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通过分子动力学模拟研究渗透剂附近水的旋转动力学

Rotational Dynamics of Water near Osmolytes by Molecular Dynamics Simulations.

作者信息

Higuchi Yuji, Saleh Md Abu, Anada Takahisa, Tanaka Masaru, Hishida Mafumi

机构信息

Research Institute for Information Technology, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.

Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan.

出版信息

J Phys Chem B. 2024 May 23;128(20):5008-5017. doi: 10.1021/acs.jpcb.3c08470. Epub 2024 May 10.

Abstract

The behavior of water molecules around organic molecules has attracted considerable attention as a crucial factor influencing the properties and functions of soft matter and biomolecules. Recently, it has been suggested that the change in protein stability upon the addition of small organic molecules (osmolytes) is dominated by the change in the water dynamics caused by the osmolyte, where the dynamics of not only the directly interacting water molecules but also the long-range hydration layer affect the protein stability. However, the relation between the long-range structure of hydration water in various solutions and the water dynamics remains unclear at the molecular level. We performed density-functional tight-binding molecular dynamics simulations to elucidate the varying rotational dynamics of water molecules in 15 osmolyte solutions. A positive correlation was observed between the rotational relaxation time and our proposed normalized parameter obtained by dividing the number of hydrogen bonds between water molecules by the number of nearest-neighbor water molecules. For the 15 osmolyte solutions, an increase or a decrease in the value of the normalized parameter for the second hydration shell tended to result in water molecules with slow and fast rotational dynamics, respectively, thus illustrating the importance of the second hydration shell for the rotational dynamics of water molecules. Our simulation results are anticipated to advance the current understanding of water dynamics around organic molecules and the long-range structure of water molecules.

摘要

有机分子周围水分子的行为作为影响软物质和生物分子性质与功能的关键因素,已引起了广泛关注。最近,有人提出,添加小分子有机分子(渗透剂)后蛋白质稳定性的变化主要由渗透剂引起的水动力学变化所主导,其中不仅直接相互作用的水分子的动力学,而且远程水化层的动力学都会影响蛋白质稳定性。然而,在分子水平上,各种溶液中水化水的远程结构与水动力学之间的关系仍不明确。我们进行了密度泛函紧束缚分子动力学模拟,以阐明15种渗透剂溶液中水分子不同的旋转动力学。通过将水分子之间的氢键数除以最近邻水分子数得到的归一化参数与旋转弛豫时间之间存在正相关关系。对于这15种渗透剂溶液,第二水化层归一化参数值的增加或减少分别倾向于导致水分子具有缓慢和快速的旋转动力学,从而说明了第二水化层对水分子旋转动力学的重要性。我们的模拟结果有望推动目前对有机分子周围水动力学和水分子远程结构的理解。

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