm at 277 K in the hanging-drops by vapour-diffusion. Further, the conditions are described that yielded the wild-type crystals with dimensions of 80 x 40 x 60 µm by self-nucleation vapour-diffusion in sitting-drops at 281 K. The wild-type and recombinant crystals prepared by seeding techniques achieved full size within 5-14 days, while the wild-type crystals grown by self-nucleation appeared after 30 days and reached their maximum size after another two months. Both the wild-type and recombinant variant crystals, the latter altered in the key catalytic and substrate-binding residues Glu220, Trp434 and Arg158/Glu161 belonged to the P43212 tetragonal space group, i.e., the space group of the native microcrystals was retained in the newly grown recombinant crystals. The crystals diffracted beyond 1.57-1.95 Å and the cell dimensions were between a = b = 99.2-100.8 Å and c = 183.2-183.6 Å. With one molecule in the asymmetric unit, the calculated Matthews coefficients were between 3.4-3.5 Å3.Da-1 and the solvent contents varied between 63.4\% and 64.5\%. The macroseeding and cross-seeding techniques are advantageous, where a limited amount of variant proteins precludes screening of crystallisation conditions, or where variant proteins could not be crystallized.}, pages = {2759--2769}, number = {7}, journaltitle = {International Journal of Molecular Sciences}, author = {Luang, Sukanya and Cairns, James R. Ketudat and Streltsov, Victor A. and Hrmova, Maria}, urldate = {2017-05-15}, date = {2010-07-19}, langid = {english}, keywords = {macro- and cross-seeding, macro- and cross-seeding, wild-type and mutant protein, wild-type and mutant protein, X-ray diffraction, X-ray diffraction}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\H4GFXAVN\\Luang et al. - 2010 - Crystallisation of Wild-Type and Variant Forms of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8BRV4QRJ\\Luang et al. - 2010 - Crystallisation of Wild-Type and Variant Forms of .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\H4GFXAVN\\Luang et al. - 2010 - Crystallisation of Wild-Type and Variant Forms of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\42XNTEHW\\Luang et al. - 2010 - Crystallisation of Wild-Type and Variant Forms of .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\K67H6VUP\\htm:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7U23GC94\\htm.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\K67H6VUP\\htm:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KIN5TZCD\\htm.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\H4GFXAVN\\Luang et al. - 2010 - Crystallisation of Wild-Type and Variant Forms of .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\K67H6VUP\\htm.html:text/html} } @article{newman_c6_2010, title = {The C6 Web Tool: A Resource for the Rational Selection of Crystallization Conditions}, volume = {10}, issn = {1528-7483}, url = {http://dx.doi.org/10.1021/cg1004209}, doi = {10.1021/cg1004209}, shorttitle = {The C6 Web Tool}, abstract = {We have created the C6 Web Tool that uses an underlying metric to compare the chemical similarity of two crystallization conditions and by extension the similarity of two crystallization screens. With over 220 crystallization screens currently available for purchase, it is difficult to know what each screen contains and when it is appropriate to use that screen. The C6 Web Tool can be found at http://c6.csiro.au and is available to the crystallization community at no charge. In addition to measuring the similarity of conditions and kits, the C6 Web Tool also provides the means to examine the conditions of a crystallization kit (or kits) in novel ways. Using the C6 Web Tool, researchers can efficiently select appropriate screens to use throughout the various stages of a crystallization project.}, pages = {2785--2792}, number = {6}, journaltitle = {Crystal Growth \& Design}, shortjournal = {Crystal Growth \& Design}, author = {Newman, Janet and Fazio, Vincent J. and Lawson, Brian and Peat, Thomas S.}, urldate = {2017-05-15}, date = {2010-06-02}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MPRAURM8\\Newman et al. - 2010 - The C6 Web Tool A Resource for the Rational Selec.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BA8RXJHU\\cg1004209.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BA8RXJHU\\cg1004209:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\G7VGQ6QX\\cg1004209.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BA8RXJHU\\cg1004209:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IJM2F6BD\\cg1004209.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MPRAURM8\\Newman et al. - 2010 - The C6 Web Tool A Resource for the Rational Selec:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MIVQ4PPN\\Newman et al. - 2010 - The C6 Web Tool A Resource for the Rational Selec.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MPRAURM8\\Newman et al. - 2010 - The C6 Web Tool A Resource for the Rational Selec:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DHN7BXPD\\Newman et al. - 2010 - The C6 Web Tool A Resource for the Rational Selec.pdf:application/pdf} } @article{oakley_structure_2010, title = {The structure of Aspergillus niger phytase {PhyA} in complex with a phytate mimetic}, volume = {397}, issn = {0006-291X}, url = {http://www.sciencedirect.com/science/article/pii/S0006291X10011277}, doi = {10.1016/j.bbrc.2010.06.024}, abstract = {Phytases hydrolyse the phosphomonoesters of phytate (myo-inositol-1,2,3,4,5,6-hexakis phosphate) and thus find uses in plant and animal production through the mobilisation of phosphorus from this source. The structure of partially deglycosylated Aspergillus niger {PhyA} is presented in apo form and in complex with the potent inhibitor myo-inositol-1,2,3,4,5,6-hexakis sulfate, which by analogy with phytate provides a snapshot of the Michaelis complex. The structure explains the enzyme’s preference for the 3′-phosphate of phytate. The apo-and inhibitor-bound forms are similar and no induced–fit mechanism operates. Furthermore the enzyme structure is apparently unaffected by the presence of glycosides on the surface. The new structures of A. niger {PhyA} are discussed in the context of protein engineering studies aimed at modulating {pH} preference and stability.}, pages = {745--749}, number = {4}, journaltitle = {Biochemical and Biophysical Research Communications}, shortjournal = {Biochemical and Biophysical Research Communications}, author = {Oakley, Aaron J.}, urldate = {2017-05-15}, date = {2010-07-09}, keywords = {3-Phytase, 3-Phytase, Aspergillus niger, Aspergillus niger, Michaelis complex, Michaelis complex, {PhyA}, {PhyA}, Phytate, Phytate, Protein Structure, Protein Structure}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ARHCGCD6\\Oakley - 2010 - The structure of Aspergillus niger phytase PhyA in:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V5I95HIN\\Oakley - 2010 - The structure of Aspergillus niger phytase PhyA in.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ARHCGCD6\\Oakley - 2010 - The structure of Aspergillus niger phytase PhyA in:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FSTW8RG7\\Oakley - 2010 - The structure of Aspergillus niger phytase PhyA in.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J93P6B2C\\S0006291X10011277:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RRIJSVA6\\S0006291X10011277.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J93P6B2C\\S0006291X10011277:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\75HIARAV\\S0006291X10011277.html:text/html;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ARHCGCD6\\Oakley - 2010 - The structure of Aspergillus niger phytase PhyA in.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J93P6B2C\\S0006291X10011277.html:text/html} } @article{oakley_structural_2010, title = {Structural and Functional Basis of Resistance to Neuraminidase Inhibitors of Influenza B Viruses}, volume = {53}, issn = {0022-2623}, url = {http://dx.doi.org/10.1021/jm100621s}, doi = {10.1021/jm100621s}, abstract = {We have identified a virus, B/Perth/211/2001, with a spontaneous mutation, D197E in the neuraminidase ({NA}), which confers cross-resistance to all {NA} inhibitors. We analyzed enzyme properties of the D197 and E197 {NAs} and compared these to a D197N {NA}, known to arise after oseltamivir treatment. Zanamivir and peramivir bound slowly to the wild type {NA}, but binding of oseltamivir was more rapid. The D197E/N mutations resulted in faster binding of all three inhibitors. Analysis of the crystal structures of D197 and E197 {NAs} with and without inhibitors showed that the D197E mutation compromised the interaction of neighboring R150 with the N-acetyl group, common to the substrate sialic acid and all {NA} inhibitors. Although rotation of the E275 in the {NA} active site occurs upon binding peramivir in both the D197 and E197 {NAs}, this does not occur upon binding oseltamivir in the E197 {NA}. Lack of the E275 rotation would also account for the loss of slow binding and the partial resistance of influenza B wild type {NAs} to oseltamivir.}, pages = {6421--6431}, number = {17}, journaltitle = {Journal of Medicinal Chemistry}, shortjournal = {J. Med. Chem.}, author = {Oakley, Aaron J. and Barrett, Susan and Peat, Thomas S. and Newman, Janet and Streltsov, Victor A. and Waddington, Lynne and Saito, Takehiko and Tashiro, Masato and {McKimm}-Breschkin, Jennifer L.}, urldate = {2017-05-15}, date = {2010-09-09}, file = {ACS Full Text PDF w/ Links:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9V4DM3R5\\Oakley et al. - 2010 - Structural and Functional Basis of Resistance to N.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KWT7VN2T\\jm100621s.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9V4DM3R5\\Oakley et al. - 2010 - Structural and Functional Basis of Resistance to N:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\R7X24GBP\\Oakley et al. - 2010 - Structural and Functional Basis of Resistance to N.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9V4DM3R5\\Oakley et al. - 2010 - Structural and Functional Basis of Resistance to N:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\54C4K82J\\Oakley et al. - 2010 - Structural and Functional Basis of Resistance to N.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KWT7VN2T\\jm100621s:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TEV6E59W\\jm100621s.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KWT7VN2T\\jm100621s:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MGKGF4EV\\jm100621s.html:text/html} } @article{oakley_identification_2010, title = {Identification and Characterization of γ-Glutamylamine Cyclotransferase, an Enzyme Responsible for γ-Glutamyl-ϵ-lysine Catabolism}, volume = {285}, issn = {0021-9258, 1083-351X}, url = {http://www.jbc.org/content/285/13/9642}, doi = {10.1074/jbc.M109.082099}, abstract = {γ-Glutamylamine cyclotransferase ({GGACT}) is an enzyme that converts γ-glutamylamines to free amines and 5-oxoproline. {GGACT} shows high activity toward γ-glutamyl-ϵ-lysine, derived from the breakdown of fibrin and other proteins cross-linked by transglutaminases. The enzyme adopts the newly identified cyclotransferase fold, observed in γ-glutamylcyclotransferase ({GGCT}), an enzyme with activity toward γ-glutamyl-α-amino acids (Oakley, A. J., Yamada, T., Liu, D., Coggan, M., Clark, A. G., and Board, P. G. (2008) J. Biol. Chem. 283, 22031–22042). Despite the absence of significant sequence identity, several residues are conserved in the active sites of {GGCT} and {GGACT}, including a putative catalytic acid/base residue ({GGACT} Glu82). The structure of {GGACT} in complex with the reaction product 5-oxoproline provides evidence for a common catalytic mechanism in both enzymes. The proposed mechanism, combined with the three-dimensional structures, also explains the different substrate specificities of these enzymes. Despite significant sequence divergence, there are at least three subfamilies in prokaryotes and eukaryotes that have conserved the {GGCT} fold and {GGCT} enzymatic activity.}, pages = {9642--9648}, number = {13}, journaltitle = {Journal of Biological Chemistry}, shortjournal = {J. Biol. Chem.}, author = {Oakley, Aaron J. and Coggan, Marjorie and Board, Philip G.}, urldate = {2017-05-15}, date = {2010-03-26}, langid = {english}, pmid = {20110353}, keywords = {5-Oxoproline, 5-Oxoproline, Crystal structure, Crystal structure, Enzyme Mechanisms, Enzyme Mechanisms, Enzymes, Enzymes, enzyme structure, enzyme structure, Gene Structure, Gene Structure, γ-Glutamylamine Cyclotransferase, γ-Glutamylamine Cyclotransferase, γ-Glutamylcyclotransferase Fold, γ-Glutamylcyclotransferase Fold, γ-Glutamyl-ϵ-lysine Dipeptides, γ-Glutamyl-ϵ-lysine Dipeptides}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A32UCIHU\\Oakley et al. - 2010 - Identification and Characterization of γ-Glutamyla:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JMAGTXGJ\\Oakley et al. - 2010 - Identification and Characterization of γ-Glutamyla.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A32UCIHU\\Oakley et al. - 2010 - Identification and Characterization of γ-Glutamyla:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z7BUGQ9U\\Oakley et al. - 2010 - Identification and Characterization of γ-Glutamyla.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PFA9TNSG\\9642:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Q44A52XF\\9642.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PFA9TNSG\\9642:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6TDFRMBG\\9642.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A32UCIHU\\Oakley et al. - 2010 - Identification and Characterization of γ-Glutamyla.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PFA9TNSG\\9642.html:text/html} } @article{pearce_identification_2010, title = {Identification and Characterization of a Misfolded Monomeric Serpin Formed at Physiological Temperature}, volume = {403}, issn = {0022-2836}, url = {http://www.sciencedirect.com/science/article/pii/S0022283610009666}, doi = {10.1016/j.jmb.2010.09.007}, abstract = {The native serpin state is kinetically trapped. However, under mildly destabilizing conditions, the conformational landscape changes, and a number of nonnative conformations with increased stability can be readily formed. The ability to undergo structural change is due to intrinsic strain within the serpin's tertiary fold, which is utilized for proteinase inhibition but renders the protein susceptible to aberrant folding and self-association. The relationship between these various conformations is poorly understood. Antichymotrypsin ({ACT}) is an inhibitory serpin that readily forms a number of inactive conformations, induced via either environmental stress or interaction with proteinases. Here we have used a variety of biophysical and structural techniques to characterize the relationship between some of these conformations. Incubation of {ACT} at physiological temperature results in the formation of a range of conformations, including both polymer and misfolded monomer. The ability to populate these nonnative states and the native conformation reflects an energy landscape that is very sensitive to the solution conditions. X-ray crystallography reveals that the misfolded monomeric conformation is in the delta conformation. Further polymerization and seeding experiments show that the delta conformation is an end point in the misfolding pathway of {ACT} and not an on-pathway intermediate formed during polymerization. The observation that {ACT} readily forms this inactive conformation at physiological temperature and {pH} suggests that it may have a role in both health and disease.}, pages = {459--467}, number = {3}, journaltitle = {Journal of Molecular Biology}, shortjournal = {Journal of Molecular Biology}, author = {Pearce, M. C. and Powers, G. A. and Feil, S. C. and Hansen, G. and Parker, M. W. and Bottomley, S. P.}, urldate = {2017-05-15}, date = {2010-10-29}, keywords = {antichymotrypsin, antichymotrypsin, conformational change, conformational change, polymerization, polymerization, protein misfolding, protein misfolding, serpin, serpin}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8BKZZNMM\\S0022283610009666:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ECIPCEKQ\\S0022283610009666.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8BKZZNMM\\S0022283610009666:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\G338UQMZ\\S0022283610009666.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KKHB28VF\\Pearce et al. - 2010 - Identification and Characterization of a Misfolded:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\H94RA4W8\\Pearce et al. - 2010 - Identification and Characterization of a Misfolded.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KKHB28VF\\Pearce et al. - 2010 - Identification and Characterization of a Misfolded:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UN3CPI8D\\Pearce et al. - 2010 - Identification and Characterization of a Misfolded.pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KKHB28VF\\Pearce et al. - 2010 - Identification and Characterization of a Misfolded.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8BKZZNMM\\S0022283610009666.html:text/html} } @article{quesada-soriano_diuretic_2011, title = {Diuretic drug binding to human glutathione transferase P1-1: potential role of Cys-101 revealed in the double mutant C47S/Y108V}, volume = {24}, issn = {1099-1352}, url = {http://onlinelibrary.wiley.com/doi/10.1002/jmr.1040/abstract}, doi = {10.1002/jmr.1040}, shorttitle = {Diuretic drug binding to human glutathione transferase P1-1}, abstract = {The diuretic drug ethacrynic acid ({EA}), both an inhibitor and substrate of pi class glutathione S-transferase ({GST} P1-1), has been tested in clinical trials as an adjuvant in chemotherapy. We recently studied the role of the active site residue Tyr-108 in binding {EA} to the enzyme and found that the analysis was complicated by covalent binding of this drug to the highly reactive Cys-47. Previous attempts to eliminate this binding by chemical modification yielded ambiguous results and therefore we decided here to produce a double mutant C47S/Y108V by site directed mutagenesis and further expression in Escherichia coli and the interaction of {EA} and its {GSH} conjugate ({EASG}) examined by calorimetric studies and X-ray diffraction. Surprisingly, in the absence of Cys-47, Cys-101 (located at the dimer interface) becomes a target for modification by {EA}, albeit at a lower conjugation rate than Cys-47. The Cys-47 → Ser mutation in the double mutant enzyme induces a positive cooperativity between the two subunits when ligands with affinity to G-site bind to enzyme. However, this mutation does not seem to affect the thermodynamic properties of ligand binding to the electrophilic binding site (H-site) and the thermal or chemical stability of this double mutant does not significantly affect the unfolding mechanism in either the absence or presence of ligand. Crystal structures of apo and an {EASG} complex are essentially identical with a few exceptions in the H-site and in the water network at the dimer interface. Copyright © 2010 John Wiley \& Sons, Ltd.}, pages = {220--234}, number = {2}, journaltitle = {Journal of Molecular Recognition}, shortjournal = {J. Mol. Recognit.}, author = {Quesada-Soriano, Indalecio and Parker, Lorien J. and Primavera, Alessandra and Wielens, Jerome and Holien, Jessica K. and Casas-Solvas, Juan M. and Vargas-Berenguel, Antonio and Aguilera, Ana M. and Nuccetelli, Marzia and Mazzetti, Anna P. and Bello, Mario Lo and Parker, Michael W. and García-Fuentes, Luis}, urldate = {2017-05-15}, date = {2011-03-01}, langid = {english}, keywords = {binding, binding, calorimetry, calorimetry, Crystallography, Crystallography, docking studies, docking studies, ethacrynic acid, ethacrynic acid, glutathione transferase, glutathione transferase, kinetic studies, kinetic studies, protein-ligand interaction, protein-ligand interaction, thermodynamic, thermodynamic}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KQFWJ5XV\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7HFNEWHT\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KQFWJ5XV\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QXNVGWIB\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UJX6N7WD\\Quesada-Soriano et al. - 2011 - Diuretic drug binding to human glutathione transfe:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5SMZ4HZS\\Quesada-Soriano et al. - 2011 - Diuretic drug binding to human glutathione transfe.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UJX6N7WD\\Quesada-Soriano et al. - 2011 - Diuretic drug binding to human glutathione transfe:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9STN5N5E\\Quesada-Soriano et al. - 2011 - Diuretic drug binding to human glutathione transfe.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UJX6N7WD\\Quesada-Soriano et al. - 2011 - Diuretic drug binding to human glutathione transfe.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KQFWJ5XV\\abstract.html:text/html} } @article{robert_germline_2010, title = {Germline humanization of a murine Aβ antibody and crystal structure of the humanized recombinant Fab fragment}, volume = {19}, issn = {1469-896X}, url = {http://onlinelibrary.wiley.com/doi/10.1002/pro.312/abstract}, doi = {10.1002/pro.312}, abstract = {Alzheimer's disease is the most common form of dementia, affecting 26 million people worldwide. The Aβ peptide (39–43 amino acids) derived from the proteolytic cleavage of the amyloid precursor protein is one of the main constituents of amyloid plaques associated with disease pathogenesis and therefore a validated target for therapy. Recently, we characterized antibody fragments (Fab and {scFvs}) derived from the murine monoclonal antibody {WO}-2, which bind the immunodominant epitope (3EFRH6) in the Aβ peptide at the N-terminus. In vitro, these fragments are able to inhibit fibril formation, disaggregate preformed amyloid fibrils, and protect neuroblastoma cells against oligomer-mediated toxicity. In this study, we describe the humanization of {WO}-2 using complementary determining region loop grafting onto the human germline gene and the determination of the three-dimensional structure by X-ray crystallography. This humanized version retains a high affinity for the Aβ peptide and therefore is a potential candidate for passive immunotherapy of Alzheimer's disease.}, pages = {299--308}, number = {2}, journaltitle = {Protein Science}, shortjournal = {Protein Science}, author = {Robert, Remy and Streltsov, Victor A. and Newman, Janet and Pearce, Lesley A. and Wark, Kim L. and Dolezal, Olan}, urldate = {2017-05-15}, date = {2010-02-01}, langid = {english}, keywords = {Alzheimer's disease, Alzheimer's disease, antibody engineering, antibody engineering, Crystal structure, Crystal structure, humanization, humanization, {SPR}, {SPR}}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RX8RRGHT\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QTPFAGQA\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RX8RRGHT\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\GIUUJC65\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UG7ZSVKK\\Robert et al. - 2010 - Germline humanization of a murine Aβ antibody and:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AU4KRF5U\\Robert et al. - 2010 - Germline humanization of a murine Aβ antibody and .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UG7ZSVKK\\Robert et al. - 2010 - Germline humanization of a murine Aβ antibody and:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FSPDVQRG\\Robert et al. - 2010 - Germline humanization of a murine Aβ antibody and .pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UG7ZSVKK\\Robert et al. - 2010 - Germline humanization of a murine Aβ antibody and .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RX8RRGHT\\abstract.html:text/html} } @article{sibarani_crystallization_2010, title = {Crystallization of dihydrodipicolinate synthase from a clinical isolate of Streptococcus pneumoniae}, volume = {66}, rights = {Copyright (c) 2010 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?fw5234}, doi = {10.1107/S174430910904771X}, abstract = {Dihydrodipicolinate synthase ({DHDPS}; {EC} 4.2.1.52) catalyzes the rate-limiting step in the (S)-lysine biosynthesis pathway of bacteria and plants. Here, the cloning of the {DHDPS} gene from a clinical isolate of Streptococcus pneumoniae ({OXC}141 strain) and the strategy used to express, purify and crystallize the recombinant enzyme are described. Diffracting crystals were grown in high-molecular-weight {PEG} precipitants using the hanging-drop vapour-diffusion method. The best crystal, from which data were collected, diffracted to beyond 2.0 Å resolution. Initially, the crystals were thought to belong to space group P42212, with unit-cell parameters a = 105.5, b = 105.5, c = 62.4 Å. However, the R factors remained high following initial processing of the data. It was subsequently shown that the data set was twinned and it was thus reprocessed in space group P2, resulting in a significant reduction in the R factors. Determination of the structure will provide insight into the design of novel antimicrobial agents targeting this important enzyme from S. pneumoniae.}, pages = {32--36}, number = {1}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Sibarani, N. E. and Gorman, M. A. and Dogovski, C. and Parker, M. W. and Perugini, M. A.}, urldate = {2017-05-15}, date = {2010-01-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A4WPF8PQ\\Sibarani et al. - 2010 - Crystallization of dihydrodipicolinate synthase fr:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SNSS76BR\\Sibarani et al. - 2010 - Crystallization of dihydrodipicolinate synthase fr.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A4WPF8PQ\\Sibarani et al. - 2010 - Crystallization of dihydrodipicolinate synthase fr:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PFCKCE4N\\Sibarani et al. - 2010 - Crystallization of dihydrodipicolinate synthase fr.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E3IDABNU\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EF9ZJD4U\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E3IDABNU\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZG8NJNFK\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A4WPF8PQ\\Sibarani et al. - 2010 - Crystallization of dihydrodipicolinate synthase fr.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\E3IDABNU\\paper.html:text/html} } @article{taylor_identification_2010, title = {Identification and characterization of two families of F420H2-dependent reductases from Mycobacteria that catalyse aflatoxin degradation}, volume = {78}, issn = {1365-2958}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07356.x/abstract}, doi = {10.1111/j.1365-2958.2010.07356.x}, abstract = {Aflatoxins are polyaromatic mycotoxins that contaminate a range of food crops as a result of fungal growth and contribute to serious health problems in the developing world because of their toxicity and mutagenicity. Although relatively resistant to biotic degradation, aflatoxins can be metabolized by certain species of Actinomycetales. However, the enzymatic basis for their breakdown has not been reported until now. We have identified nine Mycobacterium smegmatis enzymes that utilize the deazaflavin cofactor F420H2 to catalyse the reduction of the α,β-unsaturated ester moiety of aflatoxins, activating the molecules for spontaneous hydrolysis and detoxification. These enzymes belong to two previously uncharacterized F420H2 dependent reductase ({FDR}-A and -B) families that are distantly related to the flavin mononucleotide ({FMN}) dependent pyridoxamine 5′-phosphate oxidases ({PNPOxs}). We have solved crystal structures of an enzyme from each {FDR} family and show that they, like the {PNPOxs}, adopt a split barrel protein fold, although the {FDRs} also possess an extended and highly charged F420H2 binding groove. A general role for these enzymes in xenobiotic metabolism is discussed, including the observation that the nitro-reductase Rv3547 from Mycobacterium tuberculosis that is responsible for the activation of bicyclic nitroimidazole prodrugs belongs to the {FDR}-A family.}, pages = {561--575}, number = {3}, journaltitle = {Molecular Microbiology}, author = {Taylor, Matthew C. and Jackson, Colin J. and Tattersall, David B. and French, Nigel and Peat, Thomas S. and Newman, Janet and Briggs, Lyndall J. and Lapalikar, Gauri V. and Campbell, Peter M. and Scott, Colin and Russell, Robyn J. and Oakeshott, John G.}, urldate = {2017-05-15}, date = {2010-11-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\22DJJW9F\\Taylor et al. - 2010 - Identification and characterization of two familie:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\9834IHAI\\Taylor et al. - 2010 - Identification and characterization of two familie.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\22DJJW9F\\Taylor et al. - 2010 - Identification and characterization of two familie:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\236DZU6E\\Taylor et al. - 2010 - Identification and characterization of two familie.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WBPC5MMK\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DFMTAW5C\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WBPC5MMK\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V4SZMRN4\\abstract.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\22DJJW9F\\Taylor et al. - 2010 - Identification and characterization of two familie.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WBPC5MMK\\abstract.html:text/html} } @article{vallotton_droplit_2010, title = {{DroplIT}, an improved image analysis method for droplet identification in high-throughput crystallization trials}, volume = {43}, rights = {Copyright (c) 2010 International Union of Crystallography}, issn = {0021-8898}, url = {http://scripts.iucr.org/cgi-bin/paper?cg5163}, doi = {10.1107/S0021889810040963}, abstract = {The application of robotics to protein crystallization trials has resulted in the production of millions of images. Manual inspection of these images to find crystals and other interesting outcomes is a major rate-limiting step. As a result there has been intense activity in developing automated algorithms to analyse these images. The very first step for most systems that have been described in the literature is to delineate each droplet. Here, a novel approach that reaches over 97\% success rate and subsecond processing times is presented. This will form the seed of a new high-throughput system to scrutinize massive crystallization campaigns automatically.}, pages = {1548--1552}, number = {6}, journaltitle = {Journal of Applied Crystallography}, shortjournal = {J Appl Cryst, J Appl Crystallogr}, author = {Vallotton, P. and Sun, C. and Lovell, D. and Fazio, V. J. and Newman, J.}, urldate = {2017-05-15}, date = {2010-12-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JHCS4FT5\\Vallotton et al. - 2010 - DroplIT, an improved image analysis method for dro:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JK72SKN3\\Vallotton et al. - 2010 - DroplIT, an improved image analysis method for dro.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JHCS4FT5\\Vallotton et al. - 2010 - DroplIT, an improved image analysis method for dro:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JK22CVUE\\Vallotton et al. - 2010 - DroplIT, an improved image analysis method for dro.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RQID4JA2\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WGW9PTF6\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RQID4JA2\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5B3TU44X\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JHCS4FT5\\Vallotton et al. - 2010 - DroplIT, an improved image analysis method for dro.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RQID4JA2\\paper.html:text/html} } @article{voss_substrate-mediated_2010, title = {Substrate-mediated Stabilization of a Tetrameric Drug Target Reveals Achilles Heel in Anthrax}, volume = {285}, issn = {0021-9258, 1083-351X}, url = {http://www.jbc.org/content/285/8/5188}, doi = {10.1074/jbc.M109.038166}, abstract = {Bacillus anthracis is a Gram-positive spore-forming bacterium that causes anthrax. With the increased threat of anthrax in biowarfare, there is an urgent need to characterize new antimicrobial targets from B. anthracis. One such target is dihydrodipicolinate synthase ({DHDPS}), which catalyzes the committed step in the pathway yielding meso-diaminopimelate and lysine. In this study, we employed {CD} spectroscopy to demonstrate that the thermostability of {DHDPS} from B. anthracis (Ba-{DHDPS}) is significantly enhanced in the presence of the substrate, pyruvate. Analytical ultracentrifugation studies show that the tetramer-dimer dissociation constant of the enzyme is 3-fold tighter in the presence of pyruvate compared with the apo form. To examine the significance of this substrate-mediated stabilization phenomenon, a dimeric mutant of Ba-{DHDPS} (L170E/G191E) was generated and shown to have markedly reduced activity compared with the wild-type tetramer. This demonstrates that the substrate, pyruvate, stabilizes the active form of the enzyme. We next determined the high resolution (2.15 Å) crystal structure of Ba-{DHDPS} in complex with pyruvate (3HIJ) and compared this to the apo structure (1XL9). Structural analyses show that there is a significant (91 Å2) increase in buried surface area at the tetramerization interface of the pyruvate-bound structure. This study describes a new mechanism for stabilization of the active oligomeric form of an antibiotic target from B. anthracis and reveals an “Achilles heel” that can be exploited in structure-based drug design.}, pages = {5188--5195}, number = {8}, journaltitle = {Journal of Biological Chemistry}, shortjournal = {J. Biol. Chem.}, author = {Voss, Jarrod E. and Scally, Stephen W. and Taylor, Nicole L. and Atkinson, Sarah C. and Griffin, Michael D. W. and Hutton, Craig A. and Parker, Michael W. and Alderton, Malcolm R. and Gerrard, Juliet A. and Dobson, Renwick C. J. and Dogovski, Con and Perugini, Matthew A.}, urldate = {2017-05-15}, date = {2010-02-19}, langid = {english}, pmid = {19948665}, keywords = {Antibiotics, Antibiotics, Biophysics, Biophysics, Enzymes, Enzymes, Enzymes/Structure, Enzymes/Structure, Methods/Circular Dichroism, Methods/Circular Dichroism, Methods/Ultracentrifugation, Methods/Ultracentrifugation, Methods/X-ray Crystallography, Methods/X-ray Crystallography}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HQ83FZU7\\Voss et al. - 2010 - Substrate-mediated Stabilization of a Tetrameric D:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ECUGCZ5E\\Voss et al. - 2010 - Substrate-mediated Stabilization of a Tetrameric D.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HQ83FZU7\\Voss et al. - 2010 - Substrate-mediated Stabilization of a Tetrameric D:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PCHNZ3U4\\Voss et al. - 2010 - Substrate-mediated Stabilization of a Tetrameric D.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZW925K6F\\5188:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\353AHDVE\\5188.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZW925K6F\\5188:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MTCD6H87\\5188.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HQ83FZU7\\Voss et al. - 2010 - Substrate-mediated Stabilization of a Tetrameric D.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZW925K6F\\5188.html:text/html} } @article{wubben_cloning_2010, title = {Cloning, expression, purification and crystallization of dihydrodipicolinate synthase from the psychrophile Shewanella benthica}, volume = {66}, rights = {Copyright (c) 2010 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?fw5275}, doi = {10.1107/S1744309110036791}, abstract = {Dihydrodipicolinate synthase ({DHDPS}) is an oligomeric enzyme that catalyzes the first committed step of the lysine-biosynthesis pathway in plants and bacteria, which yields essential building blocks for cell-wall and protein synthesis. {DHDPS} is therefore of interest to drug-discovery research as well as to studies that probe the importance of quaternary structure to protein function, stability and dynamics. Accordingly, {DHDPS} from the psychrophilic (cold-dwelling) organism Shewanella benthica (Sb-{DHDPS}) was cloned, expressed, purified and crystallized. The best crystals of Sb-{DHDPS} were grown in 200 {mM} ammonium sulfate, 100 {mM} bis-tris {pH} 5.0–6.0, 23–26\%(w/v) {PEG} 3350, 0.02\%(w/v) sodium azide and diffracted to beyond 2.5 Å resolution. Processing of diffraction data to 2.5 Å resolution resulted in a unit cell with space group P212121 and dimensions a = 73.1, b = 84.0, c = 143.7 Å. These studies of the first {DHDPS} enzyme to be characterized from a bacterial psychrophile will provide insight into the molecular evolution of enzyme structure and dynamics.}, pages = {1511--1516}, number = {11}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Wubben, J. M. and Dogovski, C. and Dobson, R. C. J. and Codd, R. and Gerrard, J. A. and Parker, M. W. and Perugini, M. A.}, urldate = {2017-05-15}, date = {2010-11-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\95TK5TN7\\Wubben et al. - 2010 - Cloning, expression, purification and crystallizat:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7KDU97IX\\Wubben et al. - 2010 - Cloning, expression, purification and crystallizat.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\95TK5TN7\\Wubben et al. - 2010 - Cloning, expression, purification and crystallizat:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8IU3AZUQ\\Wubben et al. - 2010 - Cloning, expression, purification and crystallizat.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JMSWKZW6\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WE5T4PM9\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JMSWKZW6\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WDRJCGTE\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\95TK5TN7\\Wubben et al. - 2010 - Cloning, expression, purification and crystallizat.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JMSWKZW6\\paper.html:text/html} } @article{xu_crystal_2010, title = {Crystal Structure of the Entire Ectodomain of gp130 {INSIGHTS} {INTO} {THE} {MOLECULAR} {ASSEMBLY} {OF} {THE} {TALL} {CYTOKINE} {RECEPTOR} {COMPLEXES}}, volume = {285}, issn = {0021-9258, 1083-351X}, url = {http://www.jbc.org/content/285/28/21214}, doi = {10.1074/jbc.C110.129502}, abstract = {gp130 is the shared signal-transducing receptor subunit for the large and important family of interleukin 6-like cytokines. Previous x-ray structures of ligand-receptor complexes of this family lack the three membrane-proximal domains that are essential for signal transduction. Here we report the crystal structure of the entire extracellular portion of human gp130 (domains 1–6, D1–D6) at 3.6 Å resolution, in an unliganded form, as well as a higher resolution structure of the membrane-proximal fibronectin type {III} domains (D4–D6) at 1.9 Å. This represents the first atomic resolution structure of the complete ectodomain of any “tall” cytokine receptor. These structures show that other than a reorientation of the D1 domain, there is little structural change in gp130 upon ligand binding. They also reveal that the interface between the D4 and D5 domains forms an acute bend in the gp130 structure. Key residues at this interface are highly conserved across the entire tall receptor family, suggesting that this acute bend may be a common feature of these receptors. Importantly, this geometry positions the C termini of the membrane-proximal fibronectin type {III} domains of the tall cytokine receptors in close proximity within the transmembrane complex, favorable for receptor-associated Janus kinases to trans-phosphorylate and activate each other.}, pages = {21214--21218}, number = {28}, journaltitle = {Journal of Biological Chemistry}, shortjournal = {J. Biol. Chem.}, author = {Xu, Yibin and Kershaw, Nadia J. and Luo, Cindy S. and Soo, Priscilla and Pocock, Michael J. and Czabotar, Peter E. and Hilton, Douglas J. and Nicola, Nicos A. and Garrett, Thomas P. J. and Zhang, Jian-Guo}, urldate = {2017-05-15}, date = {2010-07-09}, langid = {english}, pmid = {20489211}, keywords = {Cell Surface Receptor, Cell Surface Receptor, Crystallography, Crystallography, Cytokine Receptor, Cytokine Receptor, Ectodomain, Ectodomain, Fibronectin Type {III} Domains, Fibronectin Type {III} Domains, gp130, gp130, Jak Kinase, Jak Kinase, Receptor Structure-Function, Receptor Structure-Function, Signal Transduction, Signal Transduction}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7PJJXM6A\\21214:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HTCMBH4I\\21214.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7PJJXM6A\\21214:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\US9T8NKZ\\21214.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AKPTRKUA\\Xu et al. - 2010 - Crystal Structure of the Entire Ectodomain of gp13:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DXM7248Q\\Xu et al. - 2010 - Crystal Structure of the Entire Ectodomain of gp13.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AKPTRKUA\\Xu et al. - 2010 - Crystal Structure of the Entire Ectodomain of gp13:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IMPAQB4Z\\Xu et al. - 2010 - Crystal Structure of the Entire Ectodomain of gp13.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AKPTRKUA\\Xu et al. - 2010 - Crystal Structure of the Entire Ectodomain of gp13.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7PJJXM6A\\21214.html:text/html} } @article{atkinson_crystallization_2009, title = {Crystallization and preliminary X-ray analysis of dihydrodipicolinate synthase from Clostridium botulinum in the presence of its substrate pyruvate}, volume = {65}, rights = {Copyright (c) 2009 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?pu5236}, doi = {10.1107/S1744309108039018}, abstract = {In this paper, the crystallization and preliminary X-ray diffraction analysis to near-atomic resolution of {DHDPS} from Clostridium botulinum crystallized in the presence of its substrate pyruvate are presented. The enzyme crystallized in a number of forms using a variety of {PEG} precipitants, with the best crystal diffracting to 1.2 Å resolution and belonging to space group C2, in contrast to the unbound form, which had trigonal symmetry. The unit-cell parameters were a = 143.4, b = 54.8, c = 94.3 Å, β = 126.3°. The crystal volume per protein weight ({VM}) was 2.3 Å3 Da−1 (based on the presence of two monomers in the asymmetric unit), with an estimated solvent content of 46\%. The high-resolution structure of the pyruvate-bound form of C. botulinum {DHDPS} will provide insight into the function and stability of this essential bacterial enzyme.}, pages = {253--255}, number = {3}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Atkinson, S. C. and Dobson, R. C. J. and Newman, J. M. and Gorman, M. A. and Dogovski, C. and Parker, M. W. and Perugini, M. A.}, urldate = {2017-05-15}, date = {2009-03-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PBN4Z75Z\\Atkinson et al. - 2009 - Crystallization and preliminary X-ray analysis of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\D6TRTI6A\\Atkinson et al. - 2009 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PBN4Z75Z\\Atkinson et al. - 2009 - Crystallization and preliminary X-ray analysis of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4ECMDA86\\Atkinson et al. - 2009 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SZRZI6EW\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EXDGEG2M\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SZRZI6EW\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\98WAEVEK\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PBN4Z75Z\\Atkinson et al. - 2009 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SZRZI6EW\\paper.html:text/html} } @article{baker_structural_2009, title = {Structural and Functional Requirements for Activity of the Tim9–Tim10 Complex in Mitochondrial Protein Import}, volume = {20}, issn = {1059-1524, 1939-4586}, url = {http://www.molbiolcell.org/content/20/3/769}, doi = {10.1091/mbc.E08-09-0903}, abstract = {The Tim9–Tim10 complex plays an essential role in mitochondrial protein import by chaperoning select hydrophobic precursor proteins across the intermembrane space. How the complex interacts with precursors is not clear, although it has been proposed that Tim10 acts in substrate recognition, whereas Tim9 acts in complex stabilization. In this study, we report the structure of the yeast Tim9–Tim10 hexameric assembly determined to 2.5 Å and have performed mutational analysis in yeast to evaluate the specific roles of Tim9 and Tim10. Like the human counterparts, each Tim9 and Tim10 subunit contains a central loop flanked by disulfide bonds that separate two extended N- and C-terminal tentacle-like helices. Buried salt-bridges between highly conserved lysine and glutamate residues connect alternating subunits. Mutation of these residues destabilizes the complex, causes defective import of precursor substrates, and results in yeast growth defects. Truncation analysis revealed that in the absence of the N-terminal region of Tim9, the hexameric complex is no longer able to efficiently trap incoming substrates even though contacts with Tim10 are still made. We conclude that Tim9 plays an important functional role that includes facilitating the initial steps in translocating precursor substrates into the intermembrane space.}, pages = {769--779}, number = {3}, journaltitle = {Molecular Biology of the Cell}, shortjournal = {Mol. Biol. Cell}, author = {Baker, Michael J. and Webb, Chaille T. and Stroud, David A. and Palmer, Catherine S. and Frazier, Ann E. and Guiard, Bernard and Chacinska, Agnieszka and Gulbis, Jacqueline M. and Ryan, Michael T.}, urldate = {2017-05-15}, date = {2009-02-01}, langid = {english}, pmid = {19037098}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KESZDRWQ\\769:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EZ3JPTK8\\769.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KESZDRWQ\\769:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WK9F7NSA\\769.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XFG5QCX2\\Baker et al. - 2009 - Structural and Functional Requirements for Activit:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\SZQX9252\\Baker et al. - 2009 - Structural and Functional Requirements for Activit.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XFG5QCX2\\Baker et al. - 2009 - Structural and Functional Requirements for Activit:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IRJBD2KH\\Baker et al. - 2009 - Structural and Functional Requirements for Activit.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XFG5QCX2\\Baker et al. - 2009 - Structural and Functional Requirements for Activit.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KESZDRWQ\\769.html:text/html} } @article{feil_crystallization_2009, title = {Crystallization and preliminary X-ray analysis of glutathione transferases from cyanobacteria}, volume = {65}, rights = {Copyright (c) 2009 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?nj5029}, doi = {10.1107/S1744309109011634}, abstract = {Glutathione S-transferases ({GSTs}) are a group of multifunctional enzymes that are found in animals, plants and microorganisms. Their primary function is to remove toxins derived from exogenous sources or the products of metabolism from the cell. Mammalian {GSTs} have been extensively studied, in contrast to bacterial {GSTs} which have received relatively scant attention. A new class of {GSTs} called Chi has recently been identified in cyanobacteria. Chi {GSTs} exhibit a high glutathionylation activity towards isothiocyanates, compounds that are normally found in plants. Here, the crystallization of two {GSTs} are presented: {TeGST} produced by Thermosynechococcus elongates {BP}-1 and {SeGST} from Synechococcus elongates {PCC} 6301. Both enzymes formed crystals that diffracted to high resolution and appeared to be suitable for further X-ray diffraction studies. The structures of these {GSTs} may shed further light on the evolution of {GST} catalytic activity and in particular why these enzymes possess catalytic activity towards plant antimicrobial compounds.}, pages = {475--477}, number = {5}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Feil, S. C. and Tang, J. and Hansen, G. and Gorman, M. A. and Wiktelius, E. and Stenberg, G. and Parker, M. W.}, urldate = {2017-05-15}, date = {2009-05-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J8EQBAQA\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5JFASC63\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J8EQBAQA\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QF4GKIFZ\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NZSHM53X\\Feil et al. - 2009 - Crystallization and preliminary X-ray analysis of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ANWII6IX\\Feil et al. - 2009 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NZSHM53X\\Feil et al. - 2009 - Crystallization and preliminary X-ray analysis of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\28U46FIA\\Feil et al. - 2009 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NZSHM53X\\Feil et al. - 2009 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J8EQBAQA\\paper.html:text/html} } @article{meikok_solid-phase_2009, title = {Solid-phase synthesis of homodimeric peptides : preparation of covalently-linked dimers of amyloid β peptide}, volume = {0}, url = {http://pubs.rsc.org/en/Content/ArticleLanding/2009/CC/B912784D}, doi = {10.1039/B912784D}, shorttitle = {Solid-phase synthesis of homodimeric peptides}, pages = {6228--6230}, number = {41}, journaltitle = {Chemical Communications}, author = {Mei Kok, W. and B. Scanlon, Denis and A. Karas, John and A. Miles, Luke and J. Tew, Deborah and W. Parker, Michael and J. Barnham, Kevin and A. Hutton, Craig}, urldate = {2017-05-15}, date = {2009}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6PUKZDWV\\Mei Kok et al. - 2009 - Solid-phase synthesis of homodimeric peptides pr:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TZ4Q7E4A\\Mei Kok et al. - 2009 - Solid-phase synthesis of homodimeric peptides pr.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6PUKZDWV\\Mei Kok et al. - 2009 - Solid-phase synthesis of homodimeric peptides pr:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NJAIFJVA\\Mei Kok et al. - 2009 - Solid-phase synthesis of homodimeric peptides pr.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\46FDBMJ3\\b912784d:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3HIZQMFC\\b912784d.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\46FDBMJ3\\b912784d:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CPXHB5TR\\b912784d.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6PUKZDWV\\Mei Kok et al. - 2009 - Solid-phase synthesis of homodimeric peptides pr.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\46FDBMJ3\\b912784d.html:text/html} } @article{kuang_spry_2009, title = {{SPRY} Domain-Containing {SOCS} Box Protein 2: Crystal Structure and Residues Critical for Protein Binding}, volume = {386}, issn = {0022-2836}, url = {http://www.sciencedirect.com/science/article/pii/S0022283608015738}, doi = {10.1016/j.jmb.2008.12.078}, shorttitle = {{SPRY} Domain-Containing {SOCS} Box Protein 2}, abstract = {The four mammalian {SPRY} (a sequence repeat in dual-specificity kinase {splA} and ryanodine receptors) domain-containing suppressor of cytokine signalling ({SOCS}) box proteins ({SSB}-1 to -4) are characterised by a C-terminal {SOCS} box and a central {SPRY} domain. The latter is a protein interaction module found in over 1600 proteins, with more than 70 encoded in the human genome. Here we report the crystal structure of the {SPRY} domain of murine {SSB}-2 and compare it with the {SSB}-2 solution structure and crystal structures of other B30.2/{SPRY} domain-containing family proteins. The structure is a bent β-sandwich, consisting of two seven-stranded β-sheets wrapped around a long loop that extends from the centre strands of the inner or concave β-sheet; it closely matches those of {GUSTAVUS} and {SSB}-4. The structure is also similar to those of two recently determined Neuralized homology repeat ({NHR}) domains (also known as {NEUZ} domains), with detailed comparisons, suggesting that the {NEUZ}/{NHR} domains form a subclass of {SPRY} domains. The binding site on {SSB}-2 for the prostate apoptosis response-4 (Par-4) protein has been mapped in finer detail using mutational analyses. Moreover, {SSB}-1 was shown to have a Par-4 binding surface similar to that identified for {SSB}-2. Structural perturbations of {SSB}-2 induced by mutations affecting its interaction with Par-4 and/or c-Met have been characterised by {NMR}. These comparisons, in conjunction with previously published dynamics data from {NMR} relaxation studies and coarse-grained dynamics simulation using normal mode analysis, further refine our understanding of the structural basis for protein recognition of {SPRY} domain-containing proteins.}, pages = {662--674}, number = {3}, journaltitle = {Journal of Molecular Biology}, shortjournal = {Journal of Molecular Biology}, author = {Kuang, Zhihe and Yao, Shenggen and Xu, Yibin and Lewis, Rowena S. and Low, Andrew and Masters, Seth L. and Willson, Tracy A. and Kolesnik, Tatiana B. and Nicholson, Sandra E. and Garrett, Thomas J. P. and Norton, Raymond S.}, urldate = {2017-05-15}, date = {2009-02-27}, keywords = {Crystal structure, Crystal structure, {NMR}, {NMR}, protein–protein interaction, protein–protein interaction, {SPRY} domain-containing {SOCS} box protein, {SPRY} domain-containing {SOCS} box protein, {SSB}-2, {SSB}-2}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6R9MWJGN\\Kuang et al. - 2009 - SPRY Domain-Containing SOCS Box Protein 2 Crystal:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ET5XRQ2N\\Kuang et al. - 2009 - SPRY Domain-Containing SOCS Box Protein 2 Crystal.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6R9MWJGN\\Kuang et al. - 2009 - SPRY Domain-Containing SOCS Box Protein 2 Crystal:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RVGF3MXH\\Kuang et al. - 2009 - SPRY Domain-Containing SOCS Box Protein 2 Crystal.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CVCQEP7T\\S0022283608015738:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VH43UEW2\\S0022283608015738.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CVCQEP7T\\S0022283608015738:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JN56USZC\\S0022283608015738.html:text/html;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6R9MWJGN\\Kuang et al. - 2009 - SPRY Domain-Containing SOCS Box Protein 2 Crystal.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CVCQEP7T\\S0022283608015738.html:text/html} } @article{lee_conformational_2009, title = {Conformational Changes in Bcl-2 Pro-survival Proteins Determine Their Capacity to Bind Ligands}, volume = {284}, issn = {0021-9258, 1083-351X}, url = {http://www.jbc.org/content/284/44/30508}, doi = {10.1074/jbc.M109.040725}, abstract = {Antagonists of anti-apoptotic Bcl-2 family members hold promise as cancer therapeutics. Apoptosis is triggered when a peptide containing a {BH}3 motif or a small molecule {BH}3 peptidomimetic, such as {ABT} 737, binds to the relevant Bcl-2 family members. {ABT}-737 is an antagonist of Bcl-2, Bcl-{xL}, and Bcl-w but not of Mcl-1. Here we describe new structures of mutant {BH}3 peptides bound to Bcl-{xL} and Mcl-1. These structures suggested a rationale for the failure of {ABT}-737 to bind Mcl-1, but a designed variant of {ABT}-737 failed to acquire binding affinity for Mcl-1. Rather, it was selective for Bcl-{xL}, a result attributable in part to significant backbone refolding and movements of helical segments in its ligand binding site. To date there are few reported crystal structures of organic ligands in complex with their pro-survival protein targets. Our structure of this new organic ligand provided insights into the structural transitions that occur within the {BH}3 binding groove, highlighting significant differences in the structural properties of members of the Bcl-2 pro-survival protein family. Such differences are likely to influence and be important in the quest for compounds capable of selectively antagonizing the different family members.}, pages = {30508--30517}, number = {44}, journaltitle = {Journal of Biological Chemistry}, shortjournal = {J. Biol. Chem.}, author = {Lee, Erinna F. and Czabotar, Peter E. and Yang, Hong and Sleebs, Brad E. and Lessene, Guillaume and Colman, Peter M. and Smith, Brian J. and Fairlie, W. Douglas}, urldate = {2017-05-15}, date = {2009-10-30}, langid = {english}, pmid = {19726685}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3WBN68W2\\30508:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\72X63PXK\\30508.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3WBN68W2\\30508:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EWIV9A6F\\30508.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6TQPEJMP\\Lee et al. - 2009 - Conformational Changes in Bcl-2 Pro-survival Prote:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\39FRN5R6\\Lee et al. - 2009 - Conformational Changes in Bcl-2 Pro-survival Prote.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6TQPEJMP\\Lee et al. - 2009 - Conformational Changes in Bcl-2 Pro-survival Prote:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4KBRNVFW\\Lee et al. - 2009 - Conformational Changes in Bcl-2 Pro-survival Prote.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6TQPEJMP\\Lee et al. - 2009 - Conformational Changes in Bcl-2 Pro-survival Prote.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\3WBN68W2\\30508.html:text/html} } @article{lee_high-resolution_2009, title = {High-Resolution Structural Characterization of a Helical α/β-Peptide Foldamer Bound to the Anti-Apoptotic Protein Bcl-{xL}}, volume = {121}, issn = {1521-3757}, url = {http://onlinelibrary.wiley.com/doi/10.1002/ange.200805761/abstract}, doi = {10.1002/ange.200805761}, abstract = {Das passt! Die erste hochaufgelöste Strukturbestimmung eines Foldamers im Komplex mit seinem Protein-Target wird beschrieben (siehe Bild; Foldamere in Stabdarstellung). Das Foldamer besteht aus α- und β-Aminosäureresten und ist an das antiapoptotische Protein Bcl-{xL} gebunden. Der Komplex ahmt den Bindungsmodus und die wichtigsten Wechselwirkungen von Komplexen natürlicher α-Peptidliganden mit Bcl-{xL} nach. Zusätzliche Kontakte über β-Aminosäurereste scheinen ebenfalls zur Bindungsaffinität beizutragen.}, pages = {4382--4386}, number = {24}, journaltitle = {Angewandte Chemie}, shortjournal = {Angewandte Chemie}, author = {Lee, Erinna F. and Sadowsky, Jack D. and Smith, Brian J. and Czabotar, Peter E. and Peterson-Kaufman, Kimberly J. and Colman, Peter M. and Gellman, Samuel H. and Fairlie, W. Douglas}, urldate = {2017-05-15}, date = {2009-06-02}, langid = {english}, keywords = {Aminosäuren, Aminosäuren, Foldamere, Foldamere, Peptide, Peptide, Protein-Protein-Wechselwirkungen, Protein-Protein-Wechselwirkungen, Röntgenbeugung, Röntgenbeugung}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N235K4CW\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HIWU5EVW\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N235K4CW\\abstract:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VVB9QMMV\\abstract.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RKUT57SH\\Lee et al. - 2009 - High-Resolution Structural Characterization of a H:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\UT2753FJ\\Lee et al. - 2009 - High-Resolution Structural Characterization of a H.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RKUT57SH\\Lee et al. - 2009 - High-Resolution Structural Characterization of a H:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8HUPNMR2\\Lee et al. - 2009 - High-Resolution Structural Characterization of a H.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RKUT57SH\\Lee et al. - 2009 - High-Resolution Structural Characterization of a H.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\N235K4CW\\abstract.html:text/html} } @article{newman_crystallization_2009, title = {Crystallization and preliminary X-ray analysis of the complexes between a Fab and two forms of human insulin-like growth factor {II}}, volume = {65}, rights = {Copyright (c) 2009 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?en5372}, doi = {10.1107/S1744309109024932}, abstract = {Elevated expression of insulin-like growth factor {II} ({IGF}-{II}) is frequently observed in a variety of human malignancies, including breast, colon and liver cancer. As {IGF}-{II} can deliver a mitogenic signal through both the type 1 insulin-like growth factor receptor ({IGF}-{IR}) and an alternately spliced form of the insulin receptor ({IR}-A), neutralizing the biological activity of this growth factor directly is an attractive therapeutic option. One method of doing this would be to find antibodies that bind tightly and specifically to the peptide, which could be used as protein therapeutics to lower the peptide levels in vivo and/or to block the peptide from binding to the {IGF}-{IR} or {IR}-A. To address this, Fabs were selected from a phage-display library using a biotinylated precursor form of the growth factor known as {IGF}-{IIE} as a target. Fabs were isolated that were specific for the E-­domain C-terminal extension and for mature {IGF}-{II}. Four Fabs selected from the library were produced, complexed with {IGF}-{II} and set up in crystallization trials. One of the Fab–{IGF}-{II} complexes (M64-F02–{IGF}-{II}) crystallized readily, yielding crystals that diffracted to 2.2 Å resolution and belonged to space group P212121, with unit-cell parameters a = 50.7, b = 106.9, c = 110.7 Å. There was one molecule of the complete complex in the asymmetric unit. The same Fab was also crystallized with a longer form of the growth factor, {IGF}-{IIE}. This complex crystallized in space group P212121, with unit-cell parameters a = 50.7, b = 107, c = 111.5 Å, and also diffracted X-rays to 2.2 Å resolution.}, pages = {945--948}, number = {9}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Newman, J. and Cohen, E. H. and Cosgrove, L. and Kopacz, K. and Dransfield, D. T. and Adams, T. E. and Peat, T. S.}, urldate = {2017-05-15}, date = {2009-09-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ABU2CFAD\\Newman et al. - 2009 - Crystallization and preliminary X-ray analysis of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HZRXITAN\\Newman et al. - 2009 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ABU2CFAD\\Newman et al. - 2009 - Crystallization and preliminary X-ray analysis of:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KQIXX3UX\\Newman et al. - 2009 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FIGBQB5Z\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\WAE5GBFH\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FIGBQB5Z\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HUUP9T9N\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ABU2CFAD\\Newman et al. - 2009 - Crystallization and preliminary X-ray analysis of .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FIGBQB5Z\\paper.html:text/html} } @article{newman_practical_2009, title = {Practical Aspects of the {SAMPL} Challenge: Providing an Extensive Experimental Data Set for the Modeling Community}, volume = {14}, issn = {1087-0571}, url = {http://dx.doi.org/10.1177/1087057109348220}, doi = {10.1177/1087057109348220}, shorttitle = {Practical Aspects of the {SAMPL} Challenge}, abstract = {To provide an experimental basis for a comprehensive molecular modeling evaluation study, 500 fragments from the Maybridge fragment library were soaked into crystals of bovine pancreatic trypsin and the structures determined by X-ray crystallography. The soaking experiments were performed in both single and pooled aliquots to determine if combination of fragments is an appropriate strategy. A further set of data was obtained from co-crystallizing the pooled fragments with the protein. X-ray diffraction data were collected on approximately 1000 crystals at the Australian Synchrotron, and these data were subsequently processed, and the preliminary analysis was performed with a custom software application (Jigsaw), which combines available software packages for structure solution and analysis.}, pages = {1245--1250}, number = {10}, journaltitle = {Journal of Biomolecular Screening}, shortjournal = {J Biomol Screen}, author = {Newman, Janet and Fazio, Vincent J. and Caradoc-Davies, Tom T. and Branson, Kim and Peat, Thomas S.}, urldate = {2017-05-15}, date = {2009-12-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A2AEEE7S\\Newman et al. - 2009 - Practical Aspects of the SAMPL Challenge Providin:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7UDXCKAT\\Newman et al. - 2009 - Practical Aspects of the SAMPL Challenge Providin.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A2AEEE7S\\Newman et al. - 2009 - Practical Aspects of the SAMPL Challenge Providin:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KGUBQJNZ\\Newman et al. - 2009 - Practical Aspects of the SAMPL Challenge Providin.pdf:application/pdf;SAGE PDF Full Text:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\A2AEEE7S\\Newman et al. - 2009 - Practical Aspects of the SAMPL Challenge Providin.pdf:application/pdf} } @article{voss_expression_2009, title = {Expression, purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Bacillus anthracis in the presence of pyruvate}, volume = {65}, rights = {Copyright (c) 2009 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?nj5027}, doi = {10.1107/S1744309109000670}, abstract = {Dihydrodipicolinate synthase ({DHDPS}) catalyses the first committed step in the lysine-biosynthesis pathway in bacteria, plants and some fungi. In this study, the expression of {DHDPS} from Bacillus anthracis (Ba-{DHDPS}) and the purification of the recombinant enzyme in the absence and presence of the substrate pyruvate are described. It is shown that {DHDPS} from B. anthracis purified in the presence of pyruvate yields greater amounts of recombinant enzyme with more than 20-fold greater specific activity compared with the enzyme purified in the absence of substrate. It was therefore sought to crystallize Ba-{DHDPS} in the presence of the substrate. Pyruvate was soaked into crystals of Ba-{DHDPS} prepared in 0.2 M sodium fluoride, 20\%(w/v) {PEG} 3350 and 0.1 M bis-tris propane {pH} 8.0. Preliminary X-ray diffraction data of the recombinant enzyme soaked with pyruvate at a resolution of 2.15 Å are presented. The pending crystal structure of the pyruvate-bound form of Ba-{DHDPS} will provide insight into the function and stability of this essential bacterial enzyme.}, pages = {188--191}, number = {2}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Voss, J. E. and Scally, S. W. and Taylor, N. L. and Dogovski, C. and Alderton, M. R. and Hutton, C. A. and Gerrard, J. A. and Parker, M. W. and Dobson, R. C. J. and Perugini, M. A.}, urldate = {2017-05-15}, date = {2009-02-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KP3QP8TM\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\R5FPRWNK\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KP3QP8TM\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\46XPRMRP\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RWSUD7C5\\Voss et al. - 2009 - Expression, purification, crystallization and prel:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\88DEQXE6\\Voss et al. - 2009 - Expression, purification, crystallization and prel.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RWSUD7C5\\Voss et al. - 2009 - Expression, purification, crystallization and prel:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\G6IXRQFU\\Voss et al. - 2009 - Expression, purification, crystallization and prel.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RWSUD7C5\\Voss et al. - 2009 - Expression, purification, crystallization and prel.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\KP3QP8TM\\paper.html:text/html} } @article{smith_structure_2006, title = {Structure of a calcium-deficient form of influenza virus neuraminidase: implications for substrate binding}, volume = {62}, rights = {Copyright (c) 2006 International Union of Crystallography}, issn = {0907-4449}, url = {http://scripts.iucr.org/cgi-bin/paper?be5059}, doi = {10.1107/S0907444906020063}, shorttitle = {Structure of a calcium-deficient form of influenza virus neuraminidase}, abstract = {The X-ray structure of influenza virus neuraminidase ({NA}) isolated from whale, subtype N9, has been determined at 2.2 Å resolution and contains a tetrameric protein in the asymmetric unit. In structures of {NA} determined previously, a calcium ion is observed to coordinate amino acids near the substrate-binding site. In three of the {NA} monomers determined here this calcium is absent, resulting in structural alterations near the substrate-binding site. These changes affect the conformation of residues that participate in several key interactions between the enzyme and substrate and provide at a molecular level the basis of the structural and functional role of calcium in substrate and inhibitor binding. Several sulfate ions were identified in complex with the protein. These are located in the active site, occupying the space reserved for the substrate (sialic acid) carboxylate, and in positions leading away from the substrate-binding site. These sites offer a new opportunity for the design of inhibitors of influenza virus {NA}.}, pages = {947--952}, number = {9}, journaltitle = {Acta Crystallographica Section D: Biological Crystallography}, shortjournal = {Acta Cryst D, Acta Cryst Sect D, Acta Crystallogr D, Acta Crystallogr Sect D, Acta Crystallogr D Biol Crystallogr, Acta Crystallogr Sect D Biol Crystallogr}, author = {Smith, B. J. and Huyton, T. and Joosten, R. P. and {McKimm}-Breschkin, J. L. and Zhang, J.-G. and Luo, C. S. and Lou, M.-Z. and Labrou, N. E. and Garrett, T. P. J.}, urldate = {2017-05-15}, date = {2006-09-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J4VNFGC2\\Smith et al. - 2006 - Structure of a calcium-deficient form of influenza:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PP2GZK5W\\Smith et al. - 2006 - Structure of a calcium-deficient form of influenza.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J4VNFGC2\\Smith et al. - 2006 - Structure of a calcium-deficient form of influenza:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RIVKCM7C\\Smith et al. - 2006 - Structure of a calcium-deficient form of influenza.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QFUGGKAP\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PSKQ3DVM\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QFUGGKAP\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6GB6ZA87\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\J4VNFGC2\\Smith et al. - 2006 - Structure of a calcium-deficient form of influenza.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QFUGGKAP\\paper.html:text/html} } @article{ward_landmarks_2006, title = {Landmarks in Insulin Research - the Determination of the Crystal Structure of the Human Insulin Receptor}, volume = {73}, url = {http://search.informit.com.au/documentSummary;dn=297064867982648;res=IELAPA}, abstract = {A multidisciplinary team from the {CSIRO} Molecular \& Health Technologies Division in Parkville has determined the molecular structure of the insulin receptor and published their findings in the prestigious international journal 'Nature'. Their findings are described as a landmark achievement and a milestone in diabetes research, facilitating future research aimed at the development of new therapies for diabetes or cancer.}, pages = {5}, number = {11}, journaltitle = {Chemistry in Australia}, author = {Ward, Colin W. and Lawrence, Michael C. and {McKern}, Neil M.}, urldate = {2017-05-15}, date = {2006-12}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\53IRR42S\\documentSummary\;dn=297064867982648\;res=IELAPA:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MG5T593N\\documentSummary\;dn=297064867982648\;res=IELAPA.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\53IRR42S\\documentSummary\;dn=297064867982648\;res=IELAPA:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\M3QHAIHA\\documentSummary\;dn=297064867982648\;res=IELAPA.html:text/html;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\53IRR42S\\documentSummary\;dn=297064867982648\;res=IELAPA.html:text/html} } @article{lee_crystal_2007, title = {Crystal structure of {ABT}-737 complexed with Bcl-{xL}: implications for selectivity of antagonists of the Bcl-2 family}, volume = {14}, rights = {© 2007 Nature Publishing Group}, issn = {1350-9047}, url = {http://www.nature.com/cdd/journal/v14/n9/abs/4402178a.html}, doi = {10.1038/sj.cdd.4402178}, shorttitle = {Crystal structure of {ABT}-737 complexed with Bcl-{xL}}, abstract = {Cell death and differentiation is a monthly research journal focused on the exciting field of programmed cell death and apoptosis. It provides a single accessible source of information for both scientists and clinicians, keeping them up-to-date with advances in the field. It encompasses programmed cell death, cell death induced by toxic agents, differentiation and the interrelation of these with cell proliferation.}, pages = {1711--1713}, number = {9}, journaltitle = {Cell Death \& Differentiation}, shortjournal = {Cell Death Differ}, author = {Lee, E. F. and Czabotar, P. E. and Smith, B. J. and Deshayes, K. and Zobel, K. and Colman, P. M. and Fairlie, W. D.}, urldate = {2017-05-15}, date = {2007-06-15}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CZAAHCCH\\Lee et al. - 2007 - Crystal structure of ABT-737 complexed with Bcl-xL:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TAW9Z8PF\\Lee et al. - 2007 - Crystal structure of ABT-737 complexed with Bcl-xL.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CZAAHCCH\\Lee et al. - 2007 - Crystal structure of ABT-737 complexed with Bcl-xL:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\B8SCKN3Z\\Lee et al. - 2007 - Crystal structure of ABT-737 complexed with Bcl-xL.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HF8S3RND\\4402178a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EU2X7STS\\4402178a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HF8S3RND\\4402178a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2V7EAEH8\\4402178a.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\CZAAHCCH\\Lee et al. - 2007 - Crystal structure of ABT-737 complexed with Bcl-xL.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\HF8S3RND\\4402178a.html:text/html} } @article{newman_initial_2007, title = {Initial evaluations of the reproducibility of vapor-diffusion crystallization}, volume = {63}, rights = {Copyright (c) 2007 International Union of Crystallography}, issn = {0907-4449}, url = {http://scripts.iucr.org/cgi-bin/paper?bw5202}, doi = {10.1107/S0907444907025784}, abstract = {Experiments were set up to test how the crystallization drop size affects the crystallization process; in the test cases studied, increasing the drop size led to increasing numbers of crystals. Other data produced from a high-throughput automation-system run were analyzed in order to gauge the effect of replication on the success of crystallization screening. With over 40-fold multiplicity, lysozyme was found to crystallize in over half of the conditions in a standard 96-condition screen. However, despite the fact that industry-standard lysozyme was used in our tests, it was rare that we obtained crystals reproducibly; this suggests that replication whilst screening might improve the success rate of macromolecular crystallization.}, pages = {826--832}, number = {7}, journaltitle = {Acta Crystallographica Section D: Biological Crystallography}, shortjournal = {Acta Cryst D, Acta Cryst Sect D, Acta Crystallogr D, Acta Crystallogr Sect D, Acta Crystallogr D Biol Crystallogr, Acta Crystallogr Sect D Biol Crystallogr}, author = {Newman, J. and Xu, J. and Willis, M. C.}, urldate = {2017-05-15}, date = {2007-07-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4UUBG7NX\\Newman et al. - 2007 - Initial evaluations of the reproducibility of vapo:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7UJQFJE9\\Newman et al. - 2007 - Initial evaluations of the reproducibility of vapo.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4UUBG7NX\\Newman et al. - 2007 - Initial evaluations of the reproducibility of vapo:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8TN6W7A2\\Newman et al. - 2007 - Initial evaluations of the reproducibility of vapo.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\47Q2ISWS\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\7D8V8BQJ\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\47Q2ISWS\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FCI3IKTU\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\4UUBG7NX\\Newman et al. - 2007 - Initial evaluations of the reproducibility of vapo.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\47Q2ISWS\\paper.html:text/html} } @article{burgess_purification_2008, title = {Purification, crystallization and preliminary X-­ray diffraction studies to near-atomic resolution of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus}, volume = {64}, rights = {Copyright (c) 2008 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?nj5016}, doi = {10.1107/S1744309108016746}, abstract = {In recent years, dihydrodipicolinate synthase ({DHDPS}; {EC} 4.2.1.52) has received considerable attention from both mechanistic and structural viewpoints. {DHDPS} is part of the diaminopimelate pathway leading to lysine, coupling (S)-aspartate-β-semialdehyde with pyruvate via a Schiff base to a conserved active-site lysine. In this paper, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of {DHDPS} from methicillin-resistant Staphylococcus aureus, an important bacterial pathogen, are reported. The enzyme was crystallized in a number of forms, predominantly from {PEG} precipitants, with the best crystal diffracting to beyond 1.45 Å resolution. The space group was P1 and the unit-cell parameters were a = 65.4, b = 67.6, c = 78.0 Å, α = 90.1, β = 68.9, γ = 72.3°. The crystal volume per protein weight ({VM}) was 2.34 Å3 Da−1, with an estimated solvent content of 47\% for four monomers per asymmetric unit. The structure of the enzyme will help to guide the design of novel therapeutics against the methicillin-resistant S. aureus pathogen.}, pages = {659--661}, number = {7}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Burgess, B. R. and Dobson, R. C. J. and Dogovski, C. and Jameson, G. B. and Parker, M. W. and Perugini, M. A.}, urldate = {2017-05-15}, date = {2008-07-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2QF5WHXI\\Burgess et al. - 2008 - Purification, crystallization and preliminary X-­r:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\Z2PKQE3J\\Burgess et al. - 2008 - Purification, crystallization and preliminary X-­r.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2QF5WHXI\\Burgess et al. - 2008 - Purification, crystallization and preliminary X-­r:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NHPDG764\\Burgess et al. - 2008 - Purification, crystallization and preliminary X-­r.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\F47WCFF9\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DXCTIM5M\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\F47WCFF9\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\U7FZUARU\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2QF5WHXI\\Burgess et al. - 2008 - Purification, crystallization and preliminary X-­r.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\F47WCFF9\\paper.html:text/html} } @article{dobson_purification_2008, title = {The purification, crystallization and preliminary X-­ray diffraction analysis of dihydrodipicolinate synthase from Clostridium botulinum}, volume = {64}, rights = {Copyright (c) 2008 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?ll5142}, doi = {10.1107/S1744309108002819}, abstract = {In recent years, dihydrodipicolinate synthase ({DHDPS}; {EC} 4.2.1.52) has received considerable attention from both mechanistic and structural viewpoints. This enzyme, which is part of the diaminopimelate pathway leading to lysine, couples (S)-aspartate-β-semialdehyde with pyruvate via a Schiff base to a conserved active-site lysine. In this paper, the expression, purification, crystallization and preliminary X-ray diffraction analysis of {DHDPS} from Clostridium botulinum, an important bacterial pathogen, are presented. The enzyme was crystallized in a number of forms, predominantly using {PEG} precipitants, with the best crystal diffracting to beyond 1.9 Å resolution and displaying P42212 symmetry. The unit-cell parameters were a = b = 92.9, c = 60.4 Å. The crystal volume per protein weight ({VM}) was 2.07 Å3 Da−1, with an estimated solvent content of 41\%. The structure of the enzyme will help guide the design of novel therapeutics against the C. botulinum pathogen.}, pages = {206--208}, number = {3}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Dobson, R. C. J. and Atkinson, S. C. and Gorman, M. A. and Newman, J. M. and Parker, M. W. and Perugini, M. A.}, urldate = {2017-05-15}, date = {2008-03-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2D5ZTW4Q\\Dobson et al. - 2008 - The purification, crystallization and preliminary:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2XHI42EW\\Dobson et al. - 2008 - The purification, crystallization and preliminary .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2D5ZTW4Q\\Dobson et al. - 2008 - The purification, crystallization and preliminary:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\5C2P4Q9B\\Dobson et al. - 2008 - The purification, crystallization and preliminary .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V9A5EHJX\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\I2AJ2UW4\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V9A5EHJX\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S8SQ4ETW\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\2D5ZTW4Q\\Dobson et al. - 2008 - The purification, crystallization and preliminary .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\V9A5EHJX\\paper.html:text/html} } @article{jackson_malonate-bound_2008, title = {Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes ({GpdQ}) and characterization of the native Fe2+ metal-ion preference}, volume = {64}, rights = {Copyright (c) 2008 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?gx5133}, doi = {10.1107/S1744309108017600}, abstract = {The structure of a malonate-bound form of the glycerophosphodiesterase from Enterobacter aerogenes, {GpdQ}, has been refined at a resolution of 2.2 Å to a final R factor of 17.1\%. The structure was originally solved to 2.9 Å resolution using {SAD} phases from Zn2+ metal ions introduced into the active site of the apoenzyme [Jackson et al. (2007), J. Mol. Biol. 367, 1047–1062]. However, the 2.9 Å resolution was insufficient to discern significant details of the architecture of the binuclear metal centre that constitutes the active site. Furthermore, kinetic analysis revealed that the enzyme lost a significant amount of activity in the presence of Zn2+, suggesting that it is unlikely to be a catalytically relevant metal ion. In this communication, a higher resolution structure of {GpdQ} is presented in which malonate is visibly coordinated in the active site and analysis of the native metal-ion preference is presented using atomic absorption spectroscopy and anomalous scattering. Catalytic implications of the structure and its Fe2+ metal-ion preference are discussed.}, pages = {681--685}, number = {8}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Jackson, C. J. and Hadler, K. S. and Carr, P. D. and Oakley, A. J. and Yip, S. and Schenk, G. and Ollis, D. L.}, urldate = {2017-05-15}, date = {2008-08-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\D2PET828\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\D8W8B8KR\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\D2PET828\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\DW3FV222\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZZUTHAJS\\Jackson et al. - 2008 - Malonate-bound structure of the glycerophosphodies:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\IFTC9ZDS\\Jackson et al. - 2008 - Malonate-bound structure of the glycerophosphodies.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZZUTHAJS\\Jackson et al. - 2008 - Malonate-bound structure of the glycerophosphodies:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TVC9JA6U\\Jackson et al. - 2008 - Malonate-bound structure of the glycerophosphodies.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZZUTHAJS\\Jackson et al. - 2008 - Malonate-bound structure of the glycerophosphodies.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\D2PET828\\paper.html:text/html} } @article{jackson_cloning_2008, title = {Cloning, expression, purification, crystallization and preliminary X-ray studies of a pyridoxine 5′-­phosphate oxidase from Mycobacterium smegmatis}, volume = {64}, rights = {Copyright (c) 2008 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?hc5054}, doi = {10.1107/S1744309108011512}, abstract = {Pyridoxine 5′-phosphate oxidases ({PNPOxs}) are known to catalyse the terminal step in pyridoxal 5′-phosphate biosynthesis in a flavin mononucleotide-dependent manner in humans and Escherichia coli. Recent reports of a putative {PNPOx} from Mycobacterium tuberculosis, Rv1155, suggest that the cofactor or catalytic mechanism may differ in Mycobacterium species. To investigate this, a putative {PNPOx} from M. smegmatis, Msmeg\_3380, has been cloned. This enzyme has been recombinantly expressed in E. coli and purified to homo­geneity. Good-quality crystals of selenomethionine-substituted Msmeg\_3380 were obtained by the hanging-drop vapour-diffusion technique and diffracted to 1.2 Å using synchrotron radiation.}, pages = {435--437}, number = {5}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Jackson, C. J. and Taylor, M. C. and Tattersall, D. B. and French, N. G. and Carr, P. D. and Ollis, D. L. and Russell, R. J. and Oakeshott, J. G.}, urldate = {2017-05-15}, date = {2008-05-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\73S67K4W\\Jackson et al. - 2008 - Cloning, expression, purification, crystallization:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\H62R8FQ5\\Jackson et al. - 2008 - Cloning, expression, purification, crystallization.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\73S67K4W\\Jackson et al. - 2008 - Cloning, expression, purification, crystallization:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FFEBBUU9\\Jackson et al. - 2008 - Cloning, expression, purification, crystallization.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AKSC28E5\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\66SEH46C\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AKSC28E5\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S7457IK5\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\73S67K4W\\Jackson et al. - 2008 - Cloning, expression, purification, crystallization.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\AKSC28E5\\paper.html:text/html} } @article{kvansakul_vaccinia_2008, title = {Vaccinia virus anti-apoptotic F1L is a novel Bcl-2-like domain-swapped dimer that binds a highly selective subset of {BH}3-containing death ligands}, volume = {15}, rights = {© 2008 Nature Publishing Group}, issn = {1350-9047}, url = {http://www.nature.com/cdd/journal/v15/n10/abs/cdd200883a.html}, doi = {10.1038/cdd.2008.83}, abstract = {Apoptosis is an important part of the host's defense mechanism for eliminating invading pathogens. Some viruses express proteins homologous in sequence and function to mammalian pro-survival Bcl-2 proteins. Anti-apoptotic F1L expressed by vaccinia virus is essential for survival of infected cells, but it bears no discernable sequence homology to proteins other than its immediate orthologues in related pox viruses. Here we report that the crystal structure of F1L reveals a Bcl-2-like fold with an unusual N-terminal extension. The protein forms a novel domain-swapped dimer in which the α1 helix is the exchanged domain. Binding studies reveal an atypical {BH}3-binding profile, with sub-micromolar affinity only for the {BH}3 peptide of pro-apoptotic Bim and low micromolar affinity for the {BH}3 peptides of Bak and Bax. This binding interaction is sensitive to F1L mutations within the predicted canonical {BH}3-binding groove, suggesting parallels between how vaccinia virus F1L and myxoma virus M11L bind {BH}3 domains. Structural comparison of F1L with other Bcl-2 family members reveals a novel sequence signature that redefines the {BH}4 domain as a structural motif present in both pro- and anti-apoptotic Bcl-2 members, including viral Bcl-2-like proteins.}, pages = {1564--1571}, number = {10}, journaltitle = {Cell Death \& Differentiation}, shortjournal = {Cell Death Differ}, author = {Kvansakul, M. and Yang, H. and Fairlie, W. D. and Czabotar, P. E. and Fischer, S. F. and Perugini, M. A. and Huang, D. C. S. and Colman, P. M.}, urldate = {2017-05-15}, date = {2008-06-13}, langid = {english}, keywords = {apoptosis, apoptosis, Bcl-2, Bcl-2, {BH}4 domain, {BH}4 domain, vaccinia virus, vaccinia virus}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8B7GXFG7\\Kvansakul et al. - 2008 - Vaccinia virus anti-apoptotic F1L is a novel Bcl-2:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\QBJAURT6\\Kvansakul et al. - 2008 - Vaccinia virus anti-apoptotic F1L is a novel Bcl-2.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8B7GXFG7\\Kvansakul et al. - 2008 - Vaccinia virus anti-apoptotic F1L is a novel Bcl-2:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C76HMWQD\\Kvansakul et al. - 2008 - Vaccinia virus anti-apoptotic F1L is a novel Bcl-2.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S39REUG4\\cdd200883a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JDJSRINH\\cdd200883a.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S39REUG4\\cdd200883a:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\PJCPVN6R\\cdd200883a.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\8B7GXFG7\\Kvansakul et al. - 2008 - Vaccinia virus anti-apoptotic F1L is a novel Bcl-2.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\S39REUG4\\cdd200883a.html:text/html} } @article{miles_amyloid-anti-amyloid-_2008, title = {Amyloid-β–Anti-Amyloid-β Complex Structure Reveals an Extended Conformation in the Immunodominant B-Cell Epitope}, volume = {377}, issn = {0022-2836}, url = {http://www.sciencedirect.com/science/article/pii/S002228360701649X}, doi = {10.1016/j.jmb.2007.12.036}, abstract = {Alzheimer's disease ({AD}) is the most common form of dementia. Amyloid-β (Aβ) peptide, generated by proteolytic cleavage of the amyloid precursor protein, is central to {AD} pathogenesis. Most pharmaceutical activity in {AD} research has focused on Aβ, its generation and clearance from the brain. In particular, there is much interest in immunotherapy approaches with a number of anti-Aβ antibodies in clinical trials. We have developed a monoclonal antibody, called {WO}2, which recognises the Aβ peptide. To this end, we have determined the three-dimensional structure, to near atomic resolution, of both the antibody and the complex with its antigen, the Aβ peptide. The structures reveal the molecular basis for {WO}2 recognition and binding of Aβ. The Aβ peptide adopts an extended, coil-like conformation across its major immunodominant B-cell epitope between residues 2 and 8. We have also studied the antibody-bound Aβ peptide in the presence of metals known to affect its aggregation state and show that {WO}2 inhibits these interactions. Thus, antibodies that target the N-terminal region of Aβ, such as {WO}2, hold promise for therapeutic development.}, pages = {181--192}, number = {1}, journaltitle = {Journal of Molecular Biology}, shortjournal = {Journal of Molecular Biology}, author = {Miles, Luke A. and Wun, Kwok S. and Crespi, Gabriela A. N. and Fodero-Tavoletti, Michelle T. and Galatis, Denise and Bagley, Christopher J. and Beyreuther, Konrad and Masters, Colin L. and Cappai, Roberto and {McKinstry}, William J. and Barnham, Kevin J. and Parker, Michael W.}, urldate = {2017-05-15}, date = {2008-03-14}, keywords = {Alzheimer's disease, Alzheimer's disease, amyloid-β antibody complex, amyloid-β antibody complex, anti-Aβ immunotherapy, anti-Aβ immunotherapy, X-ray crystallography, X-ray crystallography}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JQMEAM5F\\S002228360701649X:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\INVKN9H8\\S002228360701649X.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JQMEAM5F\\S002228360701649X:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\BAG72G93\\S002228360701649X.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TBK47P3J\\Miles et al. - 2008 - Amyloid-β–Anti-Amyloid-β Complex Structure Reveals:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\C5FWGFAP\\Miles et al. - 2008 - Amyloid-β–Anti-Amyloid-β Complex Structure Reveals.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TBK47P3J\\Miles et al. - 2008 - Amyloid-β–Anti-Amyloid-β Complex Structure Reveals:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T6NVGJNQ\\Miles et al. - 2008 - Amyloid-β–Anti-Amyloid-β Complex Structure Reveals.pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TBK47P3J\\Miles et al. - 2008 - Amyloid-β–Anti-Amyloid-β Complex Structure Reveals.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JQMEAM5F\\S002228360701649X.html:text/html} } @article{newman_phoenito_2008, title = {Phoenito experiments: combining the strengths of commercial crystallization automation}, volume = {64}, rights = {Copyright (c) 2008 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?bw5251}, doi = {10.1107/S1744309108029667}, shorttitle = {Phoenito experiments}, abstract = {The use of crystallization robots for initial screening in macromolecular crystallization is well established. This paper describes how four general optimization techniques, growth-rate modulation, fine screening, seeding and additive screening, have been adapted for automation in a medium-throughput crystallization service facility. The use of automation for more challenging optimization experiments is discussed, as is a novel way of using both the Mosquito and the Phoenix nano-dispensing robots during the setup of a single crystallization plate. This dual-dispenser technique plays to the strengths of both machines.}, pages = {991--996}, number = {11}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Newman, J. and Pham, T. M. and Peat, T. S.}, urldate = {2017-05-15}, date = {2008-11-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JMWHBNZV\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\6G432F2D\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JMWHBNZV\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\EX9ER89B\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MFRIP3AE\\Newman et al. - 2008 - Phoenito experiments combining the strengths of c:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JZ8AH2NM\\Newman et al. - 2008 - Phoenito experiments combining the strengths of c.pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MFRIP3AE\\Newman et al. - 2008 - Phoenito experiments combining the strengths of c:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\FDAG99NT\\Newman et al. - 2008 - Phoenito experiments combining the strengths of c.pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\MFRIP3AE\\Newman et al. - 2008 - Phoenito experiments combining the strengths of c.pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\JMWHBNZV\\paper.html:text/html} } @article{wun_crystallization_2008, title = {Crystallization and preliminary X-ray diffraction analysis of the Fab fragment of {WO}2, an antibody specific for the Aβ peptides associated with Alzheimer's disease}, volume = {64}, rights = {Copyright (c) 2008 International Union of Crystallography}, issn = {1744-3091}, url = {http://scripts.iucr.org/cgi-bin/paper?bw5237}, doi = {10.1107/S1744309108011718}, abstract = {The murine monoclonal antibody {WO}2 specifically binds the N-terminal region of the amyloid β peptide (Aβ) associated with Alzheimer's disease. This region of Aβ has been shown to be the immunodominant B-cell epitope of the peptide and hence is considered to be a basis for the development of immunotherapeutic strategies against this prevalent cause of dementia. Structural studies have been undertaken in order to characterize the molecular basis for antibody recognition of this important epitope. Here, details of the crystallization and X-ray analysis of the Fab fragment of the unliganded {WO}2 antibody in two crystal forms and of the complexes that it forms with the truncated Aβ peptides Aβ1–16 and Aβ1–28 are presented. These crystals were all obtained using the hanging-drop vapour-diffusion method at 295 K. Crystals of {WO}2 Fab were grown in polyethylene glycol solutions containing {ZnSO}4; they belonged to the orthorhombic space group P212121 and diffracted to 1.6 Å resolution. The complexes of {WO}2 Fab with either Aβ1–­16 or Aβ1–28 were cocrystallized from polyethylene glycol solutions. These two complex crystals grew in the same space group, P212121, and diffracted to 1.6 Å resolution. A second crystal form of {WO}2 Fab was grown in the presence of the sparingly soluble Aβ1–42 in {PEG} 550 {MME}. This second form belonged to space group P21 and diffracted to 1.9 Å resolution.}, pages = {438--441}, number = {5}, journaltitle = {Acta Crystallographica Section F: Structural Biology and Crystallization Communications}, shortjournal = {Acta Cryst F, Acta Cryst Sect F, Acta Crystallogr F, Acta Crystallogr Sect F, Acta Cryst F Struct Biol Cryst Commun, Acta Cryst Sect F Struct Biol Cryst Commun, Acta Crystallogr Sect F Struct Biol Cryst Commun}, author = {Wun, K. S. and Miles, L. A. and Crespi, G. a. N. and Wycherley, K. and Ascher, D. B. and Barnham, K. J. and Cappai, R. and Beyreuther, K. and Masters, C. L. and Parker, M. W. and {McKinstry}, W. J.}, urldate = {2017-05-15}, date = {2008-05-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\K37DAAZ5\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\VFR29ZU7\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\K37DAAZ5\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T39CDIBJ\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZFAWJ885\\Wun et al. - 2008 - Crystallization and preliminary X-ray diffraction:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\G2QN3NQ7\\Wun et al. - 2008 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZFAWJ885\\Wun et al. - 2008 - Crystallization and preliminary X-ray diffraction:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\TQJ2NTNP\\Wun et al. - 2008 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\ZFAWJ885\\Wun et al. - 2008 - Crystallization and preliminary X-ray diffraction .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\K37DAAZ5\\paper.html:text/html} } @article{peat_tapping_2005, title = {Tapping the Protein Data Bank for crystallization information}, volume = {61}, rights = {Copyright (c) 2005 International Union of Crystallography}, issn = {0907-4449}, url = {http://scripts.iucr.org/cgi-bin/paper?en5128}, doi = {10.1107/S0907444905033202}, abstract = {A database application has been developed for the collection of crystallographic information. This database (the {BDP}) has been populated with the information found in the Protein Data Bank ({PDB}). The tool has been used to store crystallization data parsed out of the {PDB} and these data may be used to extend the crystallization information found in the Biological Macromolecule Crystallization Database ({BMCD}) and could be used to refine crystallization methodology. A standard is proposed for describing a crystallization experiment that will ease future crystallization data collations and analyses.}, pages = {1662--1669}, number = {12}, journaltitle = {Acta Crystallographica Section D: Biological Crystallography}, shortjournal = {Acta Cryst D, Acta Cryst Sect D, Acta Crystallogr D, Acta Crystallogr Sect D, Acta Crystallogr D Biol Crystallogr, Acta Crystallogr Sect D Biol Crystallogr}, author = {Peat, T. S. and Christopher, J. A. and Newman, J.}, urldate = {2017-05-16}, date = {2005-12-01}, langid = {english}, file = {C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RR7S6QCX\\Peat et al. - 2005 - Tapping the Protein Data Bank for crystallization:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\D6KS4I4D\\Peat et al. - 2005 - Tapping the Protein Data Bank for crystallization .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RR7S6QCX\\Peat et al. - 2005 - Tapping the Protein Data Bank for crystallization:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\NECTWGMU\\Peat et al. - 2005 - Tapping the Protein Data Bank for crystallization .pdf:application/pdf;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XCSTDQ4E\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XHM2DIF3\\paper.html:text/html;C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XCSTDQ4E\\paper:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\T2A353VD\\paper.html:text/html;Full Text PDF:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\RR7S6QCX\\Peat et al. - 2005 - Tapping the Protein Data Bank for crystallization .pdf:application/pdf;Snapshot:C\:\\Users\\Mar815\\AppData\\Roaming\\Zotero\\Zotero\\Profiles\\58qhyszv.default\\zotero\\storage\\XCSTDQ4E\\paper.html:text/html} } @online{center_for_history_and_new_media_zotero_????-1, title = {Zotero Quick Start Guide}, url = {http://zotero.org/support/quick_start_guide}, author = {Center for History \{and\} New Media} }