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Simulation Study of the Contribution of Oligomer/Oligomer Binding to Capsid Assembly Kinetics

Tiequan Zhang ^* and Russell Schwartz ^* 

^* Department of Biological Sciences and Computer Science Department, Carnegie Mellon University, Pittsburgh, Pennsylvania

Correspondence: Address reprint requests to Russell Schwartz, Tel.: 412-268-3971; Fax: 412-268-7129; E-mail: russells{at}andrew.cmu.edu.

The process by which hundreds of identical capsid proteins self-assemble into icosahedral structures is complex and poorly understood. Establishing constraints on the assembly pathways is crucial to building reliable theoretical models. For example, it is currently an open question to what degree overall assembly kinetics are dominated by one or a few most efficient pathways versus the enormous number theoretically possible. The importance of this question, however, is often overlooked due to the difficulties of addressing it in either theoretical or experimental practice. We apply a computer model based on a discrete-event simulation method to evaluate the contributions of nondominant pathways to overall assembly kinetics. This is accomplished by comparing two possible assembly models: one allowing growth to proceed only by the accretion of individual assembly subunits and the other allowing the binding of sterically compatible assembly intermediates any sizes. Simulations show that the two models perform almost identically under low binding rate conditions, where growth is strongly nucleation-limited, but sharply diverge under conditions of higher association rates or coat protein concentrations. The results suggest the importance of identifying the actual binding pattern if one is to build reliable models of capsid assembly or other complex self-assembly processes.

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