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.
Highlights
Non-enveloped icosahedral viruses often contain binding sites for divalent cations, usually Ca2z
Author Summary We have studied the capsid of satellite tobacco necrosis virus using large scale molecular dynamics simulations, where the atomic motions of 1,2 million particles were tracked over one microsecond
The aim of this work was to probe the dynamic behavior of a virus capsid over timescales that are more than an order of magnitude longer than what has been reported from simulations of viruses previously [16,17,18], and therewith to investigate the role of the structural calcium ions in initiating the dissolution of the satellite tobacco necrosis virus
Summary
Non-enveloped icosahedral viruses often contain binding sites for divalent cations, usually Ca2z. The ions are typically bound between coat proteins or on the icosahedral symmetry axes. This is broadly observed in three plant virus taxa: the family Tombusviridae (and an associate satellite virus), the genus Sobemoviruses and the family Bromoviridae [1,2,3,4]. An expanded cowpea chlorotic mottle virus (CCMV) virion was imaged with cryo-electron microscopy at 29 Aand interpreted using rigid body fitting of the high-resolution structures of the native proteins [4]. The dynamic nature of the swelling process as well as the limited resolution of swollen virus particles structures prompted us to perform a simulation study of the capsid of STNV, with and without bound Ca2z, over one microsecond. The simulations allowed us to reproduce the swelling behavior upon removal of the calcium in silico and develop an atomistic description of the process
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