蛋白质动力学理论研究中的计算机模拟方法

COMPUTER SIMULATION METHODS IN PROTEIN DYNAMICS STUDY

蛋白质是生物体中一种十分重要的高分子物质。蛋白质分子有着自身所特有的化学、物理结构;在溶液中蛋白质分子不仅自身不同部分间存在着相互作用,而且还与溶剂分子间发生着复杂的相互作用,这些都很大程度上影响到分子的结构和演变过程。为了对蛋白质分子进行模拟,很有必要建立适当的描述蛋白质分子结构的模型,引入合理的模型基元间的相互作用,并采用有效的方法进行模拟,本着贴近现实和方便模拟的原则,在本文中我们系统地总结了近年来蛋白质动力学及其物理特性,特别对其模型、势能及模拟方法进行了着重介绍。为了增加一些感性认识,文中还就实验分析、折叠的协作性、搜寻保守残基和动力学过程的熵效应和阻挫效应等几个专题进行了应用介绍。

It is well known that the protein is a kind of magic material in the living system. The structure of protein molecule has its own characteristics. Generally the protein molecule in some kind of solution will encounter a lot of complicated interactions which come not only from the other parts of the molecule but also from the solvent. All the interactions affect the stucture of molecules and the path for the molecules to follow. To give simulations to molecule, proper models,potentials and work procedurs are needed. In this article,the details are given. Then the discussions on the topics,such as analysis of experimental data, cooperativity of folding process,searching of conserve residuals and entropic effect -frustration in dynamics, are introduced.