Molecular dynamics study of T=3 capsid assembly

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.

18 pages, 10 figures (minor changes)

References in corpus (5)

• Virus shapes and buckling transitions in spherical shells
• Understanding the Concentration Dependence of Viral Capsid Assembly Kinetics - the Origin of the Lag Time and Identifying the Critical Nucleus Size
• Stochastic kinetics of viral capsid assembly based on detailed protein structures
• Molecular dynamics simulation of reversibly self-assembling shells in solution using trapezoidal particles
• Enhanced molecular dynamics performance with a programmable graphics processor