Virus capsid dissolution studied by microsecond molecular dynamics simulations

PLoS Comput Biol. 2012;8(5):e1002502. doi: 10.1371/journal.pcbi.1002502. Epub 2012 May 10.


Dissolution of many plant viruses is thought to start with swelling of the capsid caused by calcium removal following infection, but no high-resolution structures of swollen capsids exist. Here we have used microsecond all-atom molecular simulations to describe the dynamics of the capsid of satellite tobacco necrosis virus with and without the 92 structural calcium ions. The capsid expanded 2.5% upon removal of the calcium, in good agreement with experimental estimates. The water permeability of the native capsid was similar to that of a phospholipid membrane, but the permeability increased 10-fold after removing the calcium, predominantly between the 2-fold and 3-fold related subunits. The two calcium binding sites close to the icosahedral 3-fold symmetry axis were pivotal in the expansion and capsid-opening process, while the binding site on the 5-fold axis changed little structurally. These findings suggest that the dissociation of the capsid is initiated at the 3-fold axis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Calcium / chemistry*
  • Capsid / chemistry*
  • Capsid / ultrastructure*
  • Computer Simulation
  • Models, Biological*
  • Models, Chemical*
  • Models, Molecular
  • Molecular Conformation
  • Tobacco necrosis satellite virus / chemistry*
  • Tobacco necrosis satellite virus / ultrastructure*


  • Calcium