Local Rules Modeling of Nucleation-Limited Virus Capsid Assembly

We describe an application of computer modeling to the study of the kinetics of virus capsid (protein shell) assembly. We examine two proposed models of the source of nucleation-limited growth, an observed growth pattern in which initiation of new capsids occurs significantly more slowly than subunit addition onto initiated capsids. We apply an abstract computer model of capsid assembly, based on the principle of local rules, to support a theoretical argument for favoring a two-conformation model over a one-conformation model. The theoretical analysis examines expected relative growth and nucleation rates and concludes that the two-conformation model should be able to support faster growth following nucleation for any fixed nucleation rate. Based on the theoretical argument, we develop predictions which are then supported by computer simulation results on a model of T=1 capsid assembly. In addition to strengthening the argument for a two-conformation model, our results demonstrate the potential value of computer simulations in comparing hypothetical models for observed biochemical behaviors.