Understanding how much solvents influence the structures and dynamics of proteins is important to understand functional mechanisms of solvated proteins. We propose a solvated potential model that approximates the potential energy of a solvated protein by projecting the solvent information into the protein structure. Using the model, we derive three properties of the solvent. First, the influence of the solvent on protein structure and dynamics, mostly by the bulk solvent, decays drastically (near-exponentially) as the distances of the solvent from the protein increase. Using this decay pattern, we suggest the economical size of solvent boxes in molecular dynamics simulations. Second, the hydration shell regulates the protein dynamics by effecting extra interactions within the protein structure. Lastly, the lowest frequency modes are determined mostly by protein structures.

中文翻译：

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溶剂对蛋白质结构和动力学的影响。

了解多少溶剂会影响蛋白质的结构和动力学对于理解溶剂化蛋白质的功能机制很重要。我们提出了一种溶剂化电势模型，该模型通过将溶剂信息投影到蛋白质结构中来近似溶剂化蛋白质的势能。使用该模型，我们得出了溶剂的三个特性。首先，随着溶剂与蛋白质之间距离的增加，溶剂对蛋白质结构和动力学的影响（主要由本体溶剂决定）急剧下降（接近指数）。使用这种衰减模式，我们建议分子动力学模拟中溶剂盒的经济大小。其次，水合壳通过影响蛋白质结构内的额外相互作用来调节蛋白质动力学。最后，