Sugar molecules play important roles as mediators of biomolecular interactions in cellular functions, disease, and infections. Molecular dynamics simulations are an indispensable tool to explore these interactions at the molecular level. The large time and length scales involved frequently necessitate the use of coarse-grained representations, which heavily depend on the parametrization of sugar–protein interactions. Here, we adjust the sugar–protein interactions in the widely used Martini 2.2 force field to reproduce the experimental osmotic second virial coefficients between sugars and proteins. In simulations of two model proteins in glucose solutions with adjusted force field parameters, we observe weak protein–sugar interactions. The sugar molecules are thus acting mainly as crowding agents, in agreement with experimental measurements. The procedure to fine-tune sugar–protein interactions is generally applicable and could also prove useful for atomistic force fields.

中文翻译：

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马提尼力场中的精制蛋白质-糖相互作用


糖分子在细胞功能、疾病和感染中作为生物分子相互作用的介质起着重要作用。分子动力学模拟是在分子水平上探索这些相互作用不可或缺的工具。所涉及的大时间和长度尺度经常需要使用粗粒度表示，这在很大程度上取决于糖-蛋白质相互作用的参数化。在这里，我们调整了广泛使用的马提尼 2.2 力场中的糖-蛋白质相互作用，以重现糖和蛋白质之间的实验渗透第二维里系数。在调整了力场参数的葡萄糖溶液中两种模型蛋白质的模拟中，我们观察到弱蛋白质-糖相互作用。因此，糖分子主要充当拥挤剂，这与实验测量一致。微调糖-蛋白质相互作用的程序通常是适用的，并且也可能被证明对原子力场有用。