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Benchmarking the Thermodynamic Analysis of Water Molecules Around a Model Beta Sheet

机译:标杆水分子的热力学分析围绕模型进行β折叠

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摘要

Water molecules play a vital role in biological and engineered systems by controlling intermolecular interactions in the aqueous phase. Inhomogeneous fluid solvation theory provides a method to quantify solvent thermodynamics from molecular dynamics or Monte Carlo simulations and provides an insight into intermolecular interactions. In this study, simulations of TIP4P-2005 and TIP5P-Ewald water molecules around a model beta sheet are used to investigate the orientational correlations and predicted thermodynamic properties of water molecules at a protein surface. This allows the method to be benchmarked and provides information about the effect of a protein on the thermodynamics of nearby water molecules. The results show that the enthalpy converges with relatively little sampling, but the entropy and thus the free energy require considerably more sampling to converge. The two water models yield a very similar pattern of hydration sites and these hydration sites have very similar thermodynamic properties, despite notable differences in their orientational preferences. The results also show that a protein surface affects the free energy of water molecules to a distance of approximately 4.0 Å, which is in line with previous work. In addition, all hydration sites have a favourable free energy with respect to bulk water, but only when the water-water entropy term is included. A new technique for calculating this term is presented and its use is expected to be very important in accurately calculating solvent thermodynamics for quantitative application.
机译:水分子通过控制水相中的分子间相互作用在生物和工程系统中起着至关重要的作用。不均匀的流体溶剂化理论提供了一种从分子动力学或蒙特卡罗模拟中量化溶剂热力学的方法,并提供对分子间相互作用的洞察。在该研究中,模拟模型β板上的Tip4P-2005和Tip5P-Ewald水分子用于研究蛋白质表面上水分子的定向相关性和预测热力学性质。这允许该方法是基准测试,并提供有关蛋白质对附近水分子热力学的影响的信息。结果表明,焓聚集在一起相对较少的采样,而是熵,因此自由能需要更多的采样来汇聚。两种水模型产生非常相似的水化位点模式,并且这些水化位点具有非常相似的热力学性质,尽管其取向偏好是显着差异。结果还表明,蛋白质表面影响水分子的自由能到约4.0埃的距离,这与先前的工作符合。此外,所有水化位点相对于散装水具有良好的自由能,但仅当包括水 - 水熵项时。提出了一种计算该术语的新技术,并且预计在准确计算用于定量应用的溶剂热力学中的使用非常重要。

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    David J. Huggins;

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  • 年(卷),期 -1(33),15
  • 年度 -1
  • 页码 1383–1392
  • 总页数 23
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