151
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Shen Y, Bryan PN, He Y, Orban J, Baker D, Bax A. De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds. Protein Sci 2010; 19:349-56. [PMID: 19998407 DOI: 10.1002/pro.303] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Proteins with high-sequence identity but very different folds present a special challenge to sequence-based protein structure prediction methods. In particular, a 56-residue three-helical bundle protein (GA(95)) and an alpha/beta-fold protein (GB(95)), which share 95% sequence identity, were targets in the CASP-8 structure prediction contest. With only 12 out of 300 submitted server-CASP8 models for GA(95) exhibiting the correct fold, this protein proved particularly challenging despite its small size. Here, we demonstrate that the information contained in NMR chemical shifts can readily be exploited by the CS-Rosetta structure prediction program and yields adequate convergence, even when input chemical shifts are limited to just amide (1)H(N) and (15)N or (1)H(N) and (1)H(alpha) values.
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Affiliation(s)
- Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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152
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Faraggi E, Yang Y, Zhang S, Zhou Y. Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction. Structure 2010; 17:1515-27. [PMID: 19913486 DOI: 10.1016/j.str.2009.09.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 09/01/2009] [Accepted: 09/03/2009] [Indexed: 11/30/2022]
Abstract
Local structures predicted from protein sequences are used extensively in every aspect of modeling and prediction of protein structure and function. For more than 50 years, they have been predicted at a low-resolution coarse-grained level (e.g., three-state secondary structure). Here, we combine a two-state classifier with real-value predictor to predict local structure in continuous representation by backbone torsion angles. The accuracy of the angles predicted by this approach is close to that derived from NMR chemical shifts. Their substitution for predicted secondary structure as restraints for ab initio structure prediction doubles the success rate. This result demonstrates the potential of predicted local structure for fragment-free tertiary-structure prediction. It further implies potentially significant benefits from using predicted real-valued torsion angles as a replacement for or supplement to the secondary-structure prediction tools used almost exclusively in many computational methods ranging from sequence alignment to function prediction.
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Affiliation(s)
- Eshel Faraggi
- Indiana University School of Informatics, Indiana University-Purdue University and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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153
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Shen Y, Bax A. Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts. JOURNAL OF BIOMOLECULAR NMR 2010; 46:199-204. [PMID: 20041279 PMCID: PMC2847849 DOI: 10.1007/s10858-009-9395-y] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 12/07/2009] [Indexed: 05/10/2023]
Abstract
We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and (13)C(beta) chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-(13)C(gamma), Promega calculates the statistical probability that a Xaa-Pro peptide bond is cis. Besides its potential as a validation tool, Promega is particularly useful for studies of larger proteins where Pro-(13)C(gamma) assignments can be challenging, and for on-going efforts to determine protein structures exclusively on the basis of backbone and (13)C(beta) chemical shifts.
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Affiliation(s)
- Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 126, Bethesda, MD, 20892-0520, USA.
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154
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De Jonge N, Hohlweg W, Garcia-Pino A, Respondek M, Buts L, Haesaerts S, Lah J, Zangger K, Loris R. Structural and thermodynamic characterization of Vibrio fischeri CcdB. J Biol Chem 2010; 285:5606-13. [PMID: 19959472 PMCID: PMC2820787 DOI: 10.1074/jbc.m109.068429] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 10/31/2009] [Indexed: 11/06/2022] Open
Abstract
CcdB(Vfi) from Vibrio fischeri is a member of the CcdB family of toxins that poison covalent gyrase-DNA complexes. In solution CcdB(Vfi) is a dimer that unfolds to the corresponding monomeric components in a two-state fashion. In the unfolded state, the monomer retains a partial secondary structure. This observation correlates well with the crystal and NMR structures of the protein, which show a dimer with a hydrophobic core crossing the dimer interface. In contrast to its F plasmid homologue, CcdB(Vfi) possesses a rigid dimer interface, and the apparent relative rotations of the two subunits are due to structural plasticity of the monomer. CcdB(Vfi) shows a number of non-conservative substitutions compared with the F plasmid protein in both the CcdA and the gyrase binding sites. Although variation in the CcdA interaction site likely determines toxin-antitoxin specificity, substitutions in the gyrase-interacting region may have more profound functional implications.
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Affiliation(s)
- Natalie De Jonge
- From Structural Biology Brussels and
- the Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Walter Hohlweg
- the Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and
| | - Abel Garcia-Pino
- From Structural Biology Brussels and
- the Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Michal Respondek
- the Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and
| | - Lieven Buts
- From Structural Biology Brussels and
- the Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Sarah Haesaerts
- From Structural Biology Brussels and
- the Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Jurij Lah
- the Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, 1000 Ljubljana, Slovenia
| | - Klaus Zangger
- the Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and
| | - Remy Loris
- From Structural Biology Brussels and
- the Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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155
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Cheung MS, Maguire ML, Stevens TJ, Broadhurst RW. DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 202:223-33. [PMID: 20015671 DOI: 10.1016/j.jmr.2009.11.008] [Citation(s) in RCA: 193] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 11/04/2009] [Accepted: 11/13/2009] [Indexed: 05/05/2023]
Abstract
This paper introduces DANGLE, a new algorithm that employs Bayesian inference to estimate the likelihood of all possible values of the backbone dihedral angles phi and psi for each residue in a query protein, based on observed chemical shifts and the conformational preferences of each amino acid type. The method provides robust estimates of phi and psi within realistic boundary ranges, an indication of the degeneracy in the relationship between shift measurements and conformation at each site, and faithful secondary structure state assignments. When a simple degeneracy-based filtering procedure is applied, DANGLE offers an ideal compromise between accuracy and coverage when compared with other shift-based dihedral angle prediction methods. In addition, per residue analysis of shift/structure degeneracy has potential to be a useful new approach for studying the properties of unfolded proteins, with sufficient sensitivity to identify regions of residual structure in the acid denatured state of apomyoglobin.
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Affiliation(s)
- Ming-Sin Cheung
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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156
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Abi-Ghanem J, Heddi B, Foloppe N, Hartmann B. DNA structures from phosphate chemical shifts. Nucleic Acids Res 2010; 38:e18. [PMID: 19942687 PMCID: PMC2817473 DOI: 10.1093/nar/gkp1061] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 10/14/2009] [Accepted: 11/01/2009] [Indexed: 01/04/2023] Open
Abstract
For B-DNA, the strong linear correlation observed by nuclear magnetic resonance (NMR) between the (31)P chemical shifts (deltaP) and three recurrent internucleotide distances demonstrates the tight coupling between phosphate motions and helicoidal parameters. It allows to translate deltaP into distance restraints directly exploitable in structural refinement. It even provides a new method for refining DNA oligomers with restraints exclusively inferred from deltaP. Combined with molecular dynamics in explicit solvent, these restraints lead to a structural and dynamical view of the DNA as detailed as that obtained with conventional and more extensive restraints. Tests with the Jun-Fos oligomer show that this deltaP-based strategy can provide a simple and straightforward method to capture DNA properties in solution, from routine NMR experiments on unlabeled samples.
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Affiliation(s)
- Joséphine Abi-Ghanem
- INTS, INSERM S-665, 6 rue Alexandre Cabanel, Paris 75015, IBPC, CNRS UPR 9080, 13 rue Pierre et Marie Curie, Paris 75005, France and 51 Natal Road, Cambridge CB1 3NY, UK
| | - Brahim Heddi
- INTS, INSERM S-665, 6 rue Alexandre Cabanel, Paris 75015, IBPC, CNRS UPR 9080, 13 rue Pierre et Marie Curie, Paris 75005, France and 51 Natal Road, Cambridge CB1 3NY, UK
| | - Nicolas Foloppe
- INTS, INSERM S-665, 6 rue Alexandre Cabanel, Paris 75015, IBPC, CNRS UPR 9080, 13 rue Pierre et Marie Curie, Paris 75005, France and 51 Natal Road, Cambridge CB1 3NY, UK
| | - Brigitte Hartmann
- INTS, INSERM S-665, 6 rue Alexandre Cabanel, Paris 75015, IBPC, CNRS UPR 9080, 13 rue Pierre et Marie Curie, Paris 75005, France and 51 Natal Road, Cambridge CB1 3NY, UK
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157
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Lehtivarjo J, Hassinen T, Korhonen SP, Peräkylä M, Laatikainen R. 4D prediction of protein (1)H chemical shifts. JOURNAL OF BIOMOLECULAR NMR 2009; 45:413-26. [PMID: 19876601 DOI: 10.1007/s10858-009-9384-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 10/09/2009] [Indexed: 05/11/2023]
Abstract
A 4D approach for protein (1)H chemical shift prediction was explored. The 4th dimension is the molecular flexibility, mapped using molecular dynamics simulations. The chemical shifts were predicted with a principal component model based on atom coordinates from a database of 40 protein structures. When compared to the corresponding non-dynamic (3D) model, the 4th dimension improved prediction by 6-7%. The prediction method achieved RMS errors of 0.29 and 0.50 ppm for Halpha and HN shifts, respectively. However, for individual proteins the RMS errors were 0.17-0.34 and 0.34-0.65 ppm for the Halpha and HN shifts, respectively. X-ray structures gave better predictions than the corresponding NMR structures, indicating that chemical shifts contain invaluable information about local structures. The (1)H chemical shift prediction tool 4DSPOT is available from http://www.uku.fi/kemia/4dspot .
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Affiliation(s)
- Juuso Lehtivarjo
- Department of Biosciences, University of Kuopio, Kuopio, Finland.
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158
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Kohlhoff KJ, Robustelli P, Cavalli A, Salvatella X, Vendruscolo M. Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances. J Am Chem Soc 2009; 131:13894-5. [DOI: 10.1021/ja903772t] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kai J. Kohlhoff
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Paul Robustelli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Andrea Cavalli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Xavier Salvatella
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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159
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Shen Y, Delaglio F, Cornilescu G, Bax A. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. JOURNAL OF BIOMOLECULAR NMR 2009; 44:213-23. [PMID: 19548092 PMCID: PMC2726990 DOI: 10.1007/s10858-009-9333-z] [Citation(s) in RCA: 2108] [Impact Index Per Article: 140.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 05/28/2009] [Indexed: 05/03/2023]
Abstract
NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between 13C, 15N and 1H chemical shifts and backbone torsion angles phi and psi (Cornilescu et al. J Biomol NMR 13 289-302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted phi and psi angles, equals +/-13 degrees . Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy.
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Affiliation(s)
- Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
| | - Frank Delaglio
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
| | | | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
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160
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Hill KK, Roemer SC, Jones DNM, Churchill MEA, Edwards DP. A progesterone receptor co-activator (JDP2) mediates activity through interaction with residues in the carboxyl-terminal extension of the DNA binding domain. J Biol Chem 2009; 284:24415-24. [PMID: 19553667 DOI: 10.1074/jbc.m109.003244] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Progesterone receptor (PR) belongs to the nuclear receptor family of ligand-dependent transcription factors and mediates the major biological effects of progesterone. Transcriptional co-activators that are recruited by PR through the carboxyl-terminal ligand binding domain have been studied extensively. Much less is known about co-activators that interact with other regions of receptors. Jun dimerization protein 2 (JDP2) is a PR co-activator that enhances the transcriptional activity of the amino-terminal domain by increasing the alpha-helical content and stability of the intrinsically disordered amino-terminal domain. To gain insights into the mechanism of JDP2 co-activation of PR, the structural basis of JDP2-PR interaction was analyzed using NMR. The smallest regions of each protein needed for efficient protein interaction were used for NMR and included the basic region plus leucine zipper (bZIP) domain of JDP2 and the core zinc modules of the PR DNA binding domain plus the intrinsically disordered carboxyl-terminal extension (CTE) of the DNA binding domain. Chemical shift changes in PR upon titration with JDP2 revealed that most of the residues involved in binding of JDP2 reside within the CTE. The importance of the CTE for binding JDP2 was confirmed by peptide competition and mutational analyses. Point mutations within CTE sites identified by NMR and a CTE domain swapping experiment also confirmed the functional importance of JDP2 interaction with the CTE for enhancement of PR transcriptional activity. These studies provide insights into the role and functional importance of the CTE for co-activator interactions.
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Affiliation(s)
- Krista K Hill
- Molecular Biology Program, School of Medicine, University of Colorado Denver, Aurora, Colorado 80045, USA
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161
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Robustelli P, Cavalli A, Dobson CM, Vendruscolo M, Salvatella X. Folding of Small Proteins by Monte Carlo Simulations with Chemical Shift Restraints without the Use of Molecular Fragment Replacement or Structural Homology. J Phys Chem B 2009; 113:7890-6. [DOI: 10.1021/jp900780b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paul Robustelli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and ICREA and Institute for Research in Biomedicine Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Andrea Cavalli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and ICREA and Institute for Research in Biomedicine Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and ICREA and Institute for Research in Biomedicine Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and ICREA and Institute for Research in Biomedicine Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Xavier Salvatella
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and ICREA and Institute for Research in Biomedicine Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
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162
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Berjanskii M, Tang P, Liang J, Cruz JA, Zhou J, Zhou Y, Bassett E, MacDonell C, Lu P, Lin G, Wishart DS. GeNMR: a web server for rapid NMR-based protein structure determination. Nucleic Acids Res 2009; 37:W670-7. [PMID: 19406927 PMCID: PMC2703936 DOI: 10.1093/nar/gkp280] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
GeNMR (GEnerate NMR structures) is a web server for rapidly generating accurate 3D protein structures using sequence data, NOE-based distance restraints and/or NMR chemical shifts as input. GeNMR accepts distance restraints in XPLOR or CYANA format as well as chemical shift files in either SHIFTY or BMRB formats. The web server produces an ensemble of PDB coordinates for the protein within 15-25 min, depending on model complexity and completeness of experimental restraints. GeNMR uses a pipeline of several pre-existing programs and servers to calculate the actual protein structure. In particular, GeNMR combines genetic algorithms for structure optimization along with homology modeling, chemical shift threading, torsion angle and distance predictions from chemical shifts/NOEs as well as ROSETTA-based structure generation and simulated annealing with XPLOR-NIH to generate and/or refine protein coordinates. GeNMR greatly simplifies the task of protein structure determination as users do not have to install or become familiar with complex stand-alone programs or obscure format conversion utilities. Tests conducted on a sample of 90 proteins from the BioMagResBank indicate that GeNMR produces high-quality models for all protein queries, regardless of the type of NMR input data. GeNMR was developed to facilitate rapid, user-friendly structure determination of protein structures via NMR spectroscopy. GeNMR is accessible at http://www.genmr.ca.
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Affiliation(s)
- Mark Berjanskii
- Department of Computing Science, University of Alberta and National Research Council, National Institute for Nanotechnology, Edmonton, AB, Canada T6G 2E8
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163
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Szymczyna BR, Taurog RE, Young MJ, Snyder JC, Johnson JE, Williamson JR. Synergy of NMR, computation, and X-ray crystallography for structural biology. Structure 2009; 17:499-507. [PMID: 19368883 PMCID: PMC2705668 DOI: 10.1016/j.str.2009.03.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2009] [Revised: 02/22/2009] [Accepted: 03/03/2009] [Indexed: 11/26/2022]
Abstract
NMR spectroscopy and X-ray crystallography are currently the two most widely applied methods for the determination of macromolecular structures at high resolution. More recently, significant advances have been made in algorithms for the de novo prediction of protein structure, and, in favorable cases, the predicted models agree extremely well with experimentally determined structures. Here, we demonstrate a synergistic combination of NMR spectroscopy, de novo structure prediction, and X-ray crystallography in an effective overall strategy for rapidly determining the structure of the coat protein C-terminal domain from the Sulfolobus islandicus rod-shaped virus (SIRV). This approach takes advantage of the most accessible aspects of each structural technique and may be widely applicable for structure determination.
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Affiliation(s)
- Blair R. Szymczyna
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, 92037
- Department of Chemistry, and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Rebecca E. Taurog
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Mark J. Young
- Department of Plant Sciences and Plant Pathology, Montana State University-Bozeman, Bozeman, Montana 59717
| | - Jamie C. Snyder
- Department of Plant Sciences and Plant Pathology, Montana State University-Bozeman, Bozeman, Montana 59717
| | - John E. Johnson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - James R. Williamson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, 92037
- Department of Chemistry, and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037
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164
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Vranken WF, Rieping W. Relationship between chemical shift value and accessible surface area for all amino acid atoms. BMC STRUCTURAL BIOLOGY 2009; 9:20. [PMID: 19341463 PMCID: PMC2678133 DOI: 10.1186/1472-6807-9-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 04/02/2009] [Indexed: 11/10/2022]
Abstract
BACKGROUND Chemical shifts obtained from NMR experiments are an important tool in determining secondary, even tertiary, protein structure. The main repository for chemical shift data is the BioMagResBank, which provides NMR-STAR files with this type of information. However, it is not trivial to link this information to available coordinate data from the PDB for non-backbone atoms due to atom and chain naming differences, as well as sequence numbering changes. RESULTS We here describe the analysis of a consistent set of chemical shift and coordinate data, in which we focus on the relationship between the per-atom solvent accessible surface area (ASA) in the reported coordinates and their reported chemical shift value. The data is available online on http://www.ebi.ac.uk/pdbe/docs/NMR/shiftAnalysis/index.html. CONCLUSION Atoms with zero per-atom ASA have a significantly larger chemical shift dispersion and often have a different chemical shift distribution compared to those that are solvent accessible. With higher per-atom ASA, the chemical shift values also tend towards random coil values. The per-atom ASA, although not the determinant of the chemical shift, thus provides a way to directly correlate chemical shift information to the atomic coordinates.
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165
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Robustelli P, Cavalli A, Vendruscolo M. Determination of protein structures in the solid state from NMR chemical shifts. Structure 2009; 16:1764-9. [PMID: 19081052 DOI: 10.1016/j.str.2008.10.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 09/26/2008] [Accepted: 10/29/2008] [Indexed: 11/29/2022]
Abstract
Solid-state NMR spectroscopy does not require proteins to form crystalline or soluble samples and can thus be applied under a variety of conditions, including precipitates, gels, and microcrystals. It has recently been shown that NMR chemical shifts can be used to determine the structures of the native states of proteins in solution. By considering the cases of two proteins, GB1 and SH3, we provide an initial demonstration here that this type of approach can be extended to the use of solid-state NMR chemical shifts to obtain protein structures in the solid state without the need for measuring interatomic distances.
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Affiliation(s)
- Paul Robustelli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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166
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Shen Y, Vernon R, Baker D, Bax A. De novo protein structure generation from incomplete chemical shift assignments. JOURNAL OF BIOMOLECULAR NMR 2009; 43:63-78. [PMID: 19034676 PMCID: PMC2683404 DOI: 10.1007/s10858-008-9288-5] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Accepted: 10/28/2008] [Indexed: 05/19/2023]
Abstract
NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments.
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Affiliation(s)
- Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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167
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Montalvao RW, Cavalli A, Salvatella X, Blundell TL, Vendruscolo M. Structure Determination of Protein−Protein Complexes Using NMR Chemical Shifts: Case of an Endonuclease Colicin−Immunity Protein Complex. J Am Chem Soc 2008; 130:15990-6. [DOI: 10.1021/ja805258z] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rinaldo W. Montalvao
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Andrea Cavalli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Xavier Salvatella
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Tom L. Blundell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
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