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Venkataraman S, Savithri HS, Murthy MRN. Recent advances in the structure and assembly of non-enveloped spherical viruses. Virology 2025; 606:110454. [PMID: 40081202 DOI: 10.1016/j.virol.2025.110454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Revised: 02/03/2025] [Accepted: 02/12/2025] [Indexed: 03/15/2025]
Abstract
Non-enveloped spherical viruses (NSVs) are characterized by their highly symmetrical capsids that serve to protect and encapsulate the genomes. The stability and functionality of the capsids determine their ability for survival and proliferation in harsh environments. Over four decades of structural studies using X-ray crystallography and NMR have provided static, high-resolution snapshots of several viruses. Recently, advances in cryo-electron microscopy, together with AI-based structure predictions and traditional methods, have aided in elucidating not only the structural details of complex NSVs but also the mechanistic processes underlying their assembly. The knowledge thus generated has been instrumental in critical understanding of the conformational changes and interactions associated with the coat proteins, the genome, and the auxiliary factors that regulate the capsid dynamics. This review seeks to summarize current literature regarding the structure and assembly of the NSVs and discusses how the data has facilitated a deeper understanding of their biology and phylogeny.
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Affiliation(s)
| | | | - M R N Murthy
- Indian Institute of Science, Bengaluru, 560012, India.
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2
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Prosper P, Rodríguez Puertas R, Guérin DMA, Branda MM. Computational method for designing vaccines applied to virus-like particles (VLPs) as epitope carriers. Vaccine 2024; 42:3916-3929. [PMID: 38782665 DOI: 10.1016/j.vaccine.2024.05.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 04/06/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024]
Abstract
Nonenveloped virus-like particles (VLPs) are self-assembled oligomeric structures composed of one or more proteins that originate from diverse viruses. Because these VLPs have similar antigenicity to the parental virus, they are successfully used as vaccines against cognate virus infection. Furthermore, after foreign antigenic sequences are inserted in their protein components (chimVLPs), some VLPs are also amenable to producing vaccines against pathogens other than the virus it originates from (these VLPs are named platform or epitope carrier). Designing chimVLP vaccines is challenging because the immunogenic response must be oriented against a given antigen without altering stimulant properties inherent to the VLP. An important step in this process is choosing the location of the sequence modifications because this must be performed without compromising the assembly and stability of the original VLP. Currently, many immunogenic data and computational tools can help guide the design of chimVLPs, thus reducing experimental costs and work. In this study, we analyze the structure of a novel VLP that originate from an insect virus and describe the putative regions of its three structural proteins amenable to insertion. For this purpose, we employed molecular dynamics (MD) simulations to assess chimVLP stability by comparing mutated and wild-type (WT) VLP protein trajectories. We applied this procedure to design a chimVLP that can serve as a prophylactic vaccine against the SARS-CoV-2 virus. The methodology described in this work is generally applicable for VLP-based vaccine development.
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Affiliation(s)
- Pascalita Prosper
- Instituto de Física Aplicada - INFAP, Universidad Nacional de San Luis/CONICET, Argentina, Av. Ejército de los Andes 950, 5700 San Luis, San Luis, Argentina
| | - Rafael Rodríguez Puertas
- Universidad del País Vasco (UPV/EHU), Dept. Farmacología, Facultad de Medicina, B° Sarriena S/N, 48940 Leioa, Vizcaya, Spain; Neurodegenerative Diseases, BioCruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Diego M A Guérin
- Universidad del País Vasco (UPV/EHU) and Instituto Biofisika (CSIC, UPV/EHU), B° Sarriena S/N, 48940 Leioa, Vizcaya, Spain
| | - María Marta Branda
- Instituto de Física Aplicada - INFAP, Universidad Nacional de San Luis/CONICET, Argentina, Av. Ejército de los Andes 950, 5700 San Luis, San Luis, Argentina.
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Brown C, Agarwal A, Luque A. pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells. Bioinformatics 2024; 40:btad761. [PMID: 38113434 PMCID: PMC10786678 DOI: 10.1093/bioinformatics/btad761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 11/01/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023] Open
Abstract
SUMMARY pyCapsid is a Python package developed to facilitate the characterization of the dynamics and quasi-rigid mechanical units of protein shells and other protein complexes. The package was developed in response to the rapid increase of high-resolution structures, particularly capsids of viruses, requiring multiscale biophysical analyses. Given a protein shell, pyCapsid generates the collective vibrations of its amino-acid residues, identifies quasi-rigid mechanical regions associated with the disassembly of the structure, and maps the results back to the input proteins for interpretation. pyCapsid summarizes the main results in a report that includes publication-quality figures. AVAILABILITY AND IMPLEMENTATION pyCapsid's source code is available under MIT License on GitHub. It is compatible with Python 3.8-3.10 and has been deployed in two leading Python package-management systems, PIP and Conda. Installation instructions and tutorials are available in the online documentation and in the pyCapsid's YouTube playlist. In addition, a cloud-based implementation of pyCapsid is available as a Google Colab notebook. pyCapsid Colab does not require installation and generates the same report and outputs as the installable version. Users can post issues regarding pyCapsid in the repository's issues section.
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Affiliation(s)
- Colin Brown
- Viral Information Institute, San Diego State University, San Diego, CA 92116, United States
- Department of Physics, San Diego State University, San Diego, CA 92116, United States
| | - Anuradha Agarwal
- Viral Information Institute, San Diego State University, San Diego, CA 92116, United States
- Computational Science Research Center, San Diego State University, San Diego, CA 92116, United States
| | - Antoni Luque
- Viral Information Institute, San Diego State University, San Diego, CA 92116, United States
- Computational Science Research Center, San Diego State University, San Diego, CA 92116, United States
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92116, United States
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
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Virion structure and in vitro genome release mechanism of dicistrovirus Kashmir bee virus. J Virol 2021; 95:JVI.01950-20. [PMID: 33658338 PMCID: PMC8139710 DOI: 10.1128/jvi.01950-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Infections of Kashmir bee virus (KBV) are lethal for honeybees and have been associated with colony collapse disorder. KBV and closely related viruses contribute to the ongoing decline in the number of honeybee colonies in North America, Europe, Australia, and other parts of the world. Despite the economic and ecological impact of KBV, its structure and infection process remain unknown. Here we present the structure of the virion of KBV determined to a resolution of 2.8 Å. We show that the exposure of KBV to acidic pH induces a reduction in inter-pentamer contacts within capsids and the reorganization of its RNA genome from a uniform distribution to regions of high and low density. Capsids of KBV crack into pieces at acidic pH, resulting in the formation of open particles lacking pentamers of capsid proteins. The large openings of capsids enable the rapid release of genomes and thus limit the probability of their degradation by RNases. The opening of capsids may be a shared mechanism for the genome release of viruses from the family Dicistroviridae ImportanceThe western honeybee (Apis mellifera) is indispensable for maintaining agricultural productivity as well as the abundance and diversity of wild flowering plants. However, bees suffer from environmental pollution, parasites, and pathogens, including viruses. Outbreaks of virus infections cause the deaths of individual honeybees as well as collapses of whole colonies. Kashmir bee virus has been associated with colony collapse disorder in the US, and no cure of the disease is currently available. Here we report the structure of an infectious particle of Kashmir bee virus and show how its protein capsid opens to release the genome. Our structural characterization of the infection process determined that therapeutic compounds stabilizing contacts between pentamers of capsid proteins could prevent the genome release of the virus.
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Virion structures and genome delivery of honeybee viruses. Curr Opin Virol 2020; 45:17-24. [PMID: 32679289 DOI: 10.1016/j.coviro.2020.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/10/2020] [Accepted: 06/18/2020] [Indexed: 10/23/2022]
Abstract
The western honeybee is the primary pollinator of numerous food crops. Furthermore, honeybees are essential for ecosystem stability by sustaining the diversity and abundance of wild flowering plants. However, the worldwide population of honeybees is under pressure from environmental stress and pathogens. Viruses from the families Iflaviridae and Dicistroviridae, together with their vector, the parasitic mite Varroa destructor, are the major threat to the world's honeybees. Dicistroviruses and iflaviruses have capsids with icosahedral symmetries. Acidic pH triggers the genome release of both dicistroviruses and iflaviruses. The capsids of iflaviruses expand, whereas those of dicistroviruses remain compact until the genome release. Furthermore, dicistroviruses use inner capsid proteins, whereas iflaviruses employ protruding domains or minor capsid proteins from the virion surface to penetrate membranes and deliver their genomes into the cell cytoplasm. The structural characterization of the infection process opens up possibilities for the development of antiviral compounds.
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Martínez M, Cooper CD, Poma AB, Guzman HV. Free Energies of the Disassembly of Viral Capsids from a Multiscale Molecular Simulation Approach. J Chem Inf Model 2019; 60:974-981. [DOI: 10.1021/acs.jcim.9b00883] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Matías Martínez
- Department of Mechanical Engineering, Universidad Técnica Federico Santa María, 2390123 Valparaíso, Chile
| | - Christopher D. Cooper
- Department of Mechanical Engineering, Universidad Técnica Federico Santa María, 2390123 Valparaíso, Chile
- Centro Científico Tecnológico de Valparaíso (CCTVal), 2390123 Valparaíso, Chile
| | - Adolfo B. Poma
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
| | - Horacio V. Guzman
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
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Structural Dynamics of Nonenveloped Virus Disassembly Intermediates. J Virol 2019; 93:JVI.01115-19. [PMID: 31484752 DOI: 10.1128/jvi.01115-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/14/2019] [Indexed: 12/16/2022] Open
Abstract
The stability of icosahedral viruses is crucial for protecting the viral genome during transit; however, successful infection requires eventual disassembly of the capsid. A comprehensive understanding of how stable, uniform icosahedrons disassemble remains elusive, mainly due to the complexities involved in isolating transient intermediates. We utilized incremental heating to systematically characterize the disassembly pathway of a model nonenveloped virus and identified an intriguing link between virus maturation and disassembly. Further, we isolated and characterized two intermediates by cryo-electron microscopy and three-dimensional reconstruction, without imposing icosahedral symmetry. The first intermediate displayed a series of major, asymmetric alterations, whereas the second showed that the act of genome release, through the 2-fold axis, is actually confined to a small section on the capsid. Our study thus presents a comprehensive structural analysis of nonenveloped virus disassembly and emphasizes the asymmetric nature of programmed conformational changes.IMPORTANCE Disassembly or uncoating of an icosahedral capsid is a crucial step during infection by nonenveloped viruses. However, the dynamic and transient nature of the disassembly process makes it challenging to isolate intermediates in a temporal, stepwise manner for structural characterization. Using controlled, incremental heating, we isolated two disassembly intermediates: "eluted particles" and "puffed particles" of an insect nodavirus, Flock House virus (FHV). Cryo-electron microscopy and three-dimensional reconstruction of the FHV disassembly intermediates indicated that disassembly-related conformational alterations are minimally global and largely local, leading to asymmetry in the particle and eventual genome release without complete disintegration of the icosahedron.
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Branda MM, Guérin DMA. Alkalinization of Icosahedral Non-enveloped Viral Capsid Interior Through Proton Channeling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:181-199. [DOI: 10.1007/978-3-030-14741-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Viso JF, Belelli P, Machado M, González H, Pantano S, Amundarain MJ, Zamarreño F, Branda MM, Guérin DMA, Costabel MD. Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly. PLoS Comput Biol 2018; 14:e1006082. [PMID: 29659564 PMCID: PMC5919690 DOI: 10.1371/journal.pcbi.1006082] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 04/26/2018] [Accepted: 03/09/2018] [Indexed: 12/04/2022] Open
Abstract
In this work, we assess a previously advanced hypothesis that predicts the existence of ion channels in the capsid of small and non-enveloped icosahedral viruses. With this purpose we examine Triatoma Virus (TrV) as a case study. This virus has a stable capsid under highly acidic conditions but disassembles and releases the genome in alkaline environments. Our calculations range from a subtle sub-atomic proton interchange to the dismantling of a large-scale system representing several million of atoms. Our results provide structure-based explanations for the three roles played by the capsid to enable genome release. First, we observe, for the first time, the formation of a hydrophobic gate in the cavity along the five-fold axis of the wild-type virus capsid, which can be disrupted by an ion located in the pore. Second, the channel enables protons to permeate the capsid through a unidirectional Grotthuss-like mechanism, which is the most likely process through which the capsid senses pH. Finally, assuming that the proton leak promotes a charge imbalance in the interior of the capsid, we model an internal pressure that forces shell cracking using coarse-grained simulations. Although qualitatively, this last step could represent the mechanism of capsid opening that allows RNA release. All of our calculations are in agreement with current experimental data obtained using TrV and describe a cascade of events that could explain the destabilization and disassembly of similar icosahedral viruses. Plant and animal small non-enveloped viruses are composed of a capsid shell that encloses the genome. One of the multiple functions played by the capsid is to protect the genome against host defenses and to withstand environmental aggressions, such as dehydration. This highly specialized capsule selectively recognizes and binds to the target tissue infected by the virus. In the viral cycle, the ultimate function of the capsid is to release the genome. Observations of many viruses demonstrate that the pH of the medium can trigger genome release. Nevertheless, the mechanism underlying this process at the atomic level is poorly understood. In this work, we computationally modeled the mechanism by which the capsid senses environmental pH and the destabilization process that permits genome release. Our calculations predict that a cavity that traverses the capsid functions as a hydrophobic gate, a feature already observed in membrane ion channels. Moreover, our results predict that this cavity behaves as a proton diode because the proton transit can only occur from the capsid interior to the exterior. In turn, our calculations describe a cascade of events that could explain the destabilization and dismantling of an insect virus, but this description could also apply to many vertebrate viruses.
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Affiliation(s)
- Juan Francisco Viso
- Departamento de Física (DF), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
- DF-UNS, Grupo de Biofísica, Instituto de Física del Sur (IFISUR, UNS/CONICET), Bahía Blanca, Argentina
| | - Patricia Belelli
- DF-UNS, Grupo de Materiales y Sistemas Catalíticos (GRUMASICA), IFISUR, Bahía Blanca, Argentina
| | - Matías Machado
- Grupo de Simulaciones Biomoleculares, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Humberto González
- Grupo de Simulaciones Biomoleculares, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Sergio Pantano
- Grupo de Simulaciones Biomoleculares, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - María Julia Amundarain
- Departamento de Física (DF), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
- DF-UNS, Grupo de Biofísica, Instituto de Física del Sur (IFISUR, UNS/CONICET), Bahía Blanca, Argentina
| | - Fernando Zamarreño
- Departamento de Física (DF), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
- DF-UNS, Grupo de Biofísica, Instituto de Física del Sur (IFISUR, UNS/CONICET), Bahía Blanca, Argentina
| | - Maria Marta Branda
- Departamento de Física (DF), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
- DF-UNS, Grupo de Materiales y Sistemas Catalíticos (GRUMASICA), IFISUR, Bahía Blanca, Argentina
| | - Diego M. A. Guérin
- Instituto Biofisika (UPV/EHU, CSIC), Department of Biochemistry and Molecular Biology, University of the Basque Country (EHU), Barrio Sarriena S/N, Leioa, Vizcaya, Spain
- * E-mail: (MDC); (DMAG)
| | - Marcelo D. Costabel
- Departamento de Física (DF), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
- DF-UNS, Grupo de Biofísica, Instituto de Física del Sur (IFISUR, UNS/CONICET), Bahía Blanca, Argentina
- * E-mail: (MDC); (DMAG)
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Martín-González N, Guérin Darvas SM, Durana A, Marti GA, Guérin DMA, de Pablo PJ. Exploring the role of genome and structural ions in preventing viral capsid collapse during dehydration. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:104001. [PMID: 29350623 PMCID: PMC7104708 DOI: 10.1088/1361-648x/aaa944] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/12/2018] [Accepted: 01/19/2018] [Indexed: 06/07/2023]
Abstract
Even though viruses evolve mainly in liquid milieu, their horizontal transmission routes often include episodes of dry environment. Along their life cycle, some insect viruses, such as viruses from the Dicistroviridae family, withstand dehydrated conditions with presently unknown consequences to their structural stability. Here, we use atomic force microscopy to monitor the structural changes of viral particles of Triatoma virus (TrV) after desiccation. Our results demonstrate that TrV capsids preserve their genome inside, conserving their height after exposure to dehydrating conditions, which is in stark contrast with other viruses that expel their genome when desiccated. Moreover, empty capsids (without genome) resulted in collapsed particles after desiccation. We also explored the role of structural ions in the dehydration process of the virions (capsid containing genome) by chelating the accessible cations from the external solvent milieu. We observed that ion suppression helps to keep the virus height upon desiccation. Our results show that under drying conditions, the genome of TrV prevents the capsid from collapsing during dehydration, while the structural ions are responsible for promoting solvent exchange through the virion wall.
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Affiliation(s)
- Natalia Martín-González
- Departamento de Física de la Materia Condensada C-III and Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
| | - Sofía M Guérin Darvas
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 48940, Leioa, Vizcaya, Spain
| | - Aritz Durana
- Instituto Biofisika (IBF, UPV/EHU, CSIC), Parque Científico de la UPV/EHU, Barrio Sarriena S/N, 48940, Leioa, Vizcaya, Spain
- Fundación Biofísica Bizkaia, Edificio Biblioteca Central UPV/EHU, Bº Sarriena S/N, 48940, Leioa, Vizcaya, Spain
| | - Gerardo A Marti
- Centro de Estudios Parasitológicos y de Vectores (CEPAVE-CCT-La Plata-CONICET-UNLP), Boulevard 120 e/61 y 62, 1900 La Plata, Argentina
| | - Diego M A Guérin
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, 48940, Leioa, Vizcaya, Spain
- Instituto Biofisika (IBF, UPV/EHU, CSIC), Parque Científico de la UPV/EHU, Barrio Sarriena S/N, 48940, Leioa, Vizcaya, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada C-III and Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
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Breach: Host Membrane Penetration and Entry by Nonenveloped Viruses. Trends Microbiol 2017; 26:525-537. [PMID: 29079499 DOI: 10.1016/j.tim.2017.09.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 09/06/2017] [Accepted: 09/26/2017] [Indexed: 11/22/2022]
Abstract
Disruption of host membranes by nonenveloped viruses, which allows the nucleocapsid or genome to enter the cytosol, is a mechanistically diverse process. Although the membrane-penetrating agents are usually small, hydrophobic or amphipathic peptides deployed from the capsid interior during entry, their manner of membrane interaction varies substantially. In this review, we discuss recent data about the molecular pathways for externalization of viral peptides amidst conformational alterations in the capsid, as well as mechanisms of membrane penetration, which is influenced by structural features of the peptides themselves as well as physicochemical properties of membranes, and other host factors. The membrane-penetrating components of nonenveloped viruses constitute an interesting class of cell-penetrating peptides, and may have potential therapeutic value for gene transfer.
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12
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Machado MR, González HC, Pantano S. MD Simulations of Viruslike Particles with Supra CG Solvation Affordable to Desktop Computers. J Chem Theory Comput 2017; 13:5106-5116. [DOI: 10.1021/acs.jctc.7b00659] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matı́as R. Machado
- Biomolecular Simulations
Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP 11400, Uruguay
| | - Humberto C. González
- Biomolecular Simulations
Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP 11400, Uruguay
| | - Sergio Pantano
- Biomolecular Simulations
Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP 11400, Uruguay
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13
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Cryo-electron Microscopy Study of the Genome Release of the Dicistrovirus Israeli Acute Bee Paralysis Virus. J Virol 2017; 91:JVI.02060-16. [PMID: 27928006 PMCID: PMC5286892 DOI: 10.1128/jvi.02060-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/21/2016] [Indexed: 01/09/2023] Open
Abstract
Viruses of the family Dicistroviridae can cause substantial economic damage by infecting agriculturally important insects. Israeli acute bee paralysis virus (IAPV) causes honeybee colony collapse disorder in the United States. High-resolution molecular details of the genome delivery mechanism of dicistroviruses are unknown. Here we present a cryo-electron microscopy analysis of IAPV virions induced to release their genomes in vitro. We determined structures of full IAPV virions primed to release their genomes to a resolution of 3.3 Å and of empty capsids to a resolution of 3.9 Å. We show that IAPV does not form expanded A particles before genome release as in the case of related enteroviruses of the family Picornaviridae. The structural changes observed in the empty IAPV particles include detachment of the VP4 minor capsid proteins from the inner face of the capsid and partial loss of the structure of the N-terminal arms of the VP2 capsid proteins. Unlike the case for many picornaviruses, the empty particles of IAPV are not expanded relative to the native virions and do not contain pores in their capsids that might serve as channels for genome release. Therefore, rearrangement of a unique region of the capsid is probably required for IAPV genome release.
IMPORTANCE Honeybee populations in Europe and North America are declining due to pressure from pathogens, including viruses. Israeli acute bee paralysis virus (IAPV), a member of the family Dicistroviridae, causes honeybee colony collapse disorder in the United States. The delivery of virus genomes into host cells is necessary for the initiation of infection. Here we present a structural cryo-electron microscopy analysis of IAPV particles induced to release their genomes. We show that genome release is not preceded by an expansion of IAPV virions as in the case of related picornaviruses that infect vertebrates. Furthermore, minor capsid proteins detach from the capsid upon genome release. The genome leaves behind empty particles that have compact protein shells.
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Honey Bee Deformed Wing Virus Structures Reveal that Conformational Changes Accompany Genome Release. J Virol 2017; 91:JVI.01795-16. [PMID: 27852845 DOI: 10.1128/jvi.01795-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/02/2016] [Indexed: 11/20/2022] Open
Abstract
The picornavirus-like deformed wing virus (DWV) has been directly linked to colony collapse; however, little is known about the mechanisms of host attachment or entry for DWV or its molecular and structural details. Here we report the three-dimensional (3-D) structures of DWV capsids isolated from infected honey bees, including the immature procapsid, the genome-filled virion, the putative entry intermediate (A-particle), and the empty capsid that remains after genome release. The capsids are decorated by large spikes around the 5-fold vertices. The 5-fold spikes had an open flower-like conformation for the procapsid and genome-filled capsids, whereas the putative A-particle and empty capsids that had released the genome had a closed tube-like spike conformation. Between the two conformations, the spikes undergo a significant hinge-like movement that we predicted using a Robetta model of the structure comprising the spike. We conclude that the spike structures likely serve a function during host entry, changing conformation to release the genome, and that the genome may escape from a 5-fold vertex to initiate infection. Finally, the structures illustrate that, similarly to picornaviruses, DWV forms alternate particle conformations implicated in assembly, host attachment, and RNA release. IMPORTANCE Honey bees are critical for global agriculture, but dramatic losses of entire hives have been reported in numerous countries since 2006. Deformed wing virus (DWV) and infestation with the ectoparasitic mite Varroa destructor have been linked to colony collapse disorder. DWV was purified from infected adult worker bees to pursue biochemical and structural studies that allowed the first glimpse into the conformational changes that may be required during transmission and genome release for DWV.
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Sánchez-Eugenia R, Durana A, López-Marijuan I, Marti GA, Guérin DMA. X-ray structure of Triatoma virus empty capsid: insights into the mechanism of uncoating and RNA release in dicistroviruses. J Gen Virol 2016; 97:2769-2779. [DOI: 10.1099/jgv.0.000580] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rubén Sánchez-Eugenia
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
| | - Aritz Durana
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
- Fundación Biofísica Bizkaia, Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
| | - Ibai López-Marijuan
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
- Fundación Biofísica Bizkaia, Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
| | - Gerardo A. Marti
- Centro de Estudios Parasitológicos y de Vectores (CEPAVE-CCT-La Plata-CONICET-UNLP), Boulevard 120 e/61 y 62, 1900 La Plata, Argentina
| | - Diego M. A. Guérin
- Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
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Penkler DL, Jiwaji M, Domitrovic T, Short JR, Johnson JE, Dorrington RA. Binding and entry of a non-enveloped T=4 insect RNA virus is triggered by alkaline pH. Virology 2016; 498:277-287. [PMID: 27614703 DOI: 10.1016/j.virol.2016.08.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/24/2016] [Accepted: 08/29/2016] [Indexed: 11/29/2022]
Abstract
Tetraviruses are small, non-enveloped, RNA viruses that exclusively infect lepidopteran insects. Their particles comprise 240 copies of a single capsid protein precursor (CP), which undergoes autoproteolytic cleavage during maturation. The molecular mechanisms of capsid assembly and maturation are well understood, but little is known about the viral infectious lifecycle due to a lack of tissue culture cell lines that are susceptible to tetravirus infection. We show here that binding and entry of the alphatetravirus, Helicoverpa armigera stunt virus (HaSV), is triggered by alkaline pH. At pH 9.0, wild-type HaSV virus particles undergo conformational changes that induce membrane-lytic activity and binding to Spodoptera frugiperda Sf9 cells. Binding is followed by entry and infection, with virus replication complexes detected by immunofluorescence microscopy within 2h post-infection and the CP after 12h. HaSV particles produced in S. frugiperda Sf9 cells are infectious. Helicoverpa armigera larval virus biofeed assays showed that pre-treatment with the V-ATPase inhibitor, Bafilomycin A1, resulted in a 50% decrease in larval mortality and stunting, while incubation of virus particles at pH 9.0 prior to infection restored infectivity. Together, these data show that HaSV, and likely other tetraviruses, requires the alkaline environment of the lepidopteran larval midgut for binding and entry into host cells.
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Affiliation(s)
- David L Penkler
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Meesbah Jiwaji
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Tatiana Domitrovic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - James R Short
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rosemary A Dorrington
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa.
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17
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Virion Structure of Israeli Acute Bee Paralysis Virus. J Virol 2016; 90:8150-9. [PMID: 27384649 PMCID: PMC5008081 DOI: 10.1128/jvi.00854-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/24/2016] [Indexed: 01/10/2023] Open
Abstract
The pollination services provided by the western honeybee (Apis mellifera) are critical for agricultural production and the diversity of wild flowering plants. However, honeybees suffer from environmental pollution, habitat loss, and pathogens, including viruses that can cause fatal diseases. Israeli acute bee paralysis virus (IAPV), from the family Dicistroviridae, has been shown to cause colony collapse disorder in the United States. Here, we present the IAPV virion structure determined to a resolution of 4.0 Å and the structure of a pentamer of capsid protein protomers at a resolution of 2.7 Å. IAPV has major capsid proteins VP1 and VP3 with noncanonical jellyroll β-barrel folds composed of only seven instead of eight β-strands, as is the rule for proteins of other viruses with the same fold. The maturation of dicistroviruses is connected to the cleavage of precursor capsid protein VP0 into subunits VP3 and VP4. We show that a putative catalytic site formed by the residues Asp-Asp-Phe of VP1 is optimally positioned to perform the cleavage. Furthermore, unlike many picornaviruses, IAPV does not contain a hydrophobic pocket in capsid protein VP1 that could be targeted by capsid-binding antiviral compounds. IMPORTANCE Honeybee pollination is required for agricultural production and to sustain the biodiversity of wild flora. However, honeybee populations in Europe and North America are under pressure from pathogens, including viruses that cause colony losses. Viruses from the family Dicistroviridae can cause honeybee infections that are lethal, not only to individual honeybees, but to whole colonies. Here, we present the virion structure of an Aparavirus, Israeli acute bee paralysis virus (IAPV), a member of a complex of closely related viruses that are distributed worldwide. IAPV exhibits unique structural features not observed in other picorna-like viruses. Capsid protein VP1 of IAPV does not contain a hydrophobic pocket, implying that capsid-binding antiviral compounds that can prevent the replication of vertebrate picornaviruses may be ineffective against honeybee virus infections.
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18
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Marchetti M, Wuite GJL, Roos WH. Atomic force microscopy observation and characterization of single virions and virus-like particles by nano-indentation. Curr Opin Virol 2016; 18:82-8. [DOI: 10.1016/j.coviro.2016.05.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 11/15/2022]
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19
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Triatoma virus recombinant VP4 protein induces membrane permeability through dynamic pores. J Virol 2015; 89:4645-54. [PMID: 25673713 DOI: 10.1128/jvi.00011-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
UNLABELLED In naked viruses, membrane breaching is a key step that must be performed for genome transfer into the target cells. Despite its importance, the mechanisms behind this process remain poorly understood. The small protein VP4, encoded by the genomes of most viruses of the order Picornavirales, has been shown to be involved in membrane alterations. Here we analyzed the permeabilization activity of the natively nonmyristoylated VP4 protein from triatoma virus (TrV), a virus belonging to the Dicistroviridae family within the Picornavirales order. The VP4 protein was produced as a C-terminal maltose binding protein (MBP) fusion to achieve its successful expression. This recombinant VP4 protein is able to produce membrane permeabilization in model membranes in a membrane composition-dependent manner. The induced permeability was also influenced by the pH, being greater at higher pH values. We demonstrate that the permeabilization activity elicited by the protein occurs through discrete pores that are inserted on the membrane. Sizing experiments using fluorescent dextrans, cryo-electron microscopy imaging, and other, additional techniques showed that recombinant VP4 forms heterogeneous proteolipidic pores rather than common proteinaceous channels. These results suggest that the VP4 protein may be involved in the membrane alterations required for genome transfer or cell entry steps during dicistrovirus infection. IMPORTANCE During viral infection, viruses need to overcome the membrane barrier in order to enter the cell and replicate their genome. In nonenveloped viruses membrane fusion is not possible, and hence, other mechanisms are implemented. Among other proteins, like the capsid-forming proteins and the proteins required for viral replication, several viruses of the order Picornaviridae contain a small protein called VP4 that has been shown to be involved in membrane alterations. Here we show that the triatoma virus VP4 protein is able to produce membrane permeabilization in model membranes by the formation of heterogeneous dynamic pores. These pores formed by VP4 may be involved in the genome transfer or cell entry steps during viral infection.
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20
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Sánchez-Eugenia R, Méndez F, Querido JFB, Silva MS, Guérin DMA, Rodríguez JF. Triatoma virus structural polyprotein expression, processing and assembly into virus-like particles. J Gen Virol 2014; 96:64-73. [PMID: 25304655 DOI: 10.1099/vir.0.071639-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In contrast to the current wealth of structural information concerning dicistrovirus particle structure, very little is known about their morphogenetic pathways. Here, we describe the expression of the two ORFs encoded by the Triatoma virus (TrV) genome. TrV, a member of the Cripavirus genus of the Dicistroviridae family, infects blood-sucking insects belonging to the Triatominae subfamily that act as vectors for the transmission of Trypanosoma cruzi, the aetiological agent of the Chagas disease. We have established a baculovirus-based model for the expression of the NS (non-structural) and P1 (structural) polyproteins. A preliminary characterization of the proteolytic processing of both polyprotein precursors has been performed using this system. We show that the proteolytic processing of the P1 polyprotein is strictly dependent upon the coexpression of the NS polyprotein, and that NS/P1 coexpression leads to the assembly of virus-like particles (VLPs) exhibiting a morphology and a protein composition akin to natural TrV empty capsids. Remarkably, the unprocessed P1 polypeptide assembles into quasi-spherical structures conspicuously larger than VLPs produced in NS/P1-coexpressing cells, likely representing a previously undescribed morphogenetic intermediate. This intermediate has not been found in members of the related Picornaviridae family currently used as a model for dicistrovirus studies, thus suggesting the existence of major differences in the assembly pathways of these two virus groups.
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Affiliation(s)
- Rubén Sánchez-Eugenia
- Unidad de Biofísica (CSIC, UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
| | - Fernando Méndez
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain
| | - Jailson F B Querido
- Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisboa, Portugal.,Fundación Biofísica Bizkaia, Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain.,Unidad de Biofísica (CSIC, UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
| | - Marcelo Sousa Silva
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, Brazil.,Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisboa, Portugal
| | - Diego M A Guérin
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco (EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain.,Unidad de Biofísica (CSIC, UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Bizkaia, Spain
| | - José F Rodríguez
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain
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21
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Molecular techniques for dicistrovirus detection without RNA extraction or purification. BIOMED RESEARCH INTERNATIONAL 2013; 2013:218593. [PMID: 23710438 PMCID: PMC3654624 DOI: 10.1155/2013/218593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 03/15/2013] [Accepted: 03/21/2013] [Indexed: 01/31/2023]
Abstract
Dicistroviridae is a new family of small, nonenveloped, and +ssRNA viruses pathogenic to both beneficial arthropods and insect pests as well. Triatoma virus (TrV), a dicistrovirus, is a pathogen of Triatoma infestans (Hemiptera: Reduviidae), one of the main vectors of Chagas disease. In this work, we report a single-step method to identify TrV, a dicistrovirus, isolated from fecal samples of triatomines. The identification method proved to be quite sensitive, even without the extraction and purification of RNA virus.
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22
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Snijder J, Uetrecht C, Rose RJ, Sanchez-Eugenia R, Marti GA, Agirre J, Guérin DMA, Wuite GJL, Heck AJR, Roos WH. Probing the biophysical interplay between a viral genome and its capsid. Nat Chem 2013; 5:502-9. [DOI: 10.1038/nchem.1627] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/15/2013] [Indexed: 11/09/2022]
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