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首页> 外文期刊>The Journal of Chemical Physics >Global and local Voronoi analysis of solvation shells of proteins
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Global and local Voronoi analysis of solvation shells of proteins

机译：蛋白质溶剂化壳的全局和局部Voronoi分析

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This paper presents the structure and dynamics of hydration shells for the three proteins: ubiquitin, calbindin, and phospholipase. The raw data derived from molecular dynamics simulations are analyzed on the basis of fully atomistic Delaunay tesselations. In order to cope with the high numerical effort for the computation of these Voronoi shells, we have implemented and optimized an intrinsically periodic algorithm. Based on this highly efficient Voronoi decomposition, a variety of properties is presented: three dimensional water and ion nuclear densities as well as the geometrical packing of water molecules are discussed. Thereby, we develop Voronoi interface surface area, the Voronoi analog of the well known solvent accessible surface area. The traditional radial distribution functions are resolved into Voronoi shells as a transient device to the new concept of shell-grained orientational order. Thus, we analyze the donor-acceptor property as well as the amount of dielectric screening. Shell dynamics is described in terms of mean residence times. In this way, a retardation factor for different shells can be derived and was compared to experimental values. All these results and properties are presented both at the global protein level as well as at the local residue level.
机译：本文介绍了三种蛋白水合壳的结构和动力学：泛素，钙结合蛋白和磷脂酶。在完全原子化的Delaunay细分基础上，分析了分子动力学模拟得出的原始数据。为了应对计算这些Voronoi壳的大量数值工作，我们实现并优化了本征周期算法。基于这种高效的Voronoi分解，提出了多种特性：讨论了水和离子的三维核密度以及水分子的几何堆积。因此，我们开发了Voronoi界面表面积，即众所周知的溶剂可及表面积的Voronoi类似物。传统的径向分布函数已分解为Voronoi壳，作为壳晶粒定向顺序新概念的过渡设备。因此，我们分析了供体-受体性质以及介电屏蔽的数量。壳动力学以平均停留时间描述。以此方式，可以得出不同壳的延迟因子，并将其与实验值进行比较。所有这些结果和特性均在全局蛋白质水平以及局部残基水平上给出。

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