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

Fingerprint

viruses
Viruses
Molecular dynamics
Hydrodynamics
hydrodynamics
Ions
molecular dynamics
membranes
Membranes
Atoms
water
atoms
ions
Flow of water
Water
simulation
mechanical properties
methodology
Mechanical properties
Molecules

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

Cite this

@article{d39211edd619435780b1fb8c539db8fb,
title = "Complete virus capsid at all-atom resolution: simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function",
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.",
keywords = "all-atom simulation of viruses, hybrid molecular dynamics/hydrodynamics, multiscale simulations",
author = "Elvira Tarasova and Ivan Korotkin and Volodymyr Farafonov and Sergey Karabasov and Dmitry Nerukh",
note = "{\circledC} 2017, Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/",
year = "2017",
month = "11",
day = "1",
doi = "10.1016/j.molliq.2017.06.124",
language = "English",
volume = "245",
pages = "109--114",
journal = "Journal of Molecular Liquids",
issn = "0167-7322",
publisher = "Elsevier",

}

Complete virus capsid at all-atom resolution : simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function. / Tarasova, Elvira; Korotkin, Ivan; Farafonov, Volodymyr; Karabasov, Sergey; Nerukh, Dmitry.

In: Journal of Molecular Liquids, Vol. 245, 01.11.2017, p. 109-114.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Complete virus capsid at all-atom resolution

T2 - simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function

AU - Tarasova, Elvira

AU - Korotkin, Ivan

AU - Farafonov, Volodymyr

AU - Karabasov, Sergey

AU - Nerukh, Dmitry

N1 - © 2017, Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/

PY - 2017/11/1

Y1 - 2017/11/1

N2 - 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.

AB - 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.

KW - all-atom simulation of viruses

KW - hybrid molecular dynamics/hydrodynamics

KW - multiscale simulations

UR - http://doi.org/10.17036/researchdata.aston.ac.uk.00000213

UR - http://www.scopus.com/inward/record.url?scp=85021802588&partnerID=8YFLogxK

UR - https://www.sciencedirect.com/science/article/pii/S0167732217311431?via%3Dihub

U2 - 10.1016/j.molliq.2017.06.124

DO - 10.1016/j.molliq.2017.06.124

M3 - Article

VL - 245

SP - 109

EP - 114

JO - Journal of Molecular Liquids

JF - Journal of Molecular Liquids

SN - 0167-7322

ER -