Abstract The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results.

中文翻译：

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守还是不守？有机溶剂中酶模拟的结晶水问题

摘要 酶在非水溶剂中的使用将生物催化剂的用途扩展到疏水底物，能够通过溶剂选择来调节反应的选择性。非水酶学还允许对水和其他溶剂在酶结构、动力学和功能中的作用进行基础研究。分子动力学模拟是该领域的强大工具，可提供有关溶剂对酶特性影响的详细原子信息。然而，不存在用于非水酶模拟的通用协议。如果您想模拟非水溶液中的酶，您保留多少和哪些结晶水？在目前的工作中，通过确定哪些结晶水分子最快速地导致平衡的蛋白质结构来解决这个问题。使用五种不同的选择和保持结晶水的方法来发现哪些结晶水导致蛋白质结构在有机溶液中更快地达到平衡结构。发现埋藏水对有机溶剂中的快速平衡贡献最大，缓慢扩散的水给出了类似的结果。