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 journalArticle

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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