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journalArticle
Adams
Luke A.
Sharma
Pooja
Mohanty
Biswaranjan
Ilyichova
Olga V.
Mulcair
Mark D.
Williams
Martin L.
Gleeson
Ellen C.
Totsika
Makrina
Doak
Bradley C.
Caria
Sofia
Rimmer
Kieran
Horne
James
Shouldice
Stephen R.
Vazirani
Mansha
Headey
Stephen J.
Plumb
Brent R.
Martin
Jennifer L.
Heras
Begoña
Simpson
Jamie S.
Scanlon
Martin J.
bakterielle Ansteckungskraft
bakterielle Ansteckungskraft
Ecdsba
Ecdsba
Fragment-basierte Wirkstoff-Forschung
Fragment-basierte Wirkstoff-Forschung
Medizinische Chemie
Medizinische Chemie
Wirkstoff-Design
Wirkstoff-Design
http://onlinelibrary.wiley.com/doi/10.1002/ange.201410341/abstract
2207-2212
February 9, 2015
2017-05-01 02:07:40
Wiley Online Library
en
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.
Application of Fragment-Based Screening to the Design of Inhibitors of Escherichia coli DsbA
127
7
Angewandte Chemie
ISSN 1521-3757
Angew. Chem.
DOI 10.1002/ange.201410341
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Liang
Yi-Lynn
Conn
Charlotte E.
Drummond
Calum J.
Darmanin
Connie
Bicontinuous cubic phase
Bicontinuous cubic phase
Butyrate receptor
Butyrate receptor
GPCR
GPCR
GPR41
GPR41
GPR43
GPR43
In meso crystallization
In meso crystallization
Monoolein
Monoolein
Phytantriol
Phytantriol
http://www.sciencedirect.com/science/article/pii/S0021979714008534
78-84
March 1, 2015
2017-05-01 02:10:46
ScienceDirect
The butyrate G-protein coupled receptors (GPCRs), GPR41 and GPR43, 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 GPR41 and GPR43 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 GPR43 for both lipids but was destabilized for GPR41 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.
Uptake of the butyrate receptors, GPR41 and GPR43, in lipidic bicontinuous cubic phases suitable for in meso crystallization
441
Journal of Colloid and Interface Science
ISSN 0021-9797
Journal of Colloid and Interface Science
DOI 10.1016/j.jcis.2014.11.006
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journalArticle
Xu
Yibin
Soo
Priscilla
Walker
Francesca
Zhang
Hui Hua
Redpath
Nicholas
Tan
Chin Wee
Nicola
Nicos A.
Adams
Timothy E.
Garrett
Thomas P.
Zhang
Jian-Guo
Burgess
Antony W.
EGFR inhibition
EGFR inhibition
leucine-rich repeat domain
leucine-rich repeat domain
LINGO-1
LINGO-1
stem cell marker
stem cell marker
http://www.sciencedirect.com/science/article/pii/S0022283615001734
1934-1948
May 22, 2015
2017-05-01 02:13:03
ScienceDirect
We have expressed and purified three soluble fragments of the human LRIG1-ECD (extracellular domain): the LRIG1-LRR (leucine-rich repeat) domain, the LRIG1-3Ig (immunoglobulin-like) domain, and the LRIG1-LRR-1Ig fragment using baculovirus vectors in insect cells. The two LRIG1 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 LRIG1-ECD using homology modelling based on the LINGO-1 structure. The LRIG1-LRR domain and the LRIG1-LRR-1Ig fragment are monomers in solution, whereas the LRIG1-3Ig domain appears to be dimeric. We could not detect any binding of the LRIG1 domains or the LRIG1-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 LRIG1-LRR-1Ig fragment binds weakly to colon cancer cells regardless of the presence of EGFRs. Similarly, neither the soluble LRIG1-LRR nor the LRIG1-3Ig domains nor the full-length LRIG1 co-expressed in HEK293 cells inhibited ligand-stimulated activation of cell-surface EGFR.
LRIG1 Extracellular Domain: Structure and Function Analysis
LRIG1 Extracellular Domain
427
10
Journal of Molecular Biology
ISSN 0022-2836
Journal of Molecular Biology
DOI 10.1016/j.jmb.2015.03.001
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journalArticle
Kershaw
Nadia J.
Church
Nicole L.
Griffin
Michael D. W.
Luo
Cindy S.
Adams
Timothy E.
Burgess
Antony W.
http://www.biochemj.org/content/468/1/159
© The Authors Journal compilation © 2015 Biochemical Society
159-166
2015/05/15
PMID: 25715738
2017-05-01 02:14:04
www.biochemj.org
en
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.
Notch ligand delta-like1: X-ray crystal structure and binding affinity
Notch ligand delta-like1
468
1
Biochemical Journal
ISSN 0264-6021, 1470-8728
DOI 10.1042/BJ20150010
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6
7
Cell Death & Disease
Cell Death Dis
DOI 10.1038/cddis.2015.141
Robin
A. Y.
Krishna Kumar
K.
Westphal
D.
Wardak
A. Z.
Thompson
G. V.
Dewson
G.
Colman
P. M.
Czabotar
P. E.
http://www.nature.com/cddis/journal/v6/n7/full/cddis2015141a.html
© 2015 Nature Publishing Group
e1809
July 9, 2015
2017-05-01 02:14:51
www.nature.com
en
The BH3-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 BimBH3 peptide bound to BaxΔC26 and structure-based mutagenesis studies. Similar to BidBH3, the BimBH3 peptide binds into the cognate surface groove of Bax using the conserved hydrophobic BH3 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 BidBH3 and BaxBH3 bound to BaxΔC21, the structure of the BimBH3 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 BH3 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.
Crystal structure of Bax bound to the BH3 peptide of Bim identifies important contacts for interaction
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Warden
Andrew C.
Williams
Michelle
Peat
Thomas S.
Seabrook
Shane A.
Newman
Janet
Dojchinov
Greg
Haritos
Victoria S.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4703901/
2015-12-21
PMID: 26687908
PMCID: PMC4703901
2017-05-01 02:15:21
PubMed Central
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.
Rational engineering of a mesohalophilic carbonic anhydrase to an extreme halotolerant biocatalyst
6
Nature Communications
ISSN 2041-1723
Nat Commun
DOI 10.1038/ncomms10278
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Baxter
Amy A.
Richter
Viviane
Lay
Fung T.
Poon
Ivan K. H.
Adda
Christopher G.
Veneer
Prem K.
Phan
Thanh Kha
Bleackley
Mark R.
Anderson
Marilyn A.
Kvansakul
Marc
Hulett
Mark D.
http://mcb.asm.org/content/35/11/1964
1964-1978
06/01/2015
PMID: 25802281
2017-05-01 02:15:50
mcb.asm.org
en
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 (NaD1) binds to a broad range of membrane phosphatidylinositol phosphates and forms an oligomeric complex with phosphatidylinositol (4,5)-bisphosphate (PIP2) that facilitates membrane lysis of both mammalian tumor and fungal cells. Here, we report that the tomato defensin TPP3 has a unique lipid binding profile that is specific for PIP2 with which it forms an oligomeric complex that is critical for cytolytic activity. Structural characterization of TPP3 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 PIP2 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 PIP2 binding and membrane permeabilization. This mechanism of innate defense may be conserved across defensins from different species.
The Tomato Defensin TPP3 Binds Phosphatidylinositol (4,5)-Bisphosphate via a Conserved Dimeric Cationic Grip Conformation To Mediate Cell Lysis
35
11
Molecular and Cellular Biology
ISSN 0270-7306, 1098-5549
Mol. Cell. Biol.
DOI 10.1128/MCB.00282-15
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468
2
Biochemical Journal
ISSN 0264-6021, 1470-8728
DOI 10.1042/BJ20150270
Mobbs
Jesse I.
Koay
Ann
Paolo
Alex Di
Bieri
Michael
Petrie
Emma J.
Gorman
Michael A.
Doughty
Larissa
Parker
Michael W.
Stapleton
David I.
Griffin
Michael D. W.
Gooley
Paul R.
http://www.biochemj.org/content/468/2/245
© The Authors Journal compilation © 2015 Biochemical Society
245-257
2015/06/01
2017-05-01 02:16:14
www.biochemj.org
en
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.
Determinants of oligosaccharide specificity of the carbohydrate-binding modules of AMP-activated protein kinase
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6
3
Cell Death & Disease
Cell Death Dis
DOI 10.1038/cddis.2015.52
Marshall
B.
Puthalakath
H.
Caria
S.
Chugh
S.
Doerflinger
M.
Colman
P. M.
Kvansakul
M.
http://www.nature.com/cddis/journal/v6/n3/abs/cddis201552a.html
© 2015 Nature Publishing Group
e1680
March 12, 2015
2017-05-01 02:17:08
www.nature.com
en
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 (BH3) domain. Instead, VAR F1L engages Bid BH3 as well as Bak and Bax BH3 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 BH3 domains reveal that variola F1L forms a domain-swapped Bcl-2 fold, which accommodates Bid and Bak BH3 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.
Variola virus F1L is a Bcl-2-like protein that unlike its vaccinia virus counterpart inhibits apoptosis independent of Bim
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Burton
D. R.
Caria
S.
Marshall
B.
Barry
M.
Kvansakul
M.
http://scripts.iucr.org/cgi-bin/paper?cb5081
Copyright (c) 2015 International Union of Crystallography
1593-1603
2015-08-01
2017-05-01 02:17:24
scripts.iucr.org
en
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, DPV022, only engages a highly restricted set of death-inducing Bcl-2 proteins, including Bim, Bax and Bak, with modest affinities. Structural analysis reveals that DPV022 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 DPV022 bound to Bim, Bak and Bax BH3 domains reveal that a partial obstruction of the binding groove is likely to be responsible for the modest affinities of DPV022 for BH3 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 DPV022 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 DPV022 that are dimeric and only bind a very limited number of death-inducing Bcl-2 proteins with modest affinities.
Structural basis of Deerpox virus-mediated inhibition of apoptosis
71
8
Acta Crystallographica Section D: Biological Crystallography
ISSN 1399-0047
Acta Cryst D
DOI 10.1107/S1399004715009402
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Ren
Bin
McKinstry
William J.
Pham
Tam
Newman
Janet
Layton
Daniel S.
Bean
Andrew G.
Chen
Zhenjun
Laurie
Karen L.
Borg
Kathryn
Barr
Ian G.
Adams
Timothy E.
Ferret
Ferret
Lymphocyte proliferation
Lymphocyte proliferation
mRNA induction
mRNA induction
Recombinant interleukin-2
Recombinant interleukin-2
X-ray structure
X-ray structure
http://www.sciencedirect.com/science/article/pii/S0145305X15300549
32-38
February 2016
2017-05-01 02:36:13
ScienceDirect
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.
Structural and functional characterisation of ferret interleukin-2
55
Developmental & Comparative Immunology
ISSN 0145-305X
Developmental & Comparative Immunology
DOI 10.1016/j.dci.2015.10.007
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14
48
Organic & Biomolecular Chemistry
DOI 10.1039/C6OB02299E
Angeli
A.
S. Peat
T.
Bartolucci
G.
Nocentini
A.
T. Supuran
C.
Carta
F.
http://pubs.rsc.org/en/Content/ArticleLanding/2016/OB/C6OB02299E
11353-11356
2016
2017-05-01 02:38:07
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Intramolecular oxidative deselenization of acylselenoureas: a facile synthesis of benzoxazole amides and carbonic anhydrase inhibitors
Intramolecular oxidative deselenization of acylselenoureas
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Christensen
Janni B.
Soares da Costa
T. P.
Faou
Pierre
Pearce
F. Grant
Panjikar
Santosh
Perugini
Matthew A.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5109050/
2016-11-15
PMID: 27845445
PMCID: PMC5109050
2017-05-01 02:38:29
PubMed Central
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.
Structure and Function of Cyanobacterial DHDPS and DHDPR
6
Scientific Reports
ISSN 2045-2322
Sci Rep
DOI 10.1038/srep37111
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6
Scientific Reports
ISSN 2045-2322
Sci Rep
DOI 10.1038/srep35198
Brewster
Jodi L.
McKellar
James L. O.
Finn
Thomas J.
Newman
Janet
Peat
Thomas S.
Gerth
Monica L.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062169/
2016-10-13
PMID: 27734909
PMCID: PMC5062169
2017-05-01 02:38:44
PubMed Central
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.
Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae
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Darmanin
Connie
Sarkar
Sampa
Castelli
Laura
Conn
Charlotte E.
http://dx.doi.org/10.1021/acs.cgd.6b00576
5014-5022
September 7, 2016
2017-05-01 02:40:35
ACS Publications
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.
Effect of Lipidic Cubic Phase Structure on Functionality of the Dopamine 2L Receptor: Implications for in Meso Crystallization
Effect of Lipidic Cubic Phase Structure on Functionality of the Dopamine 2L Receptor
16
9
Crystal Growth & Design
ISSN 1528-7483
Crystal Growth & Design
DOI 10.1021/acs.cgd.6b00576
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journalArticle
Hag
Leonie van 't
Knoblich
Konstantin
Seabrook
Shane A.
Kirby
Nigel M.
Mudie
Stephen T.
Lau
Deborah
Li
Xu
Gras
Sally L.
Mulet
Xavier
Call
Matthew E.
Call
Melissa J.
Drummond
Calum J.
Conn
Charlotte E.
http://rsta.royalsocietypublishing.org/content/374/2072/20150125
© 2016 The Author(s). http://royalsocietypublishing.org/licencePublished by the Royal Society. All rights reserved.
20150125
2016/07/28
PMID: 27298442
2017-05-01 02:41:00
rsta.royalsocietypublishing.org
en
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 DAP12-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’.
Exploring the in meso crystallization mechanism by characterizing the lipid mesophase microenvironment during the growth of single transmembrane α-helical peptide crystals
374
2072
Phil. Trans. R. Soc. A
ISSN 1364-503X, 1471-2962
Phil. Trans. R. Soc. A
DOI 10.1098/rsta.2015.0125
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journalArticle
Lee
Erinna F.
Grabow
Stephanie
Chappaz
Stephane
Dewson
Grant
Hockings
Colin
Kluck
Ruth M.
Debrincat
Marlyse A.
Gray
Daniel H.
Witkowski
Matthew T.
Evangelista
Marco
Pettikiriarachchi
Anne
Bouillet
Philippe
Lane
Rachael M.
Czabotar
Peter E.
Colman
Peter M.
Smith
Brian J.
Kile
Benjamin T.
Fairlie
W. Douglas
apoptosis
apoptosis
Bak
Bak
Bcl-2
Bcl-2
Bcl-xL
Bcl-xL
BH3
BH3
http://genesdev.cshlp.org/content/30/10/1240
1240-1250
05/15/2016
PMID: 27198225
2017-05-01 02:41:35
genesdev.cshlp.org
en
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, BakQ75L 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.
Physiological restraint of Bak by Bcl-xL is essential for cell survival
30
10
Genes & Development
ISSN 0890-9369, 1549-5477
Genes Dev.
DOI 10.1101/gad.279414.116
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Hunt
Cameron J.
Tanksale
Akshat
Haritos
Victoria S.
https://link.springer.com/article/10.1007/s00253-015-7044-9
1777-1787
2016/02/01
2017-05-01 02:42:14
link.springer.com
en
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 BL21 in two forms: with and without its putative signal peptide. The truncated form was found to have <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 >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.
Biochemical characterization of a halotolerant feruloyl esterase from Actinomyces spp.: refolding and activity following thermal deactivation
Biochemical characterization of a halotolerant feruloyl esterase from Actinomyces spp.
100
4
Applied Microbiology and Biotechnology
ISSN 0175-7598, 1432-0614
Appl Microbiol Biotechnol
DOI 10.1007/s00253-015-7044-9
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Dennis
Matthew L.
Pitcher
Noel P.
Lee
Michael D.
DeBono
Aaron J.
Wang
Zhong-Chang
Harjani
Jitendra R.
Rahmani
Raphaël
Cleary
Ben
Peat
Thomas S.
Baell
Jonathan B.
Swarbrick
James D.
http://dx.doi.org/10.1021/acs.jmedchem.6b00002
5248-5263
June 9, 2016
2017-05-01 02:43:16
ACS Publications
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.
Structural Basis for the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase from Staphylococcus aureus and Escherichia coli
59
11
Journal of Medicinal Chemistry
ISSN 0022-2623
J. Med. Chem.
DOI 10.1021/acs.jmedchem.6b00002
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Broughton
Sophie E.
Hercus
Timothy R.
Nero
Tracy L.
Dottore
Mara
McClure
Barbara J.
Dhagat
Urmi
Taing
Houng
Gorman
Michael A.
King-Scott
Jack
Lopez
Angel F.
Parker
Michael W.
http://www.sciencedirect.com/science/article/pii/S0969212616301241
1271-1281
August 2, 2016
2017-05-01 02:44:21
ScienceDirect
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.
Conformational Changes in the GM-CSF Receptor Suggest a Molecular Mechanism for Affinity Conversion and Receptor Signaling
24
8
Structure
ISSN 0969-2126
Structure
DOI 10.1016/j.str.2016.05.017
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59
11
Journal of Medicinal Chemistry
ISSN 0022-2623
J. Med. Chem.
DOI 10.1021/acs.jmedchem.6b00443
Mujumdar
Prashant
Teruya
Kanae
Tonissen
Kathryn F.
Vullo
Daniela
Supuran
Claudiu T.
Peat
Thomas S.
Poulsen
Sally-Ann
http://dx.doi.org/10.1021/acs.jmedchem.6b00443
5462-5470
June 9, 2016
2017-05-01 02:44:51
ACS Publications
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.
An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition, and Protein X-ray Structures of Psammaplin C
An Unusual Natural Product Primary Sulfonamide
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journalArticle
Anasir
Mohd Ishtiaq
Caria
Sofia
Skinner
Michael A.
Kvansakul
Marc
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
http://www.jbc.org/content/early/2017/04/14/jbc.M116.768879
jbc.M116.768879
2017-04-14
PMID: 28411240
2017-05-01 02:47:41
www.jbc.org
en
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 FPV039, which is a potent apoptosis inhibitor, but the precise molecular mechanism by which FPV039 inhibits apoptosis is unknown. To understand how fowlpox virus inhibits apoptosis we examined FPV039 using isothermal titration calorimetry, small-angle X-ray scattering and X-ray crystallography. Here, we report that the fowlpox virus pro-survival protein FPV039 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, FPV039 engaged with cellular pro-apoptotic Bcl-2 with affinities comparable to those of Bcl-2's endogenous cellular counterparts. Structural studies revealed that FPV039 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 FPV039 is a pan Bcl-2 protein inhibitor that can engage all host BH3-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 FPV039-mediated apoptosis inhibition.
Structural Basis of Apoptosis Inhibition by the Fowlpox Virus Protein FPV039
Journal of Biological Chemistry
ISSN 0021-9258, 1083-351X
J. Biol. Chem.
DOI 10.1074/jbc.M116.768879
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Peat
Thomas S.
Balotra
Sahil
Wilding
Matthew
Hartley
Carol J.
Newman
Janet
Scott
Colin
atrazine
atrazine
evolution
evolution
hydrolase
hydrolase
phylogenetic analysis
phylogenetic analysis
structure-activity relationships
structure-activity relationships
triazine
triazine
http://aem.asm.org/content/83/9/e03365-16
e03365-16
05/01/2017
PMID: 28235873
2017-05-01 02:47:57
aem.asm.org
en
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.
High-Resolution X-Ray Structures of Two Functionally Distinct Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes
83
9
Applied and Environmental Microbiology
ISSN 0099-2240, 1098-5336
Appl. Environ. Microbiol.
DOI 10.1128/AEM.03365-16
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Banjara
Suresh
Caria
Sofia
Dixon
Linda K.
Hinds
Mark G.
Kvansakul
Marc
http://jvi.asm.org/content/early/2017/01/04/JVI.02228-16
JVI.02228-16
2017-01-04
PMID: 28053104
2017-05-01 02:48:34
jvi.asm.org
en
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 BH3 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.
Structural insight into African Swine Fever virus A179L mediated inhibition of apoptosis
Journal of Virology
ISSN 0022-538X, 1098-5514
J. Virol.
DOI 10.1128/JVI.02228-16
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8
1
Cell Death & Disease
Cell Death Dis
DOI 10.1038/cddis.2016.469
Caria
Sofia
Hinds
Mark G.
Kvansakul
Marc
http://www.nature.com/cddis/journal/v8/n1/abs/cddis2016469a.html
© 2017 Nature Publishing Group
e2543
January 12, 2017
2017-05-01 02:48:57
www.nature.com
en
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 BHP2, 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 BHP2 from G. cydonium is able to bind the BH3 motif of a pro-apoptotic Bcl-2 protein, LB-Bak-2 of the sponge L. baicalensis. Furthermore, we determined the crystal structure of BHP2 bound to LB-Bak-2, which revealed that using a binding groove conserved across all pro-survival Bcl-2 proteins, BHP2 binds multi-motif Bax-like proteins through their BH3-binding regions. However, BHP2 discriminates against BH3-only bearing proteins by blocking access to a hydrophobic pocket that is critical for BH3 motif binding in pro-survival Bcl-2 proteins from higher organisms. This differential binding mode is reflected in a structure-based phylogenetic comparison of BHP2 with other Bcl-2 family members, which revealed that BHP2 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.
Structural insight into an evolutionarily ancient programmed cell death regulator – the crystal structure of marine sponge BHP2 bound to LB-Bak-2
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Rosa
Nicholas
Ristic
Marko
Seabrook
Shane A.
Lovell
David
Lucent
Del
Newman
Janet
http://dx.doi.org/10.1177/1087057115584059
898-905
August 1, 2015
2017-05-01 03:23:33
SAGE Journals
en
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.
Meltdown: A Tool to Help in the Interpretation of Thermal Melt Curves Acquired by Differential Scanning Fluorimetry
Meltdown
20
7
Journal of Biomolecular Screening
ISSN 1087-0571
J Biomol Screen
DOI 10.1177/1087057115584059
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journalArticle
Knoblich
Konstantin
Park
Soohyung
Lutfi
Mariam
van ’t Hag
Leonie
Conn
Charlotte E.
Seabrook
Shane A.
Newman
Janet
Czabotar
Peter E.
Im
Wonpil
Call
Matthew E.
Call
Melissa J.
http://www.sciencedirect.com/science/article/pii/S2211124715004623
1184-1192
May 26, 2015
2017-05-01 03:25:03
ScienceDirect
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 DAP12, 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.
Transmembrane Complexes of DAP12 Crystallized in Lipid Membranes Provide Insights into Control of Oligomerization in Immunoreceptor Assembly
11
8
Cell Reports
ISSN 2211-1247
Cell Reports
DOI 10.1016/j.celrep.2015.04.045
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81
2
Applied and Environmental Microbiology
ISSN 0099-2240, 1098-5336
Appl. Environ. Microbiol.
DOI 10.1128/AEM.02783-14
Newman
Janet
Cowieson
Nathan P.
French
Nigel G.
Campbell
Peter M.
Briggs
Lyndall J.
Warden
Andrew C.
Easton
Christopher J.
Peat
Thomas S.
Scott
Colin
http://aem.asm.org/content/81/2/470
470-480
01/15/2015
PMID: 25362066
2017-05-01 03:26:43
aem.asm.org
en
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.
X-Ray Structure of the Amidase Domain of AtzF, the Allophanate Hydrolase from the Cyanuric Acid-Mineralizing Multienzyme Complex
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journalArticle
Ristic
M.
Rosa
N.
Seabrook
S. A.
Newman
J.
http://scripts.iucr.org/cgi-bin/paper?rl5104
Copyright (c) 2015 International Union of Crystallography
1359-1364
2015-10-01
2017-05-01 03:27:26
scripts.iucr.org
en
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.
Formulation screening by differential scanning fluorimetry: how often does it work?
Formulation screening by differential scanning fluorimetry
71
10
Acta Crystallographica Section F: Structural Biology Communications
ISSN 2053-230X
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
DOI 10.1107/S2053230X15012662
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82
13
Applied and Environmental Microbiology
ISSN 0099-2240, 1098-5336
Appl. Environ. Microbiol.
DOI 10.1128/AEM.00665-16
Wilding
Matthew
Peat
Thomas S.
Newman
Janet
Scott
Colin
http://aem.asm.org/content/82/13/3846
3846-3856
07/01/2016
PMID: 27107110
2017-05-01 03:30:39
aem.asm.org
en
We previously isolated the transaminase KES23458 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 KES23458 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, KES23460. Unlike the transaminase, the dehydrogenase was shown to be quite selective, catalyzing the oxidation of malonic acid semialdehyde, formed from β-alanine transamination via KES23458. 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 KES23458 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.
A β-Alanine Catabolism Pathway Containing a Highly Promiscuous ω-Transaminase in the 12-Aminododecanate-Degrading Pseudomonas sp. Strain AAC
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9
2
Nanoscale
DOI 10.1039/C6NR07634C
Zabara
Alexandru
G. Meikle
Thomas
Newman
Janet
S. Peat
Thomas
E. Conn
Charlotte
J. Drummond
Calum
http://pubs.rsc.org/en/Content/ArticleLanding/2017/NR/C6NR07634C
754-763
2017
2017-05-01 03:31:36
pubs.rsc.org
en
The nanoscience behind the art of in-meso crystallization of membrane proteins
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70
3
Acta Crystallographica Section F: Structural Biology Communications
ISSN 2053-230X
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
DOI 10.1107/S2053230X13034705
Balotra
S.
Newman
J.
French
N. G.
Briggs
L. J.
Peat
T. S.
Scott
C.
http://scripts.iucr.org/cgi-bin/paper?no5038
http://creativecommons.org/licenses/by/2.0/uk
310-315
2014-03-01
2017-05-15 03:57:45
scripts.iucr.org
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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°.
Crystallization and preliminary X-ray diffraction analysis of the amidase domain of allophanate hydrolase from Pseudomonas sp. strain ADP
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70
2
Acta Crystallographica Section D: Biological Crystallography
ISSN 1399-0047
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
DOI 10.1107/S1399004713031052
Kenny
P. W.
Newman
J.
Peat
T. S.
http://scripts.iucr.org/cgi-bin/paper?kw5081
Copyright (c) 2014 International Union of Crystallography
565-571
2014-02-01
2017-05-15 03:58:19
scripts.iucr.org
en
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.
Nitrate in the active site of protein tyrosine phosphatase 1B is a putative mimetic of the transition state
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14
4
Crystal Growth & Design
ISSN 1528-7483
Crystal Growth & Design
DOI 10.1021/cg4018954
van ’t Hag
Leonie
Darmanin
Connie
Le
Tu C.
Mudie
Stephen
Conn
Charlotte E.
Drummond
Calum J.
http://dx.doi.org/10.1021/cg4018954
1771-1781
April 2, 2014
2017-05-15 04:09:22
ACS Publications
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.
In Meso Crystallization: Compatibility of Different Lipid Bicontinuous Cubic Mesophases with the Cubic Crystallization Screen in Aqueous Solution
In Meso Crystallization
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journalArticle
Peat
Thomas S.
Dolezal
Olan
Newman
Janet
Mobley
David
Deadman
John J.
https://link.springer.com/article/10.1007/s10822-014-9721-7
347-362
2014/04/01
2017-05-15 04:10:25
link.springer.com
en
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 SAMPL4 challenge. This paper describes the methods used to obtain these data and the chemistry involved.
Interrogating HIV integrase for compounds that bind- a SAMPL challenge
28
4
Journal of Computer-Aided Molecular Design
ISSN 0920-654X, 1573-4951
J Comput Aided Mol Des
DOI 10.1007/s10822-014-9721-7
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Atkinson
Sarah C.
Hor
Lilian
Dogovski
Con
Dobson
Renwick C. J.
Perugini
Matthew A.
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
http://onlinelibrary.wiley.com/doi/10.1002/prot.24539/abstract
1869-1883
September 1, 2014
2017-05-15 04:11:14
Wiley Online Library
en
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 dapA7 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.
Identification of the bona fide DHDPS from a common plant pathogen
82
9
Proteins: Structure, Function, and Bioinformatics
ISSN 1097-0134
Proteins
DOI 10.1002/prot.24539
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8
Journal of Medicinal Chemistry
ISSN 0022-2623
J. Med. Chem.
DOI 10.1021/jm500255y
Moeker
Janina
Peat
Thomas S.
Bornaghi
Laurent F.
Vullo
Daniela
Supuran
Claudiu T.
Poulsen
Sally-Ann
http://dx.doi.org/10.1021/jm500255y
3522-3531
April 24, 2014
2017-05-15 04:11:31
ACS Publications
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 > 50 000 nM) compared to saccharin. This >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.
Cyclic Secondary Sulfonamides: Unusually Good Inhibitors of Cancer-Related Carbonic Anhydrase Enzymes
Cyclic Secondary Sulfonamides
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70
5
Acta Crystallographica Section F: Structural Biology Communications
ISSN 2053-230X
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
DOI 10.1107/S2053230X14007250
North
R. A.
Seizova
S.
Stampfli
A.
Kessans
S. A.
Suzuki
H.
Griffin
M. D. W.
Kvansakul
M.
Dobson
R. C. J.
http://scripts.iucr.org/cgi-bin/paper?no5047
Copyright (c) 2014 International Union of Crystallography
643-649
2014-05-01
2017-05-15 04:11:44
scripts.iucr.org
en
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 BL21 (DE3) 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.
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of N-acetylmannosamine kinase from methicillin-resistant Staphylococcus aureus
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70
5
Acta Crystallographica Section F: Structural Biology Communications
ISSN 2053-230X
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
DOI 10.1107/S2053230X14007699
Oliver
M. R.
Crowther
J. M.
Leeman
M. M.
Kessans
S. A.
North
R. A.
Donovan
K. A.
Griffin
M. D. W.
Suzuki
H.
Hudson
A. O.
Kasanmascheff
M.
Dobson
R. C. J.
http://scripts.iucr.org/cgi-bin/paper?hc5170
Copyright (c) 2014 International Union of Crystallography
663-668
2014-05-01
2017-05-15 04:16:06
scripts.iucr.org
en
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 DapDc1) and At5g11880 (encoding DapDc2) were cloned from genomic DNA and the recombinant proteins were expressed and purified from Escherichia coli Rosetta (DE3) cells. The crystals of DapDc1 and DapDc2 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.
The purification, crystallization and preliminary X-ray diffraction analysis of two isoforms of meso-diaminopimelate decarboxylase from Arabidopsis thaliana
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457
3
Biochemical Journal
ISSN 0264-6021, 1470-8728
DOI 10.1042/BJ20131270
Murphy
James M.
Lucet
Isabelle S.
Hildebrand
Joanne M.
Tanzer
Maria C.
Young
Samuel N.
Sharma
Pooja
Lessene
Guillaume
Alexander
Warren S.
Babon
Jeffrey J.
Silke
John
Czabotar
Peter E.
http://www.biochemj.org/content/457/3/369
© The Authors Journal compilation © 2014 Biochemical Society
369-377
2014/02/01
PMID: 24219132
2017-05-15 04:16:26
www.biochemj.org
en
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.
Insights into the evolution of divergent nucleotide-binding mechanisms among pseudokinases revealed by crystal structures of human and mouse MLKL
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Richter
Viviane
Palmer
Catherine S.
Osellame
Laura D.
Singh
Abeer P.
Elgass
Kirstin
Stroud
David A.
Sesaki
Hiromi
Kvansakul
Marc
Ryan
Michael T.
http://jcb.rupress.org/content/204/4/477
© 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/).
477-486
2014/02/17
PMID: 24515348
2017-05-15 04:16:42
jcb.rupress.org
en
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, MiD49, and MiD51. MiD49/51 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 MiD51, which adopts a nucleotidyltransferase fold. Although MiD51 lacks catalytic residues for transferase activity, it specifically binds guanosine diphosphate and adenosine diphosphate. MiD51 mutants unable to bind nucleotides were still able to recruit Drp1. Disruption of an additional region in MiD51 that is not part of the nucleotidyltransferase fold blocked Drp1 recruitment and assembly of MiD51 into foci. MiD51 foci are also dependent on the presence of Drp1, and after scission they are distributed to daughter organelles, supporting the involvement of MiD51 in the fission apparatus.
Structural and functional analysis of MiD51, a dynamin receptor required for mitochondrial fission
204
4
J Cell Biol
ISSN 0021-9525, 1540-8140
J Cell Biol
DOI 10.1083/jcb.201311014
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70
7
Acta Crystallographica Section F: Structural Biology Communications
ISSN 2053-230X
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
DOI 10.1107/S2053230X1401262X
Luft
J. R.
Newman
J.
Snell
E. H.
http://scripts.iucr.org/cgi-bin/paper?en5551
http://creativecommons.org/licenses/by/2.0/uk
835-853
2014-07-01
2017-05-15 04:16:58
scripts.iucr.org
en
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.
Crystallization screening: the influence of history on current practice
Crystallization screening
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7
Acta Crystallographica Section D: Biological Crystallography
ISSN 1399-0047
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
DOI 10.1107/S1399004714009626
Ren
B.
Peat
T. S.
Streltsov
V. A.
Pollard
M.
Fernley
R.
Grusovin
J.
Seabrook
S.
Pilling
P.
Phan
T.
Lu
L.
Lovrecz
G. O.
Graham
L. D.
Hill
R. J.
http://scripts.iucr.org/cgi-bin/paper?mn5062
Copyright (c) 2014 International Union of Crystallography
1954-1964
2014-07-01
2017-05-15 04:17:08
scripts.iucr.org
en
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.
Unprecedented conformational flexibility revealed in the ligand-binding domains of the Bovicola ovis ecdysone receptor (EcR) and ultraspiracle (USP) subunits
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Brouwer
Jason M.
Westphal
Dana
Dewson
Grant
Robin
Adeline Y.
Uren
Rachel T.
Bartolo
Ray
Thompson
Geoff V.
Colman
Peter M.
Kluck
Ruth M.
Czabotar
Peter E.
http://www.sciencedirect.com/science/article/pii/S1097276514006091
938-946
September 18, 2014
2017-05-15 04:17:18
ScienceDirect
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 BH3-only proteins interact directly with Bak and Bax. Recently published crystal structures reveal that Bax separates into core and latch domains in response to BH3 peptides. The distinguishing characteristics of BH3 peptides capable of directly activating Bax were also elucidated. Here we identify specific BH3 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 BH3 peptides.
Bak Core and Latch Domains Separate during Activation, and Freed Core Domains Form Symmetric Homodimers
55
6
Molecular Cell
ISSN 1097-2765
Molecular Cell
DOI 10.1016/j.molcel.2014.07.016
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8
Acta Crystallographica Section F: Structural Biology Communications
ISSN 2053-230X
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
DOI 10.1107/S2053230X14016574
Calero
G.
Cohen
A. E.
Luft
J. R.
Newman
J.
Snell
E. H.
http://scripts.iucr.org/cgi-bin/paper?en5553
http://creativecommons.org/licenses/by/2.0/uk
993-1008
2014-08-01
2017-05-15 04:17:26
scripts.iucr.org
en
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.
Identifying, studying and making good use of macromolecular crystals
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Chen
Pengyu
Seabrook
Shane A.
Epa
V. Chandana
Kurabayashi
Katsuo
Barnard
Amanda S.
Winkler
David A.
Kirby
Jason K.
Ke
Pu Chun
http://dx.doi.org/10.1021/jp506135m
22069-22078
September 25, 2014
2017-05-15 04:17:40
ACS Publications
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.
Contrasting Effects of Nanoparticle Binding on Protein Denaturation
118
38
The Journal of Physical Chemistry C
ISSN 1932-7447
J. Phys. Chem. C
DOI 10.1021/jp506135m
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80
13
Applied and Environmental Microbiology
ISSN 0099-2240, 1098-5336
Appl. Environ. Microbiol.
DOI 10.1128/AEM.00916-14
Jackson
Colin J.
Coppin
Christopher W.
Carr
Paul D.
Aleksandrov
Alexey
Wilding
Matthew
Sugrue
Elena
Ubels
Joanna
Paks
Michael
Newman
Janet
Peat
Thomas S.
Russell
Robyn J.
Field
Martin
Weik
Martin
Oakeshott
John G.
Scott
Colin
http://aem.asm.org/content/80/13/4003
4003-4011
07/01/2014
PMID: 24771025
2017-05-15 04:17:51
aem.asm.org
en
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.
300-Fold Increase in Production of the Zn2+-Dependent Dechlorinase TrzN in Soluble Form via Apoenzyme Stabilization
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Mele
K.
Li
R.
Fazio
V. J.
Newman
J.
http://scripts.iucr.org/cgi-bin/paper?aj5232
Copyright (c) 2014 International Union of Crystallography
1097-1106
2014-06-01
2017-05-15 04:18:01
scripts.iucr.org
en
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.
Quantifying the quality of the experiments used to grow protein crystals: the iQC suite
Quantifying the quality of the experiments used to grow protein crystals
47
3
Journal of Applied Crystallography
ISSN 1600-5767
J Appl Cryst, J Appl Crystallogr
DOI 10.1107/S1600576714009728
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Newman
Janet
Peat
Thomas S.
Savage
G. Paul
http://www.publish.csiro.au/CH/CH14199
1813-1817
2014/12/24
2017-05-15 04:18:11
www.publish.csiro.au
en
Australian Journal of Chemistry - an International Journal for Chemical Science publishes research papers from all fields of chemical science.
What’s in a Name? Moving Towards a Limited Vocabulary for Macromolecular Crystallisation
What’s in a Name?
67
12
Australian Journal of Chemistry
ISSN 1445-0038
Aust. J. Chem.
DOI 10.1071/CH14199
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289
52
Journal of Biological Chemistry
ISSN 0021-9258, 1083-351X
J. Biol. Chem.
DOI 10.1074/jbc.M114.610758
Lee
Erinna F.
Dewson
Grant
Evangelista
Marco
Pettikiriarachchi
Anne
Gold
Grace J.
Zhu
Haoran
Colman
Peter M.
Fairlie
W. Douglas
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
http://www.jbc.org/content/289/52/36001
36001-36017
12/26/2014
PMID: 25371206
2017-05-15 04:18:19
www.jbc.org
en
Bcl-2 homology 3 (BH3) 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 BH3 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 “BH3-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 BH3 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.
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 (BH3) Domains
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journalArticle
70
10
Acta Crystallographica Section F: Structural Biology Communications
ISSN 2053-230X
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
DOI 10.1107/S2053230X1401841X
Fazio
V. J.
Peat
T. S.
Newman
J.
http://scripts.iucr.org/cgi-bin/paper?en5555
Copyright (c) 2014 International Union of Crystallography
1303-1311
2014-10-01
2017-05-15 04:18:50
scripts.iucr.org
en
The REMARK280 field of the Protein Data Bank is the richest open source of successful crystallization information. The REMARK280 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.
A drunken search in crystallization space
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57
22
Journal of Medicinal Chemistry
ISSN 0022-2623
J. Med. Chem.
DOI 10.1021/jm501417f
Dennis
Matthew L.
Chhabra
Sandeep
Wang
Zhong-Chang
Debono
Aaron
Dolezal
Olan
Newman
Janet
Pitcher
Noel P.
Rahmani
Raphael
Cleary
Ben
Barlow
Nicholas
Hattarki
Meghan
Graham
Bim
Peat
Thomas S.
Baell
Jonathan B.
Swarbrick
James D.
http://dx.doi.org/10.1021/jm501417f
9612-9626
November 26, 2014
2017-05-15 04:19:02
ACS Publications
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 >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.
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
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bookSection
Methods in Molecular Biology
1261
ISBN 978-1-4939-2229-1
Structural Proteomics
Springer New York
Owens
Raymond J.
Fazio
VincentJ.
Peat
ThomasS.
Newman
Janet
Crystallization screening
Crystallization screening
Differential scanning fluorimetry
Differential scanning fluorimetry
Proteins
Proteins
http://dx.doi.org/10.1007/978-1-4939-2230-7_8
©2015 Springer Science+Business Media New York
141-156
January 1, 2015
DOI: 10.1007/978-1-4939-2230-7_8
2017-05-15 04:20:00
Springer Link
English
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.
Crystallization: Digging into the Past to Learn Lessons for the Future
Crystallization
The following values have no corresponding Zotero field:<br/>periodical: Structural Proteomics
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journalArticle
Ivask
Angela
Voelcker
Nicolas H.
Seabrook
Shane A.
Hor
Maryam
Kirby
Jason K.
Fenech
Michael
Davis
Thomas P.
Ke
Pu Chun
http://dx.doi.org/10.1021/acs.chemrestox.5b00052
1023-1035
May 18, 2015
2017-05-15 04:20:10
ACS Publications
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 (IC50) 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.
DNA Melting and Genotoxicity Induced by Silver Nanoparticles and Graphene
28
5
Chemical Research in Toxicology
ISSN 0893-228X
Chem. Res. Toxicol.
DOI 10.1021/acs.chemrestox.5b00052
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journalArticle
6
Nature Communications
ISSN 2041-1723
DOI 10.1038/ncomms7253
Srivastava
Monika
Duan
Guowen
Kershaw
Nadia J.
Athanasopoulos
Vicki
Yeo
Janet H. C.
Ose
Toyoyuki
Hu
Desheng
Brown
Simon H. J.
Jergic
Slobodan
Patel
Hardip R.
Pratama
Alvin
Richards
Sashika
Verma
Anil
Jones
E. Yvonne
Heissmeyer
Vigo
Preiss
Thomas
Dixon
Nicholas E.
Chong
Mark M. W.
Babon
Jeffrey J.
Vinuesa
Carola G.
http://www.nature.com/ncomms/2015/150220/ncomms7253/full/ncomms7253.html
© 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
6253
2015-02-20
2017-05-15 04:20:32
www.nature.com
en
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.
Roquin binds microRNA-146a and Argonaute2 to regulate microRNA homeostasis
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3
Journal of Medicinal Chemistry
ISSN 0022-2623
J. Med. Chem.
DOI 10.1021/jm501798g
Tanpure
Rajendra P.
Ren
Bin
Peat
Thomas S.
Bornaghi
Laurent F.
Vullo
Daniela
Supuran
Claudiu T.
Poulsen
Sally-Ann
http://dx.doi.org/10.1021/jm501798g
1494-1501
February 12, 2015
2017-05-15 04:20:58
ACS Publications
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.
Carbonic Anhydrase Inhibitors with Dual-Tail Moieties To Match the Hydrophobic and Hydrophilic Halves of the Carbonic Anhydrase Active Site
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journalArticle
17
3
Physical Chemistry Chemical Physics
DOI 10.1039/C4CP04996A
Wang
Bo
A. Seabrook
Shane
Nedumpully-Govindan
Praveen
Chen
Pengyu
Yin
Hong
Waddington
Lynne
Chandana Epa
V.
A. Winkler
David
K. Kirby
Jason
Ding
Feng
Chun Ke
Pu
http://pubs.rsc.org/en/Content/ArticleLanding/2015/CP/C4CP04996A
1728-1739
2015
2017-05-15 04:21:07
pubs.rsc.org
en
Thermostability and reversibility of silver nanoparticle–protein binding
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23
7
Structure
ISSN 0969-2126
Structure
DOI 10.1016/j.str.2015.04.016
Menting
John G.
Lawrence
Callum F.
Kong
Geoffrey K. -W.
Margetts
Mai B.
Ward
Colin W.
Lawrence
Michael C.
http://www.sciencedirect.com/science/article/pii/S0969212615001744
1271-1282
July 7, 2015
2017-05-15 04:21:45
ScienceDirect
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 (αCT) 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 αCT peptide bound to an IR L1 plus cysteine-rich domain construct (IR310.T). These structures, refined at 3.0-Å resolution, prove congruent to respective existing structures of insulin-complexed IR310.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.
Structural Congruency of Ligand Binding to the Insulin and Insulin/Type 1 Insulin-like Growth Factor Hybrid Receptors
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13
3
Crystal Growth & Design
ISSN 1528-7483
Crystal Growth & Design
DOI 10.1021/cg301755a
Chan
Michelle
Fazio
Vincent J.
Newman
Janet
http://dx.doi.org/10.1021/cg301755a
1290-1294
March 6, 2013
2017-05-15 04:25:46
ACS Publications
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.
Using Graphs to Represent Crystallization Conditions
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journalArticle
Chhabra
Sandeep
Barlow
Nicholas
Dolezal
Olan
Hattarki
Meghan K.
Newman
Janet
Peat
Thomas S.
Graham
Bim
Swarbrick
James D.
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
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0059535
e59535
02-Apr-2013
2017-05-15 04:25:57
PLoS Journals
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) (IC50 ∼ 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.
Exploring the Chemical Space around 8-Mercaptoguanine as a Route to New Inhibitors of the Folate Biosynthesis Enzyme HPPK
8
4
PLOS ONE
ISSN 1932-6203
PLOS ONE
DOI 10.1371/journal.pone.0059535
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2017-05-15 04:26:00
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Czabotar
Peter E.
Westphal
Dana
Dewson
Grant
Ma
Stephen
Hockings
Colin
Fairlie
W. Douglas
Lee
Erinna F.
Yao
Shenggen
Robin
Adeline Y.
Smith
Brian J.
Huang
David C. S.
Kluck
Ruth M.
Adams
Jerry M.
Colman
Peter M.
http://www.sciencedirect.com/science/article/pii/S009286741201553X
519-531
January 31, 2013
2017-05-15 04:27:52
ScienceDirect
Summary
In stressed cells, apoptosis ensues when Bcl-2 family members Bax or Bak oligomerize and permeabilize the mitochondrial outer membrane. Certain BH3-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 BaxΔC21 treated with detergents and BH3 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 BH3 domains and reveal how they can activate Bax via its groove by favoring release of its BH3 domain. Furthermore, Bax helices α2–α5 alone adopted a symmetric homodimer structure, supporting the proposal that two Bax molecules insert their BH3 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.
Bax Crystal Structures Reveal How BH3 Domains Activate Bax and Nucleate Its Oligomerization to Induce Apoptosis
152
3
Cell
ISSN 0092-8674
Cell
DOI 10.1016/j.cell.2012.12.031
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456
2
Biochemical Journal
ISSN 0264-6021, 1470-8728
DOI 10.1042/BJ20121425
D’Cruz
Akshay A.
Kershaw
Nadia J.
Chiang
Jessica J.
Wang
May K.
Nicola
Nicos A.
Babon
Jeffrey J.
Gack
Michaela U.
Nicholson
Sandra E.
http://www.biochemj.org/content/456/2/231
© The Authors Journal compilation © 2013 Biochemical Society
231-240
2013/12/01
PMID: 24015671
2017-05-15 04:28:03
www.biochemj.org
en
TRIM (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. TRIM25 [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 TRIM25 at its N-terminal CARDs (caspase recruitment domains), leading to type I interferon production. The interaction with RIG-I is dependent on the TRIM25 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 TRIM25 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 TRIM25 B30.2 domain as being critical for binding to the RIG-I CARDs.
Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain: a key component of antiviral signalling
Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain
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Desbois
S.
Seabrook
S. A.
Newman
J.
http://scripts.iucr.org/cgi-bin/paper?dp5039
http://creativecommons.org/licenses/by/2.0/uk
201-208
2013-02-01
2017-05-15 04:28:20
scripts.iucr.org
en
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.
Some practical guidelines for UV imaging in the protein crystallization laboratory
69
2
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309112048634
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66
12
Australian Journal of Chemistry
ISSN 1445-0038
Aust. J. Chem.
DOI 10.1071/CH13302
Dolezal
Olan
Doughty
Larissa
Hattarki
Meghan K.
Fazio
Vincent J.
Caradoc-Davies
Tom T.
Newman
Janet
Peat
Thomas S.
http://www.publish.csiro.au/ch/ch13302
1507-1517
2014/01/10
2017-05-15 04:28:29
www.publish.csiro.au
en
Australian Journal of Chemistry - an International Journal for Chemical Science publishes research papers from all fields of chemical science.
Fragment Screening for the Modelling Community: SPR, ITC, and Crystallography
Fragment Screening for the Modelling Community
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journalArticle
Kershaw
Nadia J.
Murphy
James M.
Liau
Nicholas P. D.
Varghese
Leila N.
Laktyushin
Artem
Whitlock
Eden L.
Lucet
Isabelle S.
Nicola
Nicos A.
Babon
Jeffrey J.
Cell signalling
Cell signalling
Cytokines
Cytokines
Structural biology
Structural biology
X-ray crystallography
X-ray crystallography
http://www.nature.com/nsmb/journal/v20/n4/abs/nsmb.2519.html
© 2013 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.
469-476
April 2013
2017-05-15 04:28:39
www.nature.com
en
The inhibitory protein SOCS3 plays a key part in the immune and hematopoietic systems by regulating signaling induced by specific cytokines. SOCS3 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 SOCS3, JAK2 (kinase domain) and a fragment of the interleukin-6 receptor β-chain. The structure shows that SOCS3 binds JAK2 and receptor simultaneously, using two opposing surfaces. While the phosphotyrosine-binding groove on the SOCS3 SH2 domain is occupied by receptor, JAK2 binds in a phosphoindependent manner to a noncanonical surface. The kinase-inhibitory region of SOCS3 occludes the substrate-binding groove on JAK2, and biochemical studies show that it blocks substrate association. These studies reveal that SOCS3 targets specific JAK–cytokine receptor pairs and explains the mechanism and specificity of SOCS action.
View full text
SOCS3 binds specific receptor–JAK complexes to control cytokine signaling by direct kinase inhibition
20
4
Nature Structural & Molecular Biology
ISSN 1545-9993
Nat Struct Mol Biol
DOI 10.1038/nsmb.2519
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13
3
Crystal Growth & Design
ISSN 1528-7483
Crystal Growth & Design
DOI 10.1021/cg301730z
Le
Tu C.
Conn
Charlotte E.
Burden
Frank R.
Winkler
David A.
http://dx.doi.org/10.1021/cg301730z
1267-1276
March 6, 2013
2017-05-15 04:28:55
ACS Publications
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.
Computational Modeling and Prediction of the Complex Time-Dependent Phase Behavior of Lyotropic Liquid Crystals under in Meso Crystallization Conditions
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13
7
Crystal Growth & Design
ISSN 1528-7483
Crystal Growth & Design
DOI 10.1021/cg400513y
Le
Tu C.
Conn
Charlotte E.
Burden
Frank R.
Winkler
David A.
http://dx.doi.org/10.1021/cg400513y
3126-3137
July 3, 2013
2017-05-15 04:29:09
ACS Publications
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.
Predicting the Effect of Lipid Structure on Mesophase Formation during in Meso Crystallization
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journalArticle
Menting
John G.
Whittaker
Jonathan
Margetts
Mai B.
Whittaker
Linda J.
Kong
Geoffrey K.-W.
Smith
Brian J.
Watson
Christopher J.
Žáková
Lenka
Kletvíková
Emília
Jiráček
Jiří
Chan
Shu Jin
Steiner
Donald F.
Dodson
Guy G.
Brzozowski
Andrzej M.
Weiss
Michael A.
Ward
Colin W.
Lawrence
Michael C.
Diabetes
Diabetes
X-ray crystallography
X-ray crystallography
http://www.nature.com/nature/journal/v493/n7431/abs/nature11781.html
© 2013 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.
241-245
January 10, 2013
2017-05-15 04:29:22
www.nature.com
en
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 (IGF1R). 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 (αCT) 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 αCT 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 IGF1R systems relevant to the design of therapeutic insulin analogues.
How insulin engages its primary binding site on the insulin receptor
493
7431
Nature
ISSN 0028-0836
Nature
DOI 10.1038/nature11781
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Mulet
Xavier
Conn
Charlotte E.
Fong
Celesta
Kennedy
Danielle F.
Moghaddam
Minoo J.
Drummond
Calum J.
http://dx.doi.org/10.1021/ar300285u
1497-1505
July 16, 2013
2017-05-15 04:29:35
ACS Publications
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.
High-Throughput Development of Amphiphile Self-Assembly Materials: Fast-Tracking Synthesis, Characterization, Formulation, Application, and Understanding
High-Throughput Development of Amphiphile Self-Assembly Materials
46
7
Accounts of Chemical Research
ISSN 0001-4842
Acc. Chem. Res.
DOI 10.1021/ar300285u
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Murphy
James M.
Czabotar
Peter E.
Hildebrand
Joanne M.
Lucet
Isabelle S.
Zhang
Jian-Guo
Alvarez-Diaz
Silvia
Lewis
Rowena
Lalaoui
Najoua
Metcalf
Donald
Webb
Andrew I.
Young
Samuel N.
Varghese
Leila N.
Tannahill
Gillian M.
Hatchell
Esme C.
Majewski
Ian J.
Okamoto
Toru
Dobson
Renwick C. J.
Hilton
Douglas J.
Babon
Jeffrey J.
Nicola
Nicos A.
Strasser
Andreas
Silke
John
Alexander
Warren S.
http://www.sciencedirect.com/science/article/pii/S1074761313003488
443-453
September 19, 2013
2017-05-15 04:29:48
ScienceDirect
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 (RIPK3)-mediated phosphorylation. Structure-guided mutation of the MLKL pseudoactive site resulted in constitutive, RIPK3-independent necroptosis, demonstrating that modification of MLKL is essential for propagation of the necroptosis pathway downstream of RIPK3.
The Pseudokinase MLKL Mediates Necroptosis via a Molecular Switch Mechanism
39
3
Immunity
ISSN 1074-7613
Immunity
DOI 10.1016/j.immuni.2013.06.018
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69
7
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309113014152
Newman
J.
Burton
D. R.
Caria
S.
Desbois
S.
Gee
C. L.
Fazio
V. J.
Kvansakul
M.
Marshall
B.
Mills
G.
Richter
V.
Seabrook
S. A.
Wu
M.
Peat
T. S.
http://scripts.iucr.org/cgi-bin/paper?wd5209
Copyright (c) 2013 International Union of Crystallography
712-718
2013-07-01
2017-05-15 04:29:59
scripts.iucr.org
en
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.
Crystallization reports are the backbone of Acta Cryst. F, but do they have any spine?
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8
3
PLOS ONE
ISSN 1932-6203
PLOS ONE
DOI 10.1371/journal.pone.0058298
Newman
Janet
Seabrook
Shane
Surjadi
Regina
Williams
Charlotte C.
Lucent
Del
Wilding
Matthew
Scott
Colin
Peat
Thomas S.
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
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058298
e58298
06-Mar-2013
2017-05-15 04:30:10
PLoS Journals
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.
Determination of the Structure of the Catabolic N-Succinylornithine Transaminase (AstC) from Escherichia coli
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81
10
Proteins: Structure, Function, and Bioinformatics
ISSN 1097-0134
Proteins
DOI 10.1002/prot.24312
Nisbet
Rebecca M.
Nuttall
Stewart D.
Robert
Remy
Caine
Joanne M.
Dolezal
Olan
Hattarki
Meghan
Pearce
Lesley A.
Davydova
Natalia
Masters
Colin L.
Varghese
Jose N.
Streltsov
Victor A.
Alzheimer's disease
Alzheimer's disease
amyloid-β
amyloid-β
Aβ crystal structure
Aβ crystal structure
Im7
Im7
WO-2 Fab
WO-2 Fab
http://onlinelibrary.wiley.com/doi/10.1002/prot.24312/abstract
1748-1758
October 1, 2013
2017-05-15 04:30:22
Wiley Online Library
en
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 WO2. 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.
Structural studies of the tethered N-terminus of the Alzheimer's disease amyloid-β peptide
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69
3
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309113003060
North
R. A.
Kessans
S. A.
Atkinson
S. C.
Suzuki
H.
Watson
A. J. A.
Burgess
B. R.
Angley
L. M.
Hudson
A. O.
Varsani
A.
Griffin
M. D. W.
Fairbanks
A. J.
Dobson
R. C. J.
http://scripts.iucr.org/cgi-bin/paper?nj5146
Copyright (c) 2013 International Union of Crystallography
306-312
2013-03-01
2017-05-15 04:30:32
scripts.iucr.org
en
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 BL21 (DE3). 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.
Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus
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Peat
Thomas S.
Balotra
Sahil
Wilding
Matthew
French
Nigel G.
Briggs
Lyndall J.
Panjikar
Santosh
Cowieson
Nathan
Newman
Janet
Scott
Colin
http://onlinelibrary.wiley.com/doi/10.1111/mmi.12249/abstract
1149-1163
June 1, 2013
2017-05-15 04:30:47
Wiley Online Library
en
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.
Cyanuric acid hydrolase: evolutionary innovation by structural concatenation
Cyanuric acid hydrolase
88
6
Molecular Microbiology
ISSN 1365-2958
Molecular Microbiology
DOI 10.1111/mmi.12249
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Polekhina
G.
Ascher
D. B.
Kok
S. F.
Beckham
S.
Wilce
M.
Waltham
M.
http://scripts.iucr.org/cgi-bin/paper?lv5025
Copyright (c) 2013 International Union of Crystallography
333-344
2013-03-01
2017-05-15 04:31:00
scripts.iucr.org
en
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.
Structure of the N-terminal domain of human thioredoxin-interacting protein
69
3
Acta Crystallographica Section D: Biological Crystallography
ISSN 0907-4449
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
DOI 10.1107/S0907444912047099
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451
2
Biochemical Journal
ISSN 0264-6021, 1470-8728
DOI 10.1042/BJ20121819
Redpath
Nicholas T.
Xu
Yibin
Wilson
Nicholas J.
Fabri
Louis J.
Baca
Manuel
Andrews
Arna E.
Braley
Hal
Lu
Ping
Ireland
Cheryl
Ernst
Robin E.
Woods
Andrea
Forrest
Gail
An
Zhiqiang
Zaller
Dennis M.
Strohl
William R.
Luo
Cindy S.
Czabotar
Peter E.
Garrett
Thomas P. J.
Hilton
Douglas J.
Nash
Andrew D.
Zhang
Jian-Guo
Nicola
Nicos A.
http://biochemj.org/lookup/doi/10.1042/BJ20121819
165-175
2013-04-15
2017-05-15 04:32:17
CrossRef
en
Production of a human neutralizing monoclonal antibody and its crystal structure in complex with ectodomain 3 of the interleukin-13 receptor α1
journalArticle
69
3
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S174430911300184X
Ren
B.
Pham
T. M.
Surjadi
R.
Robinson
C. P.
Le
T.
Chandry
P. S.
Peat
T. S.
McKinstry
W. J.
http://scripts.iucr.org/cgi-bin/paper?wd5200
Copyright (c) 2013 International Union of Crystallography
275-279
2013-03-01
2017-05-15 04:32:25
scripts.iucr.org
en
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 SPP1, 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 ASCC454, 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.
Expression, purification, crystallization and preliminary X-ray diffraction analysis of a lactococcal bacteriophage small terminase subunit
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Ryan
Timothy M.
Caine
Joanne
Mertens
Haydyn D. T.
Kirby
Nigel
Nigro
Julie
Breheney
Kerry
Waddington
Lynne J.
Streltsov
Victor A.
Curtain
Cyril
Masters
Colin L.
Roberts
Blaine R.
https://peerj.com/articles/73
e73
2013-05-07
2017-05-15 04:32:35
peerj.com
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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.
Ammonium hydroxide treatment of Aβ produces an aggregate free solution suitable for biophysical and cell culture characterization
1
PeerJ
ISSN 2167-8359
PeerJ
DOI 10.7717/peerj.73
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7
PLOS ONE
ISSN 1932-6203
PLOS ONE
DOI 10.1371/journal.pone.0069228
Schulze
Monika-Sarah E. D.
Anders
Anne-Kathrin
Sethi
Dhruv K.
Call
Melissa J.
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
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069228
e69228
25-Jul-2013
2017-05-15 04:32:53
PLoS Journals
Peptide presentation by MHC class II is of critical importance to the function of CD4+ 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-DR1 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-DR1 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-DR1: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.
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
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Seabrook
Shane A.
Newman
Janet
http://dx.doi.org/10.1021/co400013v
387-392
August 12, 2013
2017-05-15 04:33:01
ACS Publications
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).
High-Throughput Thermal Scanning for Protein Stability: Making a Good Technique More Robust
High-Throughput Thermal Scanning for Protein Stability
15
8
ACS Combinatorial Science
ISSN 2156-8952
ACS Comb. Sci.
DOI 10.1021/co400013v
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69
4
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309113006143
Wu
M.
Peng
X.
Wen
H.
Wang
Q.
Chen
Q.
McKinstry
W. J.
Ren
B.
http://scripts.iucr.org/cgi-bin/paper?bo5119
Copyright (c) 2013 International Union of Crystallography
456-459
2013-04-01
2017-05-15 04:33:10
scripts.iucr.org
en
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.
Expression, purification, crystallization and preliminary X-ray analysis of tannase from Lactobacillus plantarum
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10
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309113024639
Siddiqui
T.
Paxman
J. J.
Dogovski
C.
Panjikar
S.
Perugini
M. A.
http://scripts.iucr.org/cgi-bin/paper?dp5053
Copyright (c) 2013 International Union of Crystallography
1177-1181
2013-10-01
2017-05-15 04:33:20
scripts.iucr.org
en
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.
Cloning to crystallization of dihydrodipicolinate synthase from the intracellular pathogen Legionella pneumophila
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1
Crystal Growth & Design
ISSN 1528-7483
Crystal Growth & Design
DOI 10.1021/cg4014569
Mele
Katarina
Lekamge
B. M. Thamali
Fazio
Vincent J.
Newman
Janet
http://pubs.acs.org/doi/abs/10.1021/cg4014569
261-269
January 2, 2014
2017-05-15 04:33:40
ACS Publications
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.
Using Time Courses To Enrich the Information Obtained from Images of Crystallization Trials
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68
4
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309112006963
Ascher
D. B.
Polekhina
G.
Parker
M. W.
http://scripts.iucr.org/cgi-bin/paper?dp5019
Copyright (c) 2012 International Union of Crystallography
468-471
2012-04-01
2017-05-15 04:36:31
scripts.iucr.org
en
Endoplasmic reticulum aminopeptidase 2 (ERAP2) is a critical enzyme involved in the final processing of MHC class I antigens. Peptide trimming by ERAP2 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 ERAP1 have provided an understanding of the `molecular-ruler' mechanism of substrate selection, little is known about the complementary activities of its homologue ERAP2 despite their sharing 49% sequence identity. In order to gain insights into the structure–function relationship of the oxytocinase subfamily, and in particular ERAP2, the luminal region of human ERAP2 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.
Crystallization and preliminary X-ray diffraction analysis of human endoplasmic reticulum aminopeptidase 2
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9
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309112033052
Atkinson
S. C.
Dogovski
C.
Dobson
R. C. J.
Perugini
M. A.
http://scripts.iucr.org/cgi-bin/paper?en5504
Copyright (c) 2012 International Union of Crystallography
1040-1047
2012-09-01
2017-05-15 04:36:52
scripts.iucr.org
en
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.
Cloning, expression, purification and crystallization of dihydrodipicolinate synthase from Agrobacterium tumefaciens
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PLOS ONE
ISSN 1932-6203
PLOS ONE
DOI 10.1371/journal.pone.0038318
Atkinson
Sarah C.
Dogovski
Con
Downton
Matthew T.
Pearce
F. Grant
Reboul
Cyril F.
Buckle
Ashley M.
Gerrard
Juliet A.
Dobson
Renwick C. J.
Wagner
John
Perugini
Matthew A.
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
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038318
e38318
25-Jun-2012
2017-05-15 04:37:02
PLoS Journals
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.
Crystal, Solution and In silico Structural Studies of Dihydrodipicolinate Synthase from the Common Grapevine
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68
12
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309112043333
Caria
S.
Chugh
S.
Nhu
D.
Lessene
G.
Kvansakul
M.
http://scripts.iucr.org/cgi-bin/paper?nj5138
Copyright (c) 2012 International Union of Crystallography
1521-1524
2012-12-01
2017-05-15 04:37:12
scripts.iucr.org
en
BHRF1 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 BHRF1 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 BHRF1 in complex with both Bim and Bak BH3 domains. Screening of a library of peptidomimetic compounds based on the benzoylurea scaffold that mimics critical Bim BH3 domain side chains against BHRF1 led to the identification of an inhibitor of BHRF1 that displays micromolar affinity. Single crystals were obtained from the co-crystallization of recombinant BHRF1 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 MX2 beamline at the Australian Synchrotron.
Crystallization and preliminary X-ray characterization of Epstein–Barr virus BHRF1 in complex with a benzoylurea peptidomimetic
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1
PLOS ONE
ISSN 1932-6203
PLOS ONE
DOI 10.1371/journal.pone.0029444
Chhabra
Sandeep
Dolezal
Olan
Collins
Brett M.
Newman
Janet
Simpson
Jamie S.
Macreadie
Ian G.
Fernley
Ross
Peat
Thomas S.
Swarbrick
James D.
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
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029444
e29444
19-Jan-2012
2017-05-15 04:37:26
PLoS Journals
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 IC50 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.
Structure of S. aureus HPPK and the Discovery of a New Substrate Site Inhibitor
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Conn
Charlotte E.
Darmanin
Connie
Mulet
Xavier
Hawley
Adrian
Drummond
Calum J.
http://pubs.rsc.org/en/content/articlelanding/2012/sm/c2sm25705j
6884-6896
2012/06/13
2017-05-15 04:38:22
pubs.rsc.org
en
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.
Effect of lipid architecture on cubic phase susceptibility to crystallisation screens
8
26
Soft Matter
ISSN 1744-6848
Soft Matter
DOI 10.1039/C2SM25705J
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7
Soft Matter
ISSN 1744-6848
Soft Matter
DOI 10.1039/C2SM07232G
Conn
Charlotte E.
Darmanin
Connie
Mulet
Xavier
Cann
Sophie Le
Kirby
Nigel
Drummond
Calum J.
http://pubs.rsc.org/en/content/articlelanding/2012/sm/c2sm07232g
2310-2321
2012/01/25
2017-05-15 04:38:59
pubs.rsc.org
en
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.
High-throughput analysis of the structural evolution of the monoolein cubic phase in situ under crystallogenesis conditions
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14
4
ACS Combinatorial Science
ISSN 2156-8952
ACS Comb. Sci.
DOI 10.1021/co2001718
Darmanin
Connie
Conn
Charlotte E.
Newman
Janet
Mulet
Xavier
Seabrook
Shane A.
Liang
Yi-Lynn
Hawley
Adrian
Kirby
Nigel
Varghese
Joseph N.
Drummond
Calum J.
http://dx.doi.org/10.1021/co2001718
247-252
April 9, 2012
2017-05-15 04:39:10
ACS Publications
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.
High-Throughput Production and Structural Characterization of Libraries of Self-Assembly Lipidic Cubic Phase Materials
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journalArticle
Davydova
Natalia
Streltsov
Victor A.
Roufail
Sally
Lovrecz
George O.
Stacker
Steven A.
Adams
Timothy E.
Achen
Marc G.
Deglycosylation
Deglycosylation
Human mature VEGF-D
Human mature VEGF-D
Lymphangiogenesis
Lymphangiogenesis
Protein expression and purification
Protein expression and purification
http://www.sciencedirect.com/science/article/pii/S1046592812000022
232-239
March 2012
2017-05-15 04:39:21
ScienceDirect
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.
Preparation of human vascular endothelial growth factor-D for structural and preclinical therapeutic studies
82
1
Protein Expression and Purification
ISSN 1046-5928
Protein Expression and Purification
DOI 10.1016/j.pep.2012.01.001
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68
1
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309111049530
Lay
F. T.
Mills
G. D.
Hulett
M. D.
Kvansakul
M.
http://scripts.iucr.org/cgi-bin/paper?pu5355
Copyright (c) 2012 International Union of Crystallography
85-88
2012-01-01
2017-05-15 04:39:30
scripts.iucr.org
en
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. NaD1, 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 NaD1 is reported. Crystals of NaD1 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°.
Crystallization and preliminary X-ray crystallographic analysis of the plant defensin NaD1
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3
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309112001510
Lay
F. T.
Veneer
P. K.
Hulett
M. D.
Kvansakul
M.
http://scripts.iucr.org/cgi-bin/paper?nj5113
Copyright (c) 2012 International Union of Crystallography
314-316
2012-03-01
2017-05-15 04:39:48
scripts.iucr.org
en
Class II defensins have been shown to have potent antifungal activity and are being exploited to protect agricultural crops against fungal pathogens. TPP3 is a poorly characterized member of the class II plant defensin family from tomato. To gain structural insight into the function of TPP3, soluble recombinant TPP3 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 rTPP3 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°.
Recombinant expression and purification of the tomato defensin TPP3 and its preliminary X-ray crystallographic analysis
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Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309112002618
Newman
J.
Bolton
E. E.
Müller-Dieckmann
J.
Fazio
V. J.
Gallagher
D. T.
Lovell
D.
Luft
J. R.
Peat
T. S.
Ratcliffe
D.
Sayle
R. A.
Snell
E. H.
Taylor
K.
Vallotton
P.
Velanker
S.
von Delft
F.
http://scripts.iucr.org/cgi-bin/paper?en5482
http://creativecommons.org/licenses/by/2.0/uk
253-258
2012-03-01
2017-05-15 04:39:57
scripts.iucr.org
en
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.
On the need for an international effort to capture, share and use crystallization screening data
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5
Journal of Computer-Aided Molecular Design
ISSN 0920-654X, 1573-4951
J Comput Aided Mol Des
DOI 10.1007/s10822-011-9521-2
Newman
Janet
Dolezal
Olan
Fazio
Vincent
Caradoc-Davies
Tom
Peat
Thomas S.
https://link.springer.com/article/10.1007/s10822-011-9521-2
497-503
2012/05/01
2017-05-15 04:40:07
link.springer.com
en
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.
The DINGO dataset: a comprehensive set of data for the SAMPL challenge
The DINGO dataset
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Acta Crystallographica Section D: Biological Crystallography
ISSN 0907-4449
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
DOI 10.1107/S0907444912018768
Newman
J.
Sayle
R. A.
Fazio
V. J.
http://scripts.iucr.org/cgi-bin/paper?be5201
Copyright (c) 2012 International Union of Crystallography
1003-1009
2012-08-01
2017-05-15 04:40:15
scripts.iucr.org
en
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.
A universal indicator dye pH assay for crystallization solutions and other high-throughput applications
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Peat
Thomas S.
Böttcher
Christine
Newman
Janet
Lucent
Del
Cowieson
Nathan
Davies
Christopher
http://www.plantcell.org/content/24/11/4525
4525-4538
2012-11-01
PMID: 23136372
2017-05-15 04:40:24
www.plantcell.org
en
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 (GH3-1) 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 GH3-1 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 GH3-1 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.
Crystal Structure of an Indole-3-Acetic Acid Amido Synthetase from Grapevine Involved in Auxin Homeostasis
24
11
The Plant Cell
ISSN , 1532-298X
Plant Cell
DOI 10.1105/tpc.112.102921
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7
PLOS ONE
ISSN 1932-6203
PLOS ONE
DOI 10.1371/journal.pone.0040147
Peat
Thomas S.
Rhodes
David I.
Vandegraaff
Nick
Le
Giang
Smith
Jessica A.
Clark
Lisa J.
Jones
Eric D.
Coates
Jonathan A. V.
Thienthong
Neeranat
Newman
Janet
Dolezal
Olan
Mulder
Roger
Ryan
John H.
Savage
G. Paul
Francis
Craig L.
Deadman
John J.
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
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040147
e40147
10-Jul-2012
2017-05-15 04:40:43
PLoS Journals
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.
Small Molecule Inhibitors of the LEDGF Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design
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2
Journal of Biomolecular Screening
ISSN 1087-0571
J Biomol Screen
DOI 10.1177/1087057112465979
Wielens
Jerome
Headey
Stephen J.
Rhodes
David I.
Mulder
Roger J.
Dolezal
Olan
Deadman
John J.
Newman
Janet
Chalmers
David K.
Parker
Michael W.
Peat
Thomas S.
Scanlon
Martin J.
http://dx.doi.org/10.1177/1087057112465979
147-159
February 1, 2013
2017-05-15 04:40:52
SAGE Journals
en
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.
Parallel Screening of Low Molecular Weight Fragment Libraries: Do Differences in Methodology Affect Hit Identification?
Parallel Screening of Low Molecular Weight Fragment Libraries
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67
12
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309111038395
Atkinson
S. C.
Dogovski
C.
Newman
J.
Dobson
R. C. J.
Perugini
M. A.
http://scripts.iucr.org/cgi-bin/paper?pu5341
Copyright (c) 2011 International Union of Crystallography
1537-1541
2011-12-01
2017-05-15 04:49:31
scripts.iucr.org
en
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.
Cloning, expression, purification and crystallization of dihydrodipicolinate synthase from the grapevine Vitis vinifera
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286
12
Journal of Biological Chemistry
ISSN 0021-9258, 1083-351X
J. Biol. Chem.
DOI 10.1074/jbc.M110.209924
Cross
Penelope J.
Dobson
Renwick C. J.
Patchett
Mark L.
Parker
Emily J.
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
http://www.jbc.org/content/286/12/10216
10216-10224
03/25/2011
PMID: 21282100
2017-05-15 04:49:40
www.jbc.org
en
The first step of the shikimate pathway for aromatic amino acid biosynthesis is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). Thermotoga maritima DAH7PS (TmaDAH7PS) 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 TmaDAH7PS 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 TmaDAH7PS 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.
Tyrosine Latching of a Regulatory Gate Affords Allosteric Control of Aromatic Amino Acid Biosynthesis
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286
9
Journal of Biological Chemistry
ISSN 0021-9258, 1083-351X
J. Biol. Chem.
DOI 10.1074/jbc.M110.161281
Czabotar
Peter E.
Lee
Erinna F.
Thompson
Geoff V.
Wardak
Ahmad Z.
Fairlie
W. Douglas
Colman
Peter M.
apoptosis
apoptosis
Cell Death
Cell Death
Crystal structure
Crystal structure
Mitochondrial Apoptosis
Mitochondrial Apoptosis
Protein Structure
Protein Structure
http://www.jbc.org/content/286/9/7123
7123-7131
03/04/2011
PMID: 21199865
2017-05-15 04:49:57
www.jbc.org
en
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 BH3-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 BH3 domain. These structures reveal canonical interactions between four signature hydrophobic amino acids from the BaxBH3 domain and the BH3-binding groove of the pro-survival proteins. In both structures, Met-74 from the Bax peptide engages with the BH3-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 BH3 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.
Mutation to Bax beyond the BH3 Domain Disrupts Interactions with Pro-survival Proteins and Promotes Apoptosis
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5
PLOS ONE
ISSN 1932-6203
PLOS ONE
DOI 10.1371/journal.pone.0020439
Dobson
Renwick C. J.
Girón
Irma
Hudson
André O.
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
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020439
e20439
25-May-2011
2017-05-15 04:50:11
PLoS Journals
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.
L,L-Diaminopimelate Aminotransferase from Chlamydomonas reinhardtii: A Target for Algaecide Development
L,L-Diaminopimelate Aminotransferase from Chlamydomonas reinhardtii
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Gorman
Michael A.
Uboldi
Alex D.
Walsh
Peter J.
Tan
Kher Shing
Hansen
Guido
Huyton
Trevor
Ji
Hong
Curtis
Joan
Kedzierski
Lukasz
Papenfuss
Anthony T.
Dogovski
Con
Perugini
Matthew A.
Simpson
Richard J.
Handman
Emanuela
Parker
Michael W.
14-3-3
14-3-3
Crystal structure
Crystal structure
HEAT
HEAT
Leishmania
Leishmania
TPR motif
TPR motif
http://onlinelibrary.wiley.com/doi/10.1002/pro.631/abstract
1060-1068
June 1, 2011
2017-05-15 04:50:23
Wiley Online Library
en
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.
Crystal structure of the Leishmania major MIX protein: A scaffold protein that mediates protein–protein interactions
Crystal structure of the Leishmania major MIX protein
20
6
Protein Science
ISSN 1469-896X
Protein Science
DOI 10.1002/pro.631
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Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309111033276
Griffin
M. D. W.
Billakanti
J. M.
Gerrard
J. A.
Dobson
R. C. J.
Pearce
F. G.
http://scripts.iucr.org/cgi-bin/paper?us5036
Copyright (c) 2011 International Union of Crystallography
1386-1390
2011-11-01
2017-05-15 04:50:38
scripts.iucr.org
en
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 DHDPS2 from Arabidopsis thaliana are reported. Diffraction-quality protein crystals belonged to space group P21212.
Crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase 2 from Arabidopsis thaliana
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Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309110053728
Gunn
N. J.
Gorman
M. A.
Dobson
R. C. J.
Parker
M. W.
Mulhern
T. D.
http://scripts.iucr.org/cgi-bin/paper?dp5002
Copyright (c) 2011 International Union of Crystallography
336-339
2011-03-01
2017-05-15 04:50:48
scripts.iucr.org
en
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 (SH2) 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 SH2 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 SH2 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°.
Purification, crystallization, small-angle X-ray scattering and preliminary X-ray diffraction analysis of the SH2 domain of the Csk-homologous kinase
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Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S174430911004844X
Hudson
A. O.
Girón
I.
Dobson
R. C. J.
http://scripts.iucr.org/cgi-bin/paper?pu5311
Copyright (c) 2011 International Union of Crystallography
140-143
2011-01-01
2017-05-15 04:50:56
scripts.iucr.org
en
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.
Crystallization and preliminary X-ray diffraction analysis of l,l-diaminopimelate aminotransferase (DapL) from Chlamydomonas reinhardtii
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Acta Crystallographica Section D: Biological Crystallography
ISSN 0907-4449
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
DOI 10.1107/S0907444911007530
Keegan
R. M.
Long
F.
Fazio
V. J.
Winn
M. D.
Murshudov
G. N.
Vagin
A. A.
http://scripts.iucr.org/cgi-bin/paper?ba5167
http://creativecommons.org/licenses/by/2.0/uk
313-323
2011-04-01
2017-05-15 04:51:05
scripts.iucr.org
en
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 CCP4 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.
Evaluating the solution from MrBUMP and BALBES
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5
Crystal Growth & Design
ISSN 1528-7483
Crystal Growth & Design
DOI 10.1021/cg1017104
Kennedy
Danielle F.
Drummond
Calum J.
Peat
Thomas S.
Newman
Janet
http://dx.doi.org/10.1021/cg1017104
1777-1785
May 4, 2011
2017-05-15 04:51:15
ACS Publications
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.
Evaluating Protic Ionic Liquids as Protein Crystallization Additives
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2
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309110051481
Laguerre
A.
Wielens
J.
Parker
M. W.
Porter
C. J. H.
Scanlon
M. J.
http://scripts.iucr.org/cgi-bin/paper?en5442
Copyright (c) 2011 International Union of Crystallography
291-295
2011-02-01
2017-05-15 04:51:26
scripts.iucr.org
en
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.
Preparation, crystallization and preliminary X-ray diffraction analysis of two intestinal fatty-acid binding proteins in the presence of 11-(dansylamino)undecanoic acid
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Lee
Erinna F.
Clarke
Oliver B.
Evangelista
Marco
Feng
Zhiping
Speed
Terence P.
Tchoubrieva
Elissaveta B.
Strasser
Andreas
Kalinna
Bernd H.
Colman
Peter M.
Fairlie
W. Douglas
http://www.pnas.org/content/108/17/6999
6999-7003
04/26/2011
PMID: 21444803
2017-05-15 04:51:36
www.pnas.org
en
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 BH3-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 “BH3 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 BH3 mimetic. A crystal structure of sjA bound to a BH3 peptide provides direct evidence for the feasibility of developing BH3 mimetics to target Bcl-2 prosurvival proteins in schistosomes, suggesting an alternative application for this class of drugs beyond cancer treatment.
Discovery and molecular characterization of a Bcl-2–regulated cell death pathway in schistosomes
108
17
Proceedings of the National Academy of Sciences
ISSN 0027-8424, 1091-6490
PNAS
DOI 10.1073/pnas.1100652108
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19
10
Structure
ISSN 0969-2126
Structure
DOI 10.1016/j.str.2011.07.015
Lee
Erinna F.
Dewson
Grant
Smith
Brian J.
Evangelista
Marco
Pettikiriarachchi
Anne
Dogovski
Con
Perugini
Matthew A.
Colman
Peter M.
Fairlie
W. Douglas
http://www.sciencedirect.com/science/article/pii/S0969212611002577
1467-1476
October 12, 2011
2017-05-15 04:51:47
ScienceDirect
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.
Crystal Structure of a BCL-W Domain-Swapped Dimer: Implications for the Function of BCL-2 Family Proteins
Crystal Structure of a BCL-W Domain-Swapped Dimer
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Lee
Erinna F.
Smith
Brian J.
Horne
W. Seth
Mayer
Kelsey N.
Evangelista
Marco
Colman
Peter M.
Gellman
Samuel H.
Fairlie
W. Douglas
apoptosis
apoptosis
BH3 domain
BH3 domain
foldamers
foldamers
Peptides
Peptides
peptidomimetics
peptidomimetics
http://onlinelibrary.wiley.com/doi/10.1002/cbic.201100314/abstract
2025-2032
September 5, 2011
2017-05-15 04:52:00
Wiley Online Library
en
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 BH3 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 BH3 domain. Comparison of our α/β-peptide:Bcl-xL structure with structures of complexes between native BH3 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 BH3-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 BH3-mimetic α/β-peptide displays prosurvival protein-binding preferences distinct from those of Puma BH3 itself, even though these two oligomers have identical side-chain sequences. Our results suggest origins for this backbone-dependent change in selectivity.
Structural Basis of Bcl-xL Recognition by a BH3-Mimetic α/β-Peptide Generated by Sequence-Based Design
12
13
ChemBioChem
ISSN 1439-7633
ChemBioChem
DOI 10.1002/cbic.201100314
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Newman
Janet
Automation
Automation
High throughput
High throughput
Protein crystallisation
Protein crystallisation
http://www.sciencedirect.com/science/article/pii/S1046202311000922
73-80
September 2011
2017-05-15 04:52:24
ScienceDirect
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.
One plate, two plates, a thousand plates. How crystallisation changes with large numbers of samples
Methods in Structural Proteomics
55
1
Methods
ISSN 1046-2023
Methods
DOI 10.1016/j.ymeth.2011.04.004
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67
1
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309110046208
Newman
J.
Pearce
L.
Lesburg
C. A.
Strickland
C.
Peat
T. S.
http://scripts.iucr.org/cgi-bin/paper?rp5058
Copyright (c) 2011 International Union of Crystallography
90-93
2011-01-01
2017-05-15 04:53:11
scripts.iucr.org
en
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.
Crystallization of an apo form of human arginase: using all the tools in the toolbox simultaneously
Crystallization of an apo form of human arginase
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79
4
Proteins: Structure, Function, and Bioinformatics
ISSN 1097-0134
Proteins
DOI 10.1002/prot.22971
Nuttall
Stewart D.
Wilkins
Michelle L.
Streltsov
Victor A.
Pontes-Braz
Luisa
Dolezal
Olan
Tran
Hung
Liu
Chun-Qiang
anthrax
anthrax
biosensor
biosensor
exosporium
exosporium
infectious disease
infectious disease
merohedral twinning
merohedral twinning
scFv complex
scFv complex
http://onlinelibrary.wiley.com/doi/10.1002/prot.22971/abstract
1306-1317
April 1, 2011
2017-05-15 04:53:33
Wiley Online Library
en
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.
Isolation, kinetic analysis, and structural characterization of an antibody targeting the Bacillus anthracis major spore surface protein BclA
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journalArticle
Pearce
F. Grant
Dobson
Renwick C. J.
Jameson
Geoffrey B.
Perugini
Matthew A.
Gerrard
Juliet A.
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
http://www.sciencedirect.com/science/article/pii/S1570963911002111
1900-1909
December 2011
2017-05-15 04:53:59
ScienceDirect
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.
Characterization of monomeric dihydrodipicolinate synthase variant reveals the importance of substrate binding in optimizing oligomerization
1814
12
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
ISSN 1570-9639
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
DOI 10.1016/j.bbapap.2011.07.016
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67
5
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309111010347
Polekhina
G.
Ascher
D. B.
Kok
S. F.
Waltham
M.
http://scripts.iucr.org/cgi-bin/paper?rl5005
Copyright (c) 2011 International Union of Crystallography
613-617
2011-05-01
2017-05-15 04:54:25
scripts.iucr.org
en
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.
Crystallization and preliminary X-ray analysis of the N-terminal domain of human thioredoxin-interacting protein
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Rhodes
David I
Peat
Thomas S
Vandegraaff
Nick
Jeevarajah
Dharshini
Le
Giang
Jones
Eric D
Smith
Jessica A
Coates
Jonathan AV
Winfeld
Lisa J
Thienthong
Neeranat
Newman
Janet
Lucent
Del
Ryan
John H
Savage
G Paul
Francis
Craig L
Deadman
John J
http://journals.sagepub.com/doi/abs/10.3851/IMP1716
155-168
April 1, 2011
2017-05-15 04:54:42
SAGE Journals
en
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.
Structural Basis for a New Mechanism of Inhibition of H I V-1 Integrase Identified by Fragment Screening and Structure-Based Design
21
4
Antiviral Chemistry and Chemotherapy
ISSN 0956-3202
Antivir Chem Chemother
DOI 10.3851/IMP1716
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12
15
ChemBioChem
ISSN 1439-7633
ChemBioChem
DOI 10.1002/cbic.201100350
Rhodes
David I.
Peat
Thomas S.
Vandegraaff
Nick
Jeevarajah
Dharshini
Newman
Janet
Martyn
John
Coates
Jonathan A. V.
Ede
Nicholas J.
Rea
Philip
Deadman
John J.
co-crystal structures
co-crystal structures
cyclic peptides
cyclic peptides
HIV-1 integrase
HIV-1 integrase
inhibitors
inhibitors
LEDGF
LEDGF
http://onlinelibrary.wiley.com/doi/10.1002/cbic.201100350/abstract
2311-2315
October 17, 2011
2017-05-15 04:54:54
Wiley Online Library
en
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.
Crystal Structures of Novel Allosteric Peptide Inhibitors of HIV Integrase Identify New Interactions at the LEDGF Binding Site
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Streltsov
Victor A.
Varghese
Joseph N.
Masters
Colin L.
Nuttall
Stewart D.
http://www.jneurosci.org/content/31/4/1419
Copyright © 2011 the authors 0270-6474/11/311419-08$15.00/0
1419-1426
2011/01/26
PMID: 21273426
2017-05-15 04:55:04
www.jneurosci.org
en
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 CDR3 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.
Crystal Structure of the Amyloid-β p3 Fragment Provides a Model for Oligomer Formation in Alzheimer's Disease
31
4
Journal of Neuroscience
ISSN 0270-6474, 1529-2401
J. Neurosci.
DOI 10.1523/JNEUROSCI.4259-10.2011
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conferencePaper
DOI 10.1109/DICTA.2011.92
2011 International Conference on Digital Image Computing: Techniques and Applications
Vallotton
P.
Lovell
D.
Newman
J.
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
513-517
December 2011
IEEE Xplore
2011 International Conference on Digital Image Computing: Techniques and Applications
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.
An Observation about Circular Shortest Paths: Dealing with Additional Constraints Using Branch and Bound
An Observation about Circular Shortest Paths
The following values have no corresponding Zotero field:<br/>periodical: 2011 International Conference on Digital Image Computing: Techniques and Applications
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2017-05-15 04:55:22
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journalArticle
67
2
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309110051006
Ve
T.
Williams
S.
Valkov
E.
Ellis
J. G.
Dodds
P. N.
Kobe
B.
http://scripts.iucr.org/cgi-bin/paper?uo5017
Copyright (c) 2011 International Union of Crystallography
237-240
2011-02-01
2017-05-15 04:55:29
scripts.iucr.org
en
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 AT1G72930 from Arabidopsis as a template.
Crystallization, X-ray diffraction analysis and preliminary structure determination of the TIR domain from the flax resistance protein L6
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108
24
Proceedings of the National Academy of Sciences
ISSN 0027-8424, 1091-6490
PNAS
DOI 10.1073/pnas.1018927108
Wong
Wilson
Skau
Colleen T.
Marapana
Danushka S.
Hanssen
Eric
Taylor
Nicole L.
Riglar
David T.
Zuccala
Elizabeth S.
Angrisano
Fiona
Lewis
Heather
Catimel
Bruno
Clarke
Oliver B.
Kershaw
Nadia J.
Perugini
Matthew A.
Kovar
David R.
Gulbis
Jacqueline M.
Baum
Jake
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
http://www.pnas.org/content/108/24/9869
9869-9874
06/14/2011
PMID: 21628589
2017-05-15 04:55:39
www.pnas.org
en
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 (PfADF1) 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 PfADF1 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, PfADF1. We show that PfADF1 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 PfADF1 is capable of efficient actin filament severing. Furthermore, this severing occurs despite PfADF1’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.
Minimal requirements for actin filament disassembly revealed by structural analysis of malaria parasite actin-depolymerizing factor 1
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66
5
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309110010857
Chhabra
S.
Newman
J.
Peat
T. S.
Fernley
R. T.
Caine
J.
Simpson
J. S.
Swarbrick
J. D.
http://scripts.iucr.org/cgi-bin/paper?bo5075
Copyright (c) 2010 International Union of Crystallography
575-578
2010-05-01
2017-05-15 04:59:47
scripts.iucr.org
en
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%.
Crystallization and preliminary X-ray analysis of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Staphylococcus aureus
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141
6
Cell
ISSN 0092-8674
Cell
DOI 10.1016/j.cell.2010.05.003
Clarke
Oliver B.
Caputo
Alessandro T.
Hill
Adam P.
Vandenberg
Jamie I.
Smith
Brian J.
Gulbis
Jacqueline M.
CELLBIO
CELLBIO
MOLNEURO
MOLNEURO
SIGNALING
SIGNALING
http://www.sciencedirect.com/science/article/pii/S0092867410005015
1018-1029
June 11, 2010
2017-05-15 04:59:57
ScienceDirect
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
Domain Reorientation and Rotation of an Intracellular Assembly Regulate Conduction in Kir Potassium Channels
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66
1
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309109047964
Dommaraju
S.
Gorman
M. A.
Dogovski
C.
Pearce
F. G.
Gerrard
J. A.
Dobson
R. C. J.
Parker
M. W.
Perugini
M. A.
http://scripts.iucr.org/cgi-bin/paper?gj5072
Copyright (c) 2010 International Union of Crystallography
57-60
2010-01-01
2017-05-15 05:00:06
scripts.iucr.org
en
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.
Cloning, expression and crystallization of dihydrodipicolinate reductase from methicillin-resistant Staphylococcus aureus
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Dransfield
Daniel T.
Cohen
Edward H.
Chang
Qing
Sparrow
Lindsay G.
Bentley
John D.
Dolezal
Olan
Xiao
Xiaowen
Peat
Thomas S.
Newman
Janet
Pilling
Patricia A.
Phan
Tram
Priebe
Ilka
Brierley
Gemma V.
Kastrapeli
Niksa
Kopacz
Kris
Martik
Diana
Wassaf
Dina
Rank
Douglas
Conley
Greg
Huang
Yan
Adams
Timothy E.
Cosgrove
Leah
http://mct.aacrjournals.org/content/9/6/1809
©2010 American Association for Cancer Research.
1809-1819
2010/06/01
PMID: 20515953
2017-05-15 05:00:15
mct.aacrjournals.org
en
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 CD31 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.
A Human Monoclonal Antibody against Insulin-Like Growth Factor-II Blocks the Growth of Human Hepatocellular Carcinoma Cell Lines In vitro and In vivo
9
6
Molecular Cancer Therapeutics
ISSN 1535-7163, 1538-8514
Mol Cancer Ther
DOI 10.1158/1535-7163.MCT-09-1134
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12
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309110041515
Ernberg
K.
McGrath
A. P.
Peat
T. S.
Adams
T. E.
Xiao
X.
Pham
T.
Newman
J.
McDonald
I. A.
Collyer
C. A.
Guss
J. M.
http://scripts.iucr.org/cgi-bin/paper?tb5032
Copyright (c) 2010 International Union of Crystallography
1572-1578
2010-12-01
2017-05-15 05:00:24
scripts.iucr.org
en
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.
A new crystal form of human vascular adhesion protein 1
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1
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309109047708
Hor
L.
Dobson
R. C. J.
Dogovski
C.
Hutton
C. A.
Perugini
M. A.
http://scripts.iucr.org/cgi-bin/paper?nj5045
Copyright (c) 2010 International Union of Crystallography
37-40
2010-01-01
2017-05-15 05:00:34
scripts.iucr.org
en
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.
Crystallization and preliminary X-ray diffraction analysis of diaminopimelate epimerase from Escherichia coli
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Kvansakul
Marc
Wei
Andrew H.
Fletcher
Jamie I.
Willis
Simon N.
Chen
Lin
Roberts
Andrew W.
Huang
David C. S.
Colman
Peter M.
Jung
Jae U.
http://dx.plos.org/10.1371/journal.ppat.1001236
e1001236
2010-12-23
2017-05-15 05:01:04
CrossRef
en
Structural Basis for Apoptosis Inhibition by Epstein-Barr Virus BHRF1
6
12
PLoS Pathogens
ISSN 1553-7374
DOI 10.1371/journal.ppat.1001236
journalArticle
11
7
International Journal of Molecular Sciences
DOI 10.3390/ijms11072759
Luang
Sukanya
Cairns
James R. Ketudat
Streltsov
Victor A.
Hrmova
Maria
macro- and cross-seeding
macro- and cross-seeding
wild-type and mutant protein
wild-type and mutant protein
X-ray diffraction
X-ray diffraction
http://www.mdpi.com/1422-0067/11/7/2759
http://creativecommons.org/licenses/by/3.0/
2759-2769
2010-07-19
2017-05-15 05:01:14
www.mdpi.com
en
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.
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
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10
6
Crystal Growth & Design
ISSN 1528-7483
Crystal Growth & Design
DOI 10.1021/cg1004209
Newman
Janet
Fazio
Vincent J.
Lawson
Brian
Peat
Thomas S.
http://dx.doi.org/10.1021/cg1004209
2785-2792
June 2, 2010
2017-05-15 05:01:26
ACS Publications
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.
The C6 Web Tool: A Resource for the Rational Selection of Crystallization Conditions
The C6 Web Tool
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journalArticle
Oakley
Aaron J.
3-Phytase
3-Phytase
Aspergillus niger
Aspergillus niger
Michaelis complex
Michaelis complex
PhyA
PhyA
Phytate
Phytate
Protein Structure
Protein Structure
http://www.sciencedirect.com/science/article/pii/S0006291X10011277
745-749
July 9, 2010
2017-05-15 05:01:38
ScienceDirect
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.
The structure of Aspergillus niger phytase PhyA in complex with a phytate mimetic
397
4
Biochemical and Biophysical Research Communications
ISSN 0006-291X
Biochemical and Biophysical Research Communications
DOI 10.1016/j.bbrc.2010.06.024
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53
17
Journal of Medicinal Chemistry
ISSN 0022-2623
J. Med. Chem.
DOI 10.1021/jm100621s
Oakley
Aaron J.
Barrett
Susan
Peat
Thomas S.
Newman
Janet
Streltsov
Victor A.
Waddington
Lynne
Saito
Takehiko
Tashiro
Masato
McKimm-Breschkin
Jennifer L.
http://dx.doi.org/10.1021/jm100621s
6421-6431
September 9, 2010
2017-05-15 05:01:51
ACS Publications
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.
Structural and Functional Basis of Resistance to Neuraminidase Inhibitors of Influenza B Viruses
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285
13
Journal of Biological Chemistry
ISSN 0021-9258, 1083-351X
J. Biol. Chem.
DOI 10.1074/jbc.M109.082099
Oakley
Aaron J.
Coggan
Marjorie
Board
Philip G.
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
http://www.jbc.org/content/285/13/9642
9642-9648
03/26/2010
PMID: 20110353
2017-05-15 05:02:12
www.jbc.org
en
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.
Identification and Characterization of γ-Glutamylamine Cyclotransferase, an Enzyme Responsible for γ-Glutamyl-ϵ-lysine Catabolism
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403
3
Journal of Molecular Biology
ISSN 0022-2836
Journal of Molecular Biology
DOI 10.1016/j.jmb.2010.09.007
Pearce
M. C.
Powers
G. A.
Feil
S. C.
Hansen
G.
Parker
M. W.
Bottomley
S. P.
antichymotrypsin
antichymotrypsin
conformational change
conformational change
polymerization
polymerization
protein misfolding
protein misfolding
serpin
serpin
http://www.sciencedirect.com/science/article/pii/S0022283610009666
459-467
October 29, 2010
2017-05-15 05:02:26
ScienceDirect
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.
Identification and Characterization of a Misfolded Monomeric Serpin Formed at Physiological Temperature
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journalArticle
Quesada-Soriano
Indalecio
Parker
Lorien J.
Primavera
Alessandra
Wielens
Jerome
Holien
Jessica K.
Casas-Solvas
Juan M.
Vargas-Berenguel
Antonio
Aguilera
Ana M.
Nuccetelli
Marzia
Mazzetti
Anna P.
Bello
Mario Lo
Parker
Michael W.
García-Fuentes
Luis
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
http://onlinelibrary.wiley.com/doi/10.1002/jmr.1040/abstract
220-234
March 1, 2011
2017-05-15 05:02:39
Wiley Online Library
en
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.
Diuretic drug binding to human glutathione transferase P1-1: potential role of Cys-101 revealed in the double mutant C47S/Y108V
Diuretic drug binding to human glutathione transferase P1-1
24
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Journal of Molecular Recognition
ISSN 1099-1352
J. Mol. Recognit.
DOI 10.1002/jmr.1040
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19
2
Protein Science
ISSN 1469-896X
Protein Science
DOI 10.1002/pro.312
Robert
Remy
Streltsov
Victor A.
Newman
Janet
Pearce
Lesley A.
Wark
Kim L.
Dolezal
Olan
Alzheimer's disease
Alzheimer's disease
antibody engineering
antibody engineering
Crystal structure
Crystal structure
humanization
humanization
SPR
SPR
http://onlinelibrary.wiley.com/doi/10.1002/pro.312/abstract
299-308
February 1, 2010
2017-05-15 05:02:54
Wiley Online Library
en
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.
Germline humanization of a murine Aβ antibody and crystal structure of the humanized recombinant Fab fragment
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1
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S174430910904771X
Sibarani
N. E.
Gorman
M. A.
Dogovski
C.
Parker
M. W.
Perugini
M. A.
http://scripts.iucr.org/cgi-bin/paper?fw5234
Copyright (c) 2010 International Union of Crystallography
32-36
2010-01-01
2017-05-15 05:03:43
scripts.iucr.org
en
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 (OXC141 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.
Crystallization of dihydrodipicolinate synthase from a clinical isolate of Streptococcus pneumoniae
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3
Molecular Microbiology
ISSN 1365-2958
DOI 10.1111/j.1365-2958.2010.07356.x
Taylor
Matthew C.
Jackson
Colin J.
Tattersall
David B.
French
Nigel
Peat
Thomas S.
Newman
Janet
Briggs
Lyndall J.
Lapalikar
Gauri V.
Campbell
Peter M.
Scott
Colin
Russell
Robyn J.
Oakeshott
John G.
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07356.x/abstract
561-575
November 1, 2010
2017-05-15 05:03:57
Wiley Online Library
en
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.
Identification and characterization of two families of F420H2-dependent reductases from Mycobacteria that catalyse aflatoxin degradation
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Vallotton
P.
Sun
C.
Lovell
D.
Fazio
V. J.
Newman
J.
http://scripts.iucr.org/cgi-bin/paper?cg5163
Copyright (c) 2010 International Union of Crystallography
1548-1552
2010-12-01
2017-05-15 05:04:10
scripts.iucr.org
en
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.
DroplIT, an improved image analysis method for droplet identification in high-throughput crystallization trials
43
6
Journal of Applied Crystallography
ISSN 0021-8898
J Appl Cryst, J Appl Crystallogr
DOI 10.1107/S0021889810040963
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285
8
Journal of Biological Chemistry
ISSN 0021-9258, 1083-351X
J. Biol. Chem.
DOI 10.1074/jbc.M109.038166
Voss
Jarrod E.
Scally
Stephen W.
Taylor
Nicole L.
Atkinson
Sarah C.
Griffin
Michael D. W.
Hutton
Craig A.
Parker
Michael W.
Alderton
Malcolm R.
Gerrard
Juliet A.
Dobson
Renwick C. J.
Dogovski
Con
Perugini
Matthew A.
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
http://www.jbc.org/content/285/8/5188
5188-5195
02/19/2010
PMID: 19948665
2017-05-15 05:04:20
www.jbc.org
en
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.
Substrate-mediated Stabilization of a Tetrameric Drug Target Reveals Achilles Heel in Anthrax
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11
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309110036791
Wubben
J. M.
Dogovski
C.
Dobson
R. C. J.
Codd
R.
Gerrard
J. A.
Parker
M. W.
Perugini
M. A.
http://scripts.iucr.org/cgi-bin/paper?fw5275
Copyright (c) 2010 International Union of Crystallography
1511-1516
2010-11-01
2017-05-15 05:04:35
scripts.iucr.org
en
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.
Cloning, expression, purification and crystallization of dihydrodipicolinate synthase from the psychrophile Shewanella benthica
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285
28
Journal of Biological Chemistry
ISSN 0021-9258, 1083-351X
J. Biol. Chem.
DOI 10.1074/jbc.C110.129502
Xu
Yibin
Kershaw
Nadia J.
Luo
Cindy S.
Soo
Priscilla
Pocock
Michael J.
Czabotar
Peter E.
Hilton
Douglas J.
Nicola
Nicos A.
Garrett
Thomas P. J.
Zhang
Jian-Guo
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
http://www.jbc.org/content/285/28/21214
21214-21218
07/09/2010
PMID: 20489211
2017-05-15 05:04:45
www.jbc.org
en
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.
Crystal Structure of the Entire Ectodomain of gp130 INSIGHTS INTO THE MOLECULAR ASSEMBLY OF THE TALL CYTOKINE RECEPTOR COMPLEXES
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3
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309108039018
Atkinson
S. C.
Dobson
R. C. J.
Newman
J. M.
Gorman
M. A.
Dogovski
C.
Parker
M. W.
Perugini
M. A.
http://scripts.iucr.org/cgi-bin/paper?pu5236
Copyright (c) 2009 International Union of Crystallography
253-255
2009-03-01
2017-05-15 05:06:27
scripts.iucr.org
en
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.
Crystallization and preliminary X-ray analysis of dihydrodipicolinate synthase from Clostridium botulinum in the presence of its substrate pyruvate
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Baker
Michael J.
Webb
Chaille T.
Stroud
David A.
Palmer
Catherine S.
Frazier
Ann E.
Guiard
Bernard
Chacinska
Agnieszka
Gulbis
Jacqueline M.
Ryan
Michael T.
http://www.molbiolcell.org/content/20/3/769
769-779
02/01/2009
PMID: 19037098
2017-05-15 05:06:36
www.molbiolcell.org
en
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.
Structural and Functional Requirements for Activity of the Tim9–Tim10 Complex in Mitochondrial Protein Import
20
3
Molecular Biology of the Cell
ISSN 1059-1524, 1939-4586
Mol. Biol. Cell
DOI 10.1091/mbc.E08-09-0903
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5
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309109011634
Feil
S. C.
Tang
J.
Hansen
G.
Gorman
M. A.
Wiktelius
E.
Stenberg
G.
Parker
M. W.
http://scripts.iucr.org/cgi-bin/paper?nj5029
Copyright (c) 2009 International Union of Crystallography
475-477
2009-05-01
2017-05-15 05:06:51
scripts.iucr.org
en
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.
Crystallization and preliminary X-ray analysis of glutathione transferases from cyanobacteria
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Chemical Communications
DOI 10.1039/B912784D
Mei Kok
W.
B. Scanlon
Denis
A. Karas
John
A. Miles
Luke
J. Tew
Deborah
W. Parker
Michael
J. Barnham
Kevin
A. Hutton
Craig
http://pubs.rsc.org/en/Content/ArticleLanding/2009/CC/B912784D
6228-6230
2009
2017-05-15 05:07:13
pubs.rsc.org
en
Solid-phase synthesis of homodimeric peptides : preparation of covalently-linked dimers of amyloid β peptide
Solid-phase synthesis of homodimeric peptides
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386
3
Journal of Molecular Biology
ISSN 0022-2836
Journal of Molecular Biology
DOI 10.1016/j.jmb.2008.12.078
Kuang
Zhihe
Yao
Shenggen
Xu
Yibin
Lewis
Rowena S.
Low
Andrew
Masters
Seth L.
Willson
Tracy A.
Kolesnik
Tatiana B.
Nicholson
Sandra E.
Garrett
Thomas J. P.
Norton
Raymond S.
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
http://www.sciencedirect.com/science/article/pii/S0022283608015738
662-674
February 27, 2009
2017-05-15 05:07:53
ScienceDirect
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.
SPRY Domain-Containing SOCS Box Protein 2: Crystal Structure and Residues Critical for Protein Binding
SPRY Domain-Containing SOCS Box Protein 2
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284
44
Journal of Biological Chemistry
ISSN 0021-9258, 1083-351X
J. Biol. Chem.
DOI 10.1074/jbc.M109.040725
Lee
Erinna F.
Czabotar
Peter E.
Yang
Hong
Sleebs
Brad E.
Lessene
Guillaume
Colman
Peter M.
Smith
Brian J.
Fairlie
W. Douglas
http://www.jbc.org/content/284/44/30508
30508-30517
10/30/2009
PMID: 19726685
2017-05-15 05:08:07
www.jbc.org
en
Antagonists of anti-apoptotic Bcl-2 family members hold promise as cancer therapeutics. Apoptosis is triggered when a peptide containing a BH3 motif or a small molecule BH3 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 BH3 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 BH3 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.
Conformational Changes in Bcl-2 Pro-survival Proteins Determine Their Capacity to Bind Ligands
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121
24
Angewandte Chemie
ISSN 1521-3757
Angewandte Chemie
DOI 10.1002/ange.200805761
Lee
Erinna F.
Sadowsky
Jack D.
Smith
Brian J.
Czabotar
Peter E.
Peterson-Kaufman
Kimberly J.
Colman
Peter M.
Gellman
Samuel H.
Fairlie
W. Douglas
Aminosäuren
Aminosäuren
Foldamere
Foldamere
Peptide
Peptide
Protein-Protein-Wechselwirkungen
Protein-Protein-Wechselwirkungen
Röntgenbeugung
Röntgenbeugung
http://onlinelibrary.wiley.com/doi/10.1002/ange.200805761/abstract
4382-4386
June 2, 2009
2017-05-15 05:08:42
Wiley Online Library
en
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.
High-Resolution Structural Characterization of a Helical α/β-Peptide Foldamer Bound to the Anti-Apoptotic Protein Bcl-xL
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65
9
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309109024932
Newman
J.
Cohen
E. H.
Cosgrove
L.
Kopacz
K.
Dransfield
D. T.
Adams
T. E.
Peat
T. S.
http://scripts.iucr.org/cgi-bin/paper?en5372
Copyright (c) 2009 International Union of Crystallography
945-948
2009-09-01
2017-05-15 05:08:52
scripts.iucr.org
en
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.
Crystallization and preliminary X-ray analysis of the complexes between a Fab and two forms of human insulin-like growth factor II
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10
Journal of Biomolecular Screening
ISSN 1087-0571
J Biomol Screen
DOI 10.1177/1087057109348220
Newman
Janet
Fazio
Vincent J.
Caradoc-Davies
Tom T.
Branson
Kim
Peat
Thomas S.
http://dx.doi.org/10.1177/1087057109348220
1245-1250
December 1, 2009
2017-05-15 05:10:04
SAGE Journals
en
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.
Practical Aspects of the SAMPL Challenge: Providing an Extensive Experimental Data Set for the Modeling Community
Practical Aspects of the SAMPL Challenge
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65
2
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309109000670
Voss
J. E.
Scally
S. W.
Taylor
N. L.
Dogovski
C.
Alderton
M. R.
Hutton
C. A.
Gerrard
J. A.
Parker
M. W.
Dobson
R. C. J.
Perugini
M. A.
http://scripts.iucr.org/cgi-bin/paper?nj5027
Copyright (c) 2009 International Union of Crystallography
188-191
2009-02-01
2017-05-15 05:12:21
scripts.iucr.org
en
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.
Expression, purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Bacillus anthracis in the presence of pyruvate
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9
Acta Crystallographica Section D: Biological Crystallography
ISSN 0907-4449
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
DOI 10.1107/S0907444906020063
Smith
B. J.
Huyton
T.
Joosten
R. P.
McKimm-Breschkin
J. L.
Zhang
J.-G.
Luo
C. S.
Lou
M.-Z.
Labrou
N. E.
Garrett
T. P. J.
http://scripts.iucr.org/cgi-bin/paper?be5059
Copyright (c) 2006 International Union of Crystallography
947-952
2006-09-01
2017-05-15 05:14:13
scripts.iucr.org
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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.
Structure of a calcium-deficient form of influenza virus neuraminidase: implications for substrate binding
Structure of a calcium-deficient form of influenza virus neuraminidase
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11
Chemistry in Australia
Ward
Colin W.
Lawrence
Michael C.
McKern
Neil M.
http://search.informit.com.au/documentSummary;dn=297064867982648;res=IELAPA
5
Dec 2006
2017-05-15 05:15:05
search.informit.com.au
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.
Landmarks in Insulin Research - the Determination of the Crystal Structure of the Human Insulin Receptor
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Lee
E. F.
Czabotar
P. E.
Smith
B. J.
Deshayes
K.
Zobel
K.
Colman
P. M.
Fairlie
W. D.
http://www.nature.com/cdd/journal/v14/n9/abs/4402178a.html
© 2007 Nature Publishing Group
1711-1713
June 15, 2007
2017-05-15 05:15:15
www.nature.com
en
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.
Crystal structure of ABT-737 complexed with Bcl-xL: implications for selectivity of antagonists of the Bcl-2 family
Crystal structure of ABT-737 complexed with Bcl-xL
14
9
Cell Death & Differentiation
ISSN 1350-9047
Cell Death Differ
DOI 10.1038/sj.cdd.4402178
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7
Acta Crystallographica Section D: Biological Crystallography
ISSN 0907-4449
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
DOI 10.1107/S0907444907025784
Newman
J.
Xu
J.
Willis
M. C.
http://scripts.iucr.org/cgi-bin/paper?bw5202
Copyright (c) 2007 International Union of Crystallography
826-832
2007-07-01
2017-05-15 05:15:22
scripts.iucr.org
en
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.
Initial evaluations of the reproducibility of vapor-diffusion crystallization
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Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309108016746
Burgess
B. R.
Dobson
R. C. J.
Dogovski
C.
Jameson
G. B.
Parker
M. W.
Perugini
M. A.
http://scripts.iucr.org/cgi-bin/paper?nj5016
Copyright (c) 2008 International Union of Crystallography
659-661
2008-07-01
2017-05-15 05:15:31
scripts.iucr.org
en
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.
Purification, crystallization and preliminary X-ray diffraction studies to near-atomic resolution of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus
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64
3
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309108002819
Dobson
R. C. J.
Atkinson
S. C.
Gorman
M. A.
Newman
J. M.
Parker
M. W.
Perugini
M. A.
http://scripts.iucr.org/cgi-bin/paper?ll5142
Copyright (c) 2008 International Union of Crystallography
206-208
2008-03-01
2017-05-15 05:15:44
scripts.iucr.org
en
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.
The purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Clostridium botulinum
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8
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309108017600
Jackson
C. J.
Hadler
K. S.
Carr
P. D.
Oakley
A. J.
Yip
S.
Schenk
G.
Ollis
D. L.
http://scripts.iucr.org/cgi-bin/paper?gx5133
Copyright (c) 2008 International Union of Crystallography
681-685
2008-08-01
2017-05-15 05:15:53
scripts.iucr.org
en
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.
Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference
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5
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309108011512
Jackson
C. J.
Taylor
M. C.
Tattersall
D. B.
French
N. G.
Carr
P. D.
Ollis
D. L.
Russell
R. J.
Oakeshott
J. G.
http://scripts.iucr.org/cgi-bin/paper?hc5054
Copyright (c) 2008 International Union of Crystallography
435-437
2008-05-01
2017-05-15 05:16:02
scripts.iucr.org
en
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.
Cloning, expression, purification, crystallization and preliminary X-ray studies of a pyridoxine 5′-phosphate oxidase from Mycobacterium smegmatis
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15
10
Cell Death & Differentiation
ISSN 1350-9047
Cell Death Differ
DOI 10.1038/cdd.2008.83
Kvansakul
M.
Yang
H.
Fairlie
W. D.
Czabotar
P. E.
Fischer
S. F.
Perugini
M. A.
Huang
D. C. S.
Colman
P. M.
apoptosis
apoptosis
Bcl-2
Bcl-2
BH4 domain
BH4 domain
vaccinia virus
vaccinia virus
http://www.nature.com/cdd/journal/v15/n10/abs/cdd200883a.html
© 2008 Nature Publishing Group
1564-1571
June 13, 2008
2017-05-15 05:16:12
www.nature.com
en
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 BH3-binding profile, with sub-micromolar affinity only for the BH3 peptide of pro-apoptotic Bim and low micromolar affinity for the BH3 peptides of Bak and Bax. This binding interaction is sensitive to F1L mutations within the predicted canonical BH3-binding groove, suggesting parallels between how vaccinia virus F1L and myxoma virus M11L bind BH3 domains. Structural comparison of F1L with other Bcl-2 family members reveals a novel sequence signature that redefines the BH4 domain as a structural motif present in both pro- and anti-apoptotic Bcl-2 members, including viral Bcl-2-like proteins.
Vaccinia virus anti-apoptotic F1L is a novel Bcl-2-like domain-swapped dimer that binds a highly selective subset of BH3-containing death ligands
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377
1
Journal of Molecular Biology
ISSN 0022-2836
Journal of Molecular Biology
DOI 10.1016/j.jmb.2007.12.036
Miles
Luke A.
Wun
Kwok S.
Crespi
Gabriela A. N.
Fodero-Tavoletti
Michelle T.
Galatis
Denise
Bagley
Christopher J.
Beyreuther
Konrad
Masters
Colin L.
Cappai
Roberto
McKinstry
William J.
Barnham
Kevin J.
Parker
Michael W.
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
http://www.sciencedirect.com/science/article/pii/S002228360701649X
181-192
March 14, 2008
2017-05-15 05:16:21
ScienceDirect
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 WO2, 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 WO2 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 WO2 inhibits these interactions. Thus, antibodies that target the N-terminal region of Aβ, such as WO2, hold promise for therapeutic development.
Amyloid-β–Anti-Amyloid-β Complex Structure Reveals an Extended Conformation in the Immunodominant B-Cell Epitope
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64
11
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309108029667
Newman
J.
Pham
T. M.
Peat
T. S.
http://scripts.iucr.org/cgi-bin/paper?bw5251
Copyright (c) 2008 International Union of Crystallography
991-996
2008-11-01
2017-05-15 05:16:30
scripts.iucr.org
en
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.
Phoenito experiments: combining the strengths of commercial crystallization automation
Phoenito experiments
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64
5
Acta Crystallographica Section F: Structural Biology and Crystallization Communications
ISSN 1744-3091
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
DOI 10.1107/S1744309108011718
Wun
K. S.
Miles
L. A.
Crespi
G. a. N.
Wycherley
K.
Ascher
D. B.
Barnham
K. J.
Cappai
R.
Beyreuther
K.
Masters
C. L.
Parker
M. W.
McKinstry
W. J.
http://scripts.iucr.org/cgi-bin/paper?bw5237
Copyright (c) 2008 International Union of Crystallography
438-441
2008-05-01
2017-05-15 05:16:46
scripts.iucr.org
en
The murine monoclonal antibody WO2 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 WO2 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 WO2 Fab were grown in polyethylene glycol solutions containing ZnSO4; they belonged to the orthorhombic space group P212121 and diffracted to 1.6 Å resolution. The complexes of WO2 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 WO2 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.
Crystallization and preliminary X-ray diffraction analysis of the Fab fragment of WO2, an antibody specific for the Aβ peptides associated with Alzheimer's disease
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12
Acta Crystallographica Section D: Biological Crystallography
ISSN 0907-4449
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
DOI 10.1107/S0907444905033202
Peat
T. S.
Christopher
J. A.
Newman
J.
http://scripts.iucr.org/cgi-bin/paper?en5128
Copyright (c) 2005 International Union of Crystallography
1662-1669
2005-12-01
2017-05-16 01:35:21
scripts.iucr.org
en
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.
Tapping the Protein Data Bank for crystallization information
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