Complete Virion Simulated: All-Atom Model of an MS2 Bacteriophage with Native Genome

Abstract

For the first time, a complete all-atom molecular dynamics (MD) model of a virus, bacteriophage MS2, in its entirety, including a protein outer shell, native genomic RNA with necessary divalent ions, and surrounding explicit aqueous solution with ions at physiological concentration, was built. The model is based on an experimentally measured cryo-EM structure, which was substantially augmented by reconstructing missing or low-resolution parts of the measured density (where the atomistic structure cannot be fit unambiguously). The model was tested by a quarter of a microsecond MD run, and various biophysical characteristics are obtained and analyzed. The developed methodology of building the model can be used for reconstructing other large biomolecular structures when experimental data are fragmented and/or of varying resolution, while the model itself can be used for studying the biology of MS2, including the dynamics of its interaction with the host bacteria.

Publication DOI: https://doi.org/10.1021/acs.jctc.3c00846
Divisions: College of Engineering & Physical Sciences > School of Computer Science and Digital Technologies > Applied Mathematics & Data Science
College of Engineering & Physical Sciences > School of Computer Science and Digital Technologies
College of Engineering & Physical Sciences
College of Engineering & Physical Sciences > Engineering for Health
Funding Information: V. F. thanks the Ministry of Education and Science of Ukraine for financial support in the frame of the project #0120U101064. V. F. and D. N. acknowledge the use of the HPC Midlands supercomputer funded by EPSRC, grant number EP/P020232/1; the access to H
Additional Information: This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see: https://doi.org/10.1021/acs.jctc.3c00846
Publication ISSN: 1549-9626
Last Modified: 30 Sep 2024 13:35
Date Deposited: 31 Oct 2023 17:04
Full Text Link:
Related URLs: https://pubs.ac ... cs.jctc.3c00846 (Publisher URL)
http://www.scop ... tnerID=8YFLogxK (Scopus URL)
PURE Output Type: Article
Published Date: 2023-11-14
Published Online Date: 2023-10-19
Accepted Date: 2023-10-01
Authors: Farafonov, Vladimir S.
Stich, Michael
Nerukh, Dmitry A. (ORCID Profile 0000-0001-9005-9919)

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Version: Accepted Version

Access Restriction: Restricted to Repository staff only until 19 October 2024.


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