The dynamic structure of protein molecules based on coupling among normal modes

基于简正模耦合的蛋白质分子动态结构

基本信息

批准号：
11680664
负责人：
ENDO Shigeru
金额：
$ 1.6万
依托单位：
Kitasato University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (C)
财政年份：
1999
资助国家：
日本
起止时间：
1999 至 2000
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-11680664/
关键词：
molecular dynamics internal coordinate dihedral angle energy transfer nonlinear effect 434 repressor

项目摘要

This research aims to investigate complicated motions of a protein systematically by the molecular dynamics with the initial velocity in the direction of each normal mode of a protein molecule from the viewpoint that linear movement of normal modes is extended to the nonlinear range. In normal mode analyses, since the number of variables describing the three-dimensional structure of a molecule decreased, internal coordinates like dihedral angles were often used. The dihedral angle coordinate system was also used for the program of molecular dynamics (FEDER/3) which we have developed.Molecular dynamics were performed in all the directions along about 300 normal modes lower than 200cm^<-1>, respectively for 434Cro and 434 repressor, and P22c2 repressor, which are homologous proteins. When the temperature per each mode was 300K (about 0.7 K for the whole molecule), the movement initialized with a mode faster than 40cm^<-1> resulted in harmonic oscillation with the fiequency expected from the mode. In higher temperature it was observed that the energy in a mode was dissipated to other modes, in which the energy had a tendency to move to modes roughly corresponding to the second harmonic. In the dynamics initialized with a mode slower than 40cm^<-1>, it was observed also in 300K that the tertiary structure was transferred to that around an energy minimum other than the energy minimum where the normal mode analysis was done. Energy minimization from low-energy states in the trajectories, which started from several different normal modes, however converged to the same energy minimum. That is, the number of energy minima near the native structure was not so many, for example of 434Cro, ones which were able to be transferred at 300K and at 1500K were seven and 32, respectively. It was proved that using this protocol the energy minima near the native structure can be systematically explored even in complicated multidimensional structural space of a protein.

这项研究旨在通过分子动力学系统地研究蛋白质的复杂运动，而初始速度则在蛋白质分子的每个正常模式的方向上从正常模式的线性运动扩展到非线性范围的方向。在正常模式分析中，由于描述分子三维结构的变量数量降低，因此经常使用内部坐标等内部坐标。二面角坐标系也用于我们开发的分子动力学程序（Feder/3）。分子动力学分别在所有方向上进行了大约300个正常模式，低于200cm^<-1>，分别针对434Cro和434抑制剂和434个抑制剂，P222C2抑制剂，以及P222C2抑制剂，这是Homeologic prote蛋白。当每种模式的温度为300K（整个分子约为0.7 k）时，以模式最初的运动速度快40厘米^<-1>导致了谐波振荡，并且该模式预期的Fiequencience。在较高的温度下，观察到模式下的能量被耗散到其他模式，其中能量具有移动到大约对应第二次谐波的模式的趋势。在使用模式慢的动力学速度慢于40厘米^<-1>的动力学中，在300K中也观察到，三级结构被转移到最低能量最小的能量最小值的最小值最小值的最小值。从几种不同的正常模式开始的轨迹中低能状态的能量最小化，但是融合到相同的能量最小值。也就是说，在天然结构附近的能量最小值的数量不多，例如434Cro，能够以300K和1500K的转移分别为7和32。事实证明，即使在蛋白质的复杂多维结构空间中，使用该方案也可以系统地探索天然结构附近的能量最小值。