Evolution of conformational changes in the dynamics of small biological molecules: a hybrid MD/RRK approach

作     者：Segev, Elad Grumbach, Mikael Gerber, Robert Benny 

作者机构：Hebrew Univ Jerusalem Dept Chem Phys IL-91904 Jerusalem Israel Hebrew Univ Jerusalem Fritz Haber Inst IL-91904 Jerusalem Israel Univ Calif Irvine Dept Chem Irvine CA 92697 USA 

出 版 物：《PHYSICAL CHEMISTRY CHEMICAL PHYSICS》 (Phys. Chem. Chem. Phys.)

年 卷 期：2006年第8卷第42期

页      面：4915-4923页

核心收录：

学科分类：081704[工学-应用化学] 07[理学] 070304[理学-物理化学(含∶化学物理)] 08[工学] 0817[工学-化学工程与技术] 0703[理学-化学] 0702[理学-物理学] 

主　　题：.hairpin dipeptide paths Reaction path timescale RRK Dijkstra algorithm small biological molecules blocked valine tripeptide blocked alanine hexapeptide 

摘      要：The dynamics of long timescale evolution of conformational changes in small biological molecules is described by a hybrid molecular dynamics/RRK algorithm. The approach employs classical trajectories for transitions between adjacent structures separated by a low barrier, and the classical statistical RRK approximation when the barrier involved is high. In determining the long-time dynamics from an initial structure to a final structure of interest, an algorithm is introduced for determining the most efficient pathways (sequence of the intermediate conformers). This method uses the Dijkstra algorithm for finding optimal paths on networks. Three applications of the method using an AMBER force field are presented: a detailed study of conformational transitions in a blocked valine dipeptide;a multiple reaction path study of the blocked valine tripeptide;and the evolution in time from the beta hairpin to alpha helix structure of a blocked alanine hexapeptide. Advantages and limitations of the method are discussed in light of the results.