Structural and Dynamic Asymmetry in Icosahedrally Symmetric Virus Capsids

Overview

Journal Curr Opin Virol

Publisher Elsevier

Specialty Microbiology

Date 2020 Jul 3

PMID 32615360

Citations 6

Authors

Asis K Jana

Eric R May

Affiliations

Soon will be listed here.

Abstract

A common characteristic of virus capsids is icosahedral symmetry, yet these highly symmetric structures can display asymmetric features within their virions and undergo asymmetric dynamics. The fields of structural and computational biology have entered a new realm in the investigation of virus infection mechanisms, with the ability to observe symmetry-breaking features. This review will cover important studies on icosahedral virus structure and dynamics, covering both symmetric and asymmetric conformational changes. However, the main emphasis of the review will be towards recent studies employing cryo-electron microscopy or molecular dynamics simulations, which can uncover asymmetric aspects of these systems relevant to understanding viral physical-chemical properties and their biological impact.

Citing Articles

Modeling Viral Capsid Assembly: A Review of Computational Strategies and Applications.

Guo W, Alarcon E, Sanchez J, Xiao C, Li L Cells. 2025; 13(24.

PMID: 39768179 PMC: 11674207. DOI: 10.3390/cells13242088.

Theoretical Studies on Assembly, Physical Stability, and Dynamics of Viruses.

Luque A, Reguera D Subcell Biochem. 2024; 105:693-741.

PMID: 39738961 DOI: 10.1007/978-3-031-65187-8_19.

The balance between fitness advantages and costs drives adaptation of bacteriophage Qβ to changes in host density at different temperatures.

Laguna-Castro M, Rodriguez-Moreno A, Llorente E, Lazaro E Front Microbiol. 2023; 14:1197085.

PMID: 37303783 PMC: 10248866. DOI: 10.3389/fmicb.2023.1197085.

Non-equilibrium virus particle dynamics: Microsecond MD simulations of the complete Flock House virus capsid under different conditions.

Jana A, Sharawy M, May E J Struct Biol. 2023; 215(2):107964.

PMID: 37105277 PMC: 10205670. DOI: 10.1016/j.jsb.2023.107964.

Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins.

Brodmerkel M, de Santis E, Uetrecht C, Caleman C, Marklund E Curr Res Struct Biol. 2022; 4:338-348.

PMID: 36440379 PMC: 9685359. DOI: 10.1016/j.crstbi.2022.10.001.

References

Baker T, Olson N, Fuller S . Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs. Microbiol Mol Biol Rev. 1999; 63(4):862-922, table of contents. PMC: 98980. DOI: 10.1128/MMBR.63.4.862-922.1999. View

Andoh Y, Yoshii N, Yamada A, Fujimoto K, Kojima H, Mizutani K . All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution. J Chem Phys. 2014; 141(16):165101. DOI: 10.1063/1.4897557. View

Gorzelnik K, Cui Z, Reed C, Jakana J, Young R, Zhang J . Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ. Proc Natl Acad Sci U S A. 2016; 113(41):11519-11524. PMC: 5068298. DOI: 10.1073/pnas.1609482113. View

Lee K, Gan L, Tsuruta H, Hendrix R, Duda R, Johnson J . Evidence that a local refolding event triggers maturation of HK97 bacteriophage capsid. J Mol Biol. 2004; 340(3):419-33. DOI: 10.1016/j.jmb.2004.05.008. View

Conway J, Duda R, Cheng N, Hendrix R, Steven A . Proteolytic and conformational control of virus capsid maturation: the bacteriophage HK97 system. J Mol Biol. 1995; 253(1):86-99. DOI: 10.1006/jmbi.1995.0538. View

Walukiewicz H, Johnson J, Schneemann A . Morphological changes in the T=3 capsid of Flock House virus during cell entry. J Virol. 2005; 80(2):615-22. PMC: 1346855. DOI: 10.1128/JVI.80.2.615-622.2006. View

Banerjee M, Khayat R, Walukiewicz H, Odegard A, Schneemann A, Johnson J . Dissecting the functional domains of a nonenveloped virus membrane penetration peptide. J Virol. 2009; 83(13):6929-33. PMC: 2698515. DOI: 10.1128/JVI.02299-08. View

Kumar C, Dey D, Ghosh S, Banerjee M . Breach: Host Membrane Penetration and Entry by Nonenveloped Viruses. Trends Microbiol. 2017; 26(6):525-537. DOI: 10.1016/j.tim.2017.09.010. View

May E, Feng J, Brooks 3rd C . Exploring the symmetry and mechanism of virus capsid maturation via an ensemble of pathways. Biophys J. 2012; 102(3):606-12. PMC: 3274788. DOI: 10.1016/j.bpj.2011.12.016. View

10.

Kilcher S, Mercer J . DNA virus uncoating. Virology. 2015; 479-480:578-90. DOI: 10.1016/j.virol.2015.01.024. View

11.

Tarasova E, Farafonov V, Khayat R, Okimoto N, Komatsu T, Taiji M . All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid's Stability. J Phys Chem Lett. 2017; 8(4):779-784. PMC: 5391438. DOI: 10.1021/acs.jpclett.6b02759. View

12.

Ho P, Reddy V . Rapid increase of near atomic resolution virus capsid structures determined by cryo-electron microscopy. J Struct Biol. 2017; 201(1):1-4. DOI: 10.1016/j.jsb.2017.10.007. View

13.

Larsson D, Liljas L, van der Spoel D . Virus capsid dissolution studied by microsecond molecular dynamics simulations. PLoS Comput Biol. 2012; 8(5):e1002502. PMC: 3349721. DOI: 10.1371/journal.pcbi.1002502. View

14.

Freddolino P, Arkhipov A, Larson S, McPherson A, Schulten K . Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure. 2006; 14(3):437-49. DOI: 10.1016/j.str.2005.11.014. View

15.

Butan C, Filman D, Hogle J . Cryo-electron microscopy reconstruction shows poliovirus 135S particles poised for membrane interaction and RNA release. J Virol. 2013; 88(3):1758-70. PMC: 3911577. DOI: 10.1128/JVI.01949-13. View

16.

Crick F, Watson J . Structure of small viruses. Nature. 1956; 177(4506):473-5. DOI: 10.1038/177473a0. View

17.

Dai X, Zhou Z . Structure of the herpes simplex virus 1 capsid with associated tegument protein complexes. Science. 2018; 360(6384). PMC: 5959011. DOI: 10.1126/science.aao7298. View

18.

Roy A, Post C . Long-distance correlations of rhinovirus capsid dynamics contribute to uncoating and antiviral activity. Proc Natl Acad Sci U S A. 2012; 109(14):5271-6. PMC: 3325699. DOI: 10.1073/pnas.1119174109. View

19.

Suhanovsky M, Teschke C . Nature's favorite building block: Deciphering folding and capsid assembly of proteins with the HK97-fold. Virology. 2015; 479-480:487-97. PMC: 4424165. DOI: 10.1016/j.virol.2015.02.055. View

20.

Conley M, Bhella D . Asymmetric analysis reveals novel virus capsid features. Biophys Rev. 2019; 11(4):603-609. PMC: 6682188. DOI: 10.1007/s12551-019-00572-9. View