MS2 bacteriophage capsid studied using all-atom molecular dynamics

Abstract

The all-atom model of an MS2 bacteriophage particle without its genome (the capsid) was built using high-resolution cryo-electron microscopy (EM) measurements for initial conformation. The structural characteristics of the capsid and the dynamics of the surrounding solution were examined using molecular dynamics simulation. The model demonstrates the overall preservation of the cryo-EM structure of the capsid at physiological conditions (room temperature and ions composition). The formation of a dense anion layer near the inner surface and a diffuse cation layer near the outer surface of the capsid was detected. The flow of water molecules and ions across the capsid through its pores were quantified, which was considerable for water and substantial for ions.

Publication DOI: https://doi.org/10.1098/rsfs.2018.0081
Divisions: Engineering & Applied Sciences > Mathematics
Engineering & Applied Sciences > Systems analytics research institute (SARI)
Additional Information: MS2 bacteriophage capsid studied using all-atom molecular dynamics. Vladimir S. Farafonov and Dmitry Nerukh. Interface Focus Vol 9 Iss 3. Published:19 April 2019https://doi.org/10.1098/rsfs.2018.0081
Uncontrolled Keywords: Flow of solution,Ions distribution,MS2 virus capsid,Biotechnology,Biophysics,Bioengineering,Biochemistry,Biomaterials,Biomedical Engineering
Full Text Link:
Related URLs: http://www.roya ... /rsfs.2018.0081 (Publisher URL)
http://www.scop ... tnerID=8YFLogxK (Scopus URL)
PURE Output Type: Article
Published Date: 2019-06-06
Published Online Date: 2019-04-19
Accepted Date: 2019-03-13
Authors: Farafonov, Vladimir S.
Nerukh, Dmitry ( 0000-0001-9005-9919)

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