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Luque D, Ortega-Esteban A, Valbuena A, Luis Vilas J, Rodríguez-Huete A, Mateu MG, Castón JR. Equilibrium Dynamics of a Biomolecular Complex Analyzed at Single-amino Acid Resolution by Cryo-electron Microscopy. J Mol Biol 2023; 435:168024. [PMID: 36828271 DOI: 10.1016/j.jmb.2023.168024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
The biological function of macromolecular complexes depends not only on large-scale transitions between conformations, but also on small-scale conformational fluctuations at equilibrium. Information on the equilibrium dynamics of biomolecular complexes could, in principle, be obtained from local resolution (LR) data in cryo-electron microscopy (cryo-EM) maps. However, this possibility had not been validated by comparing, for a same biomolecular complex, LR data with quantitative information on equilibrium dynamics obtained by an established solution technique. In this study we determined the cryo-EM structure of the minute virus of mice (MVM) capsid as a model biomolecular complex. The LR values obtained correlated with crystallographic B factors and with hydrogen/deuterium exchange (HDX) rates obtained by mass spectrometry (HDX-MS), a gold standard for determining equilibrium dynamics in solution. This result validated a LR-based cryo-EM approach to investigate, with high spatial resolution, the equilibrium dynamics of biomolecular complexes. As an application of this approach, we determined the cryo-EM structure of two mutant MVM capsids and compared their equilibrium dynamics with that of the wild-type MVM capsid. The results supported a previously suggested linkage between mechanical stiffening and impaired equilibrium dynamics of a virus particle. Cryo-EM is emerging as a powerful approach for simultaneously acquiring information on the atomic structure and local equilibrium dynamics of biomolecular complexes.
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Affiliation(s)
- Daniel Luque
- Spanish National Microbiology Centre, Institute of Health Carlos III, Madrid, Spain
| | - Alvaro Ortega-Esteban
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose Luis Vilas
- Biocomputing Unit, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain.
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Xu N, Doerschuk PC. Reconstruction of Stochastic 3D Signals With Symmetric Statistics From 2D Projection Images Motivated by Cryo-Electron Microscopy. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2019; 28:5479-5494. [PMID: 31095482 DOI: 10.1109/tip.2019.2915631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cryo-electron microscopy provides 2D projection images of the 3D electron scattering intensity of many instances of the particle under study (e.g., a virus). Both symmetry (rotational point groups) and heterogeneity are important aspects of biological particles and both aspects can be combined by describing the electron scattering intensity of the particle as a stochastic process with a symmetric probability law and, therefore, symmetric moments. A maximum likelihood estimator implemented by an expectation-maximization algorithm is described, which estimates the unknown statistics of the electron scattering intensity stochastic process from the images of instances of the particle. The algorithm is demonstrated on the bacteriophage HK97 and the virus [Formula: see text]. The results are contrasted with the existing algorithms, which assume that each instance of the particle has the symmetry rather than the less restrictive assumption that the probability law has the symmetry.
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Xu N, Veesler D, Doerschuk PC, Johnson JE. Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data. J Struct Biol 2018; 202:129-141. [PMID: 29331608 DOI: 10.1016/j.jsb.2017.12.013] [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: 10/04/2017] [Revised: 12/24/2017] [Accepted: 12/27/2017] [Indexed: 10/18/2022]
Abstract
The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation.
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Affiliation(s)
- Nan Xu
- School of Electrical and Computer Engineering, Cornell University, United States
| | - David Veesler
- Department of Biochemistry, University of Washington, United States
| | - Peter C Doerschuk
- Meinig School of Biomedical Engineering and School of Electrical and Computer Engineering, Cornell University, Phillips Hall Room 305, Ithaca, NY 14853, United States.
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, United States
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Doerschuk PC. Statistical characterization of ensembles of symmetric virus particles: 3-D stochastic signal reconstruction from electron microscope images. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2017; 2016:3977-3980. [PMID: 28269156 DOI: 10.1109/embc.2016.7591598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Stochastic models of nano-biomachines have been studied by 3-D reconstruction from cryo electron microscopy images in recent years. The image data is the projection of many heterogeneous instances of the object under study (e.g., a virus). Initial reconstruction algorithms require different instances of the object, while still heterogeneous, to have the same symmetry. This paper presents a maximum likelihood reconstruction approach which allows each object to lack symmetry while constraining the statistics of the ensemble of objects to have symmetry. This algorithm is demonstrated on bacteriophage HK97 and is contrasted with the former algorithm. Reconstruction results show that the proposed algorithm provides estimates that make more biological sense.
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Penkler DL, Jiwaji M, Domitrovic T, Short JR, Johnson JE, Dorrington RA. Binding and entry of a non-enveloped T=4 insect RNA virus is triggered by alkaline pH. Virology 2016; 498:277-287. [PMID: 27614703 DOI: 10.1016/j.virol.2016.08.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/24/2016] [Accepted: 08/29/2016] [Indexed: 11/29/2022]
Abstract
Tetraviruses are small, non-enveloped, RNA viruses that exclusively infect lepidopteran insects. Their particles comprise 240 copies of a single capsid protein precursor (CP), which undergoes autoproteolytic cleavage during maturation. The molecular mechanisms of capsid assembly and maturation are well understood, but little is known about the viral infectious lifecycle due to a lack of tissue culture cell lines that are susceptible to tetravirus infection. We show here that binding and entry of the alphatetravirus, Helicoverpa armigera stunt virus (HaSV), is triggered by alkaline pH. At pH 9.0, wild-type HaSV virus particles undergo conformational changes that induce membrane-lytic activity and binding to Spodoptera frugiperda Sf9 cells. Binding is followed by entry and infection, with virus replication complexes detected by immunofluorescence microscopy within 2h post-infection and the CP after 12h. HaSV particles produced in S. frugiperda Sf9 cells are infectious. Helicoverpa armigera larval virus biofeed assays showed that pre-treatment with the V-ATPase inhibitor, Bafilomycin A1, resulted in a 50% decrease in larval mortality and stunting, while incubation of virus particles at pH 9.0 prior to infection restored infectivity. Together, these data show that HaSV, and likely other tetraviruses, requires the alkaline environment of the lepidopteran larval midgut for binding and entry into host cells.
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Affiliation(s)
- David L Penkler
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Meesbah Jiwaji
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Tatiana Domitrovic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - James R Short
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rosemary A Dorrington
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa.
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Doerschuk PC, Gong Y, Xu N, Domitrovic T, Johnson JE. Virus particle dynamics derived from CryoEM studies. Curr Opin Virol 2016; 18:57-63. [DOI: 10.1016/j.coviro.2016.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 02/29/2016] [Indexed: 12/13/2022]
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Gong Y, Veesler D, Doerschuk PC, Johnson JE. Effect of the viral protease on the dynamics of bacteriophage HK97 maturation intermediates characterized by variance analysis of cryo EM particle ensembles. J Struct Biol 2016; 193:188-195. [DOI: 10.1016/j.jsb.2015.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 10/22/2022]
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An encapsidated viral protein and its role in RNA packaging by a non-enveloped animal RNA virus. Virology 2015; 476:323-333. [PMID: 25577149 DOI: 10.1016/j.virol.2014.12.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 12/12/2014] [Accepted: 12/17/2014] [Indexed: 11/23/2022]
Abstract
Alphatetraviruses are small (+) ssRNA viruses with non-enveloped, icosahedral, T=4 particles that assemble from 240 copies of a single capsid protein precursor. This study is focused on the mechanisms underlying selection and packaging of genomic vRNAs by Helicoverpa armigera stunt virus. We demonstrate that the viral protein, p17, is packaged at low levels (between 4 and 8 copies per capsid) raising the possibility of icosahedral asymmetry in wild-type particles. p17 promotes packaging of vRNA2 by virus-like particles (VLPs) generated from plasmid-expressed vRNA2. The 5' and 3' UTRs of RNA2 are not required for encapsidation. VLPs produced by recombinant baculoviruses package vRNA2 at detectable levels even in the absence of p17 and apparently excluding baculoviral transcripts. This suggests a role for p17 in vRNA selectivity. This is one of few examples of the packaging of a minor non-structural protein by (+) ssRNA animal viruses.
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Berman HM, Gabanyi MJ, Groom CR, Johnson JE, Murshudov GN, Nicholls RA, Reddy V, Schwede T, Zimmerman MD, Westbrook J, Minor W. Data to knowledge: how to get meaning from your result. IUCRJ 2015; 2:45-58. [PMID: 25610627 PMCID: PMC4285880 DOI: 10.1107/s2052252514023306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 10/22/2014] [Indexed: 05/19/2023]
Abstract
Structural and functional studies require the development of sophisticated 'Big Data' technologies and software to increase the knowledge derived and ensure reproducibility of the data. This paper presents summaries of the Structural Biology Knowledge Base, the VIPERdb Virus Structure Database, evaluation of homology modeling by the Protein Model Portal, the ProSMART tool for conformation-independent structure comparison, the LabDB 'super' laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results.
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Affiliation(s)
- Helen M. Berman
- Center for Integrative Proteomics Research, Department of Chemistry and Chemical Biology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
| | - Margaret J. Gabanyi
- Center for Integrative Proteomics Research, Department of Chemistry and Chemical Biology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
| | - Colin R. Groom
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - John E. Johnson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Robert A. Nicholls
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Vijay Reddy
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Torsten Schwede
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
- SIB-Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Matthew D. Zimmerman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - John Westbrook
- Center for Integrative Proteomics Research, Department of Chemistry and Chemical Biology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
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Assembly and maturation of a T = 4 quasi-equivalent virus is guided by electrostatic and mechanical forces. Viruses 2014; 6:3348-62. [PMID: 25153346 PMCID: PMC4147699 DOI: 10.3390/v6083348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/15/2014] [Accepted: 08/18/2014] [Indexed: 11/17/2022] Open
Abstract
Nudaurelia capensis w virus (NωV) is a eukaryotic RNA virus that is well suited for the study of virus maturation. The virus initially assembles at pH 7.6 into a marginally stable 480-Å procapsid formed by 240 copies of a single type of protein subunit. During maturation, which occurs during apoptosis at pH 5.0, electrostatic forces guide subunit trajectories into a robust 410-Å virion that is buttressed by subunit associated molecular switches. We discuss the competing factors in the virus capsid of requiring near-reversible interactions during initial assembly to avoid kinetic traps, while requiring robust stability to survive in the extra-cellular environment. In addition, viruses have a variety of mechanisms to deliver the genome, which must remain off while still inside the infected cell, yet turn on under the proper conditions of infection. We conclude that maturation is the process that provides a solution to these conflicting requirements through a program that is encoded in the procapsid and that leads to stability and infectivity.
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