TCBG Seminar

A novel coarse-grain model that captures protein backbone structure and its application to simulate the self-assembly of HIV capsid proteins

Professor Bo Chen
Department of Physics
University of Central Florida
Orlando, FL

Monday, August 26, 2013
3:00 pm (CT)
3269 Beckman Institute


Proteins are the main machinery to drive various activities for organisms. Instead of working alone, they usually orchestrate to achieve the designed functions that can extend over a wide range of time scale. For the instance of viral capsids, which are the sentinels for the viral genome materials, they are constructed from a large number of identical viral capsid proteins and essential for the infectivity of viruses. Up to date, the self-assembly process of viral capsid remains largely a mystery and a great challenge to scientists. The assembly speed of viral capsids is usually too fast for direct characterizations by experimental techniques, while the complexity and time span is beyond all-atom simulation at current computation technology. We invented a novel coarse-grain model that can capture the protein backbone structure. Initial Monte Carlo simulations based on this model can simulate the self-assembly of HIV capsid proteins when the molecular motions are restricted within a plane. The HIV capsid proteins can self-assemble into tubes in vitro and cones in vivo, both of which were confirmed by structural studies to be constructed from hexameric lattice of the protein. Our simulations predicted that the trimers of dimeric subunits are the critical species of transient intermediates along the assembly pathway and self-assembly are foiled as the interaction at the trimeric interface becomes repulsive. With recent improvements, our model simulates hundreds of capsid proteins self assembles with full freedom of 3D motions, which paves the way to understand the formation of curvature and the morphology of the capsids.

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