title: All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid'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.
authors.affiliation: Immanuel Kant Baltic Federal University , A. Nevskogo Street 14, Kaliningrad, 236041, Russian Federation.
authors.forename: Elvira
authors.initials: E
authors.lastname: Tarasova
authors.affiliation: Department of Physical Chemistry, V.N. Karazin Kharkiv National University , Svobody Square 4, Kharkiv, 61022, Ukraine.
authors.forename: Vladimir
authors.identifier: http://orcid.org/0000-0003-0785-9582
authors.initials: V
authors.lastname: Farafonov
authors.affiliation: Department of Chemistry and Biochemistry, City College of New York , New York, New York 10031, United States.
authors.forename: Reza
authors.initials: R
authors.lastname: Khayat
authors.affiliation: Laboratory for Computational Molecular Design, Computational Biology Research Core, RIKEN Quantitative Biology Center (QBiC) , QBiC Building B, 6-2-4 Furuedai, Suita, Osaka 565-0874, Japan.
authors.forename: Noriaki
authors.initials: N
authors.lastname: Okimoto
authors.affiliation: Laboratory for Computational Molecular Design, Computational Biology Research Core, RIKEN Quantitative Biology Center (QBiC) , QBiC Building B, 6-2-4 Furuedai, Suita, Osaka 565-0874, Japan.
authors.forename: Teruhisa S
authors.initials: TS
authors.lastname: Komatsu
authors.affiliation: Laboratory for Computational Molecular Design, Computational Biology Research Core, RIKEN Quantitative Biology Center (QBiC) , QBiC Building B, 6-2-4 Furuedai, Suita, Osaka 565-0874, Japan.
authors.forename: Makoto
authors.initials: M
authors.lastname: Taiji
authors.affiliation: Systems Analytics Research Institute, Aston University , Birmingham, B4 7ET, United Kingdom.
authors.forename: Dmitry
authors.identifier: http://orcid.org/0000-0001-9005-9919
authors.initials: D
authors.lastname: Nerukh