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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Sánchez Rodríguez F, Chojnowski G, Keegan RM, Rigden DJ. Using deep-learning predictions of inter-residue distances for model validation. Acta Crystallogr D Struct Biol 2022; 78:1412-1427. [PMID: 36458613 PMCID: PMC9716559 DOI: 10.1107/s2059798322010415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/28/2022] [Indexed: 11/27/2022] Open
Abstract
Determination of protein structures typically entails building a model that satisfies the collected experimental observations and its deposition in the Protein Data Bank. Experimental limitations can lead to unavoidable uncertainties during the process of model building, which result in the introduction of errors into the deposited model. Many metrics are available for model validation, but most are limited to consideration of the physico-chemical aspects of the model or its match to the experimental data. The latest advances in the field of deep learning have enabled the increasingly accurate prediction of inter-residue distances, an advance which has played a pivotal role in the recent improvements observed in the field of protein ab initio modelling. Here, new validation methods are presented based on the use of these precise inter-residue distance predictions, which are compared with the distances observed in the protein model. Sequence-register errors are particularly clearly detected and the register shifts required for their correction can be reliably determined. The method is available in the ConKit package (https://www.conkit.org).
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Affiliation(s)
- Filomeno Sánchez Rodríguez
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom,Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Ronan M. Keegan
- UKRI–STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom,Correspondence e-mail:
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3
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Atanasova M, Nicholls RA, Joosten RP, Agirre J. Updated restraint dictionaries for carbohydrates in the pyranose form. Acta Crystallogr D Struct Biol 2022; 78:455-465. [PMID: 35362468 PMCID: PMC8972801 DOI: 10.1107/s2059798322001103] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
Restraint dictionaries are used during macromolecular structure refinement to encapsulate intramolecular connectivity and geometric information. These dictionaries allow previously determined `ideal' values of features such as bond lengths, angles and torsions to be used as restraint targets. During refinement, restraints influence the model to adopt a conformation that agrees with prior observation. This is especially important when refining crystal structures of glycosylated proteins, as their resolutions tend to be worse than those of nonglycosylated proteins. Pyranosides, the overwhelming majority component in all forms of protein glycosylation, often display conformational errors in crystal structures. Whilst many of these flaws usually relate to model building, refinement issues may also have their root in suboptimal restraint dictionaries. In order to avoid subsequent misinterpretation and to improve the quality of all pyranose monosaccharide entries in the CCP4 Monomer Library, new dictionaries with improved ring torsion restraints, coordinates reflecting the lowest-energy ring pucker and updated geometry have been produced and evaluated. These new dictionaries are now part of the CCP4 Monomer Library and will be released with CCP4 version 8.0.
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Affiliation(s)
- Mihaela Atanasova
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Robert A. Nicholls
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robbie P. Joosten
- Biochemistry Department, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
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4
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Roversi P, Tronrud DE. Ten things I `hate' about refinement. Acta Crystallogr D Struct Biol 2021; 77:1497-1515. [PMID: 34866607 PMCID: PMC8647177 DOI: 10.1107/s2059798321011700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/04/2021] [Indexed: 12/05/2022] Open
Abstract
Macromolecular refinement is an optimization process that aims to produce the most likely macromolecular structural model in the light of experimental data. As such, macromolecular refinement is one of the most complex optimization problems in wide use. Macromolecular refinement programs have to deal with the complex relationship between the parameters of the atomic model and the experimental data, as well as a large number of types of prior knowledge about chemical structure. This paper draws attention to areas of unfinished business in the field of macromolecular refinement. In it, we describe ten refinement topics that we think deserve attention and discuss directions leading to macromolecular refinement software that would make the best use of modern computer resources to meet the needs of structural biologists of the twenty-first century.
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Affiliation(s)
- Pietro Roversi
- Institute of Agricultural Biology and Biotechnology, IBBA–CNR Unit of Milano, Via Bassini 15, I-20133 Milano, Italy
- Leicester Institute of Chemical and Structural Biology and Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7HR, United Kingdom
| | - Dale E. Tronrud
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
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5
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Andersson I, Carlsson GH, Hasse D. Structural Analysis of Strigolactone-Related Gene Products. Methods Mol Biol 2021; 2309:245-257. [PMID: 34028692 DOI: 10.1007/978-1-0716-1429-7_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Structural knowledge of biological macromolecules is essential for understanding their function and for modifying that function by engineering. Protein crystallography is a powerful method for elucidating molecular structures of proteins, but it is essential that the investigator has a basic knowledge of good practices and of the major pitfalls in the technique. Here we describe issues specific for the case of structural studies of strigolactone (SL) receptor structure and function, and in particular the difficulties associated with capturing complexes of SL receptors with the SL hormone ligand in the crystal.
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Affiliation(s)
- Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden. .,Arctic University of Norway, Tromsø, Norway. .,Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic.
| | - Gunilla H Carlsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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6
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Meirson T, Bomze D, Markel G. Structural basis of SARS-CoV-2 spike protein induced by ACE2. Bioinformatics 2021; 37:929-936. [PMID: 32818261 PMCID: PMC7558967 DOI: 10.1093/bioinformatics/btaa744] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/20/2020] [Accepted: 08/14/2020] [Indexed: 12/24/2022] Open
Abstract
Motivation The recent emergence of the novel SARS-coronavirus 2 (SARS-CoV-2) and its international
spread pose a global health emergency. The spike (S) glycoprotein binds ACE2 and
promotes SARS-CoV-2 entry into host cells. The trimeric S protein binds the receptor
using the receptor-binding domain (RBD) causing conformational changes in S protein that
allow priming by host cell proteases. Unraveling the dynamic structural features used by
SARS-CoV-2 for entry might provide insights into viral transmission and reveal novel
therapeutic targets. Using structures determined by X-ray crystallography and cryo-EM,
we performed structural analysis and atomic comparisons of the different conformational
states adopted by the SARS-CoV-2-RBD. Results Here, we determined the key structural components induced by the receptor and
characterized their intramolecular interactions. We show that κ-helix (polyproline-II)
is a predominant structure in the binding interface and in facilitating the conversion
to the active form of the S protein. We demonstrate a series of conversions between
switch-like κ-helix and β-strand, and conformational variations in a set of short
α-helices which affect the hinge region. These conformational changes lead to an
alternating pattern in conserved disulfide bond configurations positioned at the hinge,
indicating a possible disulfide exchange, an important allosteric switch implicated in
viral entry of various viruses, including HIV and murine coronavirus. The structural
information presented herein enables to inspect and understand the important dynamic
features of SARS-CoV-2-RBD and propose a novel potential therapeutic strategy to block
viral entry. Overall, this study provides guidance for the design and optimization of
structure-based intervention strategies that target SARS-CoV-2. Availability We have implemented the proposed methods in an R package freely available at https://github.com/Grantlab/bio3d Supplementary information Supplementary data are
available at Bioinformatics online.
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Affiliation(s)
- Tomer Meirson
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Ramat-Gan 526260, Israel.,The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | | | - Gal Markel
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Ramat-Gan 526260, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
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7
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Lawrence C, Grishaev A. Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR. RNA (NEW YORK, N.Y.) 2020; 26:2051-2061. [PMID: 32917774 PMCID: PMC7668244 DOI: 10.1261/rna.074617.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 08/19/2020] [Indexed: 06/01/2023]
Abstract
Determination of structure of RNA via NMR is complicated in large part by the lack of a precise parameterization linking the observed chemical shifts to the underlying geometric parameters. In contrast to proteins, where numerous high-resolution crystal structures serve as coordinate templates for this mapping, such models are rarely available for smaller oligonucleotides accessible via NMR, or they exhibit crystal packing and counter-ion binding artifacts that prevent their use for the chemical shifts analysis. On the other hand, NMR-determined structures of RNA often are not solved at the density of restraints required to precisely define the variable degrees of freedom. In this study we sidestep the problems of direct parameterization of the RNA chemical shifts/structure relationship and examine the effects of imposing local fragmental coordinate similarity restraints based on similarities of the experimental secondary ribose 13C/1H chemical shifts instead. The effect of such chemical shift similarity (CSS) restraints on the structural accuracy is assessed via residual dipolar coupling (RDC)-based cross-validation. Improvements in the coordinate accuracy are observed for all of the six RNA constructs considered here as test cases, which argues for routine inclusion of these terms during NMR-based oligonucleotide structure determination. Such accuracy improvements are expected to facilitate derivation of the chemical shift/structure relationships for RNA.
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Affiliation(s)
- Chad Lawrence
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, USA
| | - Alexander Grishaev
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, USA
- Biomolecular Measurement Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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8
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Rochira W, Agirre J. Iris: Interactive all-in-one graphical validation of 3D protein model iterations. Protein Sci 2020; 30:93-107. [PMID: 32964594 PMCID: PMC7737763 DOI: 10.1002/pro.3955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 11/12/2022]
Abstract
Iris validation is a Python package created to represent comprehensive per‐residue validation metrics for entire protein chains in a compact, readable and interactive view. These metrics can either be calculated by Iris, or by a third‐party program such as MolProbity. We show that those parts of a protein model requiring attention may generate ripples across the metrics on the diagram, immediately catching the modeler's attention. Iris can run as a standalone tool, or be plugged into existing structural biology software to display per‐chain model quality at a glance, with a particular emphasis on evaluating incremental changes resulting from the iterative nature of model building and refinement. Finally, the integration of Iris into the CCP4i2 graphical user interface is provided as a showcase of its pluggable design.
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Affiliation(s)
- William Rochira
- Department of Chemistry, York Structural Biology Laboratory, University of York, York, UK
| | - Jon Agirre
- Department of Chemistry, York Structural Biology Laboratory, University of York, York, UK
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9
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Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr D Struct Biol 2019; 75:861-877. [PMID: 31588918 PMCID: PMC6778852 DOI: 10.1107/s2059798319011471] [Citation(s) in RCA: 3310] [Impact Index Per Article: 662.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 08/15/2019] [Indexed: 12/16/2022] Open
Abstract
Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
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Affiliation(s)
- Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew L. Baker
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gábor Bunkóczi
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | - Vincent B. Chen
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Tristan I. Croll
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | - Bradley Hintze
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Li-Wei Hung
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Swati Jain
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Airlie J. McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert D. Oeffner
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | - Billy K. Poon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | | | | | - Massimo D. Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Duncan H. Stockwell
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | - Thomas C. Terwilliger
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Alexandre G. Urzhumtsev
- Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 67404 Illkirch, France
- Faculté des Sciences et Technologies, Université de Lorraine, BP 239, 54506 Vandoeuvre-lès-Nancy, France
| | | | | | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
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10
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ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths. J Comput Aided Mol Des 2019; 33:705-727. [PMID: 31435895 DOI: 10.1007/s10822-019-00216-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/06/2019] [Indexed: 10/26/2022]
Abstract
The possible functions of a protein are strongly related to its structural rearrangements in the presence of other molecules or environmental changes. Hence, the evaluation of transition paths of proteins, which encodes conformational changes between stable states, is important since it may reveal the underlying mechanisms of the biochemical processes related to these motions. During the last few decades, different geometry-based methods have been proposed to predict such transition paths. However, in the cases where the solution requires complex motions, these methods, which typically constrain only locally the molecular structures, could produce physically irrelevant solutions involving self-intersection. Recently, we have proposed ART-RRT, an efficient method for finding ligand-unbinding pathways. It relies on the exploration of energy valleys in low-dimensional spaces, taking advantage of some mechanisms inspired from computer graphics to ensure the consistency of molecular structures. This article extends ART-RRT to the problem of finding probable conformational transition between two stable states for proteins. It relies on a bidirectional exploration rooted on the two end states and introduces an original strategy to attempt connections between the explored regions. The resulting method is able to produce at low computational cost biologically realistic paths free from self-intersection. These paths can serve as valuable input to other advanced methods for the study of proteins. A better understanding of conformational changes of proteins is important since it may reveal the underlying mechanisms of the biochemical processes related to such motions. Recently, the ART-RRT method has been introduced for finding ligand-unbinding pathways. This article presents an adaptation of the method for finding probable conformational transition between two stable states of a protein. The method is not only computationally cost-effective but also able to produce biologically realistic paths which are free from self-intersection.
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11
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Urzhumtsev AG, Lunin VY. Introduction to crystallographic refinement of macromolecular atomic models. CRYSTALLOGR REV 2019. [DOI: 10.1080/0889311x.2019.1631817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alexandre G. Urzhumtsev
- Centre for Integrative Biology, IGBMC, CNRS–INSERM–UdS, Illkirch, France
- Département de Physique, Faculté des Sciences et des Technologies, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Vladimir Y. Lunin
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
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12
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Leng J, Shoura M, McLeish TCB, Real AN, Hardey M, McCafferty J, Ranson NA, Harris SA. Securing the future of research computing in the biosciences. PLoS Comput Biol 2019; 15:e1006958. [PMID: 31095554 PMCID: PMC6521984 DOI: 10.1371/journal.pcbi.1006958] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Improvements in technology often drive scientific discovery. Therefore, research requires sustained investment in the latest equipment and training for the researchers who are going to use it. Prioritising and administering infrastructure investment is challenging because future needs are difficult to predict. In the past, highly computationally demanding research was associated primarily with particle physics and astronomy experiments. However, as biology becomes more quantitative and bioscientists generate more and more data, their computational requirements may ultimately exceed those of physical scientists. Computation has always been central to bioinformatics, but now imaging experiments have rapidly growing data processing and storage requirements. There is also an urgent need for new modelling and simulation tools to provide insight and understanding of these biophysical experiments. Bioscience communities must work together to provide the software and skills training needed in their areas. Research-active institutions need to recognise that computation is now vital in many more areas of discovery and create an environment where it can be embraced. The public must also become aware of both the power and limitations of computing, particularly with respect to their health and personal data.
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Affiliation(s)
- Joanna Leng
- School of Computing, University of Leeds, Leeds, United Kingdom
| | - Massa Shoura
- School of Pathology, Stanford University, Palo Alto, California, United States of America
| | | | - Alan N. Real
- Advanced Research Computing, University of Durham, Durham, United Kingdom
| | - Mariann Hardey
- Advanced Research Computing, University of Durham, Durham, United Kingdom
- School of Business, University of Durham, Durham, United Kingdom
| | | | - Neil A. Ranson
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Sarah A. Harris
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom
- * E-mail:
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13
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Singh S, Sevalkar RR, Sarkar D, Karthikeyan S. Characteristics of the essential pathogenicity factor Rv1828, a MerR family transcription regulator from Mycobacterium tuberculosis. FEBS J 2018; 285:4424-4444. [PMID: 30306715 DOI: 10.1111/febs.14676] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/02/2018] [Accepted: 10/08/2018] [Indexed: 01/16/2023]
Abstract
The gene Rv1828 in Mycobacterium tuberculosis is shown to be essential for the pathogen and encodes for an uncharacterized protein. In this study, we have carried out biochemical and structural characterization of Rv1828 at the molecular level to understand its mechanism of action. The Rv1828 is annotated as helix-turn-helix (HTH)-type MerR family transcription regulator based on its N-terminal amino acid sequence similarity. The MerR family protein binds to a specific DNA sequence in the spacer region between -35 and -10 elements of a promoter through its N-terminal domain (NTD) and acts as transcriptional repressor or activator depending on the absence or presence of effector that binds to its C-terminal domain (CTD). A characteristic feature of MerR family protein is its ability to bind to 19 ± 1 bp DNA sequence in the spacer region between -35 and -10 elements which is otherwise a suboptimal length for transcription initiation by RNA polymerase. Here, we show the Rv1828 through its NTD binds to a specific DNA sequence that exists on its own as well as in other promoter regions. Moreover, the crystal structure of CTD of Rv1828, determined by single-wavelength anomalous diffraction method, reveals a distinctive dimerization. The biochemical and structural analysis reveals that Rv1828 specifically binds to an everted repeat through its winged-HTH motif. Taken together, we demonstrate that the Rv1828 encodes for a MerR family transcription regulator.
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Affiliation(s)
- Suruchi Singh
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Ritesh Rajesh Sevalkar
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Dibyendu Sarkar
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Subramanian Karthikeyan
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
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14
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Woitowich NC, Halavaty AS, Waltz P, Kupitz C, Valera J, Tracy G, Gallagher KD, Claesson E, Nakane T, Pandey S, Nelson G, Tanaka R, Nango E, Mizohata E, Owada S, Tono K, Joti Y, Nugent AC, Patel H, Mapara A, Hopkins J, Duong P, Bizhga D, Kovaleva SE, St. Peter R, Hernandez CN, Ozarowski WB, Roy-Chowdhuri S, Yang JH, Edlund P, Takala H, Ihalainen J, Brayshaw J, Norwood T, Poudyal I, Fromme P, Spence JCH, Moffat K, Westenhoff S, Schmidt M, Stojković EA. Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome. IUCRJ 2018; 5:619-634. [PMID: 30224965 PMCID: PMC6126659 DOI: 10.1107/s2052252518010631] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 07/23/2018] [Indexed: 05/11/2023]
Abstract
Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxo-bacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruiting-body formation of this photomorphogenic bacterium. SaBphP1 lacks a conserved histidine (His) in the chromophore-binding domain that stabilizes the Pr state in the classical BphPs. Instead it contains a threonine (Thr), a feature that is restricted to several myxobacterial phytochromes and is not evolutionarily understood. SaBphP1 structures of the chromophore binding domain (CBD) and the complete photosensory core module (PCM) in wild-type and Thr-to-His mutant forms reveal details of the molecular mechanism of the Pr/Pfr transition associated with the physiological response of this myxobacterium to red light. Specifically, key structural differences in the CBD and PCM between the wild-type and the Thr-to-His mutant involve essential chromophore contacts with proximal amino acids, and point to how the photosignal is transduced through the rest of the protein, impacting the essential enzymatic activity in the photomorphogenic response of this myxobacterium.
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Affiliation(s)
| | - Andrei S. Halavaty
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Patricia Waltz
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | | | - Joseph Valera
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Gregory Tracy
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Kevin D. Gallagher
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Elin Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Suraj Pandey
- Department of Physics, University of Wisconsin, Milwaukee, WI, USA
| | - Garrett Nelson
- Center for Applied Structural Discovery, Arizona State University, 85287 Tempe, AZ, USA
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan
| | - Kensure Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Angela C. Nugent
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Hardik Patel
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Ayesha Mapara
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - James Hopkins
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Phu Duong
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Dorina Bizhga
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | | | - Rachael St. Peter
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | | | | | | | - Jay-How Yang
- Center for Applied Structural Discovery, Arizona State University, 85287 Tempe, AZ, USA
| | - Petra Edlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Heikki Takala
- Faculty of Medicine, Anatomy, University of Helsinki, 00014 Helsinki, Finland
- Nanoscience Center, Department of Biological and Environmental Sciences, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | - Janne Ihalainen
- Nanoscience Center, Department of Biological and Environmental Sciences, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | | | - Tyler Norwood
- Department of Physics, University of Wisconsin, Milwaukee, WI, USA
| | - Ishwor Poudyal
- Department of Physics, University of Wisconsin, Milwaukee, WI, USA
| | - Petra Fromme
- Center for Applied Structural Discovery, Arizona State University, 85287 Tempe, AZ, USA
| | - John C. H. Spence
- Center for Applied Structural Discovery, Arizona State University, 85287 Tempe, AZ, USA
| | - Keith Moffat
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Marius Schmidt
- Department of Physics, University of Wisconsin, Milwaukee, WI, USA
| | - Emina A. Stojković
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
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15
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Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A. New tools for the analysis and validation of cryo-EM maps and atomic models. Acta Crystallogr D Struct Biol 2018; 74:814-840. [PMID: 30198894 PMCID: PMC6130467 DOI: 10.1107/s2059798318009324] [Citation(s) in RCA: 453] [Impact Index Per Article: 75.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 06/27/2018] [Indexed: 11/25/2022] Open
Abstract
Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required. Here, new computational methods and tools implemented in PHENIX are discussed, including d99 to estimate resolution, phenix.auto_sharpen to improve maps and phenix.mtriage to analyze cryo-EM maps. It is suggested that cryo-EM half-maps and masks should be deposited to facilitate the evaluation and validation of cryo-EM-derived atomic models and maps. The application of these tools to deposited cryo-EM atomic models and maps is also presented.
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Affiliation(s)
- Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai, 200444, People’s Republic of China
| | - Bruno P. Klaholz
- Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Billy K. Poon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas C. Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
| | - Alexandre Urzhumtsev
- Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
- Faculté des Sciences et Technologies, Université de Lorraine, BP 239, 54506 Vandoeuvre-lès-Nancy, France
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16
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Nguyen MK, Jaillet L, Redon S. Generating conformational transition paths with low potential-energy barriers for proteins. J Comput Aided Mol Des 2018; 32:853-867. [PMID: 30069648 DOI: 10.1007/s10822-018-0137-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/19/2018] [Indexed: 10/28/2022]
Abstract
The knowledge of conformational transition paths in proteins can be useful for understanding protein mechanisms. Recently, we have introduced the As-Rigid-As-Possible (ARAP) interpolation method, for generating interpolation paths between two protein conformations. The method was shown to preserve well the rigidity of the initial conformation along the path. However, because the method is totally geometry-based, the generated paths may be inconsistent because the atom interactions are ignored. Therefore, in this article, we would like to introduce a new method to generate conformational transition paths with low potential-energy barriers for proteins. The method is composed of three processing stages. First, ARAP interpolation is used for generating an initial path. Then, the path conformations are enhanced by a clash remover. Finally, Nudged Elastic Band, a path-optimization method, is used to produce a low-energy path. Large energy reductions are found in the paths obtained from the method than in those obtained from the ARAP interpolation method alone. The results also show that ARAP interpolation is a good candidate for generating an initial path because it leads to lower potential-energy paths than two other common methods for path interpolation.
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Affiliation(s)
- Minh Khoa Nguyen
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK, 38000, Grenoble, France
| | - Léonard Jaillet
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK, 38000, Grenoble, France.
| | - Stéphane Redon
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK, 38000, Grenoble, France
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17
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Croll TI. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D Struct Biol 2018; 74:519-530. [PMID: 29872003 PMCID: PMC6096486 DOI: 10.1107/s2059798318002425] [Citation(s) in RCA: 856] [Impact Index Per Article: 142.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 02/09/2018] [Indexed: 01/19/2023] Open
Abstract
This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.
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Affiliation(s)
- Tristan Ian Croll
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
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18
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Chen L, He J, Sazzed S, Walker R. An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains. Molecules 2018. [PMID: 29518032 PMCID: PMC5967250 DOI: 10.3390/molecules23030610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) is a structure determination method for large molecular complexes. As more and more atomic structures are determined using this technique, it is becoming possible to perform statistical characterization of side-chain conformations. Two data sets were involved to characterize block lengths for each of the 18 types of amino acids. One set contains 9131 structures resolved using X-ray crystallography from density maps with better than or equal to 1.5 Å resolutions, and the other contains 237 protein structures derived from cryo-EM density maps with 2–4 Å resolutions. The results show that the normalized probability density function of block lengths is similar between the X-ray data set and the cryo-EM data set for most of the residue types, but differences were observed for ARG, GLU, ILE, LYS, PHE, TRP, and TYR for which conformations with certain shorter block lengths are more likely to be observed in the cryo-EM set with 2–4 Å resolutions.
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Affiliation(s)
- Lin Chen
- Department of Mathematics and Computer Science, Elizabeth City State University, Elizabeth City, NC 27909, USA.
| | - Jing He
- Department of Computer Science, Old Dominion University; Norfolk, VA 23529, USA.
| | - Salim Sazzed
- Department of Computer Science, Old Dominion University; Norfolk, VA 23529, USA.
| | - Rayshawn Walker
- Department of Mathematics and Computer Science, Elizabeth City State University, Elizabeth City, NC 27909, USA.
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19
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Smart OS, Horský V, Gore S, Svobodová Vařeková R, Bendová V, Kleywegt GJ, Velankar S. Validation of ligands in macromolecular structures determined by X-ray crystallography. Acta Crystallogr D Struct Biol 2018; 74:228-236. [PMID: 29533230 PMCID: PMC5947763 DOI: 10.1107/s2059798318002541] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 02/12/2018] [Indexed: 01/19/2023] Open
Abstract
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) play a crucial role in structure-guided drug discovery and design, and also provide atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. The quality with which small-molecule ligands have been modelled in Protein Data Bank (PDB) entries has been, and continues to be, a matter of concern for many investigators. Correctly interpreting whether electron density found in a binding site is compatible with the soaked or co-crystallized ligand or represents water or buffer molecules is often far from trivial. The Worldwide PDB validation report (VR) provides a mechanism to highlight any major issues concerning the quality of the data and the model at the time of deposition and annotation, so the depositors can fix issues, resulting in improved data quality. The ligand-validation methods used in the generation of the current VRs are described in detail, including an examination of the metrics to assess both geometry and electron-density fit. It is found that the LLDF score currently used to identify ligand electron-density fit outliers can give misleading results and that better ligand-validation metrics are required.
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Affiliation(s)
- Oliver S. Smart
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, England
| | - Vladimír Horský
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Swanand Gore
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, England
| | - Radka Svobodová Vařeková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Veronika Bendová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Institute of Mathematics and Statistics, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Gerard J. Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, England
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, England
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20
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Wlodawer A, Dauter Z, Porebski PJ, Minor W, Stanfield R, Jaskolski M, Pozharski E, Weichenberger CX, Rupp B. Detect, correct, retract: How to manage incorrect structural models. FEBS J 2018; 285:444-466. [PMID: 29113027 PMCID: PMC5799025 DOI: 10.1111/febs.14320] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/01/2017] [Indexed: 12/13/2022]
Abstract
The massive technical and computational progress of biomolecular crystallography has generated some adverse side effects. Most crystal structure models, produced by crystallographers or well-trained structural biologists, constitute useful sources of information, but occasional extreme outliers remind us that the process of structure determination is not fail-safe. The occurrence of severe errors or gross misinterpretations raises fundamental questions: Why do such aberrations emerge in the first place? How did they evade the sophisticated validation procedures which often produce clear and dire warnings, and why were severe errors not noticed by the depositors themselves, their supervisors, referees and editors? Once detected, what can be done to either correct, improve or eliminate such models? How do incorrect models affect the underlying claims or biomedical hypotheses they were intended, but failed, to support? What is the long-range effect of the propagation of such errors? And finally, what mechanisms can be envisioned to restore the validity of the scientific record and, if necessary, retract publications that are clearly invalidated by the lack of experimental evidence? We suggest that cognitive bias and flawed epistemology are likely at the root of the problem. By using examples from the published literature and from public repositories such as the Protein Data Bank, we provide case summaries to guide correction or improvement of structural models. When strong claims are unsustainable because of a deficient crystallographic model, removal of such a model and even retraction of the affected publication are necessary to restore the integrity of the scientific record.
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Affiliation(s)
- Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Przemyslaw J. Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Robyn Stanfield
- Department of Structural and Computational Biology, BCC206, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, Poznan, 61-614, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan, 61-704, Poland
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Bernhard Rupp
- CVMO, k.-k.Hofkristallamt, 991 Audrey Place, Vista, CA, 92084, USA
- Department of Genetic Epidemiology, Medical University Innsbruck, Schöpfstr. 41, Innsbruck, 6020, Austria
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21
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Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ. Validation of Structures in the Protein Data Bank. Structure 2017; 25:1916-1927. [PMID: 29174494 PMCID: PMC5718880 DOI: 10.1016/j.str.2017.10.009] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/08/2017] [Accepted: 10/27/2017] [Indexed: 11/01/2022]
Abstract
The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. The reports provide useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them. The validation module is also available as a stand-alone web server and as a programmatically accessible web service. A growing number of journals require the official wwPDB validation reports (produced at biocuration) to accompany manuscripts describing macromolecular structures. Upon public release of the structure, the validation report becomes part of the public PDB archive. Geometric quality scores for proteins in the PDB archive have improved over the past decade.
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Affiliation(s)
- Swanand Gore
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eduardo Sanz García
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Pieter M S Hendrickx
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - John D Westbrook
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Huanwang Yang
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zukang Feng
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kumaran Baskaran
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John M Berrisford
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brian P Hudson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yasuyo Ikegawa
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Naohiro Kobayashi
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Catherine L Lawson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Steve Mading
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lora Mak
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Abhik Mukhopadhyay
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas J Oldfield
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ardan Patwardhan
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ezra Peisach
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Gaurav Sahni
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Monica R Sekharan
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sanchayita Sen
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Chenghua Shao
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Oliver S Smart
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eldon L Ulrich
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Reiko Yamashita
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Martha Quesada
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jasmine Y Young
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Haruki Nakamura
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - John L Markley
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Helen M Berman
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Stephen K Burley
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gerard J Kleywegt
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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22
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van Montfort RLM, Workman P. Structure-based drug design: aiming for a perfect fit. Essays Biochem 2017; 61:431-437. [PMID: 29118091 PMCID: PMC5869280 DOI: 10.1042/ebc20170052] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 10/17/2017] [Accepted: 10/18/2017] [Indexed: 02/07/2023]
Abstract
Knowledge of the three-dimensional structure of therapeutically relevant targets has informed drug discovery since the first protein structures were determined using X-ray crystallography in the 1950s and 1960s. In this editorial we provide a brief overview of the powerful impact of structure-based drug design (SBDD), which has its roots in computational and structural biology, with major contributions from both academia and industry. We describe advances in the application of SBDD for integral membrane protein targets that have traditionally proved very challenging. We emphasize the major progress made in fragment-based approaches for which success has been exemplified by over 30 clinical drug candidates and importantly three FDA-approved drugs in oncology. We summarize the articles in this issue that provide an excellent snapshot of the current state of the field of SBDD and fragment-based drug design and which offer key insights into exciting new developments, such as the X-ray free-electron laser technology, cryo-electron microscopy, open science approaches and targeted protein degradation. We stress the value of SBDD in the design of high-quality chemical tools that are used to interrogate biology and disease pathology, and to inform target validation. We emphasize the need to maintain the scientific rigour that has been traditionally associated with structural biology and extend this to other methods used in drug discovery. This is particularly important because the quality and robustness of any form of contributory data determines its usefulness in accelerating drug design, and therefore ultimately in providing patient benefit.
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Affiliation(s)
- Rob L M van Montfort
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, U.K.
- Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, U.K
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, U.K.
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23
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A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun 2017; 8:15123. [PMID: 28436492 PMCID: PMC5413968 DOI: 10.1038/ncomms15123] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/03/2017] [Indexed: 12/02/2022] Open
Abstract
In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous (‘weak' or ‘noisy') density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state—even from inaccurate maps—by subtracting a proportion of the confounding ‘ground state'; changed states are objectively identified from statistical analysis of density distributions. The method is completely general, implying new best practice for all changed-state studies, including the routine collection of multiple ground-state crystals. More generally, these results demonstrate: the incompleteness of atomic models; that single data sets contain insufficient information to model them fully; and that accuracy requires further map-deconvolution approaches. Building a ligand into a weak region of an electron density map of a protein is a subjective process. Here, the authors present a new method to obtain a clear electron density for a bound ligand based on multi-crystal experiments and 3D background correction.
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24
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Weichenberger CX, Pozharski E, Rupp B. Twilight reloaded: the peptide experience. Acta Crystallogr D Struct Biol 2017; 73:211-222. [PMID: 28291756 PMCID: PMC5349433 DOI: 10.1107/s205979831601620x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 10/12/2016] [Indexed: 01/20/2024] Open
Abstract
The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallographic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein-peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electron-density-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided.
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Affiliation(s)
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Bernhard Rupp
- k.k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
- Department of Genetic Epidemiology, Medical University Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
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25
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Eyal Z, Matzov D, Krupkin M, Paukner S, Riedl R, Rozenberg H, Zimmerman E, Bashan A, Yonath A. A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism. Sci Rep 2016; 6:39004. [PMID: 27958389 PMCID: PMC5154188 DOI: 10.1038/srep39004] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/16/2016] [Indexed: 01/07/2023] Open
Abstract
The increasing appearance of pathogenic bacteria with antibiotic resistance is a global threat. Consequently, clinically available potent antibiotics that are active against multidrug resistant pathogens are becoming exceedingly scarce. Ribosomes are a main target for antibiotics, and hence are an objective for novel drug development. Lefamulin, a semi-synthetic pleuromutilin compound highly active against multi-resistant pathogens, is a promising antibiotic currently in phase III trials for the treatment of community-acquired bacterial pneumonia in adults. The crystal structure of the Staphylococcus aureus large ribosomal subunit in complex with lefamulin reveals its protein synthesis inhibition mechanism and the rationale for its potency. In addition, analysis of the bacterial and eukaryotes ribosome structures around the pleuromutilin binding pocket has elucidated the key for the drug's selectivity.
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Affiliation(s)
- Zohar Eyal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miri Krupkin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | | | - Haim Rozenberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ella Zimmerman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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26
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Kachhap S, Priyadarshini P, Singh B. Molecular dynamics simulations show altered secondary structure of clawless in binary complex with DNA providing insights into aristaless-clawless-DNA ternary complex formation. J Biomol Struct Dyn 2016; 35:1153-1167. [PMID: 27058822 DOI: 10.1080/07391102.2016.1175967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Aristaless (Al) and clawless (Cll) homeodomains that are involved in leg development in Drosophila melanogaster are known to bind cooperatively to 5'-(T/C)TAATTAA(T/A)(T/A)G-3' DNA sequence, but the mechanism of their binding to DNA is unknown. Molecular dynamics (MD) studies have been carried out on binary, ternary, and reconstructed protein-DNA complexes involving Al, Cll, and DNA along with binding free energy analysis of these complexes. Analysis of MD trajectories of Cll-3A01, binary complex reveals that C-terminal end of helixIII of Cll, unwind in the absence of Al and remains so in reconstructed ternary complex, Cll-3A01-Al. In addition, this change in secondary structure of Cll does not allow it to form protein-protein interactions with Al in the ternary reconstructed complex. However, secondary structure of Cll and its interactions are maintained in other reconstructed ternary complex, Al-3A01-Cll where Cll binds to Al-3A01, binary complex to form ternary complex. These interactions as observed during MD simulations compare well with those observed in ternary crystal structure. Thus, this study highlights the role of helixIII of Cll and protein-protein interactions while proposing likely mechanism of recognition in ternary complex, Al-Cll-DNA.
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Affiliation(s)
- Sangita Kachhap
- a Bioinformatics Centre , Council of Scientific & Industrial Research - Institute of Microbial Technology , Sector 39A, Chandigarh , India
| | - Pragya Priyadarshini
- a Bioinformatics Centre , Council of Scientific & Industrial Research - Institute of Microbial Technology , Sector 39A, Chandigarh , India
| | - Balvinder Singh
- a Bioinformatics Centre , Council of Scientific & Industrial Research - Institute of Microbial Technology , Sector 39A, Chandigarh , India
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27
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Eyal Z, Matzov D, Krupkin M, Wekselman I, Paukner S, Zimmerman E, Rozenberg H, Bashan A, Yonath A. Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus. Proc Natl Acad Sci U S A 2015; 112:E5805-14. [PMID: 26464510 PMCID: PMC4629319 DOI: 10.1073/pnas.1517952112] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus.
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Affiliation(s)
- Zohar Eyal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miri Krupkin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Itai Wekselman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Ella Zimmerman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Haim Rozenberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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28
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New method to compute Rcomplete enables maximum likelihood refinement for small datasets. Proc Natl Acad Sci U S A 2015; 112:8999-9003. [PMID: 26150515 DOI: 10.1073/pnas.1502136112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The crystallographic reliability index [Formula: see text] is based on a method proposed more than two decades ago. Because its calculation is computationally expensive its use did not spread into the crystallographic community in favor of the cross-validation method known as [Formula: see text]. The importance of [Formula: see text] has grown beyond a pure validation tool. However, its application requires a sufficiently large dataset. In this work we assess the reliability of [Formula: see text] and we compare it with k-fold cross-validation, bootstrapping, and jackknifing. As opposed to proper cross-validation as realized with [Formula: see text], [Formula: see text] relies on a method of reducing bias from the structural model. We compare two different methods reducing model bias and question the widely spread notion that random parameter shifts are required for this purpose. We show that [Formula: see text] has as little statistical bias as [Formula: see text] with the benefit of a much smaller variance. Because the calculation of [Formula: see text] is based on the entire dataset instead of a small subset, it allows the estimation of maximum likelihood parameters even for small datasets. [Formula: see text] enables maximum likelihood-based refinement to be extended to virtually all areas of crystallographic structure determination including high-pressure studies, neutron diffraction studies, and datasets from free electron lasers.
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29
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Islam Z, Kumar A, Singh S, Salmon L, Karthikeyan S. Structural basis for competitive inhibition of 3,4-dihydroxy-2-butanone-4-phosphate synthase from Vibrio cholerae. J Biol Chem 2015; 290:11293-308. [PMID: 25792735 DOI: 10.1074/jbc.m114.611830] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Indexed: 11/06/2022] Open
Abstract
The riboflavin biosynthesis pathway has been shown to be essential in many pathogens and is absent in humans. Therefore, enzymes involved in riboflavin synthesis are considered as potential antibacterial drug targets. The enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes one of the two committed steps in the riboflavin pathway and converts d-ribulose 5-phosphate (Ru5P) to l-3,4-dihydroxy-2-butanone 4-phosphate and formate. Moreover, DHBPS is shown to be indispensable for Mycobacterium, Salmonella, and Helicobacter species. Despite the essentiality of this enzyme in bacteria, no inhibitor has been identified hitherto. Here, we describe kinetic and crystal structure characterization of DHBPS from Vibrio cholerae (vDHBPS) with a competitive inhibitor 4-phospho-d-erythronohydroxamic acid (4PEH) at 1.86-Å resolution. In addition, we also report the structural characterization of vDHBPS in its apo form and in complex with its substrate and substrate plus metal ions at 1.96-, 1.59-, and 2.04-Å resolution, respectively. Comparison of these crystal structures suggests that 4PEH inhibits the catalytic activity of DHBPS as it is unable to form a proposed intermediate that is crucial for DHBPS activity. Furthermore, vDHBPS structures complexed with substrate and metal ions reveal that, unlike Candida albicans, binding of substrate to vDHBPS induces a conformational change from an open to closed conformation. Interestingly, the position of second metal ion, which is different from that of Methanococcus jannaschii, strongly supports an active role in the catalytic mechanism. Thus, the kinetic and structural characterization of vDHBPS reveals the molecular mechanism of inhibition shown by 4PEH and that it can be explored further for designing novel antibiotics.
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Affiliation(s)
- Zeyaul Islam
- From the CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160 036, India and
| | - Adarsh Kumar
- From the CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160 036, India and
| | - Suruchi Singh
- From the CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160 036, India and
| | - Laurent Salmon
- Laboratoire de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, Université Paris-Sud, CNRS UMR8182, F-91405 Orsay, France
| | - Subramanian Karthikeyan
- From the CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160 036, India and
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31
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Wang J. On the validation of crystallographic symmetry and the quality of structures. Protein Sci 2014; 24:621-32. [PMID: 25352397 DOI: 10.1002/pro.2595] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/20/2014] [Accepted: 10/24/2014] [Indexed: 11/06/2022]
Abstract
In 2008, Zwart and colleagues observed that the fraction of the structures deposited in the PDB alleged to have "pseudosymmetry" or "special noncrystallographic symmetry" (NCS) was about 6%, and that this percentage was rising annually. A few years later, Poon and colleagues found that 2% of all the crystal structures in the PDB belonged to higher symmetry space groups than those assigned to them. Here, I report an analysis of the X-ray diffraction data deposited for this class of structures, which shows that most of the "pseudosymmetry" and "special NCS" that has been reported is in fact true crystallographic symmetry (CS). This distinction is important because the credibility of crystal structures depends heavily on quality control statistics such as Rfree that are unreliable when they are computed incorrectly, which they often are when CS is misidentified as "special NCS" or "pseudosymmetry". When mistakes of this kind are made, artificially low values of Rfree can give unjustified confidence in the accuracy of the reported structures.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
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32
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Pražnikar J, Turk D. Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures. ACTA ACUST UNITED AC 2014; 70:3124-34. [PMID: 25478831 PMCID: PMC4257616 DOI: 10.1107/s1399004714021336] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 09/25/2014] [Indexed: 11/12/2022]
Abstract
The maximum-likelihood free-kick target, which calculates model error estimates from the work set and a randomly displaced model, proved superior in the accuracy and consistency of refinement of crystal structures compared with the maximum-likelihood cross-validation target, which calculates error estimates from the test set and the unperturbed model. The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. They utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of Rfree or may leave it out completely.
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Affiliation(s)
- Jure Pražnikar
- Department of Biochemistry and Molecular and Structural Biology, Institute Joǽef Stefan, Jamova 39, 1000 Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Institute Joǽef Stefan, Jamova 39, 1000 Ljubljana, Slovenia
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33
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Jain R, Rajashankar KR, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Crystal structure of yeast DNA polymerase ε catalytic domain. PLoS One 2014; 9:e94835. [PMID: 24733111 PMCID: PMC3986358 DOI: 10.1371/journal.pone.0094835] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 03/20/2014] [Indexed: 01/20/2023] Open
Abstract
DNA polymerase ε (Polε) is a multi-subunit polymerase that contributes to genomic stability via its roles in leading strand replication and the repair of damaged DNA. Here we report the ternary structure of the Polε catalytic subunit (Pol2) bound to a nascent G:C base pair (Pol2G:C). Pol2G:C has a typical B-family polymerase fold and embraces the template-primer duplex with the palm, fingers, thumb and exonuclease domains. The overall arrangement of domains is similar to the structure of Pol2T:A reported recently, but there are notable differences in their polymerase and exonuclease active sites. In particular, we observe Ca2+ ions at both positions A and B in the polymerase active site and also observe a Ca2+ at position B of the exonuclease site. We find that the contacts to the nascent G:C base pair in the Pol2G:C structure are maintained in the Pol2T:A structure and reflect the comparable fidelity of Pol2 for nascent purine-pyrimidine and pyrimidine-purine base pairs. We note that unlike that of Pol3, the shape of the nascent base pair binding pocket in Pol2 is modulated from the major grove side by the presence of Tyr431. Together with Pol2T:A, our results provide a framework for understanding the structural basis of high fidelity DNA synthesis by Pol2.
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Affiliation(s)
- Rinku Jain
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Kanagalaghatta R. Rajashankar
- Department of Chemistry and Chemical Biology, Cornell University and NE-CAT, Advanced Photon Source, Argonne, Illinois, United States of America
| | - Angeliki Buku
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Robert E. Johnson
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Aneel K. Aggarwal
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
- * E-mail:
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34
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Crystal structure analysis of EstA from Arthrobacter sp. Rue61a--an insight into catalytic promiscuity. FEBS Lett 2014; 588:1154-60. [PMID: 24613918 DOI: 10.1016/j.febslet.2014.02.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 02/11/2014] [Accepted: 02/15/2014] [Indexed: 12/22/2022]
Abstract
In this article we analyze the reasons for catalytic promiscuity of a type VIII esterase with β-lactamase fold and the ability to cleave β-lactams. We compared the structure of this enzyme to those of an esterase of the same type without any lactamase ability, an esterase with moderate lactamase ability, and a class C β-lactamase with similar fold. Our results show that for these enzymes, the difference in the substrate specificity is sterically driven.
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35
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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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36
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Crystal structures of interleukin 17A and its complex with IL-17 receptor A. Nat Commun 2013; 4:1888. [PMID: 23695682 DOI: 10.1038/ncomms2880] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 04/12/2013] [Indexed: 02/06/2023] Open
Abstract
The constituent polypeptides of the interleukin-17 family form six different homodimeric cytokines (IL-17A-F) and the heterodimeric IL-17A/F. Their interactions with IL-17 receptors A-E (IL-17RA-E) mediate host defenses while also contributing to inflammatory and autoimmune responses. IL-17A and IL-17F both preferentially engage a receptor complex containing one molecule of IL-17RA and one molecule of IL-17RC. More generally, IL-17RA appears to be a shared receptor that pairs with other members of its family to allow signaling of different IL-17 cytokines. Here we report crystal structures of homodimeric IL-17A and its complex with IL-17RA. Binding to IL-17RA at one side of the IL-17A molecule induces a conformational change in the second, symmetry-related receptor site of IL-17A. This change favors, and is sufficient to account for, the selection of a different receptor polypeptide to complete the cytokine-receptor complex. The structural results are supported by biophysical studies with IL-17A variants produced by site-directed mutagenesis.
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Wlodawer A, Minor W, Dauter Z, Jaskolski M. Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination. FEBS J 2013; 280:5705-36. [PMID: 24034303 DOI: 10.1111/febs.12495] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/12/2013] [Accepted: 08/20/2013] [Indexed: 12/28/2022]
Abstract
The number of macromolecular structures deposited in the Protein Data Bank now approaches 100,000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation.
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Affiliation(s)
- Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD, USA
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A novel role for coenzyme A during hydride transfer in 3-hydroxy-3-methylglutaryl-coenzyme A reductase. Biochemistry 2013; 52:5195-205. [PMID: 23802607 PMCID: PMC4007485 DOI: 10.1021/bi400335g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In this study, we take advantage of the ability of HMG-CoA reductase (HMGR) from Pseudomonas mevalonii to remain active while in its crystallized form to study the changing interactions between the ligands and protein as the first reaction intermediate is created. HMG-CoA reductase catalyzes one of the few double oxidation-reduction reactions in intermediary metabolism that take place in a single active site. Our laboratory has undertaken an exploration of this reaction space using structures of HMG-CoA reductase complexed with various substrate, nucleotide, product, and inhibitor combinations. With a focus in this publication on the first hydride transfer, our structures follow this reduction reaction as the enzyme converts the HMG-CoA thioester from a flat sp(2)-like geometry to a pyramidal thiohemiacetal configuration consistent with a transition to an sp(3) orbital. This change in the geometry propagates through the coenzyme A (CoA) ligand whose first amide bond is rotated 180° where it anchors a web of hydrogen bonds that weave together the nucleotide, the reaction intermediate, the enzyme, and the catalytic residues. This creates a stable intermediate structure prepared for nucleotide exchange and the second reduction reaction within the HMG-CoA reductase active site. Identification of this reaction intermediate provides a template for the development of an inhibitor that would act as an antibiotic effective against the HMG-CoA reductase of methicillin-resistant Staphylococcus aureus.
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Warren GL, Do TD, Kelley BP, Nicholls A, Warren SD. Essential considerations for using protein-ligand structures in drug discovery. Drug Discov Today 2012; 17:1270-81. [PMID: 22728777 DOI: 10.1016/j.drudis.2012.06.011] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/01/2012] [Accepted: 06/14/2012] [Indexed: 11/16/2022]
Abstract
Protein-ligand structures are the core data required for structure-based drug design (SBDD). Understanding the error present in this data is essential to the successful development of SBDD tools. Methods for assessing protein-ligand structure quality and a new set of identification criteria are presented here. When these criteria were applied to a set of 728 structures previously used to validate molecular docking software, only 17% were found to be acceptable. Structures were re-refined to maintain internal consistency in the comparison and assessment of the quality criteria. This process resulted in Iridium, a highly trustworthy protein-ligand structure database to be used for development and validation of structure-based design tools for drug discovery.
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Vyas R, Tewari R, Weiss MS, Karthikeyan S. Structures of ternary complexes of aspartate-semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis H37Rv. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:671-9. [PMID: 22683789 DOI: 10.1107/s0907444912007330] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 02/18/2012] [Indexed: 11/10/2022]
Abstract
Aspartate-semialdehyde dehydrogenase (Asd; ASADH; EC 1.2.1.11) is the enzyme that lies at the first branch point in the biosynthetic pathway of important amino acids including lysine and methionine and the cell-wall component diaminopimelate (DAP). The enzymatic reaction of ASADH is the reductive dephosphorylation of aspartyl-β-phosphate (ABP) to aspartate β-semialdehyde (ASA). Since the aspartate pathway is absolutely essential for the survival of many microbes and is absent in humans, the enzymes involved in this pathway can be considered to be potential antibacterial drug targets. In this work, the structure of ASADH from Mycobacterium tuberculosis H37Rv (Mtb-ASADH) has been determined in complex with glycerol and sulfate at 2.18 Å resolution and in complex with S-methyl-L-cysteine sulfoxide (SMCS) and sulfate at 1.95 Å resolution. The overall structure of Mtb-ASADH is similar to those of its orthologues. However, in the Mtb-ASADH-glycerol complex structure the glycerol molecule is noncovalently bound to the active-site residue Cys130, while in the Mtb-ASADH-SMCS complex structure the SMCS (Cys) is covalently linked to Cys130. The Mtb-ASADH-SMCS complex structurally mimics one of the intermediate steps in the proposed mechanism of ASADH enzyme catalysis. Comparison of the two complex structures revealed that the amino acids Glu224 and Arg249 undergo conformational changes upon binding of glycerol. Moreover, the structures reported here may help in the development of species-specific antibacterial drug molecules against human pathogens.
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Affiliation(s)
- Rajan Vyas
- Department of Biotechnology, Panjab University, Chandigarh 160 014, India
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Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD. Towards automated crystallographic structure refinement with phenix.refine. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:352-67. [PMID: 22505256 PMCID: PMC3322595 DOI: 10.1107/s0907444912001308] [Citation(s) in RCA: 3968] [Impact Index Per Article: 330.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 01/11/2012] [Indexed: 11/10/2022]
Abstract
phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.
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Affiliation(s)
- Pavel V Afonine
- Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA.
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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: 79] [Impact Index Per Article: 6.6] [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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Abstract
Water plays a crucial role in the mediation of protein-ligand interactions, as underscored by the fact that most X-ray crystal structures (of sufficient resolution) of protein-ligand complexes possess water molecules at the protein-ligand interface. In this chapter, the accuracy and reliability of ordered waters observed in crystal structures is discussed. Additionally, the thermodynamic aspects of the inclusion of water in ligand binding to proteins is described, with the goal of providing practical guidelines for dealing with ordered water molecules during structure-guided lead optimization.
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Abstract
Cryo-electron microscopy (cryo-EM) in combination with single-particle analysis has begun to complement crystallography in the study of large macromolecules at near-atomic resolution. Furthermore, advances in cryo-electron tomography have made possible the study of macromolecules within their cellular environment. Single-particle and tomographic studies will become even more useful when technologies for improving the signal-to-noise ratio such as direct electron detectors and phase plates become widely available. Automated image acquisition has significantly reduced the time and effort required to determine the structures of macromolecular assemblies. As a result, the number of structures determined by cryo-EM is growing exponentially. However, there is an urgent need for improved criteria for validating both the reconstruction process and the atomic models derived from cryo-EM data. Another major challenge will be mitigating the effects of anisotropy caused by the missing wedge and the excessively low signal-to-noise ratio for tomographic data. Parallels between the development of macromolecular crystallography and cryo-EM have been used to tentatively predict the future of cryo-EM.
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Affiliation(s)
- Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
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Complexin cross-links prefusion SNAREs into a zigzag array. Nat Struct Mol Biol 2011; 18:927-33. [PMID: 21785414 PMCID: PMC3410656 DOI: 10.1038/nsmb.2101] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 05/19/2011] [Indexed: 01/07/2023]
Abstract
Complexin prevents SNAREs from releasing neurotransmitters until an action potential arrives at the synapse. To understand the mechanism for this inhibition, we determined the structure of complexin bound to a mimetic of a prefusion SNAREpin lacking the portion of the v-SNARE that zippers last to trigger fusion. The 'central helix' of complexin is anchored to one SNARE complex, while its 'accessory helix' extends away at ~45° and bridges to a second complex, occupying the vacant v-SNARE binding site to inhibit fusion. We expected the accessory helix to compete with the v-SNARE for t-SNARE binding but found instead that the interaction occurs intermolecularly. Thus, complexin organizes the SNAREs into a zigzag topology that, when interposed between the vesicle and plasma membranes, is incompatible with fusion.
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Structural basis for pH dependent monomer–dimer transition of 3,4-dihydroxy 2-butanone-4-phosphate synthase domain from Mycobacterium tuberculosis. J Struct Biol 2011; 174:374-84. [DOI: 10.1016/j.jsb.2011.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/13/2011] [Accepted: 01/31/2011] [Indexed: 11/22/2022]
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Alvarenga PH, Francischetti IMB, Calvo E, Sá-Nunes A, Ribeiro JMC, Andersen JF. The function and three-dimensional structure of a thromboxane A2/cysteinyl leukotriene-binding protein from the saliva of a mosquito vector of the malaria parasite. PLoS Biol 2010; 8:e1000547. [PMID: 21152418 PMCID: PMC2994686 DOI: 10.1371/journal.pbio.1000547] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 10/08/2010] [Indexed: 12/04/2022] Open
Abstract
A salivary protein from a malaria-transmitting mosquito uses a single domain to bind to thromboxane A2 and cysteinyl leukotrienes and prevent blood clotting and inflammation in the host on which it feeds. The highly expressed D7 protein family of mosquito saliva has previously been shown to act as an anti-inflammatory mediator by binding host biogenic amines and cysteinyl leukotrienes (CysLTs). In this study we demonstrate that AnSt-D7L1, a two-domain member of this group from Anopheles stephensi, retains the CysLT binding function seen in the homolog AeD7 from Aedes aegypti but has lost the ability to bind biogenic amines. Unlike any previously characterized members of the D7 family, AnSt-D7L1 has acquired the important function of binding thromboxane A2 (TXA2) and its analogs with high affinity. When administered to tissue preparations, AnSt-D7L1 abrogated Leukotriene C4 (LTC4)-induced contraction of guinea pig ileum and contraction of rat aorta by the TXA2 analog U46619. The protein also inhibited platelet aggregation induced by both collagen and U46619 when administered to stirred platelets. The crystal structure of AnSt-D7L1 contains two OBP-like domains and has a structure similar to AeD7. In AnSt-D7L1, the binding pocket of the C-terminal domain has been rearranged relative to AeD7, making the protein unable to bind biogenic amines. Structures of the ligand complexes show that CysLTs and TXA2 analogs both bind in the same hydrophobic pocket of the N-terminal domain. The TXA2 analog U46619 is stabilized by hydrogen bonding interactions of the ω-5 hydroxyl group with the phenolic hydroxyl group of Tyr 52. LTC4 and occupies a very similar position to LTE4 in the previously determined structure of its complex with AeD7. As yet, it is not known what, if any, new function has been acquired by the rearranged C-terminal domain. This article presents, to our knowledge, the first structural characterization of a protein from mosquito saliva that inhibits collagen mediated platelet activation. When feeding, a female mosquito must inhibit the blood clotting and inflammatory responses of the host. To do this, the insect produces salivary proteins that neutralize key host molecules participating in clotting and inflammation. Here, we describe a salivary protein AnSt-D7L1 that scavenges both thomboxane A2 and cysteinyl leukotrienes, two substances involved in blood vessel constriction, platelet aggregation, and inflammatory responses to an insect bite. We produced this protein in bacteria and showed that it tightly binds both these molecules, inhibiting the processes in which they are involved. We then determined its structure using X-ray crystallography and showed that there is a single binding site in one domain of the protein, accommodating both thromboxane A2 and cysteinyl leukotrienes, and that this site is responsible for the scavenging effect of the protein. These studies reveal the structural features of proteins needed to bind to key molecules of potential pharmacological importance and add to our understanding of the process of mosquito blood feeding, which is essential for transmission of the malaria parasite.
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Affiliation(s)
- Patricia H. Alvarenga
- Laboratory of Malaria and Vector Research, National Institutes of Health, National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
- Laboratório de Bioquímica e Fisiologia de Artrópodes, Departamento de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | - Ivo M. B. Francischetti
- Laboratory of Malaria and Vector Research, National Institutes of Health, National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Eric Calvo
- Laboratory of Malaria and Vector Research, National Institutes of Health, National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - Anderson Sá-Nunes
- Laboratory of Malaria and Vector Research, National Institutes of Health, National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
- Laboratório de Imunologia Experimental, Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - José M. C. Ribeiro
- Laboratory of Malaria and Vector Research, National Institutes of Health, National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
| | - John F. Andersen
- Laboratory of Malaria and Vector Research, National Institutes of Health, National Institute of Allergy and Infectious Diseases, Rockville, Maryland, United States of America
- * E-mail:
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Stiebritz MT, Wengrzik S, Klein DL, Richter JP, Srebrzynski A, Weiler S, Muller YA. Computational Design of a Chain-Specific Tetracycline Repressor Heterodimer. J Mol Biol 2010; 403:371-85. [DOI: 10.1016/j.jmb.2010.07.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 07/14/2010] [Accepted: 07/27/2010] [Indexed: 11/25/2022]
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Type IIA topoisomerase inhibition by a new class of antibacterial agents. Nature 2010; 466:935-40. [DOI: 10.1038/nature09197] [Citation(s) in RCA: 514] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Accepted: 05/20/2010] [Indexed: 11/08/2022]
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50
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Gorbalenya AE, Lieutaud P, Harris MR, Coutard B, Canard B, Kleywegt GJ, Kravchenko AA, Samborskiy DV, Sidorov IA, Leontovich AM, Jones TA. Practical application of bioinformatics by the multidisciplinary VIZIER consortium. Antiviral Res 2010; 87:95-110. [PMID: 20153379 PMCID: PMC7172516 DOI: 10.1016/j.antiviral.2010.02.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 02/03/2010] [Accepted: 02/04/2010] [Indexed: 01/03/2023]
Abstract
This review focuses on bioinformatics technologies employed by the EU-sponsored multidisciplinary VIZIER consortium (Comparative Structural Genomics of Viral Enzymes Involved in Replication, FP6 PROJECT: 2004-511960, active from 1 November 2004 to 30 April 2009), to achieve its goals. From the management of the information flow of the project, to bioinformatics-mediated selection of RNA viruses and prediction of protein targets, to the analysis of 3D protein structures and antiviral compounds, these technologies provided a communication framework and integrated solutions for steady and timely advancement of the project. RNA viruses form a large class of major pathogens that affect humans and domestic animals. Such RNA viruses as HIV, Influenza virus and Hepatitis C virus are of prime medical concern today, but the identities of viruses that will threaten human population tomorrow are far from certain. To contain outbreaks of common or newly emerging infections, prototype drugs against viruses representing the Virus Universe must be developed. This concept was championed by the VIZIER project which brought together experts in diverse fields to produce a concerted and sustained effort for identifying and validating targets for antivirus therapy in dozens of RNA virus lineages.
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Affiliation(s)
- Alexander E. Gorbalenya
- Molecular Virology Laboratory, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, P.O. Box 9600, E4-P, 2300 RC Leiden, The Netherlands
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Philippe Lieutaud
- Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 6098, AFMB-CNRS-ESIL, Case 925, 163 Avenue de Luminy, 13288 Marseille, France
| | - Mark R. Harris
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Bruno Coutard
- Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 6098, AFMB-CNRS-ESIL, Case 925, 163 Avenue de Luminy, 13288 Marseille, France
| | - Bruno Canard
- Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 6098, AFMB-CNRS-ESIL, Case 925, 163 Avenue de Luminy, 13288 Marseille, France
| | - Gerard J. Kleywegt
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Alexander A. Kravchenko
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - Dmitry V. Samborskiy
- Molecular Virology Laboratory, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, P.O. Box 9600, E4-P, 2300 RC Leiden, The Netherlands
| | - Igor A. Sidorov
- Molecular Virology Laboratory, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, P.O. Box 9600, E4-P, 2300 RC Leiden, The Netherlands
| | - Andrey M. Leontovich
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia
| | - T. Alwyn Jones
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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