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首页> 外文期刊>Journal of chemical theory and computation: JCTC >Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets
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Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets

机译:约束口袋中平移水-水相关熵的空间分解

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A number of computational tools available today compute the thermodynamic properties of water at surfaces and in binding pockets by using inhomogeneous solvation theory (IST) to analyze explicit-solvent simulations. Such methods enable qualitative spatial mappings of both energy and entropy around a solute of interest and can also be applied quantitatively. However, the entropy estimates of existing methods have, to date, been almost entirely limited to the first-order terms in the IST's entropy expansion. These first-order terms account for localization and orientation of water molecules in the field of the solute but not for the modification of water water correlations by the solute. Here, we present an extension of the Grid Inhomogeneous Solvation Theory (GIST) approach which accounts for water water translational correlations. The method involves rewriting the two-point density of water in terms of a conditional density and utilizes the efficient nearest-neighbor entropy estimation approach. Spatial maps of this second order term, for water in and around the synthetic host cucurbit[7]uril and in the binding pocket of the enzyme Factor Xa, reveal mainly negative contributions, indicating solute-induced water water correlations relative to bulk water; particularly strong signals are obtained for sites at the entrances of cavities or pockets. This second-order term thus enters with the same, negative, sign as the first order translational and orientational terms. Numerical and convergence properties of the methodology are examined.
机译:通过使用非均质溶剂化理论(IST)分析显式溶剂模拟,当今可用的许多计算工具可计算表面和结合袋中水的热力学性质。这样的方法可以围绕感兴趣的溶质进行能量和熵的定性空间映射,并且也可以定量应用。然而,迄今为止,现有方法的熵估计几乎完全限于IST熵扩展中的一阶项。这些一阶项说明了溶质领域中水分子的定位和取向,但没有说明溶质对水与水的相关性的修改。在这里,我们提出了网格非均匀溶剂化理论(GIST)方法的扩展,该方法解释了水与水之间的平移相关性。该方法涉及根据条件密度重写水的两点密度,并利用有效的最近邻熵估计方法。对于合成宿主葫芦[7]尿嘧啶及其周围以及酶因子Xa的结合口袋中的水,该二级术语的空间图主要显示出负贡献,表明溶质诱导的水与散装水的相关性;对于空腔或凹穴入口处的位置,可以获得特别强的信号。因此,该二阶术语以与一阶平移和定向术语相同的负号输入。研究了该方法的数值和收敛性质。

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