All-atom molecular dynamics simulations of entire virus capsid reveal the role of ion distribution in capsid’s stability

Tarasova, Elvira, Farafonov, Vladimir, Khayat, Reza, Okimoto, Noriaki, Komatsu, Teruhisa, Taiji, Makoto and Nerukh, Dmitry (2017). All-atom molecular dynamics simulations of entire virus capsid reveal the role of ion distribution in capsid’s stability. Journal of Physical Chemistry Letters, 8 (4), pp. 779-784.

Abstract

Present experimental methods do not have sufficient resolution to investigate all processes in virus particles at atomistic details. We report the results of molecular dynamics simulations and analyze the connection between the number of ions inside an empty capsid of PCV2 virus and its stability. We compare the crystallographic structures of the capsids with unresolved N-termini and without them in realistic conditions (room temperature and aqueous solution) and show that the structure is preserved. We find that the chloride ions play a key role in the stability of the capsid. A low number of chloride ions results in loss of the native icosahedral symmetry, while an optimal number of chloride ions create a neutralizing layer next to the positively charged inner surface of the capsid. Understanding the dependence of the capsid stability on the distribution of the ions will help clarify the details of the viral life cycle that is ultimately connected to the role of packaged viral genome inside the capsid.

Publication DOI: https://doi.org/10.1021/acs.jpclett.6b02759
Dataset DOI: https://doi.org/10.17036/6e8e1a26-aa8d-4cfc-aed1-551b081cd391
Divisions: Engineering & Applied Sciences > Systems analytics research institute (SARI)
Engineering & Applied Sciences > Mathematics
Additional Information: This document is the Accepted Manuscript version of a Published Work that appeared in final form in J. Phys. Chem. Lett., copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/acs.jpclett.6b02759 Funding: Royal Society of Chemistry (Researcher Mobility Fellowship, 550074); Great Britain Sasakawa Foundation (4679); 5 top 100 Russian Academic Excellence Project at the Immanuel Kant Baltic Federal University; NIH National Institute of General Medical Sciences and National Institute of Allergy and Infectious Diseases (5SC1AI114843); National Institute on Minority Health and Health Disparities (5G12MD007603-30); and UK High-End Computing Consortium for Biomolecular Simulation (grant number EP/L000253/1). he supporting data of this study are stored at the University of Aston. Details of how to request access to these data are provided in the documentation available from the University of Aston research data repository at http://dx.doi.org/10.17036/6e8e1a26-aa8d-4cfc-aed1-551b081cd391
Uncontrolled Keywords: Materials Science(all)
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Related URLs: http://www.scopus.com/inward/record.url?scp=85013059451&partnerID=8YFLogxK (Scopus URL)
Published Date: 2017-01-27
Authors: Tarasova, Elvira
Farafonov, Vladimir
Khayat, Reza
Okimoto, Noriaki
Komatsu, Teruhisa
Taiji, Makoto
Nerukh, Dmitry ( 0000-0001-9005-9919)

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