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Enhanced Sampling and Applications in Protein Folding in Explicit Solvent
2012-08-01  【 】【打印】【关闭
Institute of Theoretical Physics
Chinese Academy of Sciences
学术报告
Title
题目
Enhanced Sampling and Applications in Protein Folding in Explicit Solvent
Speaker
报告人
Prof. Jianpeng Ma
Department of Biochemistry and Molecular Biology, Baylor College Medicine; Department of Bioengineering, Rice University
Date
日期
2012-08-01 AM 10:00 Wednesday
Venue
地点
Conference Hall 322, ITP/理论物理所322报告厅
Abstract
摘要

We report a single-copy tempering method for simulating large complex systems. In a generalized ensemble, the method uses runtime estimate of the thermal average energy computed from a novel integral identity to guide a continuous temperature-space random walk. We first validated the method in a two-dimensional Ising model and a Lennard-Jones liquid system. It was then applied to folding of three small proteins, trpzip2, trp-cage, and villin headpiece in explicit solvent. Within 0.5 ~ 1 microsecond, all three systems were folded into atomic accuracy: the alpha carbon root mean square deviations of the best folded conformations from the native states were 0.2, 0.4, and 0.4 Å, for trpzip2, trp-cage, and villin headpiece, respectively. Discussion of folding much larger helical proteins in explicit solvent will also be given.

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