TY - JOUR
T1 - Complete Virion Simulated: All-Atom Model of an MS2 Bacteriophage with Native Genome
AU - Farafonov, Vladimir S.
AU - Stich, Michael
AU - Nerukh, Dmitry A.
N1 - 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
PY - 2023/11/14
Y1 - 2023/11/14
N2 - 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.
AB - 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.
UR - https://pubs.acs.org/doi/10.1021/acs.jctc.3c00846
UR - http://www.scopus.com/inward/record.url?scp=85176971989&partnerID=8YFLogxK
U2 - 10.1021/acs.jctc.3c00846
DO - 10.1021/acs.jctc.3c00846
M3 - Article
SN - 1549-9618
VL - 19
SP - 7924
EP - 7933
JO - Journal of Chemical Theory and Computation
JF - Journal of Chemical Theory and Computation
IS - 21
ER -