Encapsulation of a polymer by an icosahedral virus

Abstract

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.

This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is expected to be published online in November 2010

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Cited by in corpus (17)

• Mechanisms of virus assembly
• Equilibrium mechanisms of self-limiting assembly
• Viral genome structures are optimal for capsid assembly
• Energies and pressures in viruses: contribution of nonspecific electrostatic interactions
• Mechanisms of kinetic trapping in self-assembly and phase transformation
• RNA topology remolds electrostatic stabilization of viruses
• Using Markov State Models to Study Self-Assembly
• Quasi-Equilibrium Self-Assembly of Small RNA Viruses
• Templated self-assembly of patchy particles
• Orientational Phase Transitions and the Assembly of Viral Capsids
• Dynamics of Self-Assembly of Model Viral Capsids in the Presence of a Fluctuating Membrane
• Functional analysis of the N-terminal basic motif of a eukaryotic satellite RNA virus capsid protein in replication and packaging
• Hierarchical assembly is more robust than egalitarian assembly in synthetic capsids
• Self-assembly of model proteins into virus capsids
• Landau Theory and the Emergence of Chirality in Viral Capsids
• Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis
• Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model