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

Elvira Tarasova; Vladimir Farafonov; Reza Khayat; Noriaki Okimoto; Teruhisa Komatsu; Makoto Taiji; Dmitry Nerukh

doi:10.1021/acs.jpclett.6b02759

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

Elvira Tarasova, Vladimir Farafonov, Reza Khayat, Noriaki Okimoto, Teruhisa Komatsu, Makoto Taiji, Dmitry Nerukh^*

^*Corresponding author for this work

Research output: Contribution to journal › Letter, comment or opinion › peer-review

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.

Original language	English
Pages (from-to)	779-784
Number of pages	5
Journal	Journal of Physical Chemistry Letters
Volume	8
Issue number	4
DOIs	https://doi.org/10.1021/acs.jpclett.6b02759
Publication status	Published - 27 Jan 2017

Bibliographical note

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

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10.1021/acs.jpclett.6b02759

All atom molecular dynamics simulations of entire virus capsid
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
Accepted author manuscript, 756 KB

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All-atom simulation of PCV2 virus capsid using molecular dynamics in explicit water
Nerukh, D. (Creator), Tarasova, E. (Creator), Farafonov, V. (Creator), Khayat, R. (Creator), Taiji, M. (Creator), Okimoto, N. (Creator) & Komatsu, T. (Creator), Aston Data Explorer, 23 Nov 2016
DOI: 10.17036/6e8e1a26-aa8d-4cfc-aed1-551b081cd391, https://pubs.acs.org/doi/10.1021/acs.jpclett.6b02759
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@article{ed761019ccba4d329957e1b5522ee5d0,

title = "All-atom molecular dynamics simulations of entire virus capsid reveal the role of ion distribution in capsid{\textquoteright}s stability",

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.",

author = "Elvira Tarasova and Vladimir Farafonov and Reza Khayat and Noriaki Okimoto and Teruhisa Komatsu and Makoto Taiji and Dmitry Nerukh",

note = "This document is the Accepted Manuscript version of a Published Work that appeared in final form in J. Phys. Chem. Lett., copyright {\textcopyright} 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 ",

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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; Nerukh, Dmitry.

In: Journal of Physical Chemistry Letters, Vol. 8, No. 4, 27.01.2017, p. 779-784.

Research output: Contribution to journal › Letter, comment or opinion › peer-review

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AU - Tarasova, Elvira

AU - Farafonov, Vladimir

AU - Khayat, Reza

AU - Okimoto, Noriaki

AU - Komatsu, Teruhisa

AU - Taiji, Makoto

AU - Nerukh, Dmitry

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PY - 2017/1/27

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N2 - 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.

AB - 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.

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JO - Journal of Physical Chemistry Letters

JF - Journal of Physical Chemistry Letters

SN - 1948-7185

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ER -

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

Abstract

Bibliographical note

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All-atom simulation of PCV2 virus capsid using molecular dynamics in explicit water

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