Visualizing global properties of a molecular dynamics trajectory.
Visualizing global properties of a molecular dynamics trajectory.
复制标题
可视化分子动力学轨迹的全局特性。
DOI：
10.1002/prot.24957
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发表时间：
2016
期刊：
影响因子：
2.9
通讯作者：
Makowski,Lee
中科院分区：
文献类型：
--
作者：
Zhou,Hao;Li,Shangyang;Makowski,Lee
Tuesday, February 10, 2014 377a the molecular behavior during the trajectory is a substantial challenge that has received relatively little attention. Here, we introduce the sigma-r plot, a plot of the standard deviation of intermolecular distances as a function of that distance. This representation of global dynamics contains within a single, onedimensional plot, the average range of motion between pairs of atoms within a macromolecule. Comparison of sigma-r plots calculated from 10 nsec trajectories of proteins representing the four major SCOP fold classes indicates significant diversity of dynamic behaviors which are recognizably different among the four classes. Differences in domain structure and molecular weight also produce recognizable features in sigma-r plots, reflective of differences in global dynamics. Plots generated from trajectories with progressively increasing simulation time reflect the increased sampling of the structural ensemble as a function of time. Single amino acid replacements can give rise to changes in global dynamics detectable through comparison of sigma-r plots. Dynamic behavior of substructures can be monitored by careful choice of interatomic vectors included in the calculation. Comparison between the sigma-r plots calculated from MD simulations and from wide angle x-ray solution scattering data is also feasible with the potential for providing direct experimental tests of the approximations required for coarse-grained MD simulations. These examples provide demonstrations of the utility of the sigma-r plot to provide a simple measure of the global dynamics of a macromolecule.
