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Journal articles on the topic 'Structural virology'

Author: Grafiati

Published: 14 December 2024

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1

Agbandje-McKenna, Mavis, and Richard Kuhn. "Current opinion in virology: structural virology." Current Opinion in Virology 1, no. 2 (August 2011): 81–83. http://dx.doi.org/10.1016/j.coviro.2011.07.001.

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2

Stuart, David. "Changing times in structural virology." Acta Crystallographica Section A Foundations and Advances 75, a2 (August 18, 2019): e18-e18. http://dx.doi.org/10.1107/s205327331909538x.

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3

Sousa, Rui. "Structural Virology 4. T7 RNA Polymerase." Uirusu 51, no. 1 (2001): 81–94. http://dx.doi.org/10.2222/jsv.51.81.

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4

Shepherd, C. M. "VIPERdb: a relational database for structural virology." Nucleic Acids Research 34, no. 90001 (January 1, 2006): D386—D389. http://dx.doi.org/10.1093/nar/gkj032.

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5

Kiss, Bálint, Dorottya Mudra, György Török, Zsolt Mártonfalvi, Gabriella Csík, Levente Herényi, and Miklós Kellermayer. "Single-particle virology." Biophysical Reviews 12, no. 5 (September 3, 2020): 1141–54. http://dx.doi.org/10.1007/s12551-020-00747-9.

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Abstract The development of advanced experimental methodologies, such as optical tweezers, scanning-probe and super-resolved optical microscopies, has led to the evolution of single-molecule biophysics, a field of science that allows direct access to the mechanistic detail of biomolecular structure and function. The extension of single-molecule methods to the investigation of particles such as viruses permits unprecedented insights into the behavior of supramolecular assemblies. Here we address the scope of viral exploration at the level of individual particles. In an era of increased awareness towards virology, single-particle approaches are expected to facilitate the in-depth understanding, and hence combating, of viral diseases.

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6

Meier, Kristina, Sigurdur R. Thorkelsson, Emmanuelle R. J. Quemin, and Maria Rosenthal. "Hantavirus Replication Cycle—An Updated Structural Virology Perspective." Viruses 13, no. 8 (August 6, 2021): 1561. http://dx.doi.org/10.3390/v13081561.

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Hantaviruses infect a wide range of hosts including insectivores and rodents and can also cause zoonotic infections in humans, which can lead to severe disease with possible fatal outcomes. Hantavirus outbreaks are usually linked to the population dynamics of the host animals and their habitats being in close proximity to humans, which is becoming increasingly important in a globalized world. Currently there is neither an approved vaccine nor a specific and effective antiviral treatment available for use in humans. Hantaviruses belong to the order Bunyavirales with a tri-segmented negative-sense RNA genome. They encode only five viral proteins and replicate and transcribe their genome in the cytoplasm of infected cells. However, many details of the viral amplification cycle are still unknown. In recent years, structural biology methods such as cryo-electron tomography, cryo-electron microscopy, and crystallography have contributed essentially to our understanding of virus entry by membrane fusion as well as genome encapsidation by the nucleoprotein. In this review, we provide an update on the hantavirus replication cycle with a special focus on structural virology aspects.

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7

Rossmann, Michael G. "Virus crystallography and structural virology: a personal perspective." Crystallography Reviews 21, no. 1-2 (November 14, 2014): 57–102. http://dx.doi.org/10.1080/0889311x.2014.957282.

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8

Khayat, Reza. "Call for Papers: Special Issue on Structural Virology." Viral Immunology 32, no. 10 (December 1, 2019): 415. http://dx.doi.org/10.1089/vim.2019.29046.cfp.

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9

Schoehn, Guy, Florian Chenavier, and Thibaut Crépin. "Advances in Structural Virology via Cryo-EM in 2022." Viruses 15, no. 6 (June 2, 2023): 1315. http://dx.doi.org/10.3390/v15061315.

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10

Dowd, Kimberly A., and Theodore C. Pierson. "The Many Faces of a Dynamic Virion: Implications of Viral Breathing on Flavivirus Biology and Immunogenicity." Annual Review of Virology 5, no. 1 (September 29, 2018): 185–207. http://dx.doi.org/10.1146/annurev-virology-092917-043300.

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Flaviviruses are arthropod-borne RNA viruses that are a significant threat to global health due to their widespread distribution, ability to cause severe disease in humans, and capacity for explosive spread following introduction into new regions. Members of this genus include dengue, tick-borne encephalitis, yellow fever, and Zika viruses. Vaccination has been a highly successful means to control flaviviruses, and neutralizing antibodies are an important component of a protective immune response. High-resolution structures of flavivirus structural proteins and virions, alone and in complex with antibodies, provide a detailed understanding of viral fusion mechanisms and virus-antibody interactions. However, mounting evidence suggests these structures provide only a snapshot of an otherwise structurally dynamic virus particle. The contribution of the structural ensemble arising from viral breathing to the biology, antigenicity, and immunity of flaviviruses is discussed, including implications for the development and evaluation of flavivirus vaccines.

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11

Doane, Frances W. "Immunoelectron Microscopy in Diagnostic Virology." Ultrastructural Pathology 11, no. 5-6 (January 1987): 681–85. http://dx.doi.org/10.3109/01913128709048454.

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12

Porat-Dahlerbruch, Gal, Amir Goldbourt, and Tatyana Polenova. "Virus Structures and Dynamics by Magic-Angle Spinning NMR." Annual Review of Virology 8, no. 1 (September 29, 2021): 219–37. http://dx.doi.org/10.1146/annurev-virology-011921-064653.

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Techniques for atomic-resolution structural biology have evolved during the past several decades. Breakthroughs in instrumentation, sample preparation, and data analysis that occurred in the past decade have enabled characterization of viruses with an unprecedented level of detail. Here we review the recent advances in magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy for structural analysis of viruses and viral assemblies. MAS NMR is a powerful method that yields information on 3D structures and dynamics in a broad range of experimental conditions. After a brief introduction, we discuss recent structural and functional studies of several viruses investigated with atomic resolution at various levels of structural organization, from individual domains of a membrane protein reconstituted into lipid bilayers to virus-like particles and intact viruses. We present examples of the unique information revealed by MAS NMR about drug binding, conduction mechanisms, interactions with cellular host factors, and DNA packaging in biologically relevant environments that are inaccessible by other methods.

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13

Yadav, Sandeep Kumar. "Electron Microscopy for Structural Determination and Analysis of Viruses." Biotechnology Kiosk 4, no. 2 (February 21, 2022): 12–25. http://dx.doi.org/10.37756/bk.22.4.2.2.

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Viruses are known to be associated with large-scale, dynamic conformational changes that take place to facilitate cell entry and genome delivery. It is also known that a replication machinery is involved in the advanced stage of the infectious cycle that enables to read and synthesize nucleic acid strands. This process results in the generation of new copies of genetic material. In this process, the function of structural proteins helps to assemble and package the appropriate contents to produce new infectious particles. Lately, there has been a great deal of research interest on structural elucidation of these events. This interest is primarily driven by the significance of virus structural identification, which helps understand these processes and also their inhibition by antiviral agents such as neutralizing antibodies and drugs. To this end, the development of electron microscopy (EM) techniques for studies in virology has played a major role for structural determination and analysis of viruses. In this mini-review, we have highlighted some of the latest developments in this field. We have briefly described important role of EM in virology. We have also discussed notable application examples of EM in elucidating various virus structures to gain insights into identification of deadly pathogens and other infectious agents and outbreaks along with anti-viral developmental strategies.

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14

Dendooven, T., and R. Lavigne. "Dip-a-Dee-Doo-Dah: Bacteriophage-Mediated Rescoring of a Harmoniously Orchestrated RNA Metabolism." Annual Review of Virology 6, no. 1 (September 29, 2019): 199–213. http://dx.doi.org/10.1146/annurev-virology-092818-015644.

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RNA turnover and processing in bacteria are governed by the structurally divergent but functionally convergent RNA degradosome, and the mechanisms have been researched extensively in Gram-positive and Gram-negative bacteria. An emerging research field focuses on how bacterial viruses hijack all aspects of the bacterial metabolism, including the host machinery of RNA metabolism. This review addresses research on phage-based influence on RNA turnover, which can act either indirectly or via dedicated effector molecules that target degradosome assemblies. The structural divergence of host RNA turnover mechanisms likely explains the limited number of phage proteins directly targeting these specialized, host-specific complexes. The unique and nonconserved structure of DIP, a phage-encoded inhibitor of the Pseudomonas degradosome, illustrates this hypothesis. However, the natural occurrence of phage-encoded mechanisms regulating RNA turnover indicates a clear evolutionary benefit for this mode of host manipulation. Further exploration of the viral dark matter of unknown phage proteins may reveal more structurally novel interference strategies that, in turn, could be exploited for biotechnological applications.

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15

Venkatakrishnan, Balasubramanian, and Adam Zlotnick. "The Structural Biology of Hepatitis B Virus: Form and Function." Annual Review of Virology 3, no. 1 (September 29, 2016): 429–51. http://dx.doi.org/10.1146/annurev-virology-110615-042238.

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16

Bengs, Suvi, Jane Marttila, Petri Susi, and Jorma Ilonen. "Elicitation of T-cell responses by structural and non-structural proteins of coxsackievirus B4." Journal of General Virology 96, no. 2 (February 1, 2015): 322–30. http://dx.doi.org/10.1099/vir.0.069062-0.

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17

Carrillo-Tripp, M., C. M. Shepherd, I. A. Borelli, S. Venkataraman, G. Lander, P. Natarajan, J. E. Johnson, C. L. Brooks, and V. S. Reddy. "VIPERdb2: an enhanced and web API enabled relational database for structural virology." Nucleic Acids Research 37, Database (January 1, 2009): D436—D442. http://dx.doi.org/10.1093/nar/gkn840.

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18

Lukashev, Alexander N., Vasilii A. Lashkevich, Olga E. Ivanova, Galina A. Koroleva, Ari E. Hinkkanen, and Jorma Ilonen. "Recombination in circulating Human enterovirus B: independent evolution of structural and non-structural genome regions." Journal of General Virology 86, no. 12 (December 1, 2005): 3281–90. http://dx.doi.org/10.1099/vir.0.81264-0.

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The complete nucleotide sequences of eight Human enterovirus B (HEV-B) strains were determined, representing five serotypes, E6, E7, E11, CVB3 and CVB5, which were isolated in the former Soviet Union between 1998 and 2002. All strains were mosaic recombinants and only the VP2–VP3–VP1 genome region was similar to that of the corresponding prototype HEV-B strains. In seven of the eight strains studied, the 2C–3D genome region was most similar to the prototype E30, EV74 and EV75 strains, whilst the remaining strain was most similar to the prototype E1 and E9 strains in the non-structural protein genome region. Most viruses also bore marks of additional recombination events in this part of the genome. In the 5′ non-translated region, all strains were more similar to the prototype E9 than to other enteroviruses. In most cases, recombination mapped to the VP4 and 2ABC genome regions. This, together with the star-like topology of the phylogenetic trees for these genome regions, identified these genome parts as recombination hot spots. These findings further support the concept of independent evolution of enterovirus genome fragments and indicate a requirement for more advanced typing approaches. A range of available phylogenetic methods was also compared for efficient detection of recombination in enteroviruses.

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19

Subramanian, Sundharraman, Kristin N. Parent, and Sarah M. Doore. "Ecology, Structure, and Evolution of Shigella Phages." Annual Review of Virology 7, no. 1 (September 29, 2020): 121–41. http://dx.doi.org/10.1146/annurev-virology-010320-052547.

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Numerous bacteriophages—viruses of bacteria, also known as phages—have been described for hundreds of bacterial species. The Gram-negative Shigella species are close relatives of Escherichia coli, yet relatively few previously described phages appear to exclusively infect this genus. Recent efforts to isolate Shigella phages have indicated these viruses are surprisingly abundant in the environment and have distinct genomic and structural properties. In addition, at least one model system used for experimental evolution studies has revealed a unique mechanism for developing faster infection cycles. Differences between these bacteriophages and other well-described model systems may mirror differences between their hosts’ ecology and defense mechanisms. In this review, we discuss the history of Shigella phages and recent developments in their isolation and characterization and the structural information available for three model systems, Sf6, Sf14, and HRP29; we also provide an overview of potential selective pressures guiding both Shigella phage and host evolution.

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20

Quemin, Emmanuelle R. J., Emily A. Machala, Benjamin Vollmer, Vojtěch Pražák, Daven Vasishtan, Rene Rosch, Michael Grange, Linda E. Franken, Lindsay A. Baker, and Kay Grünewald. "Cellular Electron Cryo-Tomography to Study Virus-Host Interactions." Annual Review of Virology 7, no. 1 (September 29, 2020): 239–62. http://dx.doi.org/10.1146/annurev-virology-021920-115935.

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Viruses are obligatory intracellular parasites that reprogram host cells upon infection to produce viral progeny. Here, we review recent structural insights into virus-host interactions in bacteria, archaea, and eukaryotes unveiled by cellular electron cryo-tomography (cryoET). This advanced three-dimensional imaging technique of vitreous samples in near-native state has matured over the past two decades and proven powerful in revealing molecular mechanisms underlying viral replication. Initial studies were restricted to cell peripheries and typically focused on early infection steps, analyzing surface proteins and viral entry. Recent developments including cryo-thinning techniques, phase-plate imaging, and correlative approaches have been instrumental in also targeting rare events inside infected cells. When combined with advances in dedicated image analyses and processing methods, details of virus assembly and egress at (sub)nanometer resolution were uncovered. Altogether, we provide a historical and technical perspective and discuss future directions and impacts of cryoET for integrative structural cell biology analyses of viruses.

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21

Young, Megan, Harry Crook, Janet Scott, and Paul Edison. "Covid-19: virology, variants, and vaccines." BMJ Medicine 1, no. 1 (March 2022): e000040. http://dx.doi.org/10.1136/bmjmed-2021-000040.

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As of 25 January 2022, over 349 million individuals have received a confirmed diagnosis of covid-19, with over 5.59 million confirmed deaths associated with the SARS-CoV-2 virus. The covid-19 pandemic has prompted an extensive global effort to study the molecular evolution of the virus and develop vaccines to prevent its spread. Although rigorous determination of SARS-CoV-2 infectivity remains elusive, owing to the continuous evolution of the virus, steps have been made to understand its genome, structure, and emerging genetic mutations. The SARS-CoV-2 genome is composed of several open reading frames and structural proteins, including the spike protein, which is essential for entry into host cells. As of 25 January 2022, the World Health Organization has reported five variants of concern, two variants of interest, and three variants under monitoring. Additional sublineages have since been identified, and are being monitored. The mutations harboured in these variants confer an increased transmissibility, severity of disease, and escape from neutralising antibodies compared with the primary strain. The current vaccine strategy, including booster doses, provides protection from severe disease. As of 24 January 2022, 33 vaccines have been approved for use in 197 countries. In this review, we discuss the genetics, structure, and transmission methods of SARS-CoV-2 and its variants, highlighting how mutations provide enhanced abilities to spread and inflict disease. This review also outlines the vaccines currently in use around the world, providing evidence for every vaccine's immunogenicity and effectiveness.

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22

Huang, Kuan-Ying A. "Structural basis for neutralization of enterovirus." Current Opinion in Virology 51 (December 2021): 199–206. http://dx.doi.org/10.1016/j.coviro.2021.10.006.

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23

Li, Xiang, Lavanya Krishnan, Peter Cherepanov, and Alan Engelman. "Structural biology of retroviral DNA integration." Virology 411, no. 2 (March 2011): 194–205. http://dx.doi.org/10.1016/j.virol.2010.12.008.

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24

Mattei, Simone, Florian KM Schur, and John AG Briggs. "Retrovirus maturation—an extraordinary structural transformation." Current Opinion in Virology 18 (June 2016): 27–35. http://dx.doi.org/10.1016/j.coviro.2016.02.008.

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25

Fukuhara, Hideo, Mwila Hilton Mwaba, and Katsumi Maenaka. "Structural characteristics of measles virus entry." Current Opinion in Virology 41 (April 2020): 52–58. http://dx.doi.org/10.1016/j.coviro.2020.04.002.

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26

Conte, Maria R., and Stephen Matthews. "Retroviral Matrix Proteins: A Structural Perspective." Virology 246, no. 2 (July 1998): 191–98. http://dx.doi.org/10.1006/viro.1998.9206.

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27

Armengol, Elisenda, Karl-Heinz Wiesmüller, Daniel Wienhold, Mathias Büttner, Eberhard Pfaff, Günther Jung, and Armin Saalmüller. "Identification of T-cell epitopes in the structural and non-structural proteins of classical swine fever virus." Journal of General Virology 83, no. 3 (March 1, 2002): 551–60. http://dx.doi.org/10.1099/0022-1317-83-3-551.

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To identify new T-cell epitopes of classical swine fever virus (CSFV), 573 overlapping, synthetic pentadecapeptides spanning 82% of the CSFV (strain Glentorf) genome sequence were synthesized and screened. In proliferation assays, 26 peptides distributed throughout the CSFV viral protein sequences were able to induce specific T-cell responses in PBMCs from a CSFV-Glentorf-infected d/d haplotype pig. Of these 26 peptides, 18 were also recognized by PBMCs from a CSFV-Alfort/187-infected d/d haplotype pig. In further experiments, it could be shown that peptide 290 (KHKVRNEVMVHWFDD), which corresponds to amino acid residues 1446–1460 of the CSFV non-structural protein NS2–3 could induce interferon-γ secretion after secondary in vitro restimulation. The major histocompatibility complex (MHC) restriction for stimulation of T-cells by this pentadecapeptide was identified as being mainly MHC class II and partially MHC class I. In cytolytic assays, CSFV-specific cytotoxic T-lymphocytes (CTLs) were able to lyse peptide 290-loaded target cells. These findings indicate the existence of a CSFV-specific helper T-cell epitope and a CTL epitope in this peptide.

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28

Twarock, R. "A tiling approach to virus capsid assembly explaining a structural puzzle in virology." Journal of Theoretical Biology 226, no. 4 (February 2004): 477–82. http://dx.doi.org/10.1016/j.jtbi.2003.10.006.

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29

Singh, Bishal Kumar, Anna Koromyslova, and Grant S. Hansman. "Structural analysis of bovine norovirus protruding domain." Virology 487 (January 2016): 296–301. http://dx.doi.org/10.1016/j.virol.2015.10.022.

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30

Gauss-Müller, Verena, Friedrich Lottspeich, and Friedrich Deinhardt. "Characterization of hepatitis A virus structural proteins." Virology 155, no. 2 (December 1986): 732–36. http://dx.doi.org/10.1016/0042-6822(86)90234-5.

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31

Brown, Jay C., and William W. Newcomb. "Herpesvirus capsid assembly: insights from structural analysis." Current Opinion in Virology 1, no. 2 (August 2011): 142–49. http://dx.doi.org/10.1016/j.coviro.2011.06.003.

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32

Hu, Liya, Sue E. Crawford, Joseph M. Hyser, Mary K. Estes, and BV Venkataram Prasad. "Rotavirus non-structural proteins: structure and function." Current Opinion in Virology 2, no. 4 (August 2012): 380–88. http://dx.doi.org/10.1016/j.coviro.2012.06.003.

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33

Schlicksup, Christopher John, and Adam Zlotnick. "Viral structural proteins as targets for antivirals." Current Opinion in Virology 45 (December 2020): 43–50. http://dx.doi.org/10.1016/j.coviro.2020.07.001.

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34

Weber, Joseph, and Henri-A. Ménard. "Immunological cross-reactivity of adenovirus structural proteins." Journal of Virological Methods 13, no. 4 (July 1986): 363–67. http://dx.doi.org/10.1016/0166-0934(86)90061-3.

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35

Francis, M. I., J. A. Szychowski, and J. S. Semancik. "Structural sites specific to citrus viroid groups." Journal of General Virology 76, no. 5 (May 1, 1995): 1081–89. http://dx.doi.org/10.1099/0022-1317-76-5-1081.

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36

Walker, P. J., and K. Kongsuwan. "Deduced structural model for animal rhabdovirus glycoproteins." Journal of General Virology 80, no. 5 (May 1, 1999): 1211–20. http://dx.doi.org/10.1099/0022-1317-80-5-1211.

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37

BAN, NENAD, STEVEN B. LARSON, and ALEXANDER McPHERSON. "Structural Comparison of the Plant Satellite Viruses." Virology 214, no. 2 (December 1995): 571–83. http://dx.doi.org/10.1006/viro.1995.0068.

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38

Ströh, Luisa J., and Thomas Krey. "Structural insights into hepatitis C virus neutralization." Current Opinion in Virology 60 (June 2023): 101316. http://dx.doi.org/10.1016/j.coviro.2023.101316.

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39

May, Aaron J., and Priyamvada Acharya. "Structural Studies of Henipavirus Glycoproteins." Viruses 16, no. 2 (January 27, 2024): 195. http://dx.doi.org/10.3390/v16020195.

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Henipaviruses are a genus of emerging pathogens that includes the highly virulent Nipah and Hendra viruses that cause reoccurring outbreaks of disease. Henipaviruses rely on two surface glycoproteins, known as the attachment and fusion proteins, to facilitate entry into host cells. As new and divergent members of the genus have been discovered and structurally characterized, key differences and similarities have been noted. This review surveys the available structural information on Henipavirus glycoproteins, complementing this with information from related biophysical and structural studies of the broader Paramyxoviridae family of which Henipaviruses are members. The process of viral entry is a primary focus for vaccine and drug development, and this review aims to identify critical knowledge gaps in our understanding of the mechanisms that drive Henipavirus fusion.

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40

Sevvana, Madhumati, Zhenyong Keck, Steven KH Foung, and Richard J. Kuhn. "Structural perspectives on HCV humoral immune evasion mechanisms." Current Opinion in Virology 49 (August 2021): 92–101. http://dx.doi.org/10.1016/j.coviro.2021.05.002.

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41

Rupp, Jonathan C., Kevin J. Sokoloski, Natasha N. Gebhart, and Richard W. Hardy. "Alphavirus RNA synthesis and non-structural protein functions." Journal of General Virology 96, no. 9 (September 1, 2015): 2483–500. http://dx.doi.org/10.1099/jgv.0.000249.

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42

Sundqvist, A., M. Berg, P. Hernandez-Jauregui, T. Linne, and J. Moreno-Lopez. "The structural proteins of a porcine paramyxovirus (LPMV)." Journal of General Virology 71, no. 3 (March 1, 1990): 609–13. http://dx.doi.org/10.1099/0022-1317-71-3-609.

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43

Strizki, J. M., and P. M. Repik. "Structural Protein Relationships Among Eastern Equine Encephalitis Viruses." Journal of General Virology 75, no. 11 (November 1, 1994): 2897–909. http://dx.doi.org/10.1099/0022-1317-75-11-2897.

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44

Devant, Jessica M., and Grant S. Hansman. "Structural heterogeneity of a human norovirus vaccine candidate." Virology 553 (January 2021): 23–34. http://dx.doi.org/10.1016/j.virol.2020.10.005.

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45

Hayden, Melody, Mark B. Adams, and Sherwood Casjens. "Bacteriophage L: Chromosome physical map and structural proteins." Virology 147, no. 2 (December 1985): 431–40. http://dx.doi.org/10.1016/0042-6822(85)90145-x.

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46

Baquero, Eduard, Aurélie A. Albertini, Patrice Vachette, Jean Lepault, Stéphane Bressanelli, and Yves Gaudin. "Intermediate conformations during viral fusion glycoprotein structural transition." Current Opinion in Virology 3, no. 2 (April 2013): 143–50. http://dx.doi.org/10.1016/j.coviro.2013.03.006.

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47

Lozano, Gloria, and Encarnación Martínez-Salas. "Structural insights into viral IRES-dependent translation mechanisms." Current Opinion in Virology 12 (June 2015): 113–20. http://dx.doi.org/10.1016/j.coviro.2015.04.008.

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48

Charleston, Bryan, and Simon P. Graham. "Recent advances in veterinary applications of structural vaccinology." Current Opinion in Virology 29 (April 2018): 33–38. http://dx.doi.org/10.1016/j.coviro.2018.02.006.

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49

Lin, William, Jeannie L. Shurgot, and Harumi Kasamatsu. "The synthesis and transport of SV40 structural proteins." Virology 154, no. 1 (October 1986): 108–20. http://dx.doi.org/10.1016/0042-6822(86)90434-4.

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50

Baron, Michael D., and Kerstin Forsell. "Oligomerisation of the structural proteins of Rubella virus." Virology 185, no. 2 (December 1991): 811–19. http://dx.doi.org/10.1016/0042-6822(91)90552-m.

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