COLLECTIVE MOTIONS IN PROTEINS - A COVARIANCE ANALYSIS OF ATOMIC FLUCTUATIONS IN MOLECULAR-DYNAMICS AND NORMAL MODE SIMULATIONS
COLLECTIVE MOTIONS IN PROTEINS - A COVARIANCE ANALYSIS OF ATOMIC FLUCTUATIONS IN MOLECULAR-DYNAMICS AND NORMAL MODE SIMULATIONS
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DOI：
10.1002/prot.340110305
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发表时间：
1991-01-01
期刊：
影响因子：
--
通讯作者：
KARPLUS, M
中科院分区：
文献类型：
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作者：
ICHIYE, T;KARPLUS, M
描述了一种从分子动力学轨迹或正常模式模拟中识别蛋白质集体运动的方法。该方法利用原子位置涨落的协方差。这是说明了牛胰蛋白酶抑制剂的分析。协方差矩阵和互相关矩阵的比较表明，在不同的模拟中的相对运动有许多相似的特征。蛋白质的许多区域，特别是二级结构区域，以相关的方式移动。非谐效应，这是包括在分子动力学模拟中，但不是在正常的分析，是在确定较大规模的集体运动，但不是更多的本地起伏有一定的重要性。在存在和不存在溶剂的分子动力学模拟的比较表明，环境是显着的长程运动。
A method is described for identifying collective motions in proteins from molecular dynamics trajectories or normal mode simulations. The method makes use of the covariances of atomic positional fluctuations. It is illustrated by an analysis of the bovine pancreatic trypsin inhibitor. Comparison of the covariance and cross-correlation matrices shows that the relative motions have many similar features in the different simulations. Many regions of the protein, especially regions of secondary structure, move in a correlated manner. Anharmonic effects, which are included in the molecular dynamics simulations but not in the normal analysis, are of some importance in determining the larger scale collective motions, but not the more local fluctuations. Comparisons of molecular dynamics simulations in the present and absence of solvent indicate that the environment is of significance for the long-range motions.