Dynamic pathways for viral capsid assembly.
We develop a class of models with which we simulate the assembly of particles into T1 capsidlike objects using Newtonian dynamics. By simulating assembly for many different values of system parameters, we vary the forces that drive assembly. For some ranges of parameters, assembly is facile; for others, assembly is dynamically frustrated by kinetic traps corresponding to malformed or incompletely formed capsids. Our simulations sample many independent trajectories at various capsomer concentrations, allowing for statistically meaningful conclusions. Depending on subunit (i.e., capsomer) geometries, successful assembly proceeds by several mechanisms involving binding of intermediates of various sizes. We discuss the relationship between these mechanisms and experimental evaluations of capsid assembly processes.
Hagan
Michael F
MF
Department of Chemistry, University of California, Berkeley, California, USA.
Chandler
David
D
D002213:Capsid / Q000737:chemistry* / Q000502:physiology* / Q000648:ultrastructure; D036022:Capsid Proteins / Q000737:chemistry* / Q000502:physiology*; D003198:Computer Simulation; D007700:Kinetics; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D046912:Multiprotein Complexes / Q000737:chemistry / Q000502:physiology / Q000648:ultrastructure; D011487:Protein Conformation; D019065:Virus Assembly / Q000502:physiology*
D036022:Capsid Proteins; D046912:Multiprotein Complexes