Noguti T, Go N
Computation Center, Faculty of Engineering, Kyushu University, Fukuoka, Japan.
Proteins. 1989;5(2):97-103. doi: 10.1002/prot.340050203.
A computer experiment of protein dynamics is carried out, which consists of two steps: (1) A Monte Carlo simulation of thermal fluctuations in the native state of a globular protein, bovine pancreatic trypsin inhibitor; and (2) a simulation of the quick freezing of fluctuating conformations into energy minima by minimization of the energy of a number of conformations sampled in the Monte Carlo simulation. From the analysis of results of the computer experiment is obtained the following picture of protein dynamics: multiple energy minima exist in the native state, and they are distributed in clusters in the conformational space. The dynamics has a hierarchical structure which has at least two levels. In the first level, dynamics is restricted within one of the clusters of minima. In the second, transitions occur among the clusters. Local parts of a protein molecule, side chains and local main chain segments, can take multiple locally stable conformations in the native state. Many minima result from combinations of these multiple local conformations. The hierarchical structure in the dynamics comes from interactions among the local parts. Protein molecules have two types of flexibility, each associated with elastic and plastic deformations, respectively.
进行了一项蛋白质动力学的计算机实验，该实验包括两个步骤：（1）对球状蛋白质牛胰蛋白酶抑制剂天然状态下的热涨落进行蒙特卡罗模拟；（2）通过最小化在蒙特卡罗模拟中采样的多个构象的能量，将波动的构象快速冻结到能量最小值。通过对计算机实验结果的分析，得到了如下蛋白质动力学图景：天然状态下存在多个能量最小值，它们在构象空间中呈簇分布。动力学具有至少两个层次的层次结构。在第一个层次中，动力学被限制在最小值簇之一内。在第二个层次中，簇之间发生转变。蛋白质分子的局部部分、侧链和局部主链片段在天然状态下可以采取多种局部稳定构象。许多最小值是由这些多种局部构象的组合产生的。动力学中的层次结构来自局部部分之间的相互作用。蛋白质分子有两种类型的柔韧性，分别与弹性和塑性变形相关。
