1
|
Beton JG, Cragnolini T, Kaleel M, Mulvaney T, Sweeney A, Topf M. Integrating model simulation tools and
cryo‐electron
microscopy. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Joseph George Beton
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Birkbeck and University College London London UK
| | - Manaz Kaleel
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Thomas Mulvaney
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Aaron Sweeney
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Maya Topf
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| |
Collapse
|
2
|
Benfrid S, Park K, Dellarole M, Voss JE, Tamietti C, Pehau‐Arnaudet G, Raynal B, Brûlé S, England P, Zhang X, Mikhailova A, Hasan M, Ungeheuer M, Petres S, Biering SB, Harris E, Sakuntabhai A, Buchy P, Duong V, Dussart P, Coulibaly F, Bontems F, Rey FA, Flamand M. Dengue virus NS1 protein conveys pro-inflammatory signals by docking onto high-density lipoproteins. EMBO Rep 2022; 23:e53600. [PMID: 35607830 PMCID: PMC10549233 DOI: 10.15252/embr.202153600] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 04/24/2022] [Accepted: 04/27/2022] [Indexed: 10/05/2023] Open
Abstract
The dengue virus nonstructural protein 1 (NS1) is a secreted virulence factor that modulates complement, activates immune cells and alters endothelial barriers. The molecular basis of these events remains incompletely understood. Here we describe a functional high affinity complex formed between NS1 and human high-density lipoproteins (HDL). Collapse of the soluble NS1 hexamer upon binding to the lipoprotein particle leads to the anchoring of amphipathic NS1 dimeric subunits into the HDL outer layer. The stable complex can be visualized by electron microscopy as a spherical HDL with rod-shaped NS1 dimers protruding from the surface. We further show that the assembly of NS1-HDL complexes triggers the production of pro-inflammatory cytokines in human primary macrophages while NS1 or HDL alone do not. Finally, we detect NS1 in complex with HDL and low-density lipoprotein (LDL) particles in the plasma of hospitalized dengue patients and observe NS1-apolipoprotein E-positive complexes accumulating overtime. The functional reprogramming of endogenous lipoprotein particles by NS1 as a means to exacerbate systemic inflammation during viral infection provides a new paradigm in dengue pathogenesis.
Collapse
Affiliation(s)
- Souheyla Benfrid
- Unité de Virologie StructuraleInstitut Pasteur and CNRS UMR3569ParisFrance
- Université Paris Descartes SorbonneParis CitéFrance
- Present address:
Laboratoire de Santé AnimaleANSES, INRA, ENVA, UMR 1161Université Paris‐EstMaisons‐AlfortFrance
| | - Kyu‐Ho Park
- Unité de Virologie StructuraleInstitut Pasteur and CNRS UMR3569ParisFrance
- Present address:
Applied Molecular VirologyInstitut Pasteur KoreaSeongnam‐siKorea
| | - Mariano Dellarole
- Unité de Virologie StructuraleInstitut Pasteur and CNRS UMR3569ParisFrance
- Present address:
Virus Biophysics LaboratoryBionanosciences Research Center (CIBION)National Scientific and Technical Research Council (CONICET)Ciudad Autónoma de Buenos AiresArgentina
| | - James E Voss
- Unité de Virologie StructuraleInstitut Pasteur and CNRS UMR3569ParisFrance
- Present address:
Department of Immunology and MicrobiologyThe Scripps Research InstituteLa JollaCAUSA
| | - Carole Tamietti
- Unité de Virologie StructuraleInstitut Pasteur and CNRS UMR3569ParisFrance
| | | | - Bertrand Raynal
- Molecular Biophysics FacilityCNRS UMR 3528Institut PasteurParisFrance
| | - Sébastien Brûlé
- Molecular Biophysics FacilityCNRS UMR 3528Institut PasteurParisFrance
| | - Patrick England
- Molecular Biophysics FacilityCNRS UMR 3528Institut PasteurParisFrance
| | - Xiaokang Zhang
- Unité de Virologie StructuraleInstitut Pasteur and CNRS UMR3569ParisFrance
- Present address:
Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulationthe Brain Cognition and Brain Disease Institute (BCBDI)Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen‐Hong Kong Institute of Brain Science‐Shenzhen Fundamental Research InstitutionsShenzhenChina
| | - Anastassia Mikhailova
- HIV Inflammation et PersistanceInstitut PasteurParisFrance
- Present address:
Division of Molecular NeurobiologyDepartment of Medical Biochemistry and BiophysicsKarolinska InstituteStockholmSweden
| | - Milena Hasan
- Cytometry and Biomarkers Unit of Technology and ServiceCB UTechSParisFrance
| | | | - Stéphane Petres
- Production and Purification of Recombinant Proteins FacilityInstitut PasteurParisFrance
| | - Scott B Biering
- Division of Infectious Diseases and VaccinologySchool of Public HealthUniversity of CaliforniaBerkeleyCAUSA
| | - Eva Harris
- Division of Infectious Diseases and VaccinologySchool of Public HealthUniversity of CaliforniaBerkeleyCAUSA
| | | | - Philippe Buchy
- Virology UnitInstitut Pasteur du CambodgeInstitut Pasteur International NetworkPhnom PenhCambodia
- Present address:
GlaxoSmithKline Vaccines R&DSingaporeSingapore
| | - Veasna Duong
- Virology UnitInstitut Pasteur du CambodgeInstitut Pasteur International NetworkPhnom PenhCambodia
| | - Philippe Dussart
- Virology UnitInstitut Pasteur du CambodgeInstitut Pasteur International NetworkPhnom PenhCambodia
| | - Fasséli Coulibaly
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVic.Australia
| | - François Bontems
- Unité de Virologie StructuraleInstitut Pasteur and CNRS UMR3569ParisFrance
- Département de Biologie et Chimie StructuralesInstitut de Chimie des Substances Naturelles, CNRS UPR2301Gif‐sur‐YvetteFrance
| | - Félix A Rey
- Unité de Virologie StructuraleInstitut Pasteur and CNRS UMR3569ParisFrance
| | - Marie Flamand
- Unité de Virologie StructuraleInstitut Pasteur and CNRS UMR3569ParisFrance
| |
Collapse
|
3
|
Joseph AP, Lagerstedt I, Patwardhan A, Topf M, Winn M. Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy. J Struct Biol 2017; 199:12-26. [PMID: 28552721 PMCID: PMC5479444 DOI: 10.1016/j.jsb.2017.05.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 05/19/2017] [Accepted: 05/23/2017] [Indexed: 11/28/2022]
Abstract
Recent developments in 3-dimensional electron microcopy (3D-EM) techniques and a concomitant drive to look at complex molecular structures, have led to a rapid increase in the amount of volume data available for biomolecules. This creates a demand for better methods to analyse the data, including improved scores for comparison, classification and integration of data at different resolutions. To this end, we developed and evaluated a set of scoring functions that compare 3D-EM volumes. To test our scores we used a benchmark set of volume alignments derived from the Electron Microscopy Data Bank. We find that the performance of different scores vary with the map-type, resolution and the extent of overlap between volumes. Importantly, adding the overlap information to the local scoring functions can significantly improve their precision and accuracy in a range of resolutions. A combined score involving the local mutual information and overlap (LMI_OV) performs best overall, irrespective of the map category, resolution or the extent of overlap, and we recommend this score for general use. The local mutual information score itself is found to be more discriminatory than cross-correlation coefficient for intermediate-to-low resolution maps or when the map size and density distribution differ significantly. For comparing map surfaces, we implemented two filters to detect the surface points, including one based on the 'extent of surface exposure'. We show that scores that compare surfaces are useful at low resolutions and for maps with evident surface features. All the scores discussed are implemented in TEMPy (http://tempy.ismb.lon.ac.uk/).
Collapse
Affiliation(s)
- Agnel Praveen Joseph
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom; Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Ingvar Lagerstedt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom; Computational Chemistry and Cheminformatics, Lilly UK, Windlesham GU20 6PH, United Kingdom
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom.
| | - Martyn Winn
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom.
| |
Collapse
|
4
|
Brown A, Long F, Nicholls RA, Toots J, Emsley P, Murshudov G. Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:136-53. [PMID: 25615868 PMCID: PMC4304694 DOI: 10.1107/s1399004714021683] [Citation(s) in RCA: 440] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 10/01/2014] [Indexed: 11/24/2022]
Abstract
The recent rapid development of single-particle electron cryo-microscopy (cryo-EM) now allows structures to be solved by this method at resolutions close to 3 Å. Here, a number of tools to facilitate the interpretation of EM reconstructions with stereochemically reasonable all-atom models are described. The BALBES database has been repurposed as a tool for identifying protein folds from density maps. Modifications to Coot, including new Jiggle Fit and morphing tools and improved handling of nucleic acids, enhance its functionality for interpreting EM maps. REFMAC has been modified for optimal fitting of atomic models into EM maps. As external structural information can enhance the reliability of the derived atomic models, stabilize refinement and reduce overfitting, ProSMART has been extended to generate interatomic distance restraints from nucleic acid reference structures, and a new tool, LIBG, has been developed to generate nucleic acid base-pair and parallel-plane restraints. Furthermore, restraint generation has been integrated with visualization and editing in Coot, and these restraints have been applied to both real-space refinement in Coot and reciprocal-space refinement in REFMAC.
Collapse
Affiliation(s)
- Alan Brown
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Fei Long
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Robert A. Nicholls
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Jaan Toots
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Garib Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| |
Collapse
|
5
|
López-Blanco JR, Chacón P. Structural modeling from electron microscopy data. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014. [DOI: 10.1002/wcms.1199] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- José Ramón López-Blanco
- Department of Biological Physical Chemistry; Rocasolano Physical Chemistry Institute, CSIC; Madrid Spain
| | - Pablo Chacón
- Department of Biological Physical Chemistry; Rocasolano Physical Chemistry Institute, CSIC; Madrid Spain
| |
Collapse
|
6
|
Saha M, Morais MC. FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps. ACTA ACUST UNITED AC 2012; 28:3265-73. [PMID: 23131460 DOI: 10.1093/bioinformatics/bts616] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a 'mosaic' backbone model of the assembly that could aid map interpretation and illuminate biological function. RESULT Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM-a computational tool that can identify folded macromolecular domains in medium to low resolution (4-15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.
Collapse
Affiliation(s)
- Mitul Saha
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 7555-0647, USA.
| | | |
Collapse
|
7
|
Zhang Q, Bettadapura R, Bajaj C. Macromolecular structure modeling from 3D EM using VolRover 2.0. Biopolymers 2012; 97:709-31. [PMID: 22696407 DOI: 10.1002/bip.22052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We review tools for structure identification and model-based refinement from three-dimensional electron microscopy implemented in our in-house software package, VOLROVER 2.0. For viral density maps with icosahedral symmetry, we segment the capsid, polymeric, and monomeric subunits using techniques based on automatic symmetry detection and multidomain fast marching. For large biomolecules without symmetry information, we again use our multidomain fast-marching method with manual or fit-based multiseeding to segment meaningful substructures. In either case, we subject the resulting segmented subunit to secondary structure detection when the EM resolution is sufficiently high, and rigid-body structure fitting when the corresponding X-ray structure is available. Secondary structure elements are identified by three techniques: our earlier volume-based and boundary-based skeletonization methods as well as a new method, currently in development, based on solving the grassfire flow equation. For rigid-body fitting, we adapt our earlier fast Fourier-based correlation scheme F2Dock. Our reported segmentation, secondary structure elements identification, and rigid-body fitting techniques, implemented in VOLROVER 2.0 are applied to the PSB 2011 cryo-EM modeling challenge data, and our results are briefly compared to similar results submitted from other research groups. The comparisons show that our techniques are equally capable of segmenting relatively accurate subunits from a viral or protein assembly, and that high segmentation quality leads in turn to higher-quality results of secondary structure elements identification and correlation-based rigid-body fitting. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 709-731, 2012.
Collapse
Affiliation(s)
- Qin Zhang
- Institute for Computational Engineering and Sciences, The University of Texas, Austin, TX 78712, USA
| | | | | |
Collapse
|
8
|
Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A. Macromolecular assembly structures by comparative modeling and electron microscopy. Methods Mol Biol 2012; 857:331-350. [PMID: 22323229 DOI: 10.1007/978-1-61779-588-6_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Advances in electron microscopy allow for structure determination of large biological machines at increasingly higher resolutions. A key step in this process is fitting component structures into the electron microscopy-derived density map of their assembly. Comparative modeling can contribute by providing atomic models of the components, via fold assignment, sequence-structure alignment, model building, and model assessment. All four stages of comparative modeling can also benefit from consideration of the density map. In this chapter, we describe numerous types of modeling problems restrained by a density map and available protocols for finding solutions. In particular, we provide detailed instructions for density map-guided modeling using the Integrative Modeling Platform (IMP), MODELLER, and UCSF Chimera.
Collapse
Affiliation(s)
- Keren Lasker
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
| | | | | | | | | | | |
Collapse
|
9
|
Bajaj C, Goswami S, Zhang Q. Detection of secondary and supersecondary structures of proteins from cryo-electron microscopy. J Struct Biol 2011; 177:367-81. [PMID: 22186625 DOI: 10.1016/j.jsb.2011.11.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 11/09/2011] [Accepted: 11/15/2011] [Indexed: 11/30/2022]
Abstract
Recent advances in three-dimensional electron microscopy (3D EM) have enabled the quantitative visualization of the structural building blocks of proteins at improved resolutions. We provide algorithms to detect the secondary structures (α-helices and β-sheets) from proteins for which the volumetric maps are reconstructed at 6-10Å resolution. Additionally, we show that when the resolution is coarser than 10Å, some of the supersecondary structures can be detected from 3D EM maps. For both these algorithms, we employ tools from computational geometry and differential topology, specifically the computation of stable/unstable manifolds of certain critical points of the distance function induced by the molecular surface. Our results connect mathematically well-defined constructions with bio-chemically induced structures observed in proteins.
Collapse
Affiliation(s)
- Chandrajit Bajaj
- Center for Computational Visualization, The Institute for Computational Engineering and Sciences, Department of Computer Science, The University of Texas at Austin, University Station C0200, Austin, TX 78712, USA.
| | | | | |
Collapse
|
10
|
Sael L, Kihara D. Improved protein surface comparison and application to low-resolution protein structure data. BMC Bioinformatics 2010; 11 Suppl 11:S2. [PMID: 21172052 PMCID: PMC3024873 DOI: 10.1186/1471-2105-11-s11-s2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expanding at a rapid pace, an urgent task is to provide reliable clues to their biological function on a large scale. Conventional approaches for structure comparison are not suitable for a real-time database search due to their slow speed. Moreover, a new challenge has arisen from recent techniques such as electron microscopy (EM), which provide low-resolution structure data. Previously, we have introduced a method for protein surface shape representation using the 3D Zernike descriptors (3DZDs). The 3DZD enables fast structure database searches, taking advantage of its rotation invariance and compact representation. The search results of protein surface represented with the 3DZD has showngood agreement with the existing structure classifications, but some discrepancies were also observed. Results The three new surface representations of backbone atoms, originally devised all-atom-surface representation, and the combination of all-atom surface with the backbone representation are examined. All representations are encoded with the 3DZD. Also, we have investigated the applicability of the 3DZD for searching protein EM density maps of varying resolutions. The surface representations are evaluated on structure retrieval using two existing classifications, SCOP and the CE-based classification. Conclusions Overall, the 3DZDs representing backbone atoms show better retrieval performance than the original all-atom surface representation. The performance further improved when the two representations are combined. Moreover, we observed that the 3DZD is also powerful in comparing low-resolution structures obtained by electron microscopy.
Collapse
Affiliation(s)
- Lee Sael
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.
| | | |
Collapse
|
11
|
An automated procedure for detecting protein folds from sub-nanometer resolution electron density. J Struct Biol 2009; 170:513-21. [PMID: 20026407 DOI: 10.1016/j.jsb.2009.12.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 12/09/2009] [Accepted: 12/15/2009] [Indexed: 11/24/2022]
Abstract
The use of sub-nanometer resolution electron density as spatial constraints for de novo and ab initio structure prediction requires knowledge of protein boundaries to accurately segment the electron density for the prediction algorithms. Here we present a procedure where even poorly segmented density can be used to determine the fold of the protein. The method is automated, fast, capable of searching for multiple copies of a protein fold, and accessible to densities encompassing more than a thousand residues. The automation is particularly powerful as it allows the procedure to take full advantage of the expanding repository in the Protein Data Bank. We have tested the method on nine segmented sub-nanometer image reconstruction electron densities. The method successfully identifies the correct fold for the six densities for which an atomic structure is known, identifies a fold that agrees with prior structural data, a fold that agrees with predictions from the Fold & Function Assignment server, and a fold that correlates with secondary structure prediction. The identified folds in the last three examples can be used as templates for comparative modeling of the bacteriophage P22 tail-machine (a 3MDa complex composed of 39 protein subunits).
Collapse
|
12
|
Heuser P, Langer GG, Lamzin VS. Interpretation of very low resolution X-ray electron-density maps using core objects. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:690-6. [PMID: 19564689 PMCID: PMC2703575 DOI: 10.1107/s090744490901991x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 05/25/2009] [Indexed: 11/11/2022]
Abstract
A novel approach to obtaining structural information from macromolecular X-ray data extending to resolutions as low as 20 A is presented. Following a simple map-segmentation procedure, the approximate shapes of the domains forming the structure are identified. A pattern-recognition comparative analysis of these shapes and those derived from the structures of domains from the PDB results in candidate structural models that can be used for a fit into the density map. It is shown that the placed candidate models can be employed for subsequent phase extension to higher resolution.
Collapse
Affiliation(s)
- Philipp Heuser
- Hamburg Unit, European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, Hamburg 22603, Germany.
| | | | | |
Collapse
|
13
|
Lindert S, Stewart PL, Meiler J. Hybrid approaches: applying computational methods in cryo-electron microscopy. Curr Opin Struct Biol 2009; 19:218-25. [PMID: 19339173 DOI: 10.1016/j.sbi.2009.02.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 02/26/2009] [Indexed: 12/20/2022]
Abstract
Recent advances in cryo-electron microscopy have led to an increasing number of high (3-5A) to medium (5-10A) resolution cryoEM density maps. These density maps contain valuable information about the protein structure but frequently require computational algorithms to aid their structural interpretation. It is these hybrid approaches between cryoEM and computational protein structure prediction algorithms that will shape protein structure elucidation from density maps.
Collapse
Affiliation(s)
- Steffen Lindert
- Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA
| | | | | |
Collapse
|
14
|
Alber F, Förster F, Korkin D, Topf M, Sali A. Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem 2008; 77:443-77. [PMID: 18318657 DOI: 10.1146/annurev.biochem.77.060407.135530] [Citation(s) in RCA: 185] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To understand the cell, we need to determine the macromolecular assembly structures, which may consist of tens to hundreds of components. First, we review the varied experimental data that characterize the assemblies at several levels of resolution. We then describe computational methods for generating the structures using these data. To maximize completeness, resolution, accuracy, precision, and efficiency of the structure determination, a computational approach is required that uses spatial information from a variety of experimental methods. We propose such an approach, defined by its three main components: a hierarchical representation of the assembly, a scoring function consisting of spatial restraints derived from experimental data, and an optimization method that generates structures consistent with the data. This approach is illustrated by determining the configuration of the 456 proteins in the nuclear pore complex (NPC) from baker's yeast. With these tools, we are poised to integrate structural information gathered at multiple levels of the biological hierarchy--from atoms to cells--into a common framework.
Collapse
Affiliation(s)
- Frank Alber
- Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158-2330, USA.
| | | | | | | | | |
Collapse
|
15
|
Sorzano COS, Jonic S, Cottevieille M, Larquet E, Boisset N, Marco S. 3D electron microscopy of biological nanomachines: principles and applications. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:995-1013. [PMID: 17611751 DOI: 10.1007/s00249-007-0203-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 06/01/2007] [Accepted: 06/11/2007] [Indexed: 11/21/2022]
Abstract
Transmission electron microscopy is a powerful technique for studying the three-dimensional (3D) structure of a wide range of biological specimens. Knowledge of this structure is crucial for fully understanding complex relationships among macromolecular complexes and organelles in living cells. In this paper, we present the principles and main application domains of 3D transmission electron microscopy in structural biology. Moreover, we survey current developments needed in this field, and discuss the close relationship of 3D transmission electron microscopy with other experimental techniques aimed at obtaining structural and dynamical information from the scale of whole living cells to atomic structure of macromolecular complexes.
Collapse
Affiliation(s)
- C O S Sorzano
- Bioengineering Lab, Escuela Politécnica Superior, Univ. San Pablo CEU, Campus Urb, Montepríncipe s/n, 28668, Boadilla del Monte, Madrid, Spain.
| | | | | | | | | | | |
Collapse
|
16
|
Dror O, Lasker K, Nussinov R, Wolfson H. EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2007; 63:42-9. [PMID: 17164525 PMCID: PMC2483490 DOI: 10.1107/s0907444906041059] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Accepted: 10/08/2006] [Indexed: 11/22/2022]
Abstract
Structural analysis of biological machines is essential for inferring their function and mechanism. Nevertheless, owing to their large size and instability, deciphering the atomic structure of macromolecular assemblies is still considered as a challenging task that cannot keep up with the rapid advances in the protein-identification process. In contrast, structural data at lower resolution is becoming more and more available owing to recent advances in cryo-electron microscopy (cryo-EM) techniques. Once a cryo-EM map is acquired, one of the basic questions asked is what are the folds of the components in the assembly and what is their configuration. Here, a novel knowledge-based computational method, named EMatch, towards tackling this task for cryo-EM maps at 6-10 A resolution is presented. The method recognizes and locates possible atomic resolution structural homologues of protein domains in the assembly. The strengths of EMatch are demonstrated on a cryo-EM map of native GroEL at 6 A resolution.
Collapse
Affiliation(s)
- Oranit Dror
- School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Keren Lasker
- School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ruth Nussinov
- Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Basic Research Program, SAIC-Frederick, Center for Cancer Research Nanobiology Program, NCI-Frederick, Building 469, Room 151, Frederick, MD 21702 USA
| | - Haim Wolfson
- School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
17
|
Lasker K, Dror O, Shatsky M, Nussinov R, Wolfson HJ. EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2007; 4:28-39. [PMID: 17277411 DOI: 10.1109/tcbb.2007.1003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Cryo-EM has become an increasingly powerful technique for elucidating the structure, dynamics, and function of large flexible macromolecule assemblies that cannot be determined at atomic resolution. However, due to the relatively low resolution of cryo-EM data, a major challenge is to identify components of complexes appearing in cryo-EM maps. Here, we describe EMatch, a novel integrated approach for recognizing structural homologues of protein domains present in a 6-10 A resolution cryo-EM map and constructing a quasi-atomic structural model of their assembly. The method is highly efficient and has been successfully validated on various simulated data. The strength of the method is demonstrated by a domain assembly of an experimental cryo-EM map of native GroEL at 6 A resolution.
Collapse
Affiliation(s)
- Keren Lasker
- School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Israel.
| | | | | | | | | |
Collapse
|
18
|
Garzón JI, Kovacs J, Abagyan R, Chacón P. ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics 2006; 23:427-33. [PMID: 17150992 DOI: 10.1093/bioinformatics/btl625] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Efficient fitting tools are needed to take advantage of a fast growth of atomic models of protein domains from crystallography or comparative modeling, and low-resolution density maps of larger molecular assemblies. Here, we report a novel fitting algorithm for the exhaustive and fast overlay of partial high-resolution models into a low-resolution density map. The method incorporates a fast rotational search based on spherical harmonics (SH) combined with a simple translational scanning. RESULTS This novel combination makes it possible to accurately dock atomic structures into low-resolution electron-density maps in times ranging from seconds to a few minutes. The high-efficiency achieved with simulated and experimental test cases preserves the exhaustiveness needed in these heterogeneous-resolution merging tools. The results demonstrate its efficiency, robustness and high-throughput coverage. AVAILABILITY http://sbg.cib.csic.es/Software/ADP_EM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- José Ignacio Garzón
- Centro de Investigaciones Biológicas, CSIC Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | | | | |
Collapse
|
19
|
Velazquez-Muriel JA, Carazo JMA. Flexible fitting in 3D-EM with incomplete data on superfamily variability. J Struct Biol 2006; 158:165-81. [PMID: 17257856 DOI: 10.1016/j.jsb.2006.10.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Revised: 09/20/2006] [Accepted: 10/13/2006] [Indexed: 11/26/2022]
Abstract
We present a substantial improvement of S-flexfit, our recently proposed method for flexible fitting in three dimensional electron microscopy (3D-EM) at a resolution range of 8-12A, together with a comparison of the method capabilities with Normal Mode Analysis (NMA), application examples and a user's guide. S-flexfit uses the evolutionary information contained in protein domain databases like CATH, by means of the structural alignment of the elements of a protein superfamily. The added development is based on a recent extension of the Singular Value Decomposition (SVD) algorithm specifically designed for situations with missing data: Incremental Singular Value Decomposition (ISVD). ISVD can manage gaps and allows considering more aminoacids in the structural alignment of a superfamily, extending the range of application and producing better models for the fitting step of our methodology. Our previous SVD-based flexible fitting approach can only take into account positions with no gaps in the alignment, being appropriate when the superfamily members are relatively similar and there are few gaps. However, with new data coming from structural proteomics works, the later situation is becoming less likely, making ISVD the technique of choice for further works. We present the results of using ISVD in the process of flexible fitting with both simulated and experimental 3D-EM maps (GroEL and Poliovirus 135S cell entry intermediate).
Collapse
Affiliation(s)
- Javier A Velazquez-Muriel
- Biocomputing Unit, National Center for Biotechnology, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | |
Collapse
|
20
|
Velazquez-Muriel JA, Valle M, Santamaría-Pang A, Kakadiaris IA, Carazo JM. Flexible Fitting in 3D-EM Guided by the Structural Variability of Protein Superfamilies. Structure 2006; 14:1115-26. [PMID: 16843893 DOI: 10.1016/j.str.2006.05.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 04/27/2006] [Accepted: 05/01/2006] [Indexed: 10/24/2022]
Abstract
A method for flexible fitting of molecular models into three-dimensional electron microscopy (3D-EM) reconstructions at a resolution range of 8-12 A is proposed. The approach uses the evolutionarily related structural variability existing among the protein domains of a given superfamily, according to structural databases such as CATH. A structural alignment of domains belonging to the superfamily, followed by a principal components analysis, is performed, and the first three principal components of the decomposition are explored. Using rigid body transformations for the secondary structure elements (SSEs) plus the cyclic coordinate descent algorithm to close the loops, stereochemically correct models are built for the structure to fit. All of the models are fitted into the 3D-EM map, and the best one is selected based on crosscorrelation measures. This work applies the method to both simulated and experimental data and shows that the flexible fitting was able to produce better results than rigid body fitting.
Collapse
Affiliation(s)
- Javier-Angel Velazquez-Muriel
- Biocomputing Unit, National Center for Biotechnology-CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | | | | | | |
Collapse
|
21
|
Topf M, Sali A. Combining electron microscopy and comparative protein structure modeling. Curr Opin Struct Biol 2005; 15:578-85. [PMID: 16118050 DOI: 10.1016/j.sbi.2005.08.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Revised: 07/01/2005] [Accepted: 08/10/2005] [Indexed: 10/25/2022]
Abstract
Recently, advances have been made in methods and applications that integrate electron microscopy density maps and comparative modeling to produce atomic structures of macromolecular assemblies. Electron microscopy can benefit from comparative modeling through the fitting of comparative models into electron microscopy density maps. Also, comparative modeling can benefit from electron microscopy through the use of intermediate-resolution density maps in fold recognition, template selection and sequence-structure alignment.
Collapse
Affiliation(s)
- Maya Topf
- Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | | |
Collapse
|
22
|
Llorca O. Introduction to 3D reconstruction of macromolecules using single particle electron microscopy. Acta Pharmacol Sin 2005; 26:1153-64. [PMID: 16174429 DOI: 10.1111/j.1745-7254.2005.00203.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Single-particle electron microscopy has now reached maturity, becoming a commonly used method in the examination of macromolecular structure. Using a small amount of purified protein, isolated molecules are observed under the electron microscope and the data collected can be averaged into a 3D reconstruction. Single-particle electron microscopy is an appropriate tool for the analysis of proteins that can only be obtained in modest quantities, like many of the large complexes currently of interest in biomedicine. Whilst the use of electron microscopy expands, new methods are being developed and improved to deal with further challenges, such as reaching higher resolutions and the combination of information at different levels of structural detail. More importantly, present methodology is still not robust enough when studying certain tricky proteins like those displaying extensive conformational flexibility and a great deal of user expertise is required, posing a threat to the consistency of the final structure. This mini review describes a brief outline of the methods currently used in the 3D analysis of macromolecules using single-particle electron microscopy, intended for those first approaching this field. A summary of methods, techniques, software, and some recent work is presented. The spectacular improvements to the technique in recent years, its advantages and limitations compared to other structural methods, and its future developments are discussed.
Collapse
Affiliation(s)
- Oscar Llorca
- Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas, Ramiro de Maeztu, 9 Campus Universidad Complutense, 28040 Madrid, Spain.
| |
Collapse
|