title: Virus capsid dissolution studied by microsecond molecular dynamics simulations.
abstract: 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.
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
authors.forename: Daniel S D
authors.initials: DS
authors.lastname: Larsson
authors.forename: Lars
authors.initials: L
authors.lastname: Liljas
authors.forename: David
authors.initials: D
authors.lastname: van der Spoel
mesh_terms: D001665:Binding Sites; D002118:Calcium / Q000737:chemistry*; D002213:Capsid / Q000737:chemistry* / Q000648:ultrastructure*; D003198:Computer Simulation; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D025641:Tobacco necrosis satellite virus / Q000737:chemistry* / Q000648:ultrastructure*
chemical_list: D002118:Calcium