Complete virus capsid at all-atom resolution: simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function

Elvira Tarasova, Ivan Korotkin, Volodymyr Farafonov, Sergey Karabasov, Dmitry Nerukh*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Simulations of complete virus capsid at atomistic details have been performed using standard Molecular Dynamics as well as original hybrid Molecular Dynamics/hydrodynamics methodologies. The results show that the capsid is stable in water solution at room temperature and ions composition similar to physiological conditions. Detailed analysis of the flow of water molecules and ions through the capsid’s wall is performed. It demonstrates that ions do not cross the capsid shell, while water exhibits substantial flows in both directions. This behaviour can be classified as a semipermeable membrane and may play a role in mechanical properties of the virus particle.
    Original languageEnglish
    Pages (from-to)109-114
    JournalJournal of Molecular Liquids
    Volume245
    Early online date29 Jun 2017
    DOIs
    Publication statusPublished - 1 Nov 2017

    Bibliographical note

    © 2017, Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/

    Keywords

    • all-atom simulation of viruses
    • hybrid molecular dynamics/hydrodynamics
    • multiscale simulations

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