1
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Flood R, Mockler NM, Thureau A, Malinska M, Crowley PB. Supramolecular Synthons in Protein-Ligand Frameworks. CRYSTAL GROWTH & DESIGN 2024; 24:2149-2156. [PMID: 38463617 PMCID: PMC10921380 DOI: 10.1021/acs.cgd.3c01480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 03/12/2024]
Abstract
Supramolecular synthons, defined as reproducible intermolecular structural units, have greatly aided small molecule crystal engineering. In this paper, we propose that supramolecular synthons guide ligand-mediated protein crystallization. The protein RSL and the macrocycle sulfonato-calix[8]arene cocrystallize in at least four ways. One of these cocrystals is a highly porous cube comprising protein nodes connected by calixarene dimers. We show that mutating an aspartic acid to an asparagine results in two new cubic assemblies that depend also on the crystallization method. One of the new cubic arrangements is mediated by calixarene trimers and has a ∼30% increased cell volume relative to the original crystal with calixarene dimers. Crystals of the sulfonato-calix[8]arene sodium salt were obtained from buffered conditions similar to those used to grow the protein-calix[8]arene cocrystals. X-ray analysis reveals a coordination polymer of the anionic calix[8]arene and sodium cation in which the macrocycle is arranged as staggered stacks of the pleated loop conformation. Remarkably, the calixarene packing arrangement is the same in the simple salt as in the protein cocrystal. With the pleated loop conformation, the calixarene presents an extended surface for binding other calixarenes (oligomerization) as well as binding to a protein patch (biomolecular complexation). Small-angle X-ray scattering data suggest pH-dependent calixarene assembly in solution. Therefore, the calix[8]arene-calix[8]arene structural unit may be regarded as a supramolecular synthon that directs at least two types of protein assembly, suggesting applications in protein crystal engineering.
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Affiliation(s)
- Ronan
J. Flood
- SSPC,
Science Foundation Ireland Research Centre for Pharmaceuticals, School
of Biological and Chemical Sciences, University
of Galway, University
Road, Galway H91 TK33, Ireland
| | - Niamh M. Mockler
- SSPC,
Science Foundation Ireland Research Centre for Pharmaceuticals, School
of Biological and Chemical Sciences, University
of Galway, University
Road, Galway H91 TK33, Ireland
| | - Aurélien Thureau
- Synchrotron
SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, Cedex, Gif-sur-Yvette 91192, France
| | - Maura Malinska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Peter B. Crowley
- SSPC,
Science Foundation Ireland Research Centre for Pharmaceuticals, School
of Biological and Chemical Sciences, University
of Galway, University
Road, Galway H91 TK33, Ireland
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2
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Through Diffusion Measurements of Molecules to a Numerical Model for Protein Crystallization in Viscous Polyethylene Glycol Solution. CRYSTALS 2022. [DOI: 10.3390/cryst12070881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Protein crystallography has become a popular method for biochemists, but obtaining high-quality protein crystals for precise structural analysis and larger ones for neutron analysis requires further technical progress. Many studies have noted the importance of solvent viscosity for the probability of crystal nucleation and for mass transportation; therefore, in this paper, we have reported on experimental results and simulation studies regarding the use of viscous polyethylene glycol (PEG) solvents for protein crystals. We investigated the diffusion rates of proteins, peptides, and small molecules in viscous PEG solvents using fluorescence correlation spectroscopy. In high-molecular-weight PEG solutions (molecular weights: 10,000 and 20,000), solute diffusion showed deviations, with a faster diffusion than that estimated by the Stokes–Einstein equation. We showed that the extent of the deviation depends on the difference between the molecular sizes of the solute and PEG solvent, and succeeded in creating equations to predict diffusion coefficients in viscous PEG solutions. Using these equations, we have developed a new numerical model of 1D diffusion processes of proteins and precipitants in a counter-diffusion chamber during crystallization processes. Examples of the application of anomalous diffusion in counter-diffusion crystallization are shown by the growth of lysozyme crystals.
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3
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Bellini D. A drug-discovery-oriented non-invasive protocol for protein crystal cryoprotection by dehydration, with application for crystallization screening. J Appl Crystallogr 2022; 55:370-379. [PMID: 35497658 PMCID: PMC8985602 DOI: 10.1107/s1600576722002382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/01/2022] [Indexed: 11/10/2022] Open
Abstract
In X-ray macromolecular crystallography, cryoprotection of crystals mounted on harvesting loops is achieved when the water in the sample solvent transitions to vitreous ice before crystalline ice forms. This is achieved by rapid cooling in liquid nitro-gen or propane. Protocols for protein crystal cryoprotection are based on either increasing the environmental pressure or reducing the water fraction in the solvent. This study presents a new protocol for cryoprotecting crystals. It is based on vapour diffusion dehydration of the crystal drop to reduce the water fraction in the solvent by adding a highly concentrated salt solution, 13 M potassium formate (KF13), directly to the reservoir. Several salt solutions were screened to identify KF13 as optimal. Cryoprotection using the KF13 protocol is non-invasive to the crystal, high throughput and easy to implement, can benefit diffraction resolution and ligand binding, and is very useful in cases with high redundancy such as drug-discovery projects which use very large compound or fragment libraries. An application of KF13 to discover new crystal hits from clear drops of equilibrated crystallization screening plates is also shown.
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Affiliation(s)
- Dom Bellini
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, Cambridgeshire CB2 0QH, United Kingdom
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4
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Abstract
The three-dimensional structure of protein is determined by analyzing diffraction data collected using X-ray beams. However, X-ray beam can damage protein crystals during data collection, lowering the quality of the crystal data. A way to prevent such damage is by treating protein crystals with cryoprotectants. The cryoprotectant stabilizes the protein crystal and prevents lowering the quality of the diffraction data. Many kinds of cryoprotectants are commercially available, and various treatment methods have also been reported. However, incorrect selection or treatment of such cryoprotectants may lead to deterioration of crystal diffraction data when using X-ray beams.
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5
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Subedi P, Paxman JJ, Wang G, Hor L, Hong Y, Verderosa AD, Whitten AE, Panjikar S, Santos-Martin CF, Martin JL, Totsika M, Heras B. Salmonella enterica BcfH Is a Trimeric Thioredoxin-Like Bifunctional Enzyme with Both Thiol Oxidase and Disulfide Isomerase Activities. Antioxid Redox Signal 2021; 35:21-39. [PMID: 33607928 DOI: 10.1089/ars.2020.8218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Aims: Thioredoxin (TRX)-fold proteins are ubiquitous in nature. This redox scaffold has evolved to enable a variety of functions, including redox regulation, protein folding, and oxidative stress defense. In bacteria, the TRX-like disulfide bond (Dsb) family mediates the oxidative folding of multiple proteins required for fitness and pathogenic potential. Conventionally, Dsb proteins have specific redox functions with monomeric and dimeric Dsbs exclusively catalyzing thiol oxidation and disulfide isomerization, respectively. This contrasts with the eukaryotic disulfide forming machinery where the modular TRX protein disulfide isomerase (PDI) mediates thiol oxidation and disulfide reshuffling. In this study, we identified and structurally and biochemically characterized a novel Dsb-like protein from Salmonella enterica termed bovine colonization factor protein H (BcfH) and defined its role in virulence. Results: In the conserved bovine colonization factor (bcf) fimbrial operon, the Dsb-like enzyme BcfH forms a trimeric structure, exceptionally uncommon among the large and evolutionary conserved TRX superfamily. This protein also displays very unusual catalytic redox centers, including an unwound α-helix holding the redox active site and a trans-proline instead of the conserved cis-proline active site loop. Remarkably, BcfH displays both thiol oxidase and disulfide isomerase activities contributing to Salmonella fimbrial biogenesis. Innovation and Conclusion: Typically, oligomerization of bacterial Dsb proteins modulates their redox function, with monomeric and dimeric Dsbs mediating thiol oxidation and disulfide isomerization, respectively. This study demonstrates a further structural and functional malleability in the TRX-fold protein family. BcfH trimeric architecture and unconventional catalytic sites permit multiple redox functions emulating in bacteria the eukaryotic PDI dual oxidoreductase activity. Antioxid. Redox Signal. 35, 21-39.
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Affiliation(s)
- Pramod Subedi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Jason J Paxman
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Geqing Wang
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Lilian Hor
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Yaoqin Hong
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Anthony D Verderosa
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Andrew E Whitten
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, Australia
| | - Santosh Panjikar
- Macromolecular Crystallography, Australian Synchrotron, ANSTO, Clayton, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Carlos F Santos-Martin
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Jennifer L Martin
- Griffith Institute for Drug Discovery, Brisbane Innovation Park, Nathan, Australia.,Vice-Chancellor's Unit, University of Wollongong, Wollongong, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
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6
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Yucel B, Robinson GK, Shepherd M. The copper‐responsive ScsC protein of
Salmonella
promotes intramacrophage survival and interacts with the arginine sensor ArtI. FEBS J 2020; 287:3827-3840. [DOI: 10.1111/febs.15285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 02/20/2020] [Accepted: 03/06/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Buke Yucel
- RAPID Group School of Biosciences University of Kent Canterbury UK
| | - Gary K. Robinson
- RAPID Group School of Biosciences University of Kent Canterbury UK
| | - Mark Shepherd
- RAPID Group School of Biosciences University of Kent Canterbury UK
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7
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Applications of X-ray Powder Diffraction in Protein Crystallography and Drug Screening. CRYSTALS 2020. [DOI: 10.3390/cryst10020054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Providing fundamental information on intra/intermolecular interactions and physicochemical properties, the three-dimensional structural characterization of biological macromolecules is of extreme importance towards understanding their mechanism of action. Among other methods, X-ray powder diffraction (XRPD) has proved its applicability and efficiency in numerous studies of different materials. Owing to recent methodological advances, this method is now considered a respectable tool for identifying macromolecular phase transitions, quantitative analysis, and determining structural modifications of samples ranging from small organics to full-length proteins. An overview of the XRPD applications and recent improvements related to the study of challenging macromolecules and peptides toward structure-based drug design is discussed. This review congregates recent studies in the field of drug formulation and delivery processes, as well as in polymorph identification and the effect of ligands and environmental conditions upon crystal characteristics. These studies further manifest the efficiency of protein XRPD for quick and accurate preliminary structural characterization.
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8
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Trampari S, Valmas A, Logotheti S, Saslis S, Fili S, Spiliopoulou M, Beckers D, Degen T, Nénert G, Fitch AN, Calamiotou M, Karavassili F, Margiolaki I. In situ detection of a novel lysozyme monoclinic crystal form upon controlled relative humidity variation. J Appl Crystallogr 2018. [DOI: 10.1107/s1600576718013936] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The effect of relative humidity (rH) on protein crystal structures, an area that has attracted high scientific interest during the past decade, is investigated in this study on hen egg-white lysozyme (HEWL) polycrystalline precipitates via in situ laboratory X-ray powder diffraction (XRPD) measurements. For this purpose, HEWL was crystallized at room temperature and pH 4.5, leading to a novel monoclinic HEWL phase which, to our knowledge, has not been reported before. Analysis of XRPD data collected upon rH variation revealed several structural modifications. These observations, on a well-studied molecule like HEWL, underline not only the high impact of humidity levels on biological crystal structures, but also the significance of in-house XRPD as an analytical tool in industrial drug development and its potential to provide information for enhancing manufacturing of pharmaceuticals.
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9
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Totsika M, Vagenas D, Paxman JJ, Wang G, Dhouib R, Sharma P, Martin JL, Scanlon MJ, Heras B. Inhibition of Diverse DsbA Enzymes in Multi-DsbA Encoding Pathogens. Antioxid Redox Signal 2018; 29:653-666. [PMID: 29237285 PMCID: PMC6067686 DOI: 10.1089/ars.2017.7104] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
AIMS DsbA catalyzes disulfide bond formation in secreted and outer membrane proteins in bacteria. In pathogens, DsbA is a major facilitator of virulence constituting a target for antivirulence antimicrobial development. However, many pathogens encode multiple and diverse DsbA enzymes for virulence factor folding during infection. The aim of this study was to determine whether our recently identified inhibitors of Escherichia coli K-12 DsbA can inhibit the diverse DsbA enzymes found in two important human pathogens and attenuate their virulence. RESULTS DsbA inhibitors from two chemical classes (phenylthiophene and phenoxyphenyl derivatives) inhibited the virulence of uropathogenic E. coli and Salmonella enterica serovar Typhimurium, encoding two and three diverse DsbA homologues, respectively. Inhibitors blocked the virulence of dsbA null mutants complemented with structurally diverse DsbL and SrgA, suggesting that they were not selective for prototypical DsbA. Structural characterization of DsbA-inhibitor complexes showed that compounds from each class bind in a similar region of the hydrophobic groove adjacent to the Cys30-Pro31-His32-Cys33 (CPHC) active site. Modeling of DsbL- and SrgA-inhibitor interactions showed that these accessory enzymes could accommodate the inhibitors in their different hydrophobic grooves, supporting our in vivo findings. Further, we identified highly conserved residues surrounding the active site for 20 diverse bacterial DsbA enzymes, which could be exploited in developing inhibitors with a broad spectrum of activity. Innovation and Conclusion: We have developed tools to analyze the specificity of DsbA inhibitors in bacterial pathogens encoding multiple DsbA enzymes. This work demonstrates that DsbA inhibitors can be developed to target diverse homologues found in bacteria. Antioxid. Redox Signal. 29, 653-666.
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Affiliation(s)
- Makrina Totsika
- 1 Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology , Queensland, Australia
| | - Dimitrios Vagenas
- 1 Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology , Queensland, Australia
| | - Jason J Paxman
- 2 Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University , Bundoora, Australia
| | - Geqing Wang
- 2 Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University , Bundoora, Australia
| | - Rabeb Dhouib
- 1 Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology , Queensland, Australia
| | - Pooja Sharma
- 3 Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Australia
| | - Jennifer L Martin
- 4 Institute for Molecular Bioscience, University of Queensland , Queensland, Australia
| | - Martin J Scanlon
- 3 Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Australia
| | - Begoña Heras
- 2 Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University , Bundoora, Australia
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10
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Bowler MG, Bowler DR, Bowler MW. Raoult's law revisited: accurately predicting equilibrium relative humidity points for humidity control experiments. J Appl Crystallogr 2017; 50:631-638. [PMID: 28381983 PMCID: PMC5377353 DOI: 10.1107/s1600576717003636] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/07/2017] [Indexed: 11/16/2022] Open
Abstract
The humidity surrounding a sample is an important variable in scientific experiments. Biological samples in particular require not just a humid atmosphere but often a relative humidity (RH) that is in equilibrium with a stabilizing solution required to maintain the sample in the same state during measurements. The controlled dehydration of macromolecular crystals can lead to significant increases in crystal order, leading to higher diffraction quality. Devices that can accurately control the humidity surrounding crystals while monitoring diffraction have led to this technique being increasingly adopted, as the experiments become easier and more reproducible. Matching the RH to the mother liquor is the first step in allowing the stable mounting of a crystal. In previous work [Wheeler, Russi, Bowler & Bowler (2012). Acta Cryst. F68, 111-114], the equilibrium RHs were measured for a range of concentrations of the most commonly used precipitants in macromolecular crystallography and it was shown how these related to Raoult's law for the equilibrium vapour pressure of water above a solution. However, a discrepancy between the measured values and those predicted by theory could not be explained. Here, a more precise humidity control device has been used to determine equilibrium RH points. The new results are in agreement with Raoult's law. A simple argument in statistical mechanics is also presented, demonstrating that the equilibrium vapour pressure of a solvent is proportional to its mole fraction in an ideal solution: Raoult's law. The same argument can be extended to the case where the solvent and solute molecules are of different sizes, as is the case with polymers. The results provide a framework for the correct maintenance of the RH surrounding a sample.
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Affiliation(s)
- Michael G. Bowler
- Department of Physics, University of Oxford, Keble Road, Oxford OX1 3RH, UK
| | - David R. Bowler
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181, Grenoble F-38042, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes–EMBL–CNRS, 71 avenue des Martyrs, CS 90181, Grenoble F-38042, France
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11
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Abstract
Protein crystallization was discovered by chance nearly 200 years ago and was developed in the late nineteenth century as a powerful purification tool, and a demonstration of chemical purity. The crystallization of proteins, nucleic acids, and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule, but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild precipitating agents such as neutral salts or polymers, and by manipulation of various parameters that include temperature, ionic strength, and pH. Also important in the crystallization process are factors that can affect the structural state of the macromolecule, such as metal ions, inhibitors, cofactors, or other conventional small molecules. A variety of approaches have been developed that combine the spectrum of factors that effect and promote crystallization, and among the most widely used are vapor diffusion, dialysis, batch, and liquid-liquid diffusion. Successes in macromolecular crystallization have multiplied rapidly in recent years due to the advent of practical, easy-to-use screening kits, and the application of laboratory robotics.
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Affiliation(s)
- Alexander McPherson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA.
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12
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Eng WS, Hocková D, Špaček P, Baszczyňski O, Janeba Z, Naesens L, Keough DT, Guddat LW. Crystal Structures of Acyclic Nucleoside Phosphonates in Complex withEscherichia coliHypoxanthine Phosphoribosyltransferase. ChemistrySelect 2016. [DOI: 10.1002/slct.201601679] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wai Soon Eng
- The School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane, Queensland 4068 Australia
| | - Dana Hocková
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i. Flemingovo nam. 2, CZ- 166 10 Prague 6 Czech Republic
| | - Petr Špaček
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i. Flemingovo nam. 2, CZ- 166 10 Prague 6 Czech Republic
| | - Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i. Flemingovo nam. 2, CZ- 166 10 Prague 6 Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i. Flemingovo nam. 2, CZ- 166 10 Prague 6 Czech Republic
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven; University of Leuven; Minderbroedersstraat 10, B- 3000 Leuven Belgium
| | - Dianne T. Keough
- The School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane, Queensland 4068 Australia
| | - Luke W. Guddat
- The School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane, Queensland 4068 Australia
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13
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Park H, Tran T, Lee JH, Park H, Disney MD. Controlled dehydration improves the diffraction quality of two RNA crystals. BMC STRUCTURAL BIOLOGY 2016; 16:19. [PMID: 27809904 PMCID: PMC5093936 DOI: 10.1186/s12900-016-0069-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/18/2016] [Indexed: 01/07/2023]
Abstract
BACKGROUND Post-crystallization dehydration methods, applying either vapor diffusion or humidity control devices, have been widely used to improve the diffraction quality of protein crystals. Despite the fact that RNA crystals tend to diffract poorly, there is a dearth of reports on the application of dehydration methods to improve the diffraction quality of RNA crystals. RESULTS We use dehydration techniques with a Free Mounting System (FMS, a humidity control device) to recover the poor diffraction quality of RNA crystals. These approaches were applied to RNA constructs that model various RNA-mediated repeat expansion disorders. CONCLUSION The method we describe herein could serve as a general tool to improve diffraction quality of RNA crystals to facilitate structure determinations.
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Affiliation(s)
- HaJeung Park
- X-ray Core Facility, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Tuan Tran
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990 Republic of Korea ,Department of Polar Sciences, University of Science and Technology, Incheon, 21990 Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990 Republic of Korea ,Department of Polar Sciences, University of Science and Technology, Incheon, 21990 Republic of Korea
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458 USA
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14
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Lafaye C, Van Molle I, Tamu Dufe V, Wahni K, Boudier A, Leroy P, Collet JF, Messens J. Sulfur Denitrosylation by an Engineered Trx-like DsbG Enzyme Identifies Nucleophilic Cysteine Hydrogen Bonds as Key Functional Determinant. J Biol Chem 2016; 291:15020-8. [PMID: 27226614 DOI: 10.1074/jbc.m116.729426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 11/06/2022] Open
Abstract
Exposure of bacteria to NO results in the nitrosylation of cysteine thiols in proteins and low molecular weight thiols such as GSH. The cells possess enzymatic systems that catalyze the denitrosylation of these modified sulfurs. An important player in these systems is thioredoxin (Trx), a ubiquitous, cytoplasmic oxidoreductase that can denitrosylate proteins in vivo and S-nitrosoglutathione (GSNO) in vitro However, a periplasmic or extracellular denitrosylase has not been identified, raising the question of how extracytoplasmic proteins are repaired after nitrosative damage. In this study, we tested whether DsbG and DsbC, two Trx family proteins that function in reducing pathways in the Escherichia coli periplasm, also possess denitrosylating activity. Both DsbG and DsbC are poorly reactive toward GSNO. Moreover, DsbG is unable to denitrosylate its specific substrate protein, YbiS. Remarkably, by borrowing the CGPC active site of E. coli Trx-1 in combination with a T200M point mutation, we transformed DsbG into an enzyme highly reactive toward GSNO and YbiS. The pKa of the nucleophilic cysteine, as well as the redox and thermodynamic properties of the engineered DsbG are dramatically changed and become similar to those of E. coli Trx-1. X-ray structural insights suggest that this results from a loss of two direct hydrogen bonds to the nucleophilic cysteine sulfur in the DsbG mutant. Our results highlight the plasticity of the Trx structural fold and reveal that the subtle change of the number of hydrogen bonds in the active site of Trx-like proteins is the key factor that thermodynamically controls reactivity toward nitrosylated compounds.
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Affiliation(s)
- Céline Lafaye
- From the de Duve Institute, Université Catholique de Louvain, B-1200 Brussels, Belgium, WELBIO, B-1200 Brussels, Belgium, the Brussels Center for Redox Biology, B-1050 Brussels, Belgium
| | - Inge Van Molle
- the Brussels Center for Redox Biology, B-1050 Brussels, Belgium, the Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050 Brussels, Belgium, the Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium, and
| | - Veronica Tamu Dufe
- From the de Duve Institute, Université Catholique de Louvain, B-1200 Brussels, Belgium, WELBIO, B-1200 Brussels, Belgium, the Brussels Center for Redox Biology, B-1050 Brussels, Belgium, the Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050 Brussels, Belgium, the Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium, and
| | - Khadija Wahni
- the Brussels Center for Redox Biology, B-1050 Brussels, Belgium, the Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050 Brussels, Belgium, the Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium, and
| | - Ariane Boudier
- the Université de Lorraine, Faculté de Pharmacie, 54000 Nancy, France
| | - Pierre Leroy
- the Université de Lorraine, Faculté de Pharmacie, 54000 Nancy, France
| | - Jean-François Collet
- From the de Duve Institute, Université Catholique de Louvain, B-1200 Brussels, Belgium, WELBIO, B-1200 Brussels, Belgium, the Brussels Center for Redox Biology, B-1050 Brussels, Belgium,
| | - Joris Messens
- the Brussels Center for Redox Biology, B-1050 Brussels, Belgium, the Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050 Brussels, Belgium, the Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium, and
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15
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Huang Q, Szebenyi DME. Improving diffraction resolution using a new dehydration method. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2016; 72:152-9. [PMID: 26841767 DOI: 10.1107/s2053230x16000261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/06/2016] [Indexed: 11/10/2022]
Abstract
The production of high-quality crystals is one of the major obstacles in determining the three-dimensional structure of macromolecules by X-ray crystallography. It is fairly common that a visually well formed crystal diffracts poorly to a resolution that is too low to be suitable for structure determination. Dehydration has proven to be an effective post-crystallization treatment for improving crystal diffraction quality. Several dehydration methods have been developed, but no single one of them is suitable for all crystals. Here, a new convenient and effective dehydration method is reported that makes use of a dehydrating solution that will not dry out in air for several hours. Using this dehydration method, the resolution of Archaeoglobus fulgidus Cas5a crystals has been increased from 3.2 to 1.95 Å and the resolution of Escherichia coli LptA crystals has been increased from <5 to 3.4 Å.
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Klingl S, Scherer M, Stamminger T, Muller YA. Controlled crystal dehydration triggers a space-group switch and shapes the tertiary structure of cytomegalovirus immediate-early 1 (IE1) protein. ACTA ACUST UNITED AC 2015; 71:1493-504. [PMID: 26143921 DOI: 10.1107/s1399004715008792] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/06/2015] [Indexed: 11/10/2022]
Abstract
Cytomegalovirus immediate-early 1 (IE1) protein is a key viral effector protein that reprograms host cells. Controlled dehydration experiments with IE1 crystals not only extended their diffraction limit from 2.85 to 2.3 Å resolution but also triggered a monoclinic to tetragonal space-group transition with only minor alterations in the unit-cell parameters. An analysis of the pre-dehydration and post-dehydration crystal structures shows how dehydration rearranges the packing of IE1 molecules to meet the unit-cell constraints of the higher lattice symmetry. The transition from P21 to P43 reduces the number of copies in the asymmetric unit from four to two, and molecules previously related by noncrystallographic symmetry merge into identical crystallographic copies in the tetragonal space group. At the same time, dehydration considerably alters the tertiary structure of one of the two remaining IE1 chains in the asymmetric unit. It appears that this conformational switch is required to compensate for a transition that is assumed to be unfavourable, namely from a highly preferred to a rarely observed space group. At the same time, the dehydration-triggered molecular reshaping could reveal an inherent molecular flexibility that possibly informs on the biological function of IE1, namely on its binding to target proteins from the host cell.
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Affiliation(s)
- Stefan Klingl
- Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestrasse 91, 91052 Erlangen, Germany
| | - Myriam Scherer
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nuremberg, Schlossgarten 4, 91054 Erlangen, Germany
| | - Thomas Stamminger
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nuremberg, Schlossgarten 4, 91054 Erlangen, Germany
| | - Yves A Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestrasse 91, 91052 Erlangen, Germany
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Kawahara K, Oki H, Fukakusa S, Maruno T, Kobayashi Y, Motooka D, Taniguchi T, Honda T, Iida T, Nakamura S, Ohkubo T. Cloning, expression, purification, crystallization and X-ray crystallographic analysis of CofB, the minor pilin subunit of CFA/III from human enterotoxigenic Escherichia coli. Acta Crystallogr F Struct Biol Commun 2015; 71:663-7. [PMID: 26057791 PMCID: PMC4461326 DOI: 10.1107/s2053230x15005890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 03/24/2015] [Indexed: 11/11/2022] Open
Abstract
Colonization factor antigen III (CFA/III) is one of the virulence factors of human enterotoxigenic Escherichia coli (ETEC) that forms the long, thin, proteinaceous fibres of type IV pili through assembly of its major and minor subunits CofA and CofB, respectively. The crystal structure of CofA has recently been reported; however, the lack of structural information for CofB, the largest among the known type IV pilin subunits, hampers a comprehensive understanding of CFA/III pili. In this study, constructs of wild-type CofB with an N-terminal truncation and the corresponding SeMet derivative were cloned, expressed, purified and crystallized. The crystals belonged to the rhombohedral space group R32, with unit-cell parameters a = b = 103.97, c = 364.57 Å for the wild-type construct and a = b = 103.47, c = 362.08 Å for the SeMet-derivatized form. Although the diffraction quality of these crystals was initially very poor, dehydration of the crystals substantially improved the resolution limit from ∼ 4.0 to ∼ 2.0 Å. The initial phase was solved by the single-wavelength anomalous dispersion (SAD) method using a dehydrated SeMet CofB crystal, which resulted in an interpretable electron-density map.
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Affiliation(s)
- Kazuki Kawahara
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroya Oki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shunsuke Fukakusa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Center for Research of Ancient Culture, Nara Women’s University, Kita-Uoya-Nishi Machi, Nara, Nara 630-8506, Japan
| | - Takahiro Maruno
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuji Kobayashi
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tooru Taniguchi
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Honda
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Iida
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tadayasu Ohkubo
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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Kang J, Park YW, Yeo HK, Lee JY. Crystallization and preliminary X-ray diffraction analysis of the arginine repressor ArgR from Bacillus halodurans. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:291-4. [PMID: 25760703 DOI: 10.1107/s2053230x15000904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 01/15/2015] [Indexed: 11/10/2022]
Abstract
The arginine repressor (ArgR) is a transcriptional regulator which regulates genes encoding proteins involved in arginine biosynthesis and the arginine catabolic pathway. ArgR from the alkaliphilic bacterium Bacillus halodurans was cloned and overexpressed in Escherichia coli. ArgR (Bh2777) from B. halodurans is composed of 149 amino-acid residues with a molecular mass of 16 836 Da. ArgR was crystallized at 296 K using 1,2-propanediol as a precipitant. Crystals of N-terminally His-tagged ArgR were obtained by the sitting-drop vapour-diffusion method. Dehydrated crystals showed a dramatic improvement in diffraction quality and diffracted to 2.35 Å resolution. The crystals belonged to the cubic space group I23, with unit-cell parameters a = b = c = 104.68 Å. The asymmetric unit contained one monomer of ArgR, which generates a trimer by the threefold axis of the space group, giving a crystal volume per mass (VM) of 2.98 Å(3) Da(-1) and a solvent content of 56.8%.
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Affiliation(s)
- Jina Kang
- Department of Life Science, Dongguk University, 30 Pildong-rho 1-gil, Jung-gu, Seoul 100-715, Republic of Korea
| | - Young Woo Park
- Department of Life Science, Dongguk University, 30 Pildong-rho 1-gil, Jung-gu, Seoul 100-715, Republic of Korea
| | - Hyun Ku Yeo
- Department of Life Science, Dongguk University, 30 Pildong-rho 1-gil, Jung-gu, Seoul 100-715, Republic of Korea
| | - Jae Young Lee
- Department of Life Science, Dongguk University, 30 Pildong-rho 1-gil, Jung-gu, Seoul 100-715, Republic of Korea
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McPherson A, Cudney B. Optimization of crystallization conditions for biological macromolecules. Acta Crystallogr F Struct Biol Commun 2014; 70:1445-67. [PMID: 25372810 PMCID: PMC4231845 DOI: 10.1107/s2053230x14019670] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 08/31/2014] [Indexed: 11/11/2022] Open
Abstract
For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success.
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Affiliation(s)
- Alexander McPherson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Bob Cudney
- Hampton Research, 34 Journey, Aliso Viejo, CA 92656-3317, USA
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Mazzorana M, Sanchez-Weatherby J, Sandy J, Lobley CMC, Sorensen T. An evaluation of adhesive sample holders for advanced crystallographic experiments. ACTA ACUST UNITED AC 2014; 70:2390-400. [PMID: 25195752 PMCID: PMC4157448 DOI: 10.1107/s1399004714014370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 06/18/2014] [Indexed: 05/28/2023]
Abstract
The hydration state of macromolecular crystals often affects their overall order and, ultimately, the quality of the X-ray diffraction pattern that they produce. Post-crystallization techniques that alter the solvent content of a crystal may induce rearrangement within the three-dimensional array making up the crystal, possibly resulting in more ordered packing. The hydration state of a crystal can be manipulated by exposing it to a stream of air at controlled relative humidity in which the crystal can equilibrate. This approach provides a way of exploring crystal hydration space to assess the diffraction capabilities of existing crystals. A key requirement of these experiments is to expose the crystal directly to the dehydrating environment by having the minimum amount of residual mother liquor around it. This is usually achieved by placing the crystal on a flat porous support (Kapton mesh) and removing excess liquid by wicking. Here, an alternative approach is considered whereby crystals are harvested using adhesives that capture naked crystals directly from their crystallization drop, reducing the process to a one-step procedure. The impact of using adhesives to ease the harvesting of different types of crystals is presented together with their contribution to background scattering and their usefulness in dehydration experiments. It is concluded that adhesive supports represent a valuable tool for mounting macromolecular crystals to be used in humidity-controlled experiments and to improve signal-to-noise ratios in diffraction experiments, and how they can protect crystals from modifications in the sample environment is discussed.
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Affiliation(s)
- Marco Mazzorana
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Juan Sanchez-Weatherby
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - James Sandy
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Carina M C Lobley
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Thomas Sorensen
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
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21
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Oka T, Hojo H. Single crystallization of an inverse bicontinuous cubic phase of a lipid. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8253-8257. [PMID: 25007349 DOI: 10.1021/la502002r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We report a simple method to produce a single crystal region of an inverse bicontinuous cubic (QII) phase of a lipid, 1-monoolein. By starting with the lipid of the sponge (L3) phase in the presence of 1,4-butanediol, we can obtain a single crystal region of the double-diamond QII phase in 1 week by controlled dilution of 1,4-butanediol. The length of the single crystal region in a 0.5 mm diameter capillary was on the order of millimeters. X-ray diffraction images of the region showed diffraction "spots", but not "rings" as in powder diffraction. The diffraction images also changed rotation angle dependently. We could assign Miller indices to all of the distinguishable diffraction spots from the region. This method would bring benefits to the basic and applied research areas of the Q phases.
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Affiliation(s)
- Toshihiko Oka
- Department of Physics, Graduate School of Science, §Nanomaterials Research Division, Research Institute of Electronics, and ‡Department of Physics, Faculty of Science, Shizuoka University , Shizuoka 422-8529, Japan
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22
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Botello-Morte L, Bes MT, Heras B, Fernández-Otal Á, Peleato ML, Fillat MF. Unraveling the redox properties of the global regulator FurA from Anabaena sp. PCC 7120: disulfide reductase activity based on its CXXC motifs. Antioxid Redox Signal 2014; 20:1396-406. [PMID: 24093463 PMCID: PMC3936511 DOI: 10.1089/ars.2013.5376] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
UNLABELLED Cyanobacterial FurA works as a global regulator linking iron homeostasis to photosynthetic metabolism and the responses to different environmental stresses. Additionally, FurA modulates several genes involved in redox homeostasis and fulfills the characteristics of a heme-sensor protein whose interaction with this cofactor negatively affects its DNA binding ability. FurA from Anabaena PCC 7120 contains five cysteine residues, four of them arranged in two redox CXXC motifs. AIMS Our goals were to analyze in depth the putative contribution of these CXXC motifs in the redox properties of FurA and to identify potential interacting partners of this regulator. RESULTS Insulin reduction assays unravel that FurA exhibits disulfide reductase activity. Simultaneous presence of both CXXC signatures greatly enhances the reduction rate, although the redox motif containing Cys(101) and Cys(104) seems a major contributor to this activity. Disulfide reductase activity was not detected in other ferric uptake regulator (Fur) proteins isolated from heterotrophic bacteria. In vivo, FurA presents different redox states involving intramolecular disulfide bonds when is partially oxidized. Redox potential values for CXXC motifs, -235 and -238 mV, are consistent with those reported for other proteins displaying disulfide reductase activity. Pull-down and two-hybrid assays unveil potential FurA interacting partners, namely phosphoribulokinase Alr4123, the hypothetical amidase-containing domain All1140 and the DNA-binding protein HU. INNOVATION A novel biochemical activity of cyanobacterial FurA based on its cysteine arrangements and the identification of novel interacting partners are reported. CONCLUSION The present study discloses a putative connection of FurA with the cyanobacterial redox-signaling pathway.
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Affiliation(s)
- Laura Botello-Morte
- 1 Department of Biochemistry and Molecular and Cell Biology, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza , Zaragoza, Spain
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Preparation, crystallization, and preliminary crystallographic analysis of wild-type and mutant human TREM-2 ectodomains linked to neurodegenerative and inflammatory diseases. Protein Expr Purif 2014; 96:32-8. [PMID: 24508568 DOI: 10.1016/j.pep.2014.01.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/28/2014] [Accepted: 01/29/2014] [Indexed: 11/22/2022]
Abstract
TREM-2 (triggering receptor expressed on myeloid cells-2) is an innate immune receptor expressed on dendritic cells, macrophages, osteoclasts, and microglia. Recent genetic studies have reported the occurrence of point mutations in TREM-2 that correlate with a dramatically increased risk for the development of neurodegenerative diseases, including Alzheimer's disease, frontotemporal dementia, and Parkinson's disease. Structural and biophysical studies of wild-type and mutant TREM-2 ectodomains are required to understand the functional consequences of these mutations. In order to facilitate these studies, we undertook the production and crystallization of these proteins. Here we demonstrate that, unlike many single Ig domain proteins, TREM-2 could not be readily refolded from bacterially-expressed inclusion bodies. Instead, we developed a mammalian-cell based expression system for the successful production of wild-type and mutant TREM-2 proteins in milligram quantities and a single-chromatography-step purification scheme that produced diffraction-quality crystals. These crystals diffract to a resolution of 3.3 Å and produce data sufficient for structure determination. We describe herein the procedures to produce wild-type and mutant human TREM-2 Ig domains in sufficient quantities for structural and biophysical studies. Such studies are crucial to understand the functional consequences of TREM-2 point mutations linked to the development of neurodegenerative diseases and, ultimately, to develop patient-specific molecular therapies to treat them.
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Middleton CL, Parker JL, Knott GJ, White MF, Bond CS. Crystal ‘Unengineering’: Reducing the Crystallisability of Sulfolobus solfataricus Hjc. Aust J Chem 2014. [DOI: 10.1071/ch14342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The protein Hjc from the thermophilic archaeon Sulfolobus solfataricus (Ss) presented many challenges to both structure solution and formation of stable complexes with its substrate, the DNA four-way or Holliday junction. As the challenges were caused by an uncharacteristically high propensity for rapid and promiscuous crystallisation, we investigated the molecular cause of this behaviour, corrected it by mutagenesis, and solved the X-ray crystal structures of the two mutants. An active site mutant SsHjcA32A crystallised in space group I23 (a 144.2 Å; 68 % solvent), and a deletion of a key crystal contact site, SsHjcδ62–63 crystallised in space group P21 (a 64.60, b 61.83, c 55.25 Å; β = 95.74°; 28 % solvent). Characterisation and comparative analysis of the structures are presented along with discussion of the pitfalls of the use of protein engineering to alter crystallisability while maintaining biological function.
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The antigen 43 structure reveals a molecular Velcro-like mechanism of autotransporter-mediated bacterial clumping. Proc Natl Acad Sci U S A 2013; 111:457-62. [PMID: 24335802 DOI: 10.1073/pnas.1311592111] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aggregation and biofilm formation are critical mechanisms for bacterial resistance to host immune factors and antibiotics. Autotransporter (AT) proteins, which represent the largest group of outer-membrane and secreted proteins in Gram-negative bacteria, contribute significantly to these phenotypes. Despite their abundance and role in bacterial pathogenesis, most AT proteins have not been structurally characterized, and there is a paucity of detailed information with regard to their mode of action. Here we report the structure-function relationships of Antigen 43 (Ag43a), a prototypic self-associating AT protein from uropathogenic Escherichia coli. The functional domain of Ag43a displays a twisted L-shaped β-helical structure firmly stabilized by a 3D hydrogen-bonded scaffold. Notably, the distinctive Ag43a L shape facilitates self-association and cell aggregation. Combining all our data, we define a molecular "Velcro-like" mechanism of AT-mediated bacterial clumping, which can be tailored to fit different bacterial lifestyles such as the formation of biofilms.
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Awad W, Svensson Birkedal G, Thunnissen MMGM, Mani K, Logan DT. Improvements in the order, isotropy and electron density of glypican-1 crystals by controlled dehydration. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2524-33. [PMID: 24311593 PMCID: PMC3852657 DOI: 10.1107/s0907444913025250] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/11/2013] [Indexed: 01/15/2023]
Abstract
The use of controlled dehydration for improvement of protein crystal diffraction quality is increasing in popularity, although there are still relatively few documented examples of success. A study has been carried out to establish whether controlled dehydration could be used to improve the anisotropy of crystals of the core protein of the human proteoglycan glypican-1. Crystals were subjected to controlled dehydration using the HC1 device. The optimal protocol for dehydration was developed by careful investigation of the following parameters: dehydration rate, final relative humidity and total incubation time Tinc. Of these, the most important was shown to be Tinc. After dehydration using the optimal protocol the crystals showed significantly reduced anisotropy and improved electron density, allowing the building of previously disordered parts of the structure.
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Affiliation(s)
- Wael Awad
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Box 124, 221 00 Lund, Sweden
- Department of Biophysics, Faculty of Science, Cairo University, Cairo, Egypt
| | - Gabriel Svensson Birkedal
- Department of Experimental Medical Science, Division of Neuroscience, Glycobiology Group, Lund University, Biomedical Center A13, 221 84 Lund, Sweden
| | - Marjolein M. G. M. Thunnissen
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Box 124, 221 00 Lund, Sweden
- MAX IV Laboratory, Lund University, Box 188, 221 00 Lund, Sweden
| | - Katrin Mani
- Department of Experimental Medical Science, Division of Neuroscience, Glycobiology Group, Lund University, Biomedical Center A13, 221 84 Lund, Sweden
| | - Derek T. Logan
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Box 124, 221 00 Lund, Sweden
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27
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Abergel C. Molecular replacement: tricks and treats. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2167-73. [PMID: 24189227 PMCID: PMC3817689 DOI: 10.1107/s0907444913015291] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 06/02/2013] [Indexed: 11/16/2022]
Abstract
Molecular replacement is the method of choice for X-ray crystallographic structure determination provided that suitable structural homologues are available in the PDB. Presently, there are ~80,000 structures in the PDB (8074 were deposited in the year 2012 alone), of which ~70% have been solved by molecular replacement. For successful molecular replacement the model must cover at least 50% of the total structure and the Cα r.m.s.d. between the core model and the structure to be solved must be less than 2 Å. Here, an approach originally implemented in the CaspR server (http://www.igs.cnrs-mrs.fr/Caspr2/index.cgi) based on homology modelling to search for a molecular-replacement solution is discussed. How the use of as much information as possible from different sources can improve the model(s) is briefly described. The combination of structural information with distantly related sequences is crucial to optimize the multiple alignment that will define the boundaries of the core domains. PDB clusters (sequences with ≥30% identical residues) can also provide information on the eventual changes in conformation and will help to explore the relative orientations assumed by protein subdomains. Normal-mode analysis can also help in generating series of conformational models in the search for a molecular-replacement solution. Of course, finding a correct solution is only the first step and the accuracy of the identified solution is as important as the data quality to proceed through refinement. Here, some possible reasons for failure are discussed and solutions are proposed using a set of successful examples.
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Affiliation(s)
- Chantal Abergel
- Information Génomique et Structurale, IGS UMR 7256, CNRS, Aix-Marseille Université, IMM, FR3479, 163 Avenue de Luminy – case 934, 13288 Marseille CEDEX 09, France
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Park S, Kim KY, Kim S, Crane BR. Crystallization and preliminary X-ray crystallographic analysis of Thermotoga maritima CheA P3-P4-P5 domains in complex with CheW. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:713-5. [PMID: 22684078 DOI: 10.1107/s174430911201826x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 04/24/2012] [Indexed: 11/10/2022]
Abstract
The CheA-CheW complex plays a key role in bacterial chemotaxis signal transduction by initiating phosphotransfer to response regulators via coupling to the chemoreceptors. CheA (P3-P4-P5 domains) and CheW from Thermotoga maritima were overexpressed in Escherichia coli and crystallized as a complex at 298 K using ammonium dihydrogen phosphate as a precipitant. X-ray diffraction data were collected to ~8 Å resolution at 100 K using synchrotron radiation. The crystal belonged to space group I222 or I2(1)2(1)2(1), with unit-cell parameters a = 184.2, b = 286.4, c = 327.7 Å. The asymmetric unit may contain six to ten CheA-CheW molecules.
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Affiliation(s)
- Sangyoun Park
- School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea
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29
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Increasing the X-ray diffraction power of protein crystals by dehydration: the case of bovine serum albumin and a survey of literature data. Int J Mol Sci 2012; 13:3782-3800. [PMID: 22489183 PMCID: PMC3317743 DOI: 10.3390/ijms13033782] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 03/07/2012] [Accepted: 03/08/2012] [Indexed: 12/19/2022] Open
Abstract
Serum albumin is one of the most widely studied proteins. It is the most abundant protein in plasma with a typical concentration of 5 g/100 mL and the principal transporter of fatty acids in plasma. While the crystal structures of human serum albumin (HSA) free and in complex with fatty acids, hemin, and local anesthetics have been characterized, no crystallographic models are available on bovine serum albumin (BSA), presumably because of the poor diffraction power of existing hexagonal BSA crystals. Here, the crystallization and diffraction data of a new BSA crystal form, obtained by the hanging drop method using MPEG 5K as precipitating agent, are presented. The crystals belong to space group C2, with unit-cell parameters a = 216.45 Å, b = 44.72 Å, c = 140.18 Å, β = 114.5°. Dehydration was found to increase the diffraction limit of BSA crystals from ~8 Å to 3.2 Å, probably by improving the packing of protein molecules in the crystal lattice. These results, together with a survey of more than 60 successful cases of protein crystal dehydration, confirm that it can be a useful procedure to be used in initial screening as a method of improving the diffraction limits of existing crystals.
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30
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Panjikar S, Stoeckigt J, O'Connor S, Warzecha H. The impact of structural biology on alkaloid biosynthesis research. Nat Prod Rep 2012; 29:1176-200. [DOI: 10.1039/c2np20057k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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31
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Wheeler MJ, Russi S, Bowler MG, Bowler MW. Measurement of the equilibrium relative humidity for common precipitant concentrations: facilitating controlled dehydration experiments. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:111-4. [PMID: 22232186 PMCID: PMC3253849 DOI: 10.1107/s1744309111054029] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 12/15/2011] [Indexed: 11/10/2022]
Abstract
The dehydration of crystals of macromolecules has long been known to have the potential to increase their diffraction quality. A number of methods exist to change the relative humidity that surrounds crystals, but for reproducible results, with complete characterization of the changes induced, a precise humidity-control device coupled with an X-ray source is required. The first step in these experiments is to define the relative humidity in equilibrium with the mother liquor of the system under study; this can often be quite time-consuming. In order to reduce the time spent on this stage of the experiment, the equilibrium relative humidity for a range of concentrations of the most commonly used precipitants has been measured. The relationship between the precipitant solution and equilibrium relative humidity is explained by Raoult's law for the equilibrium vapour pressure of water above a solution. The results also have implications for the choice of cryoprotectant and solutions used to dehydrate crystals. For the most commonly used precipitants (10-30% PEG 2000-8000), the starting point will be a relative humidity of 99.5%.
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Affiliation(s)
- Matthew J. Wheeler
- Structural Biology Group, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble, France
| | - Silvia Russi
- European Molecular Biology Laboratory, Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Michael G. Bowler
- Department of Physics, University of Oxford, Keble Road, Oxford OX1 3RH, England
| | - Matthew W. Bowler
- Structural Biology Group, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble, France
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Rojviriya C, Pratumrat T, Saper MA, Yuvaniyama J. Improved X-ray diffraction from Bacillus megaterium penicillin G acylase crystals through long cryosoaking dehydration. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1570-4. [PMID: 22139169 PMCID: PMC3232142 DOI: 10.1107/s1744309111040462] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 10/01/2011] [Indexed: 11/10/2022]
Abstract
Penicillin G acylase from Bacillus megaterium (BmPGA) is currently used in the pharmaceutical industry as an alternative to PGA from Escherichia coli (EcPGA) for the hydrolysis of penicillin G to produce 6-aminopenicillanic acid (6-APA), a penam nucleus for semisynthetic penicillins. Despite the significant differences in amino-acid sequence between PGAs from Gram-positive and Gram-negative bacteria, a representative PGA structure of Gram-positive origin has never been reported. In this study, crystallization and diffraction studies of BmPGA are described. Poor diffraction patterns with blurred spots at higher resolution were typical for BmPGA crystals cryocooled after a brief immersion in cryoprotectant solution. Overnight soaking in the same cryo-solution substantially improved both the mosaicity and resolution limit through the establishment of a new crystal-packing equilibrium. A crystal of BmPGA diffracted X-rays to 2.20 Å resolution and belonged to the monoclinic space group P2(1) with one molecule of BmPGA in the asymmetric unit.
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Affiliation(s)
- Catleya Rojviriya
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Rama 6 Road, Phayathai, Bangkok 10400, Thailand
| | - Thunyaluck Pratumrat
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Rama 6 Road, Phayathai, Bangkok 10400, Thailand
| | - Mark A. Saper
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
| | - Jirundon Yuvaniyama
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Rama 6 Road, Phayathai, Bangkok 10400, Thailand
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34
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Andres SN, Junop MS. Crystallization and preliminary X-ray diffraction analysis of the human XRCC4-XLF complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1399-402. [PMID: 22102241 PMCID: PMC3212460 DOI: 10.1107/s1744309111033549] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 08/17/2011] [Indexed: 11/10/2022]
Abstract
XRCC4 and XLF are key proteins in the repair of DNA double-strand breaks through nonhomologous end-joining. Together, they form a complex that stimulates the ligation of double-strand breaks. Owing to the suggested filamentous nature of this complex, structural studies via X-ray crystallography have proven difficult. Multiple truncations of the XLF and XRCC4 proteins were cocrystallized, but yielded low-resolution diffraction (~20 Å). However, a combination of microseeding, dehydration and heavy metals improved the diffraction of XRCC4(Δ157)-XLF(Δ224) crystals to 3.9 Å resolution. Although molecular replacement alone was unable to produce a solution, when combined with the anomalous signal from tantalum bromide clusters initial phasing was successfully obtained.
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Affiliation(s)
- Sara N. Andres
- Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | - Murray S. Junop
- Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
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35
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Inducing phase changes in crystals of macromolecules: Status and perspectives for controlled crystal dehydration. J Struct Biol 2011; 175:236-43. [DOI: 10.1016/j.jsb.2011.03.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 02/25/2011] [Accepted: 03/01/2011] [Indexed: 11/22/2022]
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36
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Heras B, Totsika M, Jarrott R, Shouldice SR, Guncar G, Achard MES, Wells TJ, Argente MP, McEwan AG, Schembri MA. Structural and functional characterization of three DsbA paralogues from Salmonella enterica serovar typhimurium. J Biol Chem 2010; 285:18423-32. [PMID: 20233716 DOI: 10.1074/jbc.m110.101360] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In prototypic Escherichia coli K-12 the introduction of disulfide bonds into folding proteins is mediated by the Dsb family of enzymes, primarily through the actions of the highly oxidizing protein EcDsbA. Homologues of the Dsb catalysts are found in most bacteria. Interestingly, pathogens have developed distinct Dsb machineries that play a pivotal role in the biogenesis of virulence factors, hence contributing to their pathogenicity. Salmonella enterica serovar (sv.) Typhimurium encodes an extended number of sulfhydryl oxidases, namely SeDsbA, SeDsbL, and SeSrgA. Here we report a comprehensive analysis of the sv. Typhimurium thiol oxidative system through the structural and functional characterization of the three Salmonella DsbA paralogues. The three proteins share low sequence identity, which results in several unique three-dimensional characteristics, principally in areas involved in substrate binding and disulfide catalysis. Furthermore, the Salmonella DsbA-like proteins also have different redox properties. Whereas functional characterization revealed some degree of redundancy, the properties of SeDsbA, SeDsbL, and SeSrgA and their expression pattern in sv. Typhimurium indicate a diverse role for these enzymes in virulence.
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Affiliation(s)
- Begoña Heras
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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Gupta V, Gupta RK, Khare G, Salunke DM, Surolia A, Tyagi AK. Structural ordering of disordered ligand-binding loops of biotin protein ligase into active conformations as a consequence of dehydration. PLoS One 2010; 5:e9222. [PMID: 20169168 PMCID: PMC2821413 DOI: 10.1371/journal.pone.0009222] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 01/23/2010] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), a dreaded pathogen, has a unique cell envelope composed of high fatty acid content that plays a crucial role in its pathogenesis. Acetyl Coenzyme A Carboxylase (ACC), an important enzyme that catalyzes the first reaction of fatty acid biosynthesis, is biotinylated by biotin acetyl-CoA carboxylase ligase (BirA). The ligand-binding loops in all known apo BirAs to date are disordered and attain an ordered structure only after undergoing a conformational change upon ligand-binding. Here, we report that dehydration of Mtb-BirA crystals traps both the apo and active conformations in its asymmetric unit, and for the first time provides structural evidence of such transformation. Recombinant Mtb-BirA was crystallized at room temperature, and diffraction data was collected at 295 K as well as at 120 K. Transfer of crystals to paraffin and paratone-N oil (cryoprotectants) prior to flash-freezing induced lattice shrinkage and enhancement in the resolution of the X-ray diffraction data. Intriguingly, the crystal lattice rearrangement due to shrinkage in the dehydrated Mtb-BirA crystals ensued structural order of otherwise flexible ligand-binding loops L4 and L8 in apo BirA. In addition, crystal dehydration resulted in a shift of approximately 3.5 A in the flexible loop L6, a proline-rich loop unique to Mtb complex as well as around the L11 region. The shift in loop L11 in the C-terminal domain on dehydration emulates the action responsible for the complex formation with its protein ligand biotin carboxyl carrier protein (BCCP) domain of ACCA3. This is contrary to the involvement of loop L14 observed in Pyrococcus horikoshii BirA-BCCP complex. Another interesting feature that emerges from this dehydrated structure is that the two subunits A and B, though related by a noncrystallographic twofold symmetry, assemble into an asymmetric dimer representing the ligand-bound and ligand-free states of the protein, respectively. In-depth analyses of the sequence and the structure also provide answers to the reported lower affinities of Mtb-BirA toward ATP and biotin substrates. This dehydrated crystal structure not only provides key leads to the understanding of the structure/function relationships in the protein in the absence of any ligand-bound structure, but also demonstrates the merit of dehydration of crystals as an inimitable technique to have a glance at proteins in action.
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Affiliation(s)
- Vibha Gupta
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Rakesh K. Gupta
- Department of Biochemistry, University of Delhi, New Delhi, India
- Department of Microbiology, University of Delhi, New Delhi, India
| | - Garima Khare
- Department of Biochemistry, University of Delhi, New Delhi, India
| | | | | | - Anil K. Tyagi
- Department of Biochemistry, University of Delhi, New Delhi, India
- * E-mail:
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38
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Radiation stability of proteinase K crystals grown by LB nanotemplate method. J Struct Biol 2009; 168:409-18. [PMID: 19686853 DOI: 10.1016/j.jsb.2009.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 07/29/2009] [Accepted: 08/12/2009] [Indexed: 11/23/2022]
Abstract
A detailed analysis of structural and intensity changes induced by X-ray radiation is presented for two types of proteinase K crystals: crystal grown by classical hanging drop method and those grown by Langmuir-Blodgett (LB) nanotemplate. The comparison of various parameters (e.g. intensity per sigma ratio, unit-cell volume, number of unique reflections, B-factors) and electron density maps as a function of radiation dose, demonstrates that crystals, grown by the LB nanotemplate method, appear to be more resistant against radiation damage than crystals grown by the classical hanging drop method.
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39
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Manjasetty BA, Turnbull AP, Panjikar S, Büssow K, Chance MR. Automated technologies and novel techniques to accelerate protein crystallography for structural genomics. Proteomics 2008; 8:612-25. [PMID: 18210369 DOI: 10.1002/pmic.200700687] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The sequence infrastructure that has arisen through large-scale genomic projects dedicated to protein analysis, has provided a wealth of information and brought together scientists and institutions from all over the world. As a consequence, the development of novel technologies and methodologies in proteomics research is helping to unravel the biochemical and physiological mechanisms of complex multivariate diseases at both a functional and molecular level. In the late sixties, when X-ray crystallography had just been established, the idea of determining protein structure on an almost universal basis was akin to an impossible dream or a miracle. Yet only forty years after, automated protein structure determination platforms have been established. The widespread use of robotics in protein crystallography has had a huge impact at every stage of the pipeline from protein cloning, over-expression, purification, crystallization, data collection, structure solution, refinement, validation and data management- all of which have become more or less automated with minimal human intervention necessary. Here, recent advances in protein crystal structure analysis in the context of structural genomics will be discussed. In addition, this review aims to give an overview of recent developments in high throughput instrumentation, and technologies and strategies to accelerate protein structure/function analysis.
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Affiliation(s)
- Babu A Manjasetty
- Case Center for Synchrotron Biosciences, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY11973, USA.
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40
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Heras B, Kurz M, Jarrott R, Shouldice SR, Frei P, Robin G, Čemažar M, Thöny-Meyer L, Glockshuber R, Martin JL. Staphylococcus aureus DsbA Does Not Have a Destabilizing Disulfide. J Biol Chem 2008; 283:4261-71. [DOI: 10.1074/jbc.m707838200] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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41
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Kurz M, Iturbe-Ormaetxe I, Jarrott R, O'Neill SL, Byriel KA, Martin JL, Heras B. Crystallization and preliminary diffraction analysis of a DsbA homologue from Wolbachia pipientis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:94-7. [PMID: 18259058 DOI: 10.1107/s1744309108000055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 01/01/2008] [Indexed: 11/10/2022]
Abstract
alpha-DsbA1 is one of two DsbA homologues encoded by the Gram-negative alpha-proteobacterium Wolbachia pipientis, an endosymbiont that can behave as a reproductive parasite in insects and as a mutualist in medically important filarial nematodes. The alpha-DsbA1 protein is thought to be important for the folding and secretion of Wolbachia proteins involved in the induction of reproductive distortions. Crystals of native and SeMet alpha-DsbA1 were grown by vapour diffusion and belong to the monoclinic space group C2, with unit-cell parameters a = 71.4, b = 49.5, c = 69.3 A, beta = 107.0 degrees and one molecule in the asymmetric unit (44% solvent content). X-ray data were recorded from native crystals to a resolution of 2.01 A using a copper anode and data from SeMet alpha-DsbA1 crystals were recorded to 2.45 A resolution using a chromium anode.
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Affiliation(s)
- M Kurz
- Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, University of Queensland, St Lucia, QLD 4072, Australia
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42
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Heras B, Kurz M, Jarrott R, Byriel KA, Jones A, Thöny-Meyer L, Martin JL. Expression and crystallization of DsbA from Staphylococcus aureus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:953-6. [PMID: 18007049 DOI: 10.1107/s174430910704821x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 10/02/2007] [Indexed: 03/15/2023]
Abstract
Bacterial Dsb proteins catalyse the in vivo formation of disulfide bonds, a critical step in the stability and activity of many proteins. Most studies on Dsb proteins have focused on Gram-negative bacteria and thus the process of oxidative folding in Gram-positive bacteria is poorly understood. To help elucidate this process in Gram-positive bacteria, DsbA from Staphylococcus aureus (SaDsbA) has been focused on. Here, the expression, purification, crystallization and preliminary diffraction analysis of SaDsbA are reported. SaDsbA crystals diffract to a resolution limit of 2.1 A and belong to the hexagonal space group P6(5) or P6(1), with unit-cell parameters a = b = 72.1, c = 92.1 A and one molecule in the asymmetric unit (64% solvent content).
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Affiliation(s)
- B Heras
- Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, University of Queensland, Brisbane QLD 4072, Australia.
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43
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Hiniker A, Ren G, Heras B, Zheng Y, Laurinec S, Jobson RW, Stuckey JA, Martin JL, Bardwell JCA. Laboratory evolution of one disulfide isomerase to resemble another. Proc Natl Acad Sci U S A 2007; 104:11670-5. [PMID: 17609373 PMCID: PMC1906722 DOI: 10.1073/pnas.0704692104] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is often difficult to determine which of the sequence and structural differences between divergent members of multigene families are functionally important. Here we use a laboratory evolution approach to determine functionally important structural differences between two distantly related disulfide isomerases, DsbC and DsbG from Escherichia coli. Surprisingly, we found single amino acid substitutions in DsbG that were able to complement dsbC in vivo and have more DsbC-like isomerase activity in vitro. Crystal structures of the three strongest point mutants, DsbG K113E, DsbG V216M, and DsbG T200M, reveal changes in highly surface-exposed regions that cause DsbG to more closely resemble the distantly related DsbC. In this case, laboratory evolution appears to have taken a direct route to allow one protein family member to complement another, with single substitutions apparently bypassing much of the need for multiple changes that took place over approximately 0.5 billion years of evolution. Our findings suggest that, for these two proteins at least, regions important in determining functional differences may represent only a tiny fraction of the overall protein structure.
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Affiliation(s)
- Annie Hiniker
- *Medical Scientist Training Program
- Program in Cellular and Molecular Biology
- Howard Hughes Medical Institute
| | - Guoping Ren
- Howard Hughes Medical Institute
- Molecular, Cellular and Developmental Biology, and
| | - Begoña Heras
- Institute for Molecular Bioscience and Australian Research Council Special Research Centre for Functional and Applied Genomics, University of Queensland, Brisbane QLD 4072, Australia
| | - Ying Zheng
- Molecular, Cellular and Developmental Biology, and
| | | | | | - Jeanne A. Stuckey
- **Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Jennifer L. Martin
- Institute for Molecular Bioscience and Australian Research Council Special Research Centre for Functional and Applied Genomics, University of Queensland, Brisbane QLD 4072, Australia
| | - James C. A. Bardwell
- Program in Cellular and Molecular Biology
- Howard Hughes Medical Institute
- Molecular, Cellular and Developmental Biology, and
- To whom correspondence should be addressed. E-mail:
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44
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Latham CF, Hu SH, Gee CL, Armishaw CJ, Alewood PF, James DE, Martin JL. Crystallization and preliminary X-ray diffraction of the Munc18c-syntaxin4 (1-29) complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:524-8. [PMID: 17554178 PMCID: PMC2335071 DOI: 10.1107/s1744309107022361] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Accepted: 05/08/2007] [Indexed: 11/10/2022]
Abstract
The production of diffraction-quality crystals of Munc18c, a protein involved in regulating vesicular exocytosis in mammals, is reported. The diffraction resolution of Munc18c crystals was optimized by (i) cocrystallizing with a peptide fragment of the Munc18c functional binding partner syntaxin4, (ii) using nanolitre free-interface diffusion crystallization-screening chips and microlitre hanging-drop vapour diffusion and (iii) applying a post-crystallization dehydration treatment. Crystals belonging to the cubic space group P2(1)3, with unit-cell parameters a = b = c = 170.8 A, alpha = beta = gamma = 90 degrees , were generated that diffract to 3.7 A resolution on a laboratory X-ray source.
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Affiliation(s)
- Catherine F. Latham
- Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Shu-Hong Hu
- Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Christine L. Gee
- Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Chris J. Armishaw
- Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Paul F. Alewood
- Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David E. James
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Jennifer L. Martin
- Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence e-mail:
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45
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Walter TS, Meier C, Assenberg R, Au KF, Ren J, Verma A, Nettleship JE, Owens RJ, Stuart DI, Grimes JM. Lysine methylation as a routine rescue strategy for protein crystallization. Structure 2007; 14:1617-22. [PMID: 17098187 PMCID: PMC7126202 DOI: 10.1016/j.str.2006.09.005] [Citation(s) in RCA: 210] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 08/28/2006] [Accepted: 09/01/2006] [Indexed: 11/24/2022]
Abstract
Crystallization remains a critical step in X-ray structure determination. Because it is not generally possible to rationally predict crystallization conditions, commercial screens have been developed which sample a wide range of crystallization space. While this approach has proved successful in many cases, a significant number of proteins fail to crystallize despite being soluble and monodispersed. It is established that chemical modification can facilitate the crystallization of otherwise intractable proteins. Here we describe a method for the reductive methylation of lysine residues which is simple, inexpensive, and efficient, and report on its application to ten proteins. We describe the effect of methylation on the physico-chemical properties of these proteins, and show that it led to diffraction-quality crystals from four proteins and structures for three that had hitherto proved refractory to crystallization. The method is suited to both low- and high-throughput laboratories.
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Affiliation(s)
- Thomas S Walter
- Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
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46
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Papanikolau Y, Papadovasilaki M, Ravelli RBG, McCarthy AA, Cusack S, Economou A, Petratos K. Structure of dimeric SecA, the Escherichia coli preprotein translocase motor. J Mol Biol 2006; 366:1545-57. [PMID: 17229438 DOI: 10.1016/j.jmb.2006.12.049] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 12/12/2006] [Accepted: 12/17/2006] [Indexed: 01/31/2023]
Abstract
SecA is the preprotein translocase ATPase subunit and a superfamily 2 (SF2) RNA helicase. Here we present the 2 A crystal structures of the Escherichia coli SecA homodimer in the apo form and in complex with ATP, ADP and adenosine 5'-[beta,gamma-imido]triphosphate (AMP-PNP). Each monomer contains the SF2 ATPase core (DEAD motor) built of two domains (nucleotide binding domain, NBD and intramolecular regulator of ATPase 2, IRA2), the preprotein binding domain (PBD), which is inserted in NBD and a carboxy-terminal domain (C-domain) linked to IRA2. The structures of the nucleotide complexes of SecA identify an interfacial nucleotide-binding cleft located between the two DEAD motor domains and residues critical for ATP catalysis. The dimer comprises two virtually identical protomers associating in an antiparallel fashion. Dimerization is mediated solely through extensive contacts of the DEAD motor domains leaving the C-domain facing outwards from the dimerization core. This dimerization mode explains the effect of functionally important mutations and is completely different from the dimerization models proposed for other SecA structures. The repercussion of these findings on translocase assembly and catalysis is discussed.
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Affiliation(s)
- Yannis Papanikolau
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, PO Box 1385, 71110 Heraklion, Greece
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47
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Sankaranarayanan R, Biswal BK, Vijayan M. A new relaxed state in horse methemoglobin characterized by crystallographic studies. Proteins 2006; 60:547-51. [PMID: 15887226 DOI: 10.1002/prot.20510] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A new relaxed state has been characterized in the crystals of horse methemoglobin grown at neutral pH at low ionic concentration and their low humidity variants. The crystals provide an example for improvement in X-ray diffraction quality with reduced solvent content. Only the classical R state has been so far observed in liganded horse hemoglobin. The state characterized in the present study lies in between the R state and the R2 state characterized earlier in liganded human hemoglobin. The results presented here, along with those of earlier studies, suggest that relaxed and tense hemoglobin can access ensembles of states.
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Affiliation(s)
- R Sankaranarayanan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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48
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Stocker A, Keis S, Cook GM, Dimroth P. Purification, crystallization, and properties of F1-ATPase complexes from the thermoalkaliphilic Bacillus sp. strain TA2.A1. J Struct Biol 2005; 152:140-5. [PMID: 16226039 DOI: 10.1016/j.jsb.2005.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 08/17/2005] [Accepted: 08/18/2005] [Indexed: 11/30/2022]
Abstract
Recently, we reported the cloning of the atp operon encoding for the F(1)F(0)-ATP synthase from the extremely thermoalkaliphilic bacterium Bacillus sp. strain TA2.A1. In this study, the genes encoding the F(1) moiety of the enzyme complex were cloned from the atp operon into the vector pTrc99A and expressed in Escherichia coli in two variant complexes, F(1)-wt consisting of subunits alpha(3)beta(3)gammadeltaepsilon and F(1)Deltadelta lacking the entire delta-subunit as a prerequisite for overproduction and crystallization trials. Both F(1)-wt and F(1)Deltadelta were successfully overproduced in E. coli and purified in high yield and purity. F(1)Deltadelta was crystallized by micro-batch screening yielding three-dimensional crystals that diffracted to a resolution of 3.1A using a synchrotron radiation source. After establishing cryo and dehydrating conditions, a complete set of diffraction data was collected from a single crystal. No crystals were obtained with F(1)-wt. Data processing of diffraction patterns showed that F(1)Deltadelta crystals belong to the orthorhombic space group P2(1)2(1)2(1) with unit cell parameters of a=121.70, b=174.80, and c=223.50A, alpha, beta, gamma=90.000. The asymmetric unit contained one molecule of bacterial F(1)Deltadelta with a corresponding volume per protein weight (V(M)) of 3.25A(3) Da(-1) and a solvent content of 62.1%. Silver staining of single crystals of F(1)Deltadelta analyzed by SDS-PAGE revealed four bands alpha, beta, gamma, and epsilon with identical M(r)-values as those found in the native F(1)F(0)-ATP synthase isolated from strain TA2.A1 membranes. ATPase assays of F(1)Deltadelta crystals exhibited latent ATP hydrolytic activity that was highly stimulated by lauryldimethylamine oxide, a hallmark of the native enzyme.
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Affiliation(s)
- Achim Stocker
- Institute of Microbiology ETH Zürich, ETH Hönggerberg, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
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Pauwels K, Loris R, Vandenbussche G, Ruysschaert JM, Wyns L, Van Gelder P. Crystallization and crystal manipulation of a steric chaperone in complex with its lipase substrate. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:791-5. [PMID: 16511160 PMCID: PMC1952342 DOI: 10.1107/s1744309105023055] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Accepted: 07/19/2005] [Indexed: 11/10/2022]
Abstract
Bacterial lipases that are secreted via the type II secretion pathway require a lipase-specific foldase in order to obtain their native and biologically active conformation in the periplasmic space. The lipase-foldase complex from Burkholderia glumae (319 and 333 residues, respectively) was crystallized in two crystal forms. One crystal form belongs to space group P3(1)21 (P3(2)21), with unit-cell parameters a = b = 122.3, c = 98.2 A. A procedure is presented which improved the diffraction of these crystals from approximately 5 to 2.95 A. For the second crystal form, which belonged to space group C2 with unit-cell parameters a = 183.0, b = 75.7, c = 116.6 A, X-ray data were collected to 1.85 A.
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Affiliation(s)
- Kris Pauwels
- Department of Molecular and Cellular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB6), Pleinlaan 2, Free University of Brussels, 1050 Brussels, Belgium.
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Mao X, Chen X. Crystallization and X-ray crystallographic analysis of human STAT1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:666-8. [PMID: 16511123 PMCID: PMC1952444 DOI: 10.1107/s1744309105017392] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Accepted: 06/02/2005] [Indexed: 11/10/2022]
Abstract
Unphosphorylated human STAT1 (1-683) has been crystallized in the presence of a phosphopeptide derived from the alpha-chain of human interferon gamma (IFNgamma) receptor. A complete data set has been collected from a KAu(CN)2-derivatized and dehydrated crystal. The crystal belonged to space group P6(1)22, with unit-cell parameters a = b = 102.6, c = 646.5 A, alpha = beta = 90, gamma = 120 degrees.
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Affiliation(s)
- Xiang Mao
- Department of Biochemistry and Molecular Biology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Box 117, Houston, TX 77030, USA
| | - Xiaomin Chen
- Department of Biochemistry and Molecular Biology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Box 117, Houston, TX 77030, USA
- Correspondence e-mail:
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