1
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Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation. IUCRJ 2024; 11:140-151. [PMID: 38358351 PMCID: PMC10916293 DOI: 10.1107/s2052252524001246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
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Affiliation(s)
| | - Paul D. Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
| | | | | | | | | | | | - Maya Topf
- Birkbeck, University of London, London, United Kingdom
| | | | | | | | | | | | | | | | - Sai J. Ganesan
- University of California at San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Ryan Pye
- EMBL-EBI, Cambridge, United Kingdom
| | | | | | | | | | | | | | | | | | - Zhe Wang
- EMBL-EBI, Cambridge, United Kingdom
| | | | | | - Martyn D. Winn
- Science and Technology Facilities Council, Research Complex at Harwell, Oxon, United Kingdom
| | - Jasmine Y. Young
- RCSB Protein Data Bank, The State University of New Jersey, NJ, USA
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2
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Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation. ARXIV 2024:arXiv:2311.17640v3. [PMID: 38076521 PMCID: PMC10705588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and consensus recommendations resulting from the workshop. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
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Affiliation(s)
| | - Paul D Adams
- Lawrence Berkeley Laboratory, Berkeley, CA, USA and University of California, Berkeley, CA, USA
| | | | - Catherine L Lawson
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | | | | | | | - Maya Topf
- Birkbeck, University of London, London, UK
| | | | | | | | | | | | | | | | - Sai J Ganesan
- University of California at San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - John D Westbrook
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | - Martyn D Winn
- Science and Technology Facilities Council, Research Complex at Harwell, Oxon, UK
| | - Jasmine Y Young
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | - Stephen K Burley
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
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3
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Roy RR, Ullmann GM. Virtual Model Compound Approach for Calculating Redox Potentials of [Fe 2S 2]-Cys 4 Centers in Proteins - Structure Quality Matters. J Chem Theory Comput 2023; 19:8930-8941. [PMID: 37974307 DOI: 10.1021/acs.jctc.3c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The midpoint potential of the [Fe2S2]-Cys4-cluster in proteins is known to vary between -200 and -450 mV. This variation is caused by the different electrostatic environment of the cluster in the respective proteins. Continuum electrostatics can quantify the impact of the protein environment on the redox potential. Thus, if the redox potential of a [Fe2S2]-Cys4-cluster model compound in aqueous solution would be known, then redox potentials in various protein complexes could be calculated. However, [Fe2S2]-Cys4-cluster models are not water-soluble, and thus, their redox potential can not be measured in aqueous solution. To overcome this problem, we introduce a method that we call Virtual Model Compound Approach (VMCA) to extrapolate the model redox potential from known redox potentials of proteins. We carefully selected high-resolution structures for our analysis and divide them into a fit set, for fitting the model redox potential, and an independent test set, to check the validity of the model redox potential. However, from our analysis, we realized that the some structures can not be used as downloaded from the PDB but had to be re-refined in order to calculate reliable redox potentials. Because of the re-refinement, we were able to significantly reduce the standard deviation of our derived model redox potential for the [Fe2S2]-Cys4-cluster from 31 mV to 10 mV. As the model redox potential, we obtained -184 mV. This model redox potential can be used to analyze the redox behavior of [Fe2S2]-Cys4-clusters in larger protein complexes.
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Affiliation(s)
- Rajeev Ranjan Roy
- Computational Biochemistry, Universitätsstr. 30, NWI, University of Bayreuth, Bayreuth, 95440, Germany
| | - G Matthias Ullmann
- Computational Biochemistry, Universitätsstr. 30, NWI, University of Bayreuth, Bayreuth, 95440, Germany
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4
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Li J, Zhang O, Lee S, Namini A, Liu ZH, Teixeira JMC, Forman-Kay JD, Head-Gordon T. Learning Correlations between Internal Coordinates to Improve 3D Cartesian Coordinates for Proteins. J Chem Theory Comput 2023; 19:4689-4700. [PMID: 36749957 PMCID: PMC10404647 DOI: 10.1021/acs.jctc.2c01270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
We consider a generic representation problem of internal coordinates (bond lengths, valence angles, and dihedral angles) and their transformation to 3-dimensional Cartesian coordinates of a biomolecule. We show that the internal-to-Cartesian process relies on correctly predicting chemically subtle correlations among the internal coordinates themselves, and learning these correlations increases the fidelity of the Cartesian representation. We developed a machine learning algorithm, Int2Cart, to predict bond lengths and bond angles from backbone torsion angles and residue types of a protein, which allows reconstruction of protein structures better than using fixed bond lengths and bond angles or a static library method that relies on backbone torsion angles and residue types in a local environment. The method is able to be used for structure validation, as we show that the agreement between Int2Cart-predicted bond geometries and those from an AlphaFold 2 model can be used to estimate model quality. Additionally, by using Int2Cart to reconstruct an IDP ensemble, we are able to decrease the clash rate during modeling. The Int2Cart algorithm has been implemented as a publicly accessible python package at https://github.com/THGLab/int2cart.
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Affiliation(s)
- Jie Li
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Oufan Zhang
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Seokyoung Lee
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ashley Namini
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5S 1A8, Canada
| | - Zi Hao Liu
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1X8, Canada
| | - João M C Teixeira
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5S 1A8, Canada
| | - Julie D Forman-Kay
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1X8, Canada
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
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5
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The reproducible normality of the crystallographic B-factor. Anal Biochem 2022; 645:114594. [DOI: 10.1016/j.ab.2022.114594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/17/2022] [Accepted: 02/08/2022] [Indexed: 11/20/2022]
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6
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Liebeschuetz JW. The Good, the Bad, and the Twisted Revisited: An Analysis of Ligand Geometry in Highly Resolved Protein-Ligand X-ray Structures. J Med Chem 2021; 64:7533-7543. [PMID: 34060310 DOI: 10.1021/acs.jmedchem.1c00228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An analysis of the rotatable bond geometry of drug-like ligand models is reported for high-resolution (<1.1 Å) crystallographic protein-ligand complexes. In cases where the ligand fit to the electron density is very good, unusual torsional geometry is rare and, most often, though not exclusively, associated with strong polar, metal, or covalent ligand-protein interactions. It is rarely associated with a torsional strain of greater than 2 kcal mol-1 by calculation. An unusual torsional geometry is more prevalent where the fit to electron density is not perfect. Multiple low-strain conformer bindings were observed in 21% of the set and, it is suggested, may also lie behind many of the 35% of single-occupancy cases, where a poor fit to the e-density was found. It is concluded that multiple conformer ligand binding is an under-recognized phenomenon in structure-based drug design and that there is a need for more robust crystallographic refinement methods to better handle such cases.
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Affiliation(s)
- John W Liebeschuetz
- Skilos Chemoinformatics, 159 Water Street, Cambridge CB4 1PB, United Kingdom.,Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Milton, Cambridge CB4 0QA, United Kingdom
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7
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Stiers KM, Graham AC, Zhu JS, Jakeman DL, Nix JC, Beamer LJ. Structural and dynamical description of the enzymatic reaction of a phosphohexomutase. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:024703. [PMID: 31041362 PMCID: PMC6443537 DOI: 10.1063/1.5092803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Enzymes are known to adopt various conformations at different points along their catalytic cycles. Here, we present a comprehensive analysis of 15 isomorphous, high resolution crystal structures of the enzyme phosphoglucomutase from the bacterium Xanthomonas citri. The protein was captured in distinct states critical to function, including enzyme-substrate, enzyme-product, and enzyme-intermediate complexes. Key residues in ligand recognition and regions undergoing conformational change are identified and correlated with the various steps of the catalytic reaction. In addition, we use principal component analysis to examine various subsets of these structures with two goals: (1) identifying sites of conformational heterogeneity through a comparison of room temperature and cryogenic structures of the apo-enzyme and (2) a priori clustering of the enzyme-ligand complexes into functionally related groups, showing sensitivity of this method to structural features difficult to detect by traditional methods. This study captures, in a single system, the structural basis of diverse substrate recognition, the subtle impact of covalent modification, and the role of ligand-induced conformational change in this representative enzyme of the α-D-phosphohexomutase superfamily.
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Affiliation(s)
- Kyle M. Stiers
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, USA
| | - Abigail C. Graham
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, USA
| | - Jian-She Zhu
- College of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 3J5, Canada
| | | | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Lesa J. Beamer
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, USA
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8
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Leonarski F, D'Ascenzo L, Auffinger P. Nucleobase carbonyl groups are poor Mg 2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey. RNA (NEW YORK, N.Y.) 2019; 25:173-192. [PMID: 30409785 PMCID: PMC6348993 DOI: 10.1261/rna.068437.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/16/2018] [Indexed: 05/04/2023]
Abstract
Precise knowledge of Mg2+ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg2+ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg2+ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg2+ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of "prior-knowledge" nucleobase Mg2+ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg2+ binding sites are fewer than expected since many of those are associated with misidentified Na+ or K+ We also emphasize that binding of Na+ and K+ to nucleic acids is much more frequent than anticipated. Overall, we provide evidence derived from X-ray structures that nucleobases are poor inner-sphere binders for Mg2+ but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline Mg2+ stereochemistry is observed, alternative placement of Na+, K+, or Ca2+ must be considered. We also critically examine the use of lanthanides (Yb3+, Tb3+) as Mg2+ substitutes in crystallography experiments.
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Affiliation(s)
- Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
| | - Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
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9
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Vila JA, Arnautova YA. 13C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information. SPRINGER SERIES ON BIO- AND NEUROSYSTEMS 2019. [PMCID: PMC7123919 DOI: 10.1007/978-3-319-95843-9_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Despite the formidable progress in Nuclear Magnetic Resonance (NMR) spectroscopy, quality assessment of NMR-derived structures remains as an important problem. Thus, validation of protein structures is essential for the spectroscopists, since it could enable them to detect structural flaws and potentially guide their efforts in further refinement. Moreover, availability of accurate and efficient validation tools would help molecular biologists and computational chemists to evaluate quality of available experimental structures and to select a protein model which is the most suitable for a given scientific problem. The 13Cα nuclei are ubiquitous in proteins, moreover, their shieldings are easily obtainable from NMR experiments and represent a rich source of encoded structural information that makes 13Cα chemical shifts an attractive candidate for use in computational methods aimed at determination and validation of protein structures. In this chapter, the basis of a novel methodology of computing, at the quantum chemical level of theory, the 13Cα shielding for the amino acid residues in proteins is described. We also identify and examine the main factors affecting the 13Cα-shielding computation. Finally, we illustrate how the information encoded in the 13C chemical shifts can be used for a number of applications, viz., from protein structure prediction of both α-helical and β-sheet conformations, to determination of the fraction of the tautomeric forms of the imidazole ring of histidine in proteins as a function of pH or to accurate detection of structural flaws, at a residue-level, in NMR-determined protein models.
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10
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Kleywegt GJ, Velankar S, Patwardhan A. Structural biology data archiving - where we are and what lies ahead. FEBS Lett 2018; 592:2153-2167. [PMID: 29749603 PMCID: PMC6019198 DOI: 10.1002/1873-3468.13086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 12/31/2022]
Abstract
For almost 50 years, structural biology has endeavoured to conserve and share its experimental data and their interpretations (usually, atomistic models) through global public archives such as the Protein Data Bank, Electron Microscopy Data Bank and Biological Magnetic Resonance Data Bank (BMRB). These archives are treasure troves of freely accessible data that document our quest for molecular or atomic understanding of biological function and processes in health and disease. They have prepared the field to tackle new archiving challenges as more and more (combinations of) techniques are being utilized to elucidate structure at ever increasing length scales. Furthermore, the field has made substantial efforts to develop validation methods that help users to assess the reliability of structures and to identify the most appropriate data for their needs. In this Review, we present an overview of public data archives in structural biology and discuss the importance of validation for users and producers of structural data. Finally, we sketch our efforts to integrate structural data with bioimaging data and with other sources of biological data. This will make relevant structural information available and more easily discoverable for a wide range of scientists.
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Affiliation(s)
- Gerard J. Kleywegt
- European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Sameer Velankar
- European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Ardan Patwardhan
- European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EMBL‐EBI)CambridgeUK
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11
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Abstract
The generation of conformations for small molecules is a problem of continuing interest in cheminformatics and computational drug discovery. This review will present an overview of methods used to sample conformational space, focusing on those methods designed for organic molecules commonly of interest in drug discovery. Different approaches to both the sampling of conformational space and the scoring of conformational stability will be compared and contrasted, with an emphasis on those methods suitable for conformer sampling of large numbers of drug-like molecules. Particular attention will be devoted to the appropriate utilization of information from experimental solid-state structures in validating and evaluating the performance of these tools. The review will conclude with some areas worthy of further investigation.
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Affiliation(s)
- Paul C D Hawkins
- OpenEye Scientific , 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States
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12
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Abstract
Nucleic acid crystallization buffers contain a large variety of chemicals fitting specific needs. Among them, anions are often solely considered for pH-regulating purposes and as cationic co-salts while their ability to directly bind to nucleic acid structures is rarely taken into account. Here we review current knowledge related to the use of anions in crystallization buffers along with data on their biological prevalence. Chloride ions are frequently identified in crystal structures but display low cytosolic concentrations. Hence, they are thought to be distant from nucleic acid structures in the cell. Sulfate ions are also frequently identified in crystal structures but their localization in the cell remains elusive. Nevertheless, the characterization of the binding properties of these ions is essential for better interpreting the solvent structure in crystals and consequently, avoiding mislabeling of electron densities. Furthermore, understanding the binding properties of these anions should help to get clues related to their potential effects in crowded cellular environments.
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Affiliation(s)
- Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, UPR 9002 CNRS/Université de Strasbourg, 15, rue René Descartes, Strasbourg Cedex, 67084, France
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13
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Improta R, Vitagliano L, Esposito L. The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis. Proteins 2015; 83:1973-86. [DOI: 10.1002/prot.24876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/24/2015] [Accepted: 08/03/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture e Bioimmagini; Consiglio Nazionale delle Ricerche (CNR); Napoli I-80134 Italy
| | - Luigi Vitagliano
- Istituto di Biostrutture e Bioimmagini; Consiglio Nazionale delle Ricerche (CNR); Napoli I-80134 Italy
| | - Luciana Esposito
- Istituto di Biostrutture e Bioimmagini; Consiglio Nazionale delle Ricerche (CNR); Napoli I-80134 Italy
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14
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Improta R, Vitagliano L, Esposito L. Bond distances in polypeptide backbones depend on the local conformation. ACTA ACUST UNITED AC 2015; 71:1272-83. [DOI: 10.1107/s1399004715005507] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/17/2015] [Indexed: 11/10/2022]
Abstract
By combining quantum-mechanical analysis of small model peptides and statistical surveys of high-resolution protein structures, a systematic conformational dependence of bond lengths in polypeptide backbones has been unveiled which involves both the peptide bond (C—O and C—N) and those bonds centred on the Cα atom. All of these bond lengths indeed display a systematic variability in the ψ angle according to both calculations and surveys of protein structures. The overall agreement between the computed and the statistical data suggests that these trends are essentially driven by local effects. The dependence of Cα distances on ψ is governed by interactions between the σ system of the Cα moiety and the C—O π system of the peptide bond. Maximum and minimum values for each bond distance are found for conformations with the specific bond perpendicular and parallel to the adjacent CONH peptide plane, respectively. On the other hand, the variability of the C—O and C—N distances is related to the strength of the interactions between the lone pair of the N atom and the C—O π* system, which is modulated by the ψ angle. The C—O and C—N distances are related but their trends are not strictly connected to peptide-bond planarity, although a correlation amongst all of these parameters is expected on the basis of the classical resonance model.
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15
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Stauber M, Jakoncic J, Berger J, Karp JM, Axelbaum A, Sastow D, Buldyrev SV, Hrnjez BJ, Asherie N. Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:427-41. [PMID: 25760593 PMCID: PMC4356360 DOI: 10.1107/s1399004714025061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 11/15/2014] [Indexed: 11/10/2022]
Abstract
Chiral control of crystallization has ample precedent in the small-molecule world, but relatively little is known about the role of chirality in protein crystallization. In this study, lysozyme was crystallized in the presence of the chiral additive 2-methyl-2,4-pentanediol (MPD) separately using the R and S enantiomers as well as with a racemic RS mixture. Crystals grown with (R)-MPD had the most order and produced the highest resolution protein structures. This result is consistent with the observation that in the crystals grown with (R)-MPD and (RS)-MPD the crystal contacts are made by (R)-MPD, demonstrating that there is preferential interaction between lysozyme and this enantiomer. These findings suggest that chiral interactions are important in protein crystallization.
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Affiliation(s)
- Mark Stauber
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
- Department of Biology, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
| | - Jean Jakoncic
- National Synchrotron Light Source, Brookhaven National Laboratory, Building 725D, Upton, NY 11973-5000, USA
| | - Jacob Berger
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
- Department of Biology, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
| | - Jerome M. Karp
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
- Department of Biology, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
| | - Ariel Axelbaum
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
- Department of Biology, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
| | - Dahniel Sastow
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
- Department of Biology, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
| | - Sergey V. Buldyrev
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
| | - Bruce J. Hrnjez
- Collegiate School, 260 West 78th Street, New York, NY 10024-6559, USA
| | - Neer Asherie
- Department of Physics, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
- Department of Biology, Yeshiva University, 2495 Amsterdam Avenue, New York, NY 10033-3312, USA
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16
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Sehnal D, Svobodová Vařeková R, Pravda L, Ionescu CM, Geidl S, Horský V, Jaiswal D, Wimmerová M, Koča J. ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. Nucleic Acids Res 2014; 43:D369-75. [PMID: 25392418 PMCID: PMC4383933 DOI: 10.1093/nar/gku1118] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Following the discovery of serious errors in the structure of biomacromolecules, structure validation has become a key topic of research, especially for ligands and non-standard residues. ValidatorDB (freely available at http://ncbr.muni.cz/ValidatorDB) offers a new step in this direction, in the form of a database of validation results for all ligands and non-standard residues from the Protein Data Bank (all molecules with seven or more heavy atoms). Model molecules from the wwPDB Chemical Component Dictionary are used as reference during validation. ValidatorDB covers the main aspects of validation of annotation, and additionally introduces several useful validation analyses. The most significant is the classification of chirality errors, allowing the user to distinguish between serious issues and minor inconsistencies. Other such analyses are able to report, for example, completely erroneous ligands, alternate conformations or complete identity with the model molecules. All results are systematically classified into categories, and statistical evaluations are performed. In addition to detailed validation reports for each molecule, ValidatorDB provides summaries of the validation results for the entire PDB, for sets of molecules sharing the same annotation (three-letter code) or the same PDB entry, and for user-defined selections of annotations or PDB entries.
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Affiliation(s)
- David Sehnal
- CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Radka Svobodová Vařeková
- CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Lukáš Pravda
- CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Crina-Maria Ionescu
- CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stanislav Geidl
- CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Vladimír Horský
- Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Deepti Jaiswal
- CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michaela Wimmerová
- CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jaroslav Koča
- CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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17
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Vranken WF. NMR structure validation in relation to dynamics and structure determination. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 82:27-38. [PMID: 25444697 DOI: 10.1016/j.pnmrs.2014.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/14/2014] [Accepted: 08/14/2014] [Indexed: 06/04/2023]
Abstract
NMR spectroscopy is a key technique for understanding the behaviour of proteins, especially highly dynamic proteins that adopt multiple conformations in solution. Overall, protein structures determined from NMR spectroscopy data constitute just over 10% of the Protein Data Bank archive. This review covers the validation of these NMR protein structures, but rather than describing currently available methodology, it focuses on concepts that are important for understanding where and how validation is most relevant. First, the inherent characteristics of the protein under study have an influence on quality and quantity of the distinct types of data that can be acquired from NMR experiments. Second, these NMR data are necessarily transformed into a model for use in a structure calculation protocol, and the protein structures that result from this reflect the types of NMR data used as well as the protein characteristics. The validation of NMR protein structures should therefore take account, wherever possible, of the inherent behavioural characteristics of the protein, the types of available NMR data, and the calculation protocol. These concepts are discussed in the context of 'knowledge based' and 'model versus data' validation, with suggestions for questions to ask and different validation categories to consider. The principal aim of this review is to stimulate discussion and to help the reader understand the relationships between the above elements in order to make informed decisions on which validation approaches are the most relevant in particular cases.
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Affiliation(s)
- Wim F Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Department of Structural Biology, VIB, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan, BC Building, 6th Floor, CP 263, 1050 Brussels, Belgium.
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18
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Vařeková RS, Jaiswal D, Sehnal D, Ionescu CM, Geidl S, Pravda L, Horský V, Wimmerová M, Koča J. MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. Nucleic Acids Res 2014; 42:W227-33. [PMID: 24848013 PMCID: PMC4086108 DOI: 10.1093/nar/gku426] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Structure validation has become a major issue in the structural biology community, and an essential step is checking the ligand structure. This paper introduces MotiveValidator, a web-based application for the validation of ligands and residues in PDB or PDBx/mmCIF format files provided by the user. Specifically, MotiveValidator is able to evaluate in a straightforward manner whether the ligand or residue being studied has a correct annotation (3-letter code), i.e. if it has the same topology and stereochemistry as the model ligand or residue with this annotation. If not, MotiveValidator explicitly describes the differences. MotiveValidator offers a user-friendly, interactive and platform-independent environment for validating structures obtained by any type of experiment. The results of the validation are presented in both tabular and graphical form, facilitating their interpretation. MotiveValidator can process thousands of ligands or residues in a single validation run that takes no more than a few minutes. MotiveValidator can be used for testing single structures, or the analysis of large sets of ligands or fragments prepared for binding site analysis, docking or virtual screening. MotiveValidator is freely available via the Internet at http://ncbr.muni.cz/MotiveValidator.
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Affiliation(s)
- Radka Svobodová Vařeková
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Deepti Jaiswal
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - David Sehnal
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Crina-Maria Ionescu
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stanislav Geidl
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Lukáš Pravda
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Vladimír Horský
- Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Michaela Wimmerová
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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19
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Stanfield RL. Determination of antibody structures. Methods Mol Biol 2014; 1131:395-406. [PMID: 24515478 DOI: 10.1007/978-1-62703-992-5_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
While antibodies share a conserved structural framework, their complementarity-determining region loops are highly variable in size and sequence. Even more variable are the potential ways these loops can be used to interact with antigen. Thus, X-ray crystal structures of antibody Fab fragments and Fab-antigen complexes are critical for a detailed understanding of the antibody-antigen recognition process. This chapter describes the basic procedures necessary for the crystallization and structure determination of antibody Fab fragments by X-ray crystallography.
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Affiliation(s)
- Robyn L Stanfield
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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20
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Rashin AA, Domagalski MJ, Zimmermann MT, Minor W, Chruszcz M, Jernigan RL. Factors correlating with significant differences between X-ray structures of myoglobin. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:481-91. [PMID: 24531482 PMCID: PMC3940193 DOI: 10.1107/s1399004713028812] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/20/2013] [Indexed: 11/10/2022]
Abstract
Validation of general ideas about the origins of conformational differences in proteins is critical in order to arrive at meaningful functional insights. Here, principal component analysis (PCA) and distance difference matrices are used to validate some such ideas about the conformational differences between 291 myoglobin structures from sperm whale, horse and pig. Almost all of the horse and pig structures form compact PCA clusters with only minor coordinate differences and outliers that are easily explained. The 222 whale structures form a few dense clusters with multiple outliers. A few whale outliers with a prominent distortion of the GH loop are very similar to the cluster of horse structures, which all have a similar GH-loop distortion apparently owing to intermolecular crystal lattice hydrogen bonds to the GH loop from residues near the distal histidine His64. The variations of the GH-loop coordinates in the whale structures are likely to be owing to the observed alternative intermolecular crystal lattice bond, with the change to the GH loop distorting bonds correlated with the binding of specific `unusual' ligands. Such an alternative intermolecular bond is not observed in horse myoglobins, obliterating any correlation with the ligands. Intermolecular bonds do not usually cause significant coordinate differences and cannot be validated as their universal cause. Most of the native-like whale myoglobin structure outliers can be correlated with a few specific factors. However, these factors do not always lead to coordinate differences beyond the previously determined uncertainty thresholds. The binding of unusual ligands by myoglobin, leading to crystal-induced distortions, suggests that some of the conformational differences between the apo and holo structures might not be `functionally important' but rather artifacts caused by the binding of `unusual' substrate analogs. The causes of P6 symmetry in myoglobin crystals and the relationship between crystal and solution structures are also discussed.
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Affiliation(s)
- Alexander A. Rashin
- BioChemComp Inc., 543 Sagamore Avenue, Teaneck, NJ 07666, USA
- LH Baker Center for Bioinformatics and Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 112 Office and Lab Bldg, Ames, IA 50011-3020, USA
| | - Marcin J. Domagalski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
| | - Michael T. Zimmermann
- LH Baker Center for Bioinformatics and Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 112 Office and Lab Bldg, Ames, IA 50011-3020, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
| | - Maksymilian Chruszcz
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Robert L. Jernigan
- LH Baker Center for Bioinformatics and Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 112 Office and Lab Bldg, Ames, IA 50011-3020, USA
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21
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Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM. Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure 2014; 21:875-81. [PMID: 23747111 DOI: 10.1016/j.str.2013.04.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 03/24/2013] [Accepted: 04/18/2013] [Indexed: 12/13/2022]
Abstract
This report presents the conclusions of the July 12-13, 2012 meeting of the Small-Angle Scattering Task Force of the worldwide Protein Data Bank (wwPDB; Berman et al., 2003) at Rutgers University in New Brunswick, New Jersey. The task force includes experts in small-angle scattering (SAS), crystallography, data archiving, and molecular modeling who met to consider questions regarding the contributions of SAS to modern structural biology. Recognizing there is a rapidly growing community of structural biology researchers acquiring and interpreting SAS data in terms of increasingly sophisticated molecular models, the task force recommends that (1) a global repository is needed that holds standard format X-ray and neutron SAS data that is searchable and freely accessible for download; (2) a standard dictionary is required for definitions of terms for data collection and for managing the SAS data repository; (3) options should be provided for including in the repository SAS-derived shape and atomistic models based on rigid-body refinement against SAS data along with specific information regarding the uniqueness and uncertainty of the model, and the protocol used to obtain it; (4) criteria need to be agreed upon for assessment of the quality of deposited SAS data and the accuracy of SAS-derived models, and the extent to which a given model fits the SAS data; (5) with the increasing diversity of structural biology data and models being generated, archiving options for models derived from diverse data will be required; and (6) thought leaders from the various structural biology disciplines should jointly define what to archive in the PDB and what complementary archives might be needed, taking into account both scientific needs and funding.
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Affiliation(s)
- Jill Trewhella
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia.
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22
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Martin OA, Arnautova YA, Icazatti AA, Scheraga HA, Vila JA. Physics-based method to validate and repair flaws in protein structures. Proc Natl Acad Sci U S A 2013; 110:16826-31. [PMID: 24082119 PMCID: PMC3801053 DOI: 10.1073/pnas.1315525110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A method that makes use of information provided by the combination of (13)C(α) and (13)C(β) chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ∼90%; and (ii) provide a set of (χ1/χ2) torsional angles that leads to optimal agreement between the observed and computed (13)C(α) and (13)C(β) chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of (χ1/χ2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed (13)C(α) and (13)C(β) chemical shifts for ∼94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range ≤ 0.5 , in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of (χ1/χ2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models.
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Affiliation(s)
- Osvaldo A. Martin
- Instituto de Matemática Aplicada San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Departamento de Física, Universidad Nacional de San Luis, 5700 San Luis, Argentina
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; and
| | | | - Alejandro A. Icazatti
- Instituto de Matemática Aplicada San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Departamento de Física, Universidad Nacional de San Luis, 5700 San Luis, Argentina
| | - Harold A. Scheraga
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; and
| | - Jorge A. Vila
- Instituto de Matemática Aplicada San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Departamento de Física, Universidad Nacional de San Luis, 5700 San Luis, Argentina
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; and
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23
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Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. Outcome of the first electron microscopy validation task force meeting. Structure 2012; 20:205-14. [PMID: 22325770 PMCID: PMC3328769 DOI: 10.1016/j.str.2011.12.014] [Citation(s) in RCA: 361] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/29/2011] [Accepted: 12/29/2011] [Indexed: 11/10/2022]
Abstract
This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Task Force organized by the Unified Data Resource for 3DEM (http://www.emdatabank.org) and held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. At the workshop, a group of scientists involved in collecting electron microscopy data, using the data to determine three-dimensional electron microscopy (3DEM) density maps, and building molecular models into the maps explored how to assess maps, models, and other data that are deposited into the Electron Microscopy Data Bank and Protein Data Bank public data archives. The specific recommendations resulting from the workshop aim to increase the impact of 3DEM in biology and medicine.
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Affiliation(s)
- Richard Henderson
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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24
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Gore S, Velankar S, Kleywegt GJ. Implementing an X-ray validation pipeline for the Protein Data Bank. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:478-83. [PMID: 22505268 PMCID: PMC3322607 DOI: 10.1107/s0907444911050359] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 11/23/2011] [Indexed: 11/10/2022]
Abstract
There is an increasing realisation that the quality of the biomacromolecular structures deposited in the Protein Data Bank (PDB) archive needs to be assessed critically using established and powerful validation methods. The Worldwide Protein Data Bank (wwPDB) organization has convened several Validation Task Forces (VTFs) to advise on the methods and standards that should be used to validate all of the entries already in the PDB as well as all structures that will be deposited in the future. The recommendations of the X-ray VTF are currently being implemented in a software pipeline. Here, ongoing work on this pipeline is briefly described as well as ways in which validation-related information could be presented to users of structural data.
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Affiliation(s)
- Swanand Gore
- Protein Data Bank in Europe (PDBe), EMBL–EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), EMBL–EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England
| | - Gerard J. Kleywegt
- Protein Data Bank in Europe (PDBe), EMBL–EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England
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25
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Merritt EA. To B or not to B: a question of resolution? ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:468-77. [PMID: 22505267 PMCID: PMC3322606 DOI: 10.1107/s0907444911028320] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 07/14/2011] [Indexed: 11/21/2022]
Abstract
A simple rule of thumb based on resolution is not adequate to identify the best treatment of atomic displacements in macromolecular structural models. The choice to use isotropic B factors, anisotropic B factors, TLS models or some combination of the three should be validated through statistical analysis of the model refinement. In choosing and refining any crystallographic structural model, there is tension between the desire to extract the most detailed information possible and the necessity to describe no more than what is justified by the observed data. A more complex model is not necessarily a better model. Thus, it is important to validate the choice of parameters as well as validating their refined values. One recurring task is to choose the best model for describing the displacement of each atom about its mean position. At atomic resolution one has the option of devoting six model parameters (a ‘thermal ellipsoid’) to describe the displacement of each atom. At medium resolution one typically devotes at most one model parameter per atom to describe the same thing (a ‘B factor’). At very low resolution one cannot justify the use of even one parameter per atom. Furthermore, this aspect of the structure may be described better by an explicit model of bulk displacements, the most common of which is the translation/libration/screw (TLS) formalism, rather than by assigning some number of parameters to each atom individually. One can sidestep this choice between atomic displacement parameters and TLS descriptions by including both treatments in the same model, but this is not always statistically justifiable. The choice of which treatment is best for a particular structure refinement at a particular resolution can be guided by general considerations of the ratio of model parameters to the number of observations and by specific statistics such as the Hamilton R-factor ratio test.
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Affiliation(s)
- Ethan A Merritt
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA.
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26
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Liebeschuetz J, Hennemann J, Olsson T, Groom CR. The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures. J Comput Aided Mol Des 2012; 26:169-83. [PMID: 22246295 PMCID: PMC3292722 DOI: 10.1007/s10822-011-9538-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 12/21/2011] [Indexed: 12/27/2022]
Abstract
The protein databank now contains the structures of over 11,000 ligands bound to proteins. These structures are invaluable in applied areas such as structure-based drug design, but are also the substrate for understanding the energetics of intermolecular interactions with proteins. Despite their obvious importance, the careful analysis of ligands bound to protein structures lags behind the analysis of the protein structures themselves. We present an analysis of the geometry of ligands bound to proteins and highlight the role of small molecule crystal structures in enabling molecular modellers to critically evaluate a ligand model's quality and investigate protein-induced strain.
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27
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Cooper DR, Porebski PJ, Chruszcz M, Minor W. X-ray crystallography: Assessment and validation of protein-small molecule complexes for drug discovery. Expert Opin Drug Discov 2011; 6:771-782. [PMID: 21779303 PMCID: PMC3138648 DOI: 10.1517/17460441.2011.585154] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION: Crystallography is the key initial component for structure-based and fragment-based drug design and can often generate leads that can be developed into high potency drugs. Therefore, huge sums of money are committed based on the outcome of crystallography experiments and their interpretation. AREAS COVERED: This review discusses how to evaluate the correctness of an X-ray structure, focusing on the validation of small molecule-protein complexes. Various types of inaccuracies found within the PDB are identified and the ramifications of these errors are discussed. The reader will gain an understanding of the key parameters that need to be inspected before a structure can be used in drug discovery efforts, as well as an appreciation of the difficulties of correctly interpreting electron density for small molecules. The reader will also be introduced to methods for validating small molecules within the context of a macromolecular structure. EXPERT OPINION: One of the reasons that ligand identification and positioning, within a macromolecular crystal structure, is so difficult is that the quality of small molecules widely varies in the PDB. For this reason, the PDB can not always be considered a reliable repository of structural information pertaining to small molecules, and this makes the derivation of general principles that govern small molecule-protein interactions more difficult.
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Affiliation(s)
- David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
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28
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Cole JC, Korb O, Olsson TSG, Liebeschuetz J. The Basis for Target-Based Virtual Screening: Protein Structures. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/9783527633326.ch4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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29
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Velankar S, Kleywegt GJ. The Protein Data Bank in Europe (PDBe): bringing structure to biology. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:324-30. [PMID: 21460450 PMCID: PMC3069747 DOI: 10.1107/s090744491004117x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 10/13/2010] [Indexed: 12/30/2022]
Abstract
The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide PDB and as such handles depositions of X-ray, NMR and EM data and structure models. PDBe also provides advanced bioinformatics services based on data from the PDB and related resources. Some of the challenges facing the PDB and its guardians are discussed, as well as some of the areas on which PDBe activities will focus in the future (advanced services, ligands, integration, validation and experimental data). Finally, some recent developments at PDBe are described.
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Affiliation(s)
- Sameer Velankar
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, England
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di Luccio E, Koehl P. A quality metric for homology modeling: the H-factor. BMC Bioinformatics 2011; 12:48. [PMID: 21291572 PMCID: PMC3213331 DOI: 10.1186/1471-2105-12-48] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 02/04/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The analysis of protein structures provides fundamental insight into most biochemical functions and consequently into the cause and possible treatment of diseases. As the structures of most known proteins cannot be solved experimentally for technical or sometimes simply for time constraints, in silico protein structure prediction is expected to step in and generate a more complete picture of the protein structure universe. Molecular modeling of protein structures is a fast growing field and tremendous works have been done since the publication of the very first model. The growth of modeling techniques and more specifically of those that rely on the existing experimental knowledge of protein structures is intimately linked to the developments of high resolution, experimental techniques such as NMR, X-ray crystallography and electron microscopy. This strong connection between experimental and in silico methods is however not devoid of criticisms and concerns among modelers as well as among experimentalists. RESULTS In this paper, we focus on homology-modeling and more specifically, we review how it is perceived by the structural biology community and what can be done to impress on the experimentalists that it can be a valuable resource to them. We review the common practices and provide a set of guidelines for building better models. For that purpose, we introduce the H-factor, a new indicator for assessing the quality of homology models, mimicking the R-factor in X-ray crystallography. The methods for computing the H-factor is fully described and validated on a series of test cases. CONCLUSIONS We have developed a web service for computing the H-factor for models of a protein structure. This service is freely accessible at http://koehllab.genomecenter.ucdavis.edu/toolkit/h-factor.
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Affiliation(s)
- Eric di Luccio
- Computer Science Department, Room 4337, Genome Center, GBSF University of California Davis 451 East Health Sciences Drive Davis, CA 95616, USA.
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Zucker F, Champ PC, Merritt EA. Validation of crystallographic models containing TLS or other descriptions of anisotropy. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:889-900. [PMID: 20693688 PMCID: PMC2917275 DOI: 10.1107/s0907444910020421] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 05/28/2010] [Indexed: 04/07/2024]
Abstract
The use of TLS (translation/libration/screw) models to describe anisotropic displacement of atoms within a protein crystal structure has become increasingly common. These models may be used purely as an improved methodology for crystallographic refinement or as the basis for analyzing inter-domain and other large-scale motions implied by the crystal structure. In either case it is desirable to validate that the crystallographic model, including the TLS description of anisotropy, conforms to our best understanding of protein structures and their modes of flexibility. A set of validation tests has been implemented that can be integrated into ongoing crystallographic refinement or run afterwards to evaluate a previously refined structure. In either case validation can serve to increase confidence that the model is correct, to highlight aspects of the model that may be improved or to strengthen the evidence supporting specific modes of flexibility inferred from the refined TLS model. Automated validation checks have been added to the PARVATI and TLSMD web servers and incorporated into the CCP4i user interface.
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Affiliation(s)
- Frank Zucker
- Biomolecular Structure Center, Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA
| | - P. Christoph Champ
- Biomolecular Structure Center, Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA
| | - Ethan A. Merritt
- Biomolecular Structure Center, Department of Biochemistry, University of Washington, Seattle, WA 98195-7742, USA
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Ginzinger SW, Weichenberger CX, Sippl MJ. Detection of unrealistic molecular environments in protein structures based on expected electron densities. JOURNAL OF BIOMOLECULAR NMR 2010; 47:33-40. [PMID: 20405167 PMCID: PMC2859164 DOI: 10.1007/s10858-010-9408-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 03/10/2010] [Indexed: 05/11/2023]
Abstract
Understanding the relationship between protein structure and biological function is a central theme in structural biology. Advances are severely hampered by errors in experimentally determined protein structures. Detection and correction of such errors is therefore of utmost importance. Electron densities in molecular structures obey certain rules which depend on the molecular environment. Here we present and discuss a new approach that relates electron densities computed from a structural model to densities expected from prior observations on identical or closely related molecular environments. Strong deviations of computed from expected densities reveal unrealistic molecular structures. Most importantly, structure analysis and error detection are independent of experimental data and hence may be applied to any structural model. The comparison to state-of-the-art methods reveals that our approach is able to identify errors that formerly remained undetected. The new technique, called RefDens, is accessible as a public web service at http://refdens.services.came.sbg.ac.at.
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Affiliation(s)
- Simon W. Ginzinger
- Department of Molecular Biology, Division of Bioinformatics, Center of Applied Molecular Engineering, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
| | - Christian X. Weichenberger
- Department of Molecular Biology, Division of Bioinformatics, Center of Applied Molecular Engineering, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
| | - Manfred J. Sippl
- Department of Molecular Biology, Division of Bioinformatics, Center of Applied Molecular Engineering, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
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Kalman M, Ben-Tal N. Quality assessment of protein model-structures using evolutionary conservation. ACTA ACUST UNITED AC 2010; 26:1299-307. [PMID: 20385730 PMCID: PMC2865859 DOI: 10.1093/bioinformatics/btq114] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Motivation: Programs that evaluate the quality of a protein structural model are important both for validating the structure determination procedure and for guiding the model-building process. Such programs are based on properties of native structures that are generally not expected for faulty models. One such property, which is rarely used for automatic structure quality assessment, is the tendency for conserved residues to be located at the structural core and for variable residues to be located at the surface. Results: We present ConQuass, a novel quality assessment program based on the consistency between the model structure and the protein's conservation pattern. We show that it can identify problematic structural models, and that the scores it assigns to the server models in CASP8 correlate with the similarity of the models to the native structure. We also show that when the conservation information is reliable, the method's performance is comparable and complementary to that of the other single-structure quality assessment methods that participated in CASP8 and that do not use additional structural information from homologs. Availability: A perl implementation of the method, as well as the various perl and R scripts used for the analysis are available at http://bental.tau.ac.il/ConQuass/. Contact:nirb@tauex.tau.ac.il Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matan Kalman
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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Rashin AA, Rashin AHL, Jernigan RL. Protein flexibility: coordinate uncertainties and interpretation of structural differences. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:1140-61. [PMID: 19923711 PMCID: PMC2777169 DOI: 10.1107/s090744490903145x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2009] [Accepted: 08/10/2009] [Indexed: 11/10/2022]
Abstract
Valid interpretations of conformational movements in protein structures determined by X-ray crystallography require that the movement magnitudes exceed their uncertainty threshold. Here, it is shown that such thresholds can be obtained from the distance difference matrices (DDMs) of 1014 pairs of independently determined structures of bovine ribonuclease A and sperm whale myoglobin, with no explanations provided for reportedly minor coordinate differences. The smallest magnitudes of reportedly functional motions are just above these thresholds. Uncertainty thresholds can provide objective criteria that distinguish between true conformational changes and apparent 'noise', showing that some previous interpretations of protein coordinate changes attributed to external conditions or mutations may be doubtful or erroneous. The use of uncertainty thresholds, DDMs, the newly introduced CDDMs (contact distance difference matrices) and a novel simple rotation algorithm allows a more meaningful classification and description of protein motions, distinguishing between various rigid-fragment motions and nonrigid conformational deformations. It is also shown that half of 75 pairs of identical molecules, each from the same asymmetric crystallographic cell, exhibit coordinate differences that range from just outside the coordinate uncertainty threshold to the full magnitude of large functional movements. Thus, crystallization might often induce protein conformational changes that are comparable to those related to or induced by the protein function.
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Vila JA, Scheraga HA. Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts. Acc Chem Res 2009; 42:1545-53. [PMID: 19572703 PMCID: PMC3396562 DOI: 10.1021/ar900068s] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two major techniques have been used to determine the three-dimensional structures of proteins: X-ray diffraction and NMR spectroscopy. In particular, the validation of NMR-derived protein structures is one of the most challenging problems in NMR spectroscopy. Therefore, researchers have proposed a plethora of methods to determine the accuracy and reliability of protein structures. Despite these proposals, there is a growing need for more sophisticated, physics-based structure validation methods. This approach will enable us to (a) characterize the "quality" of the NMR-derived ensemble as a whole by a single parameter, (b) unambiguously identify flaws in the sequence at a residue level, and (c) provide precise information, such as sets of backbone and side-chain torsional angles, that we can use to detect local flaws. Rather than reviewing all of the existing validation methods, this Account describes the contributions of our research group toward a solution of the long-standing problem of both global and local structure validation of NMR-derived protein structures. We emphasize a recently introduced physics-based methodology that makes use of observed and computed (13)C(alpha) chemical shifts (at the density functional theory (DFT) level of theory) for an accurate validation of protein structures in solution and in crystals. By assessing the ability of computed (13)C(alpha) chemical shifts to reproduce observed (13)C(alpha) chemical shifts of a single structure or ensemble of structures in solution and in crystals, we accomplish a global validation by using the conformationally averaged root-mean-square deviation, ca-rmsd, as a scoring function. In addition, the method enables us to provide local validation by identifying a set of individual amino acid conformations for which the computed and observed (13)C(alpha) chemical shifts do not agree within a certain error range and may represent a nonreliable fold of the protein model. Although it is computationally intensive, our validation method has several advantages, which we illustrate through a series of applications. This method makes use of the (13)C(alpha) chemical shifts, not shielding, that are ubiquitous to proteins and can be computed precisely from the phi, psi, and chi torsional angles. There is no need for a priori knowledge of the oligomeric state of the protein, and no knowledge-based information or additional NMR data are required. The primary limitation at this point is the computational cost of such calculations. However, we anticipate that enhancements in the speed of calculating these chemical shifts coupled with the ever-increasing computational power should soon make this a standard method accessible to the general NMR community.
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Affiliation(s)
- Jorge A. Vila
- Baker Laboratory of Chemistry and Chemical Biology, Cornell
University, Ithaca NY, 14853-1301, USA
- Universidad Nacional de San Luis, IMASL-CONICET,
Ejército de Los Andes 950-5700 San Luis-Argentina
| | - Harold A. Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell
University, Ithaca NY, 14853-1301, USA
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Read RJ, Kleywegt GJ. Case-controlled structure validation. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:140-7. [PMID: 19171969 PMCID: PMC2631636 DOI: 10.1107/s0907444908041085] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 12/05/2008] [Indexed: 11/10/2022]
Abstract
Although many factors influence the quality of a macromolecular crystal structure, validation criteria are usually only calibrated using one of these factors, the resolution. For many purposes this is sufficient, but there are times when one wishes to compare one set of structures with another and the comparison may be invalidated by systematic differences between the sets in factors other than resolution. This problem can be circumvented by borrowing from medicine the idea of the case-matched control: each structure of interest is matched with a control structure that has similar values for all relevant factors considered in this study. In addition to resolution, these include the size of the structure (as measured by the volume of the asymmetric unit) and the year of deposition. This approach has been applied to address two questions: whether structures from structural genomics efforts reach the same level of quality as structures from traditional sources and whether the impact factor of the journal in which a structure is published correlates with structure quality. In both cases, once factors influencing quality have been controlled in the comparison, there is little evidence for a systematic difference in quality.
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Affiliation(s)
- Randy J Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, England.
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