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首页> 外文期刊>The Journal of Chemical Physics >Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study
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Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study

机译：蛋白质水合层溶剂化动力学中不同时间尺度的起源：模拟研究

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摘要

In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics, we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems, namely, lysozyme, myoglobin, and sweet protein monellin. In these experiments, we mutate the charges of the neighbouring amino acid side chains of certain natural probes (tryptophan) and also freeze the side chain motions. In order to distinguish between different contributions, we decompose the total solvation energy response in terms of various components present in the system. This allows us to capture the interplay among different self-and cross-energy correlation terms. Freezing the protein motions removes the slowest component that results from side chain fluctuations, but a part of slowness remains. This leads to the conclusion that the slowcomponent approximately in the 20-80 ps range arises from slow water molecules present in the hydration layer. While the more than 100 ps component has multiple origins, namely, adjacent charges in amino acid side chains, hydrogen bonded water molecules and a dynamically coupled motion between side chain and water. In addition, the charges enforce a structural ordering of nearby water molecules and helps to form a local long-lived hydrogen bonded network. Further separation of the spatial and temporal responses in solvation dynamics reveals different roles of hydration and bulk water. We find that the hydration layer water molecules are largely responsible for the slow component, whereas the initial ultrafast decay arises predominantly (approximately 80%) due to the bulk. This agrees with earlier theoretical observations. We also attempt to rationalise our results with the help of a molecular hydrodynamic theory that was developed using classical time dependent density functional theory in a semi-quantitative manner. Published by AIP Publishing.
机译：为了在求解动态中查询观察到的多个时间尺度的微观起源，我们进行了几个计算机实验。我们在三种蛋白水系统中进行原子分子动力学模拟，即溶菌酶，肌红蛋白和甜蛋白单蛋白。在这些实验中，我们突变了某些天然探针（色氨酸）的相邻氨基酸侧链的指控，并冻结侧链运动。为了区分不同的贡献，我们根据系统中存在的各种组分来分解总溶剂化能量响应。这允许我们捕获不同的自我和交叉能相关项之间的相互作用。冷冻蛋白质运动消除了由侧链波动导致的最慢的组件，而是仍然存在疲软​​的一部分。这导致得出结论，大致在20-80ps范围内的慢性慢性来自水合层中存在的缓慢水分子。虽然100多个PS组分具有多种起源，即氨基酸侧链，氢键水分子和侧链和水之间的动态耦合运动的相邻电荷。此外，该电荷强制了附近水分子的结构排序，并有助于形成局部长寿命的氢键网络。溶剂化动力学中的空间和时间响应的进一步分离揭示了水合和散热的不同作用。我们发现水合层水分子很大程度上对缓慢的组分负责，而初始超快衰变主要由散装引起的（约80％）。这同意了早期的理论观察。我们还试图在分子流体动力学理论的帮助下使用经典时间依赖密度泛函理论以半定量方式进行合理化。通过AIP发布发布。

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