报告题目：Computational Investigation of Molecular Machinery: Structure, Dynamics, and Function
报告人：Yanxin Liu， University of Illinois at Urbana-Champaign
时间：10：00 am，Nov. 9th，2011
Molecular dynamics simulation has been successfully applied to many biological systems to investigate the relation between structure, dynamics, and unction. I will present what we can learn from molecular dynamics simulation through two case studies:protein folding and motor proteins.In the case of protein folding, a five-helix bundle lambda repressor fragment is chosen as a model system. It is known to be a fast folding protein experimentally with folding time 15 microseconds. The protein folded ab initio into its native state in the simulation, revealing the folding process with unprecedented spatial and temporal resolution, rendering it as the largest protein one can fold on a computer. For the motor protein, stepping mechanism of myosin VI is investigated. We demonstrated how myosin VI realize its large step size with a short lever arm (or legs). If time permits, I will give a brief introduction of molecule dynamics flexible fitting (MDFF), a computational method that can fit high- resolution X-ray crystallographic structure into cryo-EM density maps.