MS2 bacteriophage capsid studied using all-atom molecular dynamics

Vladimir S. Farafonov, Dmitry Nerukh

Research output: Contribution to journalArticlepeer-review


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.
Original languageEnglish
Article number20180081
JournalInterface Focus
Issue number3
Early online date19 Apr 2019
Publication statusPublished - 6 Jun 2019

Bibliographical note

MS2 bacteriophage capsid studied using all-atom molecular dynamics. Vladimir S. Farafonov and Dmitry Nerukh. Interface Focus Vol 9 Iss 3. Published:19 April 2019


  • Flow of solution
  • Ions distribution
  • MS2 virus capsid


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