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

Vladimir S. Farafonov, Michael Stich, Dmitry A. Nerukh

Research output: Contribution to journalArticlepeer-review


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.
Original languageEnglish
Pages (from-to)7924-7933
Number of pages10
JournalJournal of Chemical Theory and Computation
Issue number21
Early online date19 Oct 2023
Publication statusPublished - 14 Nov 2023

Bibliographical note

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:


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