209g Molecular Dynamics Simulations of Viral Capsid Self-Assembly

Hung D. Nguyen and Charles L. Brooks III. Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, TPC6, La Jolla, CA 92037

For about half of the known virus families, the coat that protects their genome in the form of DNA or RNA is a ‘spherical' or icosahedral capsid which is composed of many copies of individual proteins that must self-assemble correctly, rapidly, and reproducibly on a biological timescale in order to propagate an infection in vivo. Elucidating the self-assembly of empty viral capsids may have the potential to assist in developing novel approaches to interfere with viral infection. We have developed a geometric model that can mimic the basic shape and interface interactions of each capsid protein for use in conjunction with the rigid-body Monte Carlo simulation method and the discontinuous molecular dynamics algorithm - a fast alternative to standard molecular dynamics. This model has allowed us to simulate the spontaneous formation of multiple complete T=1 viral capsids simultaneously in relatively large systems containing many capsid proteins. Also, our simulation results are able to capture in general features of self-assembly as observed in experiments on a variety of viruses. Detailed analysis on the kinetics and thermodynamics of capsid self-assembly will be presented.


Web Page: www.scripps.edu/~hdnguyen/index.html