UC San Diego

Proteins carry out most cell functions and thus it is important to understand protein dynamics, in practice, knowing how they fold and how they interact. Within the framework of energy landscape theory and the funnel concept, we used domain swapping as an example of protein interaction to demonstrate the physical principles that underlie protein interaction and aggregation. As a direct biological implication, a novel structural model for the infectious prion was proposed under the name of "domain- swapping trimeric prion". Along the line of course-grained modeling for protein interaction, we also utilized atomic simulations to study the detail of folding dynamics using beta-hairpin as a model system. To reduce the high- dimensional folding problem, we introduced an "effective stochastic dynamics" approach to characterize the folding kinetics by using one or two functional reaction coordinates. This method provides a general framework to understand the dynamics of relevant biological systems