Molecular dynamics study of T=3 capsid assembly

TL;DR

This study uses molecular dynamics simulations to model the self-assembly of T=3 virus capsids, revealing detailed intermediate structures and successful formation of complete shells with minimal errors.

Contribution

It introduces a detailed molecular dynamics model that includes reversible bonding and explicit solvent to simulate virus capsid assembly.

Findings

Successful formation of complete capsids in simulations

Intermediate structures identified during assembly

Minimal formation of incorrect or incomplete clusters

Abstract

Molecular dynamics simulation is used to model the self-assembly of polyhedral shells containing 180 trapezoidal particles that correspond to the T=3 virus capsid. Three kinds of particle, differing only slightly in shape, are used to account for the effect of quasi-equivalence. Bond formation between particles is reversible and an explicit atomistic solvent is included. Under suitable conditions the simulations are able to produce complete shells, with the majority of unused particles remaining as monomers, and practically no other clusters. There are also no incorrectly assembled clusters. The simulations reveal details of intermediate structures along the growth pathway, information that is relevant for interpreting experiment.