  The coat proteins of many viruses spontaneously form icosahedral capsids
around nucleic acids or other polymers. Elucidating the role of the packaged
polymer in capsid formation could promote biomedical efforts to block viral
replication and enable use of capsids in nanomaterials applications. To this
end, we perform Brownian dynamics on a coarse-grained model that describes the
dynamics of icosahedral capsid assembly around a flexible polymer. We identify
several mechanisms by which the polymer plays an active role in its
encapsulation, including cooperative polymer-protein motions. These mechanisms
are related to experimentally controllable parameters such as polymer length,
protein concentration, and solution conditions. Furthermore, the simulations
demonstrate that assembly mechanisms are correlated to encapsulation
efficiency, and we present a phase diagram that predicts assembly outcomes as a
function of experimental parameters. We anticipate that our simulation results
will provide a framework for designing in vitro assembly experiments on
single-stranded RNA virus capsids.
