1
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Comas-Garcia M. How structural biology has changed our understanding of icosahedral viruses. J Virol 2024:e0111123. [PMID: 39291975 DOI: 10.1128/jvi.01111-23] [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: 09/19/2024] Open
Abstract
Cryo-electron microscopy and tomography have allowed us to unveil the remarkable structure of icosahedral viruses. However, in the past few years, the idea that these viruses must have perfectly symmetric virions, but in some cases, it might not be true. This has opened the door to challenging paradigms in structural virology and raised new questions about the biological implications of "unusual" or "defective" symmetries and structures. Also, the continual improvement of these technologies, coupled with more rigorous sample purification protocols, improvements in data processing, and the use of artificial intelligence, has allowed solving the structure of sub-viral particles in highly heterogeneous samples and finding novel symmetries or structural defects. In this review, I initially analyzed the case of the symmetry and composition of hepatitis B virus-produced spherical sub-viral particles. Then, I focused on Alphaviruses as an example of "imperfect" icosahedrons and analyzed how structural biology has changed our understanding of the Alphavirus assembly and some biological implications arising from these discoveries.
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Affiliation(s)
- Mauricio Comas-Garcia
- Science Department, Autonomous University of San Luis Potosi, San Luis Potosí, Mexico
- High-Resolution Microscopy Section, Research Center for Health Sciences and Biomedicine, Autonomous University of San Luis Potosi, San Luis Potosi, Mexico
- Translational and Molecular Medicine Section, Research Center for Health Sciences and Biomedicine, Autonomous University of San Luis Potosi, San Luis Potosí, Mexico
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2
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Zhang C, Wu H, Feng H, Zhang YA, Tu J. Grass carp reovirus VP56 and VP35 induce formation of viral inclusion bodies for replication. iScience 2024; 27:108684. [PMID: 38188516 PMCID: PMC10767200 DOI: 10.1016/j.isci.2023.108684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/14/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Viral inclusion bodies (VIBs) are subcellular structures required for efficient viral replication. How type II grass carp reovirus (GCRV-II), the mainly prevalent strain, forms VIBs is unknown. In this study, we found that GCRV-II infection induced punctate VIBs in grass carp ovary (GCO) cells and that non-structural protein 38 (NS38) functioned as a participant in VIB formation. Furthermore, VP56 and VP35 induced VIBs and recruited other viral proteins via the N-terminal of VP56 and the middle domain of VP35. Additionally, we found that the newly synthesized viral RNAs co-localized with VP56 and VP35 in VIBs during infection. Taken together, VP56 and VP35 induce VIB formation and recruit other viral proteins and viral RNAs to the VIBs for viral replication, which helps identify new targets for developing anti-GCRV-II drugs to disrupt viral replication.
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Affiliation(s)
- Chu Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Hui Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Hao Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Yong-An Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Jiagang Tu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
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3
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Lata K, Charles S, Mangala Prasad V. Advances in computational approaches to structure determination of alphaviruses and flaviviruses using cryo-electron microscopy. J Struct Biol 2023; 215:107993. [PMID: 37414374 DOI: 10.1016/j.jsb.2023.107993] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/15/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Advancements in the field of cryo-electron microscopy (cryo-EM) have greatly contributed to our current understanding of virus structures and life cycles. In this review, we discuss the application of single particle cryo-electron microscopy (EM) for the structure elucidation of small enveloped icosahedral viruses, namely, alpha- and flaviviruses. We focus on technical advances in cryo-EM data collection, image processing, three-dimensional reconstruction, and refinement strategies for obtaining high-resolution structures of these viruses. Each of these developments enabled new insights into the alpha- and flavivirus architecture, leading to a better understanding of their biology, pathogenesis, immune response, immunogen design, and therapeutic development.
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Affiliation(s)
- Kiran Lata
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Sylvia Charles
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Vidya Mangala Prasad
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India; Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, Karnataka 560012, India
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4
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Williamson LE, Bandyopadhyay A, Bailey K, Sirohi D, Klose T, Julander JG, Kuhn RJ, Crowe JE. Structural constraints link differences in neutralization potency of human anti-Eastern equine encephalitis virus monoclonal antibodies. Proc Natl Acad Sci U S A 2023; 120:e2213690120. [PMID: 36961925 PMCID: PMC10068833 DOI: 10.1073/pnas.2213690120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/10/2023] [Indexed: 03/26/2023] Open
Abstract
Selection and development of monoclonal antibody (mAb) therapeutics against pathogenic viruses depends on certain functional characteristics. Neutralization potency, or the half-maximal inhibitory concentration (IC50) values, is an important characteristic of candidate therapeutic antibodies. Structural insights into the bases of neutralization potency differences between antiviral neutralizing mAbs are lacking. In this report, we present cryo-electron microscopy (EM) reconstructions of three anti-Eastern equine encephalitis virus (EEEV) neutralizing human mAbs targeting overlapping epitopes on the E2 protein, with greater than 20-fold differences in their respective IC50 values. From our structural and biophysical analyses, we identify several constraints that contribute to the observed differences in the neutralization potencies. Cryo-EM reconstructions of EEEV in complex with these Fab fragments reveal structural constraints that dictate intravirion or intervirion cross-linking of glycoprotein spikes by their IgG counterparts as a mechanism of neutralization. Additionally, we describe critical features for the recognition of EEEV by these mAbs including the epitope-paratope interaction surface, occupancy, and kinetic differences in on-rate for binding to the E2 protein. Each constraint contributes to the extent of EEEV inhibition for blockade of virus entry, fusion, and/or egress. These findings provide structural and biophysical insights into the differences in mechanism and neutralization potencies of these antibodies, which help inform rational design principles for candidate vaccines and therapeutic antibodies for all icosahedral viruses.
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Affiliation(s)
- Lauren E. Williamson
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN37232
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN37232
| | - Abhishek Bandyopadhyay
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN47907
| | - Kevin Bailey
- Institute for Antiviral Research, Utah State University, Logan, UT84335
| | - Devika Sirohi
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN47907
| | - Thomas Klose
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN47907
| | | | - Richard J. Kuhn
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN47907
| | - James E. Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN37232
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN37232
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN37232
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5
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Chen CL, Klose T, Sun C, Kim AS, Buda G, Rossmann MG, Diamond MS, Klimstra WB, Kuhn RJ. Cryo-EM structures of alphavirus conformational intermediates in low pH-triggered prefusion states. Proc Natl Acad Sci U S A 2022; 119:e2114119119. [PMID: 35867819 PMCID: PMC9335222 DOI: 10.1073/pnas.2114119119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 06/03/2022] [Indexed: 01/24/2023] Open
Abstract
Alphaviruses can cause severe human arthritis and encephalitis. During virus infection, structural changes of viral glycoproteins in the acidified endosome trigger virus-host membrane fusion for delivery of the capsid core and RNA genome into the cytosol to initiate virus translation and replication. However, mechanisms by which E1 and E2 glycoproteins rearrange in this process remain unknown. Here, we investigate prefusion cryoelectron microscopy (cryo-EM) structures of eastern equine encephalitis virus (EEEV) under acidic conditions. With models fitted into the low-pH cryo-EM maps, we suggest that E2 dissociates from E1, accompanied by a rotation (∼60°) of the E2-B domain (E2-B) to expose E1 fusion loops. Cryo-EM reconstructions of EEEV bound to a protective antibody at acidic and neutral pH suggest that stabilization of E2-B prevents dissociation of E2 from E1. These findings reveal conformational changes of the glycoprotein spikes in the acidified host endosome. Stabilization of E2-B may provide a strategy for antiviral agent development.
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Affiliation(s)
- Chun-Liang Chen
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Chengqun Sun
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261
| | - Arthur S. Kim
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Geeta Buda
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Michael G. Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - William B. Klimstra
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261
| | - Richard J. Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
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6
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Capsid-E2 Interactions Rescue Core Assembly in Viruses That Cannot Form Cytoplasmic Nucleocapsid Cores. J Virol 2021; 95:e0106221. [PMID: 34495691 DOI: 10.1128/jvi.01062-21] [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: 11/20/2022] Open
Abstract
Alphavirus capsid proteins (CPs) have two domains: the N-terminal domain (NTD), which interacts with the viral RNA, and the C-terminal domain (CTD), which forms CP-CP interactions and interacts with the cytoplasmic domain of the E2 spike protein (cdE2). In this study, we examine how mutations in the CP NTD affect CP CTD interactions with cdE2. We changed the length and/or charge of the NTD of Ross River virus CP and found that changing the charge of the NTD has a greater impact on core and virion assembly than changing the length of the NTD. The NTD CP insertion mutants are unable to form cytoplasmic cores during infection, but they do form cores or core-like structures in virions. Our results are consistent with cdE2 having a role in core maturation during virion assembly and rescuing core formation when cytoplasmic cores are not assembled. We go on to find that the isolated cores from some mutant virions are now assembly competent in that they can be disassembled and reassembled back into cores. These results show how the two domains of CP may have distinct yet coordinated roles. IMPORTANCE Structural viral proteins have multiple roles during entry and assembly. The capsid protein (CP) of alphaviruses has one domain that interacts with the viral genome and another domain that interacts with the E2 spike protein. In this work, we determined that the length and/or charge of the CP affects cytoplasmic core formation. However, defects in cytoplasmic core formation can be overcome by E2-CP interactions, thus assembling a core or core-like complex in the virion. In the absence of both cytoplasmic cores and CP-E2 interactions, CP is not even packaged in the released virions, but some infectious particles are still released, presumably as RNA packaged in a glycoprotein-containing membrane shell. This suggests that the virus has multiple mechanisms in place to ensure the viral genome is surrounded by a capsid core during its life cycle.
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7
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Martín-Bravo M, Llorente JMG, Hernández-Rojas J, Wales DJ. Minimal Design Principles for Icosahedral Virus Capsids. ACS NANO 2021; 15:14873-14884. [PMID: 34492194 PMCID: PMC8939845 DOI: 10.1021/acsnano.1c04952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Indexed: 06/13/2023]
Abstract
The geometrical structures of single- and multiple-shell icosahedral virus capsids are reproduced as the targets that minimize the cost corresponding to relatively simple design functions. Capsid subunits are first identified as building blocks at a given coarse-grained scale and then represented in these functions as point particles located on an appropriate number of concentric spherical surfaces. Minimal design cost is assigned to optimal spherical packings of the particles. The cost functions are inspired by the packings favored for the Thomson problem, which minimize the electrostatic potential energy between identical charged particles. In some cases, icosahedral symmetry constraints are incorporated as external fields acting on the particles. The simplest cost functions can be obtained by separating particles in disjoint nonequivalent sets with distinct interactions, or by introducing interacting holes (the absence of particles). These functions can be adapted to reproduce any capsid structure found in real viruses. Structures absent in Nature require significantly more complex designs. Measures of information content and complexity are assigned to both the cost functions and the capsid geometries. In terms of these measures, icosahedral structures and the corresponding cost functions are the simplest solutions.
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Affiliation(s)
- Manuel Martín-Bravo
- Departamento
de Física and IUdEA, Universidad
de La Laguna, 38205 Tenerife, Spain
| | | | | | - David J. Wales
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
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8
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Hasan SS, Dey D, Singh S, Martin M. The Structural Biology of Eastern Equine Encephalitis Virus, an Emerging Viral Threat. Pathogens 2021; 10:pathogens10080973. [PMID: 34451437 PMCID: PMC8400090 DOI: 10.3390/pathogens10080973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/21/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022] Open
Abstract
Alphaviruses are arboviruses that cause arthritis and encephalitis in humans. Eastern Equine Encephalitis Virus (EEEV) is a mosquito-transmitted alphavirus that is implicated in severe encephalitis in humans with high mortality. However, limited insights are available into the fundamental biology of EEEV and residue-level details of its interactions with host proteins. In recent years, outbreaks of EEEV have been reported mainly in the United States, raising concerns about public safety. This review article summarizes recent advances in the structural biology of EEEV based mainly on single-particle cryogenic electron microscopy (cryoEM) structures. Together with functional analyses of EEEV and related alphaviruses, these structural investigations provide clues to how EEEV interacts with host proteins, which may open avenues for the development of therapeutics.
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Affiliation(s)
- S. Saif Hasan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore, MD 21201, USA; (D.D.); (S.S.); (M.M.)
- Center for Biomolecular Therapeutics, University of Maryland School of Medicine, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, 22. S. Greene St., Baltimore, MD 21201, USA
- Correspondence:
| | - Debajit Dey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore, MD 21201, USA; (D.D.); (S.S.); (M.M.)
| | - Suruchi Singh
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore, MD 21201, USA; (D.D.); (S.S.); (M.M.)
| | - Matthew Martin
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore, MD 21201, USA; (D.D.); (S.S.); (M.M.)
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9
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Cryo-EM structure of the mature and infective Mayaro virus at 4.4 Å resolution reveals features of arthritogenic alphaviruses. Nat Commun 2021; 12:3038. [PMID: 34031424 PMCID: PMC8144435 DOI: 10.1038/s41467-021-23400-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/27/2021] [Indexed: 12/19/2022] Open
Abstract
Mayaro virus (MAYV) is an emerging arbovirus of the Americas that may cause a debilitating arthritogenic disease. The biology of MAYV is not fully understood and largely inferred from related arthritogenic alphaviruses. Here, we present the structure of MAYV at 4.4 Å resolution, obtained from a preparation of mature, infective virions. MAYV presents typical alphavirus features and organization. Interactions between viral proteins that lead to particle formation are described together with a hydrophobic pocket formed between E1 and E2 spike proteins and conformational epitopes specific of MAYV. We also describe MAYV glycosylation residues in E1 and E2 that may affect MXRA8 host receptor binding, and a molecular “handshake” between MAYV spikes formed by N262 glycosylation in adjacent E2 proteins. The structure of MAYV is suggestive of structural and functional complexity among alphaviruses, which may be targeted for specificity or antiviral activity. Mayaro virus (MAYV) is an emerging arbovirus in Central and South America that is transmitted by mosquitoes and causes arthritogenic disease. Here, the authors present the 4.4 Å resolution cryo-EM structure of MAYV and describe specific features of the virus, which could be exploited for the design of MAYV-specific diagnostics and therapeutics.
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10
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Johnson JE, Olson AJ. Icosahedral virus structures and the protein data bank. J Biol Chem 2021; 296:100554. [PMID: 33744290 PMCID: PMC8081926 DOI: 10.1016/j.jbc.2021.100554] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 11/30/2022] Open
Abstract
The structural study of icosahedral viruses has a long and impactful history in both crystallographic methodology and molecular biology. The evolution of the Protein Data Bank has paralleled and supported these studies providing readily accessible formats dealing with novel features associated with viral particle symmetries and subunit interactions. This overview describes the growth in size and complexity of icosahedral viruses from the first early studies of small RNA plant viruses and human picornaviruses up to the larger and more complex bacterial phage, insect, and human disease viruses such as Zika, hepatitis B, Adeno and Polyoma virus. The analysis of icosahedral viral capsid protein domain folds has shown striking similarities, with the beta jelly roll motif observed across multiple evolutionarily divergent species. The icosahedral symmetry of viruses drove the development of noncrystallographic symmetry averaging as a powerful phasing method, and the constraints of maintaining this symmetry resulted in the concept of quasi-equivalence in viral structures. Symmetry also played an important early role in demonstrating the power of cryo-electron microscopy as an alternative to crystallography in generating atomic resolution structures of these viruses. The Protein Data Bank has been a critical resource for assembling and disseminating these structures to a wide community, and the virus particle explorer (VIPER) was developed to enable users to easily generate and view complete viral capsid structures from their asymmetric building blocks. Finally, we share a personal perspective on the early use of computer graphics to communicate the intricacies, interactions, and beauty of these virus structures.
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Affiliation(s)
- John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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11
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12
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Cryo-EM structure of eastern equine encephalitis virus in complex with heparan sulfate analogues. Proc Natl Acad Sci U S A 2020; 117:8890-8899. [PMID: 32245806 DOI: 10.1073/pnas.1910670117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Eastern equine encephalitis virus (EEEV), a mosquito-borne icosahedral alphavirus found mainly in North America, causes human and equine neurotropic infections. EEEV neurovirulence is influenced by the interaction of the viral envelope protein E2 with heparan sulfate (HS) proteoglycans from the host's plasma membrane during virus entry. Here, we present a 5.8-Å cryoelectron microscopy (cryo-EM) structure of EEEV complexed with the HS analog heparin. "Peripheral" HS binding sites were found to be associated with the base of each of the E2 glycoproteins that form the 60 quasi-threefold spikes (q3) and the 20 sites associated with the icosahedral threefold axes (i3). In addition, there is one HS site at the vertex of each q3 and i3 spike (the "axial" sites). Both the axial and peripheral sites are surrounded by basic residues, suggesting an electrostatic mechanism for HS binding. These residues are highly conserved among EEEV strains, and therefore a change in these residues might be linked to EEEV neurovirulence.
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13
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Saredy JJ, Chim FY, Lyski ZL, Ahearn YP, Bowers DF. Confocal Analysis of the Distribution and Persistence of Sindbis Virus (TaV-GFP) Infection in Midguts of Aedes aegypti Mosquitoes. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2020; 26:267-274. [PMID: 32189602 DOI: 10.1017/s1431927620001270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biological transmission of arthropod-borne viruses (arboviruses) to vertebrate hosts by hematophagous insects poses a global threat because such arboviruses can result in a range of serious public health infectious diseases. Sindbis virus (SINV), the prototype Alphavirus, was used to track infections in the posterior midgut (PMG) of Aedes aegypti adult mosquitoes. Females were fed viremic blood containing a virus reporter, SINV [Thosea asigna virus-green fluorescent protein (TaV-GFP)], that leaves a fluorescent signal in infected cells. We assessed whole-mount PMGs to identify primary foci, secondary target tissues, distribution, and virus persistence. Following a viremic blood meal, PMGs were dissected and analyzed at various days of post blood-feeding. We report that virus foci indicated by GFP in midgut epithelial cells resulted in a 9.8% PMG infection and a 10.8% dissemination from these infected guts. The number of virus foci ranged from 1 to 3 per individual PMG and was more prevalent in the PMG-middle > PMG-frontal > PMG-caudal regions. SINV TaV-GFP was first observed in the PMG (primary target tissue) at 3 days post blood-feeding, was sequestered in circumscribed foci, replicated in PMG peristaltic muscles (secondary target tissue) following dissemination, and GFP was observed to persist in PMGs for 30 days postinfection.
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Affiliation(s)
- Jason J Saredy
- Department of Biology, Temple University, Philadelphia, PA19122, USA
| | - Florence Y Chim
- Saft America Inc., 13575 Waterworks St., Jacksonville, FL32221, USA
| | - Zoë L Lyski
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR97239, USA
| | - Yani P Ahearn
- Department of Biology, University of North Florida, 1 UNF Drive, Jacksonville, FL32224, USA
| | - Doria F Bowers
- Department of Biology, University of North Florida, 1 UNF Drive, Jacksonville, FL32224, USA
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14
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Puranik N, Rani R, Singh VA, Tomar S, Puntambekar HM, Srivastava P. Evaluation of the Antiviral Potential of Halogenated Dihydrorugosaflavonoids and Molecular Modeling with nsP3 Protein of Chikungunya Virus (CHIKV). ACS OMEGA 2019; 4:20335-20345. [PMID: 31815237 PMCID: PMC6893968 DOI: 10.1021/acsomega.9b02900] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/06/2019] [Indexed: 06/10/2023]
Abstract
Antiviral therapy is crucial for the circumvention of viral epidemics. The unavailability of a specific antiviral drug against the chikungunya virus (CHIKV) disease has created an alarming situation to identify or develop potent chemical molecules for remedial management of CHIKV. In the present investigation, in silico studies of dihydrorugosaflavonoid derivatives (5a-f) with non-structural protein-3 (nsP3) were carried out. nsP3 replication protein has recently been considered as a possible antiviral target in which crucial inhibitors fit into the adenosine-binding pocket of the macrodomain. The 4'-halogenated dihydrorugosaflavonoids displayed intrinsic binding with the nsp3 macrodomain (PDB ID: 3GPO) of CHIKV. Compounds 5c and 5d showed docking scores of -7.54 and -6.86 kcal mol-1, respectively. Various in vitro assays were performed to confirm their (5a-f) antiviral potential against CHIKV. The non-cytotoxic dose was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and was found to be <100 μM. The compounds 5c and 5d showed their inhibitory potential for CHIKV, which was determined through cytopathic effect assay and plaque reduction assay, which show inhibition up to 95 and 92% for 70 μM concentration of the compounds, respectively. The quantitative real-time polymerase chain reaction assay result confirmed the ability of 5c and 5d to reduce the viral RNA level at 70 μM concentration of compounds to nearly 95 and 93% concentration, respectively, in cells with CHIKV infection. Further, the CHIKV-inhibitory capacity of these compounds was corroborated by execution of immunofluorescence assay. The executed work will be meaningful for the future research of studied dihydrorugosaflavonoids against prime antiviral entrants, leading to remedial management to preclude CHIKV infection.
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Affiliation(s)
- Ninad
V. Puranik
- Bioprospecting Group, Agharkar Research Institute, G. G. Agarkar Road, Pune 411004, Maharashtra, India
- Savitribai
Phule Pune University, Ganeshkhind, Pune 411007, India
| | - Ruchi Rani
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Vedita Anand Singh
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Shailly Tomar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Hemalata M. Puntambekar
- Bioprospecting Group, Agharkar Research Institute, G. G. Agarkar Road, Pune 411004, Maharashtra, India
- Savitribai
Phule Pune University, Ganeshkhind, Pune 411007, India
| | - Pratibha Srivastava
- Bioprospecting Group, Agharkar Research Institute, G. G. Agarkar Road, Pune 411004, Maharashtra, India
- Savitribai
Phule Pune University, Ganeshkhind, Pune 411007, India
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15
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Cryo-EM Structures of Eastern Equine Encephalitis Virus Reveal Mechanisms of Virus Disassembly and Antibody Neutralization. Cell Rep 2019; 25:3136-3147.e5. [PMID: 30540945 PMCID: PMC6302666 DOI: 10.1016/j.celrep.2018.11.067] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/01/2018] [Accepted: 11/15/2018] [Indexed: 01/08/2023] Open
Abstract
Alphaviruses are enveloped pathogens that cause arthritis and encephalitis. Here, we report a 4.4-Å cryoelectron microscopy (cryo-EM) structure of eastern equine encephalitis virus (EEEV), an alphavirus that causes fatal encephalitis in humans. Our analysis provides insights into viral entry into host cells. The envelope protein E2 showed a binding site for the cellular attachment factor heparan sulfate. The presence of a cryptic E2 glycan suggests how EEEV escapes surveillance by lectin-expressing myeloid lineage cells, which are sentinels of the immune system. A mechanism for nucleocapsid core release and disassembly upon viral entry was inferred based on pH changes and capsid dissociation from envelope proteins. The EEEV capsid structure showed a viral RNA genome binding site adjacent to a ribosome binding site for viral genome translation following genome release. Using five Fab-EEEV complexes derived from neutralizing antibodies, our investigation provides insights into EEEV host cell interactions and protective epitopes relevant to vaccine design. EEEV cryo-EM structure shows the basis of receptor binding and pH-triggered disassembly Cryptic envelope protein glycosylation interferes with immune detection EEEV RNA genome binding site on capsid protein has an extended conformation Antibody inhibition of EEEV entry involves cross-linking of viral envelope proteins
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16
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Dharmavaram S, She SB, Lázaro G, Hagan MF, Bruinsma R. Gaussian curvature and the budding kinetics of enveloped viruses. PLoS Comput Biol 2019; 15:e1006602. [PMID: 31433804 PMCID: PMC6736314 DOI: 10.1371/journal.pcbi.1006602] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 09/10/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023] Open
Abstract
The formation of a membrane-enveloped virus starts with the assembly of a curved layer of capsid proteins lining the interior of the plasma membrane (PM) of the host cell. This layer develops into a spherical shell (capsid) enveloped by a lipid-rich membrane. In many cases, the budding process stalls prior to the release of the virus. Recently, Brownian dynamics simulations of a coarse-grained model system reproduced protracted pausing and stalling, which suggests that the origin of pausing/stalling is to be found in the physics of the budding process. Here, we propose that the pausing/stalling observed in the simulations can be understood as a purely kinetic phenomenon associated with the neck geometry. A geometrical potential energy barrier develops during the budding that must be overcome by capsid proteins diffusing along the membrane prior to incorporation into the capsid. The barrier is generated by a conflict between the positive Gauss curvature of the assembling capsid and the negative Gauss curvature of the neck region. A continuum theory description is proposed and is compared with the Brownian simulations of the budding of enveloped viruses. Despite intense study, the life-cycle of the HIV-1 virus continues to pose mysteries. One of these is the fact that the assembly of an HIV-1 virus along the plasma membrane (PM) of the host cell—the budding process—stalls prior to release of the virus. Many other important viral pathogens with a surrounding lipid membrane envelope display similar stalling. Combining numerical and analytical methods, we demonstrate that the neck-like shape of the membrane that forms prior to release of the virus creates a barrier that blocks the proteins required for the assembly process from reaching the budding virus. An improved understanding of the physics of the blocking process could enable new strategies to combat enveloped viruses.
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Affiliation(s)
- Sanjay Dharmavaram
- Department of Mathematics, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Selene Baochen She
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Guillermo Lázaro
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Michael Francis Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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17
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Johnson JE. Michael G. Rossmann (1930–2019): Leadership in structural biology for 60 years. Protein Sci 2019. [DOI: 10.1002/pro.3671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- John E. Johnson
- Department of Integrative Structural and Computational BiologyThe Scripps Research Institute La Jolla California 92037
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18
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Dunbar CA, Rayaprolu V, Wang JCY, Brown CJ, Leishman E, Jones-Burrage S, Trinidad JC, Bradshaw HB, Clemmer DE, Mukhopadhyay S, Jarrold MF. Dissecting the Components of Sindbis Virus from Arthropod and Vertebrate Hosts: Implications for Infectivity Differences. ACS Infect Dis 2019; 5:892-902. [PMID: 30986033 DOI: 10.1021/acsinfecdis.8b00356] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Sindbis virus (SINV) is an enveloped, single-stranded RNA virus, which is transmitted via mosquitos to a wide range of vertebrate hosts. SINV produced by vertebrate, baby hamster kidney (BHK) cells is more than an order of magnitude less infectious than SINV produced from mosquito (C6/36) cells. The cause of this difference is poorly understood. In this study, charge detection mass spectrometry was used to determine the masses of intact SINV particles isolated from BHK and C6/36 cells. The measured masses are substantially different: 52.88 MDa for BHK derived SINV and 50.69 MDa for C6/36 derived. Further analysis using several mass spectrometry-based methods and biophysical approaches indicates that BHK derived SINV has a substantially higher mass than C6/36 derived because in the lipid bilayer, there is a higher portion of lipids containing long chain fatty acids. The difference in lipid composition could influence the organization of the lipid bilayer. As a result, multiple stages of the viral lifecycle may be affected including assembly and budding, particle stability during transmission, and fusion events, all of which could contribute to the differences in infectivity.
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Affiliation(s)
- Carmen A. Dunbar
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Vamseedhar Rayaprolu
- Department of Biology, Indiana University, Jordan Hall, 1001 East Third Street, Bloomington, Indiana 47405, United States
| | - Joseph C.-Y. Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall, 212 South Hawthorne Drive, Bloomington, Indiana 47405, United States
| | - Christopher J. Brown
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Emma Leishman
- Department of Psychological and Brain Sciences, Indiana University, 1101 East Tenth Street, Bloomington, Indiana 47405, United States
| | - Sara Jones-Burrage
- Department of Biology, Indiana University, Jordan Hall, 1001 East Third Street, Bloomington, Indiana 47405, United States
| | - Jonathan C. Trinidad
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Heather B. Bradshaw
- Department of Psychological and Brain Sciences, Indiana University, 1101 East Tenth Street, Bloomington, Indiana 47405, United States
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Suchetana Mukhopadhyay
- Department of Biology, Indiana University, Jordan Hall, 1001 East Third Street, Bloomington, Indiana 47405, United States
| | - Martin F. Jarrold
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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19
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Arnold E, Wu H, Johnson JE. Michael G. Rossmann (1930-2019), pioneer in macromolecular and virus crystallography: scientist, mentor and friend. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:523-527. [PMID: 31205014 DOI: 10.1107/s2059798319008398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Michael George Rossmann, who made monumental contributions to science, passed away peacefully in West Lafayette, Indiana on 14 May 2019 at the age of 88, following a courageous five-year battle with cancer. Michael was born in Frankfurt, Germany on 30 July 1930. As a young boy, he emigrated to England with his mother just as World War II ignited. Michael was a highly innovative and energetic person, well known for his intensity, persistence and focus in pursuing his research goals. Michael was a towering figure in crystallography as a highly distinguished faculty member at Purdue University for 55 years. Michael made many seminal contributions to crystallography in a career that spanned the entirety of structural biology, beginning in the 1950s at Cambridge where the first protein structures were determined in the laboratories of Max Perutz (hemoglobin, 1960) and John Kendrew (myoglobin, 1958). Michael's work was central in establishing and defining the field of structural biology, which amazingly has described the structures of a vast array of complex biological molecules and assemblies in atomic detail. Knowledge of three-dimensional biological structure has important biomedical significance including understanding the basis of health and disease at the molecular level, and facilitating the discovery of many drugs.
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Affiliation(s)
- Eddy Arnold
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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20
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Cryo-EM Structure of Chikungunya Virus in Complex with the Mxra8 Receptor. Cell 2019; 177:1725-1737.e16. [PMID: 31080061 DOI: 10.1016/j.cell.2019.04.006] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/22/2019] [Accepted: 04/01/2019] [Indexed: 11/21/2022]
Abstract
Mxra8 is a receptor for multiple arthritogenic alphaviruses that cause debilitating acute and chronic musculoskeletal disease in humans. Herein, we present a 2.2 Å resolution X-ray crystal structure of Mxra8 and 4 to 5 Å resolution cryo-electron microscopy reconstructions of Mxra8 bound to chikungunya (CHIKV) virus-like particles and infectious virus. The Mxra8 ectodomain contains two strand-swapped Ig-like domains oriented in a unique disulfide-linked head-to-head arrangement. Mxra8 binds by wedging into a cleft created by two adjacent CHIKV E2-E1 heterodimers in one trimeric spike and engaging a neighboring spike. Two binding modes are observed with the fully mature VLP, with one Mxra8 binding with unique contacts. Only the high-affinity binding mode was observed in the complex with infectious CHIKV, as viral maturation and E3 occupancy appear to influence receptor binding-site usage. Our studies provide insight into how Mxra8 binds CHIKV and creates a path for developing alphavirus entry inhibitors.
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21
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Lázaro GR, Mukhopadhyay S, Hagan MF. Why Enveloped Viruses Need Cores-The Contribution of a Nucleocapsid Core to Viral Budding. Biophys J 2019; 114:619-630. [PMID: 29414708 DOI: 10.1016/j.bpj.2017.11.3782] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/11/2017] [Accepted: 11/27/2017] [Indexed: 11/17/2022] Open
Abstract
During the lifecycle of many enveloped viruses, a nucleocapsid core buds through the cell membrane to acquire an outer envelope of lipid membrane and viral glycoproteins. However, the presence of a nucleocapsid core is not required for assembly of infectious particles. To determine the role of the nucleocapsid core, we develop a coarse-grained computational model with which we investigate budding dynamics as a function of glycoprotein and nucleocapsid interactions, as well as budding in the absence of a nucleocapsid. We find that there is a transition between glycoprotein-directed budding and nucleocapsid-directed budding that occurs above a threshold strength of nucleocapsid interactions. The simulations predict that glycoprotein-directed budding leads to significantly increased size polydispersity and particle polymorphism. This polydispersity can be explained by a theoretical model accounting for the competition between bending energy of the membrane and the glycoprotein shell. The simulations also show that the geometry of a budding particle leads to a barrier to subunit diffusion, which can result in a stalled, partially budded state. We present a phase diagram for this and other morphologies of budded particles. Comparison of these structures against experiments could establish bounds on whether budding is directed by glycoprotein or nucleocapsid interactions. Although our model is motivated by alphaviruses, we discuss implications of our results for other enveloped viruses.
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Affiliation(s)
- Guillermo R Lázaro
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts
| | | | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts.
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22
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San Martín C. Virus Maturation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:129-158. [DOI: 10.1007/978-3-030-14741-9_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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Alphavirus Nucleocapsid Packaging and Assembly. Viruses 2018; 10:v10030138. [PMID: 29558394 PMCID: PMC5869531 DOI: 10.3390/v10030138] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/11/2018] [Accepted: 03/13/2018] [Indexed: 12/18/2022] Open
Abstract
Alphavirus nucleocapsids are assembled in the cytoplasm of infected cells from 240 copies of the capsid protein and the approximately 11 kb positive strand genomic RNA. However, the challenge of how the capsid specifically selects its RNA package and assembles around it has remained an elusive one to solve. In this review, we will summarize what is known about the alphavirus capsid protein, the packaging signal, and their roles in the mechanism of packaging and assembly. We will review the discovery of the packaging signal and how there is as much evidence for, as well as against, its requirement to specify packaging of the genomic RNA. Finally, we will compare this model with those of other viral systems including particular reference to a relatively new idea of RNA packaging based on the presence of multiple minimal packaging signals throughout the genome known as the two stage mechanism. This review will provide a basis for further investigating the fundamental ways of how RNA viruses are able to select their own cargo from the relative chaos that is the cytoplasm.
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24
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Brown RS, Wan JJ, Kielian M. The Alphavirus Exit Pathway: What We Know and What We Wish We Knew. Viruses 2018; 10:E89. [PMID: 29470397 PMCID: PMC5850396 DOI: 10.3390/v10020089] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 12/28/2022] Open
Abstract
Alphaviruses are enveloped positive sense RNA viruses and include serious human pathogens, such as the encephalitic alphaviruses and Chikungunya virus. Alphaviruses are transmitted to humans primarily by mosquito vectors and include species that are classified as emerging pathogens. Alphaviruses assemble highly organized, spherical particles that bud from the plasma membrane. In this review, we discuss what is known about the alphavirus exit pathway during a cellular infection. We describe the viral protein interactions that are critical for virus assembly/budding and the host factors that are involved, and we highlight the recent discovery of cell-to-cell transmission of alphavirus particles via intercellular extensions. Lastly, we discuss outstanding questions in the alphavirus exit pathway that may provide important avenues for future research.
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Affiliation(s)
- Rebecca S Brown
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Judy J Wan
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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25
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Sharma R, Kesari P, Kumar P, Tomar S. Structure-function insights into chikungunya virus capsid protein: Small molecules targeting capsid hydrophobic pocket. Virology 2018; 515:223-234. [DOI: 10.1016/j.virol.2017.12.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 12/03/2017] [Accepted: 12/20/2017] [Indexed: 10/18/2022]
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26
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Erdemci-Tandogan G, Orland H, Zandi R. RNA Base Pairing Determines the Conformations of RNA Inside Spherical Viruses. PHYSICAL REVIEW LETTERS 2017; 119:188102. [PMID: 29219580 DOI: 10.1103/physrevlett.119.188102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Indexed: 05/21/2023]
Abstract
Many simple RNA viruses enclose their genetic material by a protein shell called the capsid. While the capsid structures are well characterized for most viruses, the structure of RNA inside the shells and the factors contributing to it remain poorly understood. We study the impact of base pairing on the conformations of RNA and find that it undergoes a swollen coil to globule continuous transition as a function of the strength of the pairing interaction. We also observe a first order transition and kink profile as a function of RNA length. All these transitions could explain the different RNA profiles observed inside viral shells.
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Affiliation(s)
- Gonca Erdemci-Tandogan
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
| | - Henri Orland
- Institut de Physique Théorique, CEA-Saclay, CEA, F-91191 Gif-sur-Yvette, France
- Beijing Computational Science Research Center, No. 10 East Xibeiwang Road, Haidan District, Beijing 100193, China
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
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27
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Ding J, Lawrence RM, Jones PV, Hogue BG, Hayes MA. Concentration of Sindbis virus with optimized gradient insulator-based dielectrophoresis. Analyst 2017; 141:1997-2008. [PMID: 26878279 DOI: 10.1039/c5an02430g] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Biotechnology, separation science, and clinical research are impacted by microfluidic devices. Separation and manipulation of bioparticles such as DNA, protein and viruses are performed on these platforms. Microfluidic systems provide many attractive features, including small sample size, rapid detection, high sensitivity and short processing time. Dielectrophoresis (DEP) and electrophoresis are especially well suited to microscale bioparticle control and have been demonstrated in many formats. In this work, an optimized gradient insulator-based DEP device was utilized for concentration of Sindbis virus, an animal virus with a diameter of 68 nm. Within only a few seconds, the concentration of Sindbis virus can be increased by two to six times in the channel under easily accessible voltages as low as about 70 V. Compared with traditional diagnostic methods used in virology, DEP-based microfluidics can enable faster isolation, detection and concentration of viruses in a single step within a short time.
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Affiliation(s)
- Jie Ding
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.
| | - Robert M Lawrence
- The Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA and Center for Applied Structural Design, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Paul V Jones
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.
| | - Brenda G Hogue
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA and The Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA and Center for Applied Structural Design, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mark A Hayes
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.
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28
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Inhibition of chikungunya virus by picolinate that targets viral capsid protein. Virology 2016; 498:265-276. [DOI: 10.1016/j.virol.2016.08.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/26/2016] [Accepted: 08/29/2016] [Indexed: 01/13/2023]
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29
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Freire JM, Veiga AS, de la Torre BG, Santos NC, Andreu D, Da Poian AT, Castanho MARB. Peptides as models for the structure and function of viral capsid proteins: Insights on dengue virus capsid. Biopolymers 2016; 100:325-36. [PMID: 23868207 DOI: 10.1002/bip.22266] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Revised: 04/11/2013] [Accepted: 04/19/2013] [Indexed: 12/24/2022]
Abstract
The structural organization of viral particles is among the most astonishing examples of molecular self-assembly in nature, involving proteins, nucleic acids, and, sometimes, lipids. Proper assembly is essential to produce well structured infectious virions. A great variety of structural arrangements can be found in viral particles. Nucleocapsids, for instance, may display highly ordered geometric shapes or consist in macroscopically amorphous packs of the viral genome. Alphavirus and flavivirus are viral genera that exemplify these extreme cases, the former comprising viral particles structured with a T = 4 icosahedral symmetry, whereas flavivirus capsids have no regular geometry. Dengue virus is a member of flavivirus genus and is used in this article to illustrate how viral protein-derived peptides can be used advantageously over full-length proteins to unravel the foundations of viral supramolecular assemblies. Membrane- and viral RNA-binding data of capsid protein-derived dengue virus peptides are used to explain the amorphous organization of the viral capsid. Our results combine bioinformatic and spectroscopic approaches using two- or three-component peptide and/or nucleic acid and/or lipid systems.
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Affiliation(s)
- João Miguel Freire
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisbon, Portugal
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30
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Wang JCY, Chen C, Rayaprolu V, Mukhopadhyay S, Zlotnick A. Self-Assembly of an Alphavirus Core-like Particle Is Distinguished by Strong Intersubunit Association Energy and Structural Defects. ACS NANO 2015; 9:8898-906. [PMID: 26275088 PMCID: PMC5683390 DOI: 10.1021/acsnano.5b02632] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Weak association energy can lead to uniform nanostructures: defects can anneal due to subunit lability. What happens when strong association energy leads to particles where defects are trapped? Alphaviruses are enveloped viruses whose icosahedral nucleocapsid core can assemble independently. We used a simplest case system to study Ross River virus (RRV) core-like particle (CLP) self-assembly using purified capsid protein and a short DNA oligomer. We find that capsid protein binds the oligomer with high affinity to form an assembly competent unit (U). Subsequently, U assembles with concentration dependence into CLPs. We determined that U-U pairwise interactions are very strong (ca. -6 kcal/mol) compared to other virus assembly systems. Assembled RRV CLPs appeared morphologically uniform and cryo-EM image reconstruction with imposed icosahedral symmetry yielded a T = 4 structure. However, 2D class averages of the CLPs show that virtually every class had disordered regions. These results suggested that irregular cores may be present in RRV virions. To test this hypothesis, we determined 2D class averages of RRV virions using authentic virions or only the core from intact virions isolated by computational masking. Virion-based class averages were symmetrical, geometric, and corresponded well to projections of image reconstructions. In core-based class averages, cores and envelope proteins in many classes were disordered. These results suggest that partly disordered components are common even in ostensibly well-ordered viruses, a biological realization of a patchy particle. Biological advantages of partly disordered complexes may arise from their ease of dissociation and asymmetry.
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Affiliation(s)
- Joseph Che-Yen Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN
| | - Chao Chen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN
| | | | | | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN
- Department of Biology, Indiana University, Bloomington, IN
- Department of Chemistry, Indiana University, Bloomington, IN
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31
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Veesler D, Kearney BM, Johnson JE. Integration of X-ray crystallography and electron cryo-microscopy in the analysis of virus structure and function. CRYSTALLOGR REV 2015. [DOI: 10.1080/0889311x.2015.1038530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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32
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Rupp JC, Sokoloski KJ, Gebhart NN, Hardy RW. Alphavirus RNA synthesis and non-structural protein functions. J Gen Virol 2015. [PMID: 26219641 DOI: 10.1099/jgv.0.000249] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The members of the genus Alphavirus are positive-sense RNA viruses, which are predominantly transmitted to vertebrates by a mosquito vector. Alphavirus disease in humans can be severely debilitating, and depending on the particular viral species, infection may result in encephalitis and possibly death. In recent years, alphaviruses have received significant attention from public health authorities as a consequence of the dramatic emergence of chikungunya virus in the Indian Ocean islands and the Caribbean. Currently, no safe, approved or effective vaccine or antiviral intervention exists for human alphavirus infection. The molecular biology of alphavirus RNA synthesis has been well studied in a few species of the genus and represents a general target for antiviral drug development. This review describes what is currently understood about the regulation of alphavirus RNA synthesis, the roles of the viral non-structural proteins in this process and the functions of cis-acting RNA elements in replication, and points to open questions within the field.
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Affiliation(s)
- Jonathan C Rupp
- Department of Biology, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Kevin J Sokoloski
- Department of Biology, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Natasha N Gebhart
- Department of Biology, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Richard W Hardy
- Department of Biology, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
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33
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Lawrence RM, Conrad CE, Zatsepin NA, Grant TD, Liu H, James D, Nelson G, Subramanian G, Aquila A, Hunter MS, Liang M, Boutet S, Coe J, Spence JCH, Weierstall U, Liu W, Fromme P, Cherezov V, Hogue BG. Serial femtosecond X-ray diffraction of enveloped virus microcrystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041720. [PMID: 26798819 PMCID: PMC4711640 DOI: 10.1063/1.4929410] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/12/2015] [Indexed: 05/22/2023]
Abstract
Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ∼700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ∼40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is an important step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | | | | | | | | | | | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California , Los Angeles, California 90089, USA
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Zheng Y, Kielian M. An alphavirus temperature-sensitive capsid mutant reveals stages of nucleocapsid assembly. Virology 2015; 484:412-420. [PMID: 26051211 DOI: 10.1016/j.virol.2015.05.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/05/2015] [Accepted: 05/12/2015] [Indexed: 11/17/2022]
Abstract
Alphaviruses have a nucleocapsid core composed of the RNA genome surrounded by an icosahedral lattice of capsid protein. An insertion after position 186 in the capsid protein produced a strongly temperature-sensitive growth phenotype. Even when the structural proteins were synthesized at the permissive temperature (28°C), subsequent incubation of the cells at the non-permissive temperature (37°C) dramatically decreased mutant capsid protein stability and particle assembly. Electron microscopy confirmed the presence of cytoplasmic nucleocapsids in mutant-infected cells cultured at the permissive temperature, but these nucleocapsids were not stable to sucrose gradient separation. In contrast, nucleocapsids isolated from mutant virus particles had similar stability to that of wildtype virus. Our data support a model in which cytoplasmic nucleocapsids go through a maturation step during packaging into virus particles. The insertion site lies in the interface between capsid proteins in the assembled nucleocapsid, suggesting the region where such a stabilizing transition occurs.
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Affiliation(s)
- Yan Zheng
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA.
| | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA.
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Ooi YS, Dubé M, Kielian M. BST2/tetherin inhibition of alphavirus exit. Viruses 2015; 7:2147-67. [PMID: 25912717 PMCID: PMC4411694 DOI: 10.3390/v7042147] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/08/2015] [Accepted: 04/17/2015] [Indexed: 11/29/2022] Open
Abstract
Alphaviruses such as chikungunya virus (CHIKV) and Semliki Forest virus (SFV) are small enveloped RNA viruses that bud from the plasma membrane. Tetherin/BST2 is an interferon-induced host membrane protein that inhibits the release of many enveloped viruses via direct tethering of budded particles to the cell surface. Alphaviruses have highly organized structures and exclude host membrane proteins from the site of budding, suggesting that their release might be insensitive to tetherin inhibition. Here, we demonstrated that exogenously-expressed tetherin efficiently inhibited the release of SFV and CHIKV particles from host cells without affecting virus entry and infection. Alphavirus release was also inhibited by the endogenous levels of tetherin in HeLa cells. While rubella virus (RuV) and dengue virus (DENV) have structural similarities to alphaviruses, tetherin inhibited the release of RuV but not DENV. We found that two recently identified tetherin isoforms differing in length at the N-terminus exhibited distinct capabilities in restricting alphavirus release. SFV exit was efficiently inhibited by the long isoform but not the short isoform of tetherin, while both isoforms inhibited vesicular stomatitis virus exit. Thus, in spite of the organized structure of the virus particle, tetherin specifically blocks alphavirus release and shows an interesting isoform requirement.
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Affiliation(s)
- Yaw Shin Ooi
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA.
| | - Mathieu Dubé
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA.
| | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA.
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36
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Harrison SC. Viral membrane fusion. Virology 2015; 479-480:498-507. [PMID: 25866377 DOI: 10.1016/j.virol.2015.03.043] [Citation(s) in RCA: 519] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 02/23/2015] [Accepted: 03/10/2015] [Indexed: 11/27/2022]
Abstract
Membrane fusion is an essential step when enveloped viruses enter cells. Lipid bilayer fusion requires catalysis to overcome a high kinetic barrier; viral fusion proteins are the agents that fulfill this catalytic function. Despite a variety of molecular architectures, these proteins facilitate fusion by essentially the same generic mechanism. Stimulated by a signal associated with arrival at the cell to be infected (e.g., receptor or co-receptor binding, proton binding in an endosome), they undergo a series of conformational changes. A hydrophobic segment (a "fusion loop" or "fusion peptide") engages the target-cell membrane and collapse of the bridging intermediate thus formed draws the two membranes (virus and cell) together. We know of three structural classes for viral fusion proteins. Structures for both pre- and postfusion conformations of illustrate the beginning and end points of a process that can be probed by single-virion measurements of fusion kinetics.
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Affiliation(s)
- Stephen C Harrison
- Boston Children׳s Hospital, Harvard Medical School, and Howard Hughes Medical Institute, 3 Blackfan Circle, Boston, MA 02115, United States.
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Residue-level resolution of alphavirus envelope protein interactions in pH-dependent fusion. Proc Natl Acad Sci U S A 2015; 112:2034-9. [PMID: 25646410 DOI: 10.1073/pnas.1414190112] [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: 12/30/2022] Open
Abstract
Alphavirus envelope proteins, organized as trimers of E2-E1 heterodimers on the surface of the pathogenic alphavirus, mediate the low pH-triggered fusion of viral and endosomal membranes in human cells. The lack of specific treatment for alphaviral infections motivates our exploration of potential antiviral approaches by inhibiting one or more fusion steps in the common endocytic viral entry pathway. In this work, we performed constant pH molecular dynamics based on an atomic model of the alphavirus envelope with icosahedral symmetry. We have identified pH-sensitive residues that cause the largest shifts in thermodynamic driving forces under neutral and acidic pH conditions for various fusion steps. A series of conserved interdomain His residues is identified to be responsible for the pH-dependent conformational changes in the fusion process, and ligand binding sites in their vicinity are anticipated to be potential drug targets aimed at inhibiting viral infections.
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Sedzik J, Jastrzebski JP, Grandis M. Glycans of myelin proteins. J Neurosci Res 2014; 93:1-18. [PMID: 25213400 DOI: 10.1002/jnr.23462] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 06/19/2014] [Accepted: 07/07/2014] [Indexed: 01/04/2023]
Abstract
Human P0 is the main myelin glycoprotein of the peripheral nervous system. It can bind six different glycans, all linked to Asn(93) , the unique glycosylation site. Other myelin glycoproteins, also with a single glycosylation site (PMP22 at Asn(36) , MOG at Asn(31) ), bind only one glycan. The MAG has 10 glycosylation sites; the glycoprotein OMgp has 11 glycosylation sites. Aside from P0, no comprehensive data are available on other myelin glycoproteins. Here we review and analyze all published data on the physicochemical structure of the glycans linked to P0, PMP22, MOG, and MAG. Most data concern bovine P0, whose glycan moieties have an MW ranging from 1,294.56 Da (GP3) to 2,279.94 Da (GP5). The pI of glycosylated P0 protein varies from pH 9.32 to 9.46. The most charged glycan is MS2 containing three sulfate groups and one glucuronic acid; whereas the least charged one is the BA2 residue. All glycans contain one fucose and one galactose. The most mannose rich are the glycans MS2 and GP4, each of them has four mannoses; OPPE1 contains five N-acetylglucosamines and one sulfated glucuronic acid; GP4 contains one sialic acid. Furthermore, human P0 variants causing both gain and loss of glycosylation have been described and cause peripheral neuropathies with variable clinical severity. In particular, the substitution T(95) →M is a very common in Europe and is associated with a late-onset axonal neuropathy. Although peripheral myelin is made up largely of glycoproteins, mutations altering glycosylation have been described only in P0. This attractive avenue of research requires further study.
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Affiliation(s)
- Jan Sedzik
- Royal Institute of Technology, Department of Chemical Engineering, Protein Crystallization Facility, Stockholm, Sweden; National Institute of Physiological Sciences, Department of Neuroscience and Bioinformatics, Okazaki, Japan
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Gopal A, Egecioglu DE, Yoffe AM, Ben-Shaul A, Rao ALN, Knobler CM, Gelbart WM. Viral RNAs are unusually compact. PLoS One 2014; 9:e105875. [PMID: 25188030 PMCID: PMC4154850 DOI: 10.1371/journal.pone.0105875] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 07/21/2014] [Indexed: 01/28/2023] Open
Abstract
A majority of viruses are composed of long single-stranded genomic RNA molecules encapsulated by protein shells with diameters of just a few tens of nanometers. We examine the extent to which these viral RNAs have evolved to be physically compact molecules to facilitate encapsulation. Measurements of equal-length viral, non-viral, coding and non-coding RNAs show viral RNAs to have among the smallest sizes in solution, i.e., the highest gel-electrophoretic mobilities and the smallest hydrodynamic radii. Using graph-theoretical analyses we demonstrate that their sizes correlate with the compactness of branching patterns in predicted secondary structure ensembles. The density of branching is determined by the number and relative positions of 3-helix junctions, and is highly sensitive to the presence of rare higher-order junctions with 4 or more helices. Compact branching arises from a preponderance of base pairing between nucleotides close to each other in the primary sequence. The density of branching represents a degree of freedom optimized by viral RNA genomes in response to the evolutionary pressure to be packaged reliably. Several families of viruses are analyzed to delineate the effects of capsid geometry, size and charge stabilization on the selective pressure for RNA compactness. Compact branching has important implications for RNA folding and viral assembly.
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Affiliation(s)
- Ajaykumar Gopal
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Defne E. Egecioglu
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Aron M. Yoffe
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Avinoam Ben-Shaul
- Institute of Chemistry & The Fritz Haber Research Center, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Ayala L. N. Rao
- Department of Plant Pathology, University of California Riverside, Riverside, California, United States of America
| | - Charles M. Knobler
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - William M. Gelbart
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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41
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Zhou ZH. Structures of viral membrane proteins by high-resolution cryoEM. Curr Opin Virol 2014; 5:111-9. [PMID: 24799302 DOI: 10.1016/j.coviro.2014.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/24/2014] [Accepted: 04/01/2014] [Indexed: 01/06/2023]
Abstract
Cryo electron microscopy (cryoEM) has emerged as an excellent tool for resolving high-resolution three-dimensional structures of membrane proteins in a lipid-containing environment with interacting partners. The near atomic resolution structures of Venezuelan equine encephalitis virus and dengue virus revealed transmembrane helices in lipid bilayers, receptor-binding glycosylation moieties, and functionally important interactions between their fusion protein and membrane-anchored chaperone protein. For pleomorphic enveloped viruses, such as human immunodeficiency virus, glycoprotein complexes can be imaged in isolation to reveal molecular interactions at different states. These high-resolution cryoEM structures have clarified important domains not previously resolved by crystallography and illustrate exciting opportunities to visualize viral membrane proteins in their native and possibly transiently stable functional states, thus uncovering mechanisms of action and informing anti-viral strategies.
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Affiliation(s)
- Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095-7364, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095-7227, USA.
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Hantavirus Gn and Gc envelope glycoproteins: key structural units for virus cell entry and virus assembly. Viruses 2014; 6:1801-22. [PMID: 24755564 PMCID: PMC4014721 DOI: 10.3390/v6041801] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/20/2014] [Accepted: 03/31/2014] [Indexed: 01/24/2023] Open
Abstract
In recent years, ultrastructural studies of viral surface spikes from three different genera within the Bunyaviridae family have revealed a remarkable diversity in their spike organization. Despite this structural heterogeneity, in every case the spikes seem to be composed of heterodimers formed by Gn and Gc envelope glycoproteins. In this review, current knowledge of the Gn and Gc structures and their functions in virus cell entry and exit is summarized. During virus cell entry, the role of Gn and Gc in receptor binding has not yet been determined. Nevertheless, biochemical studies suggest that the subsequent virus-membrane fusion activity is accomplished by Gc. Further, a class II fusion protein conformation has been predicted for Gc of hantaviruses, and novel crystallographic data confirmed such a fold for the Rift Valley fever virus (RVFV) Gc protein. During virus cell exit, the assembly of different viral components seems to be established by interaction of Gn and Gc cytoplasmic tails (CT) with internal viral ribonucleocapsids. Moreover, recent findings show that hantavirus glycoproteins accomplish important roles during virus budding since they self-assemble into virus-like particles. Collectively, these novel insights provide essential information for gaining a more detailed understanding of Gn and Gc functions in the early and late steps of the hantavirus infection cycle.
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Abstract
This review is a partially personal account of the discovery of virus structure and its implication for virus function. Although I have endeavored to cover all aspects of structural virology and to acknowledge relevant individuals, I know that I have favored taking examples from my own experience in telling this story. I am anxious to apologize to all those who I might have unintentionally offended by omitting their work. The first knowledge of virus structure was a result of Stanley's studies of tobacco mosaic virus (TMV) and the subsequent X-ray fiber diffraction analysis by Bernal and Fankuchen in the 1930s. At about the same time it became apparent that crystals of small RNA plant and animal viruses could diffract X-rays, demonstrating that viruses must have distinct and unique structures. More advances were made in the 1950s with the realization by Watson and Crick that viruses might have icosahedral symmetry. With the improvement of experimental and computational techniques in the 1970s, it became possible to determine the three-dimensional, near-atomic resolution structures of some small icosahedral plant and animal RNA viruses. It was a great surprise that the protecting capsids of the first virus structures to be determined had the same architecture. The capsid proteins of these viruses all had a 'jelly-roll' fold and, furthermore, the organization of the capsid protein in the virus were similar, suggesting a common ancestral virus from which many of today's viruses have evolved. By this time a more detailed structure of TMV had also been established, but both the architecture and capsid protein fold were quite different to that of the icosahedral viruses. The small icosahedral RNA virus structures were also informative of how and where cellular receptors, anti-viral compounds, and neutralizing antibodies bound to these viruses. However, larger lipid membrane enveloped viruses did not form sufficiently ordered crystals to obtain good X-ray diffraction. Starting in the 1990s, these enveloped viruses were studied by combining cryo-electron microscopy of the whole virus with X-ray crystallography of their protein components. These structures gave information on virus assembly, virus neutralization by antibodies, and virus fusion with and entry into the host cell. The same techniques were also employed in the study of complex bacteriophages that were too large to crystallize. Nevertheless, there still remained many pleomorphic, highly pathogenic viruses that lacked the icosahedral symmetry and homogeneity that had made the earlier structural investigations possible. Currently some of these viruses are starting to be studied by combining X-ray crystallography with cryo-electron tomography.
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Administration of E2 and NS1 siRNAs inhibit chikungunya virus replication in vitro and protects mice infected with the virus. PLoS Negl Trop Dis 2013; 7:e2405. [PMID: 24040429 PMCID: PMC3764232 DOI: 10.1371/journal.pntd.0002405] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 07/23/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Chikungunya virus (CHIKV) has reemerged as a life threatening pathogen and caused large epidemics in several countries. So far, no licensed vaccine or effective antivirals are available and the treatment remains symptomatic. In this context, development of effective and safe prophylactics and therapeutics assumes priority. METHODS We evaluated the efficacy of the siRNAs against ns1 and E2 genes of CHIKV both in vitro and in vivo. Four siRNAs each, targeting the E2 (Chik-1 to Chik-4) and ns1 (Chik-5 to Chik-8) genes were designed and evaluated for efficiency in inhibiting CHIKV growth in vitro and in vivo. Chik-1 and Chik-5 siRNAs were effective in controlling CHIKV replication in vitro as assessed by real time PCR, IFA and plaque assay. CONCLUSIONS CHIKV replication was completely inhibited in the virus-infected mice when administered 72 hours post infection. The combination of Chik-1 and Chik-5 siRNAs exhibited additive effect leading to early and complete inhibition of virus replication. These findings suggest that RNAi capable of inhibiting CHIKV growth might constitute a new therapeutic strategy for controlling CHIKV infection and transmission.
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45
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Fusion of mApple and Venus fluorescent proteins to the Sindbis virus E2 protein leads to different cell-binding properties. Virus Res 2013; 177:138-46. [PMID: 23916968 DOI: 10.1016/j.virusres.2013.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/12/2013] [Accepted: 07/17/2013] [Indexed: 11/23/2022]
Abstract
Fluorescent proteins (FPs) are widely used in real-time single virus particle studies to visualize, track and quantify the spatial and temporal parameters of viral pathways. However, potential functional differences between the wild type and the FP-tagged virus may specifically affect particular stages in the virus life-cycle. In this work, we genetically modified the E2 spike protein of Sindbis virus (SINV) with two FPs. We inserted mApple, a red FP, or Venus, a yellow FP, at the N-terminus of the E2 protein of SINV to make SINV-Apple and SINV-Venus. Our results indicate that SINV-Apple and SINV-Venus have similar levels of infectivity and are morphologically similar to SINV-wild-type by negative stain transmission electron microscopy. Both mutants are highly fluorescent and have excellent single-particle tracking properties. However, despite these similarities, when measuring cell entry at the single-particle level, we found that SINV-Apple and SINV-Venus are different in their interaction with the cell surface and FPs are not always interchangeable. We went on to determine that the FP changes the net surface charge on the virus particles, the folding of the spike proteins, and the conformation of the spikes on the virus particle surface, ultimately leading to different cell-binding properties between SINV-Apple and SINV-Venus. Our results are consistent with recent findings that FPs may alter the biological and cellular localization properties of bacterial proteins to which they are fused.
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46
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Characterization of an early-stage fusion intermediate of Sindbis virus using cryoelectron microscopy. Proc Natl Acad Sci U S A 2013; 110:13362-7. [PMID: 23898184 DOI: 10.1073/pnas.1301911110] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The sequential steps in the alphavirus membrane fusion pathway have been postulated based on the prefusion and postfusion crystal structures of the viral fusion protein E1 in conjunction with biochemical studies. However, the molecular structures of the hypothesized fusion intermediates have remained obscure due to difficulties inherent in the dynamic nature of the process. We developed an experimental system that uses liposomes as the target membrane to capture Sindbis virus, a prototypical alphavirus, in its membrane-binding form at pH 6.4. Cryoelectron micrograph analyses and 3D reconstructions showed that the virus retains its overall icosahedral structure at this mildly acidic pH, except in the membrane-binding region, where monomeric E1 associates with the target membrane and the E2 glycoprotein retains its original trimeric organization. The remaining E2 trimers may hinder E1 homotrimerization and are a potential target for antiviral drugs.
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Abstract
Enveloped viruses rely on fusion proteins in their envelope to fuse the viral membrane to the host-cell membrane. This key step in viral entry delivers the viral genome into the cytoplasm for replication. Although class II fusion proteins are genetically and structurally unrelated to class I fusion proteins, they use the same physical principles and topology as other fusion proteins to drive membrane fusion. Exposure of a fusion loop first allows it to insert into the host-cell membrane. Conserved hydrophobic residues in the fusion loop act as an anchor, which penetrates only partway into the outer bilayer leaflet of the host-cell membrane. Subsequent folding back of the fusion protein on itself directs the C-terminal viral transmembrane anchor towards the fusion loop. This fold-back forces the host-cell membrane (held by the fusion loop) and the viral membrane (held by the C-terminal transmembrane anchor) against each other, resulting in membrane fusion. In class II fusion proteins, the fold-back is triggered by the reduced pH of an endosome, and is accompanied by the assembly of fusion protein monomers into trimers. The fold-back occurs by domain rearrangement rather than by an extensive refolding of secondary structure, but this domain rearrangement and the assembly of monomers into trimers together bury a large surface area. The energy that is thus released exerts a bending force on the apposed viral and cellular membranes, causing them to bend towards each other and, eventually, to fuse.
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Affiliation(s)
- Stefan Pöhlmann
- grid.10423.340000000095299877Institute for Virology, Hannover Medical School, Hannover, Germany ,grid.418215.b0000000085027018German Primate Center, Göttingen, Germany
| | - Graham Simmons
- grid.266102.10000000122976811Blood Systems Research Institute, and Department of Laboratory Medicine, University of California San Francisco, San Francisco, California USA
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48
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Roehrig JT, Butrapet S, Liss NM, Bennett SL, Luy BE, Childers T, Boroughs KL, Stovall JL, Calvert AE, Blair CD, Huang CYH. Mutation of the dengue virus type 2 envelope protein heparan sulfate binding sites or the domain III lateral ridge blocks replication in Vero cells prior to membrane fusion. Virology 2013; 441:114-25. [DOI: 10.1016/j.virol.2013.03.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 01/11/2013] [Accepted: 03/16/2013] [Indexed: 10/27/2022]
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49
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Brandler S, Ruffié C, Combredet C, Brault JB, Najburg V, Prevost MC, Habel A, Tauber E, Desprès P, Tangy F. A recombinant measles vaccine expressing chikungunya virus-like particles is strongly immunogenic and protects mice from lethal challenge with chikungunya virus. Vaccine 2013; 31:3718-25. [PMID: 23742993 DOI: 10.1016/j.vaccine.2013.05.086] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/16/2013] [Accepted: 05/21/2013] [Indexed: 12/26/2022]
Abstract
Chikungunya virus (CHIKV), a mosquito-transmitted alphavirus, recently reemerged in the Indian Ocean, India and Southeast Asia, causing millions of cases of severe polyarthralgia. No specific treatment to prevent disease or vaccine to limit epidemics is currently available. Here we describe a recombinant live-attenuated measles vaccine (MV) expressing CHIKV virus-like particles comprising capsid and envelope structural proteins from the recent CHIKV strain La Reunion. Immunization of mice susceptible to measles virus induced high titers of CHIKV antibodies that neutralized several primary isolates. Specific cellular immune responses were also elicited. A single immunization with this vaccine candidate protected all mice from a lethal CHIKV challenge, and passive transfer of immune sera conferred protection to naïve mice. Measles vaccine is one of the safest and most effective human vaccines. A recombinant MV-CHIKV virus could make a safe and effective vaccine against chikungunya that deserves to be further tested in human trials.
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Affiliation(s)
- Samantha Brandler
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS URA 3015, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
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Differential protein partitioning within the herpesvirus tegument and envelope underlies a complex and variable virion architecture. Proc Natl Acad Sci U S A 2013; 110:E1613-20. [PMID: 23569236 DOI: 10.1073/pnas.1221896110] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The herpesvirus virion is a multilayered structure consisting of a DNA-filled capsid, tegument, and envelope. Detailed reconstructions of the capsid are possible based on its icosahedral symmetry, but the surrounding tegument and envelope layers lack regular architecture. To circumvent limitations of symmetry-based ultrastructural reconstruction methods, a fluorescence approach was developed using single-particle imaging combined with displacement measurements at nanoscale resolution. An analysis of 11 tegument and envelope proteins defined the composition and plasticity of symmetric and asymmetric elements of the virion architecture. The resulting virion protein map ascribes molecular composition to density profiles previously acquired by traditional ultrastructural methods, and provides a way forward to examine the dynamics of the virion architecture during infection.
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