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

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.

All-atom simulation of viruses, Hybrid molecular dynamics/hydrodynamics, Multiscale simulations

10.1016/j.molliq.2017.06.124

0167-7322

109-114

Tarasova, Elvira

41aef7af-8878-4340-b7b7-398f3536e7fe

Korotkin, Ivan

1ca96363-075e-41d9-a0c1-153c8c0cc31a

Farafonov, Vladimir

207a6c3e-4af2-4f1e-8a8c-7db7dc00ed17

Karabasov, Sergey

39acae29-1474-4567-a51c-af177ad0fe72

Nerukh, Dmitry

75d91f2c-d211-469d-b13b-d0fc7fe2b219

1 November 2017

Tarasova, Elvira

41aef7af-8878-4340-b7b7-398f3536e7fe

Korotkin, Ivan

1ca96363-075e-41d9-a0c1-153c8c0cc31a

Farafonov, Vladimir

207a6c3e-4af2-4f1e-8a8c-7db7dc00ed17

Karabasov, Sergey

39acae29-1474-4567-a51c-af177ad0fe72

Nerukh, Dmitry

75d91f2c-d211-469d-b13b-d0fc7fe2b219

Tarasova, Elvira, Korotkin, Ivan, Farafonov, Vladimir, Karabasov, Sergey and Nerukh, Dmitry (2017) Complete virus capsid at all-atom resolution: Simulations using molecular dynamics and hybrid molecular dynamics/hydrodynamics methods reveal semipermeable membrane function. Journal of Molecular Liquids, 245, 109-114. (doi:10.1016/j.molliq.2017.06.124).

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Accepted/In Press date: 28 June 2017

e-pub ahead of print date: 29 June 2017

Published date: 1 November 2017

Additional Information: Funding Information: E.T. acknowledges support from the Royal Society of Chemistry (Researcher Mobility Fellowship, 550074), the Great Britain Sasakawa Foundation (grant 4679 ), and the 5 top 100 Russian Academic Excellence Project at the Immanuel Kant Baltic Federal University ( 5-100 ). This work used the ARCHER UK National Supercomputing Service ( http://www.archer.ac.uk ) funded by the UK High-End Computing Consortium for Biomolecular Simulation (grant number EP/L000253/1), the RIKEN Integrated Cluster of Clusters (RICC) and HOKUSAI GreatWave system. I.K. gratefully acknowledges the financial support of European Commission under the Marie Curie Individual Fellowship ( H2020-MSCA-IF-2015-700276 “HIPPOGRIFFE” project). The 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://doi.org/10.17036/researchdata.aston.ac.uk.00000213 Funding Information: This work used the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk) funded by the UK High-End Computing Consortium for Biomolecular Simulation (grant number EP/L000253/1), the RIKEN Integrated Cluster of Clusters (RICC) and HOKUSAI GreatWave system. I.K. gratefully acknowledges the financial support of European Commission under the Marie Curie Individual Fellowship (H2020-MSCA-IF-2015-700276 ?HIPPOGRIFFE? project). Publisher Copyright: © 2017 Elsevier B.V.

Keywords: All-atom simulation of viruses, Hybrid molecular dynamics/hydrodynamics, Multiscale simulations