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Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules

机译:计算机中偶极子场的大涡状结构 水和生物分子间偶极桥的模型

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摘要

We propose a framework to describe the cooperative orientational motions of water molecules in liquid water and around solute molecules in water solutions. From molecular dynamics (MD) simulation a new quantity “site-dipole field” is defined as the averaged orientation of water molecules that pass through each spatial position. In the site-dipole field of bulk water we found large vortex-like structures of more than 10 Å in size. Such coherent patterns persist more than 300 ps although the orientational memory of individual molecules is quickly lost. A 1-ns MD simulation of systems consisting of two amino acids shows that the fluctuations of site-dipole field of solvent are pinned around the amino acids, resulting in a stable dipole-bridge between side-chains of amino acids. The dipole-bridge is significantly formed even for the side-chain separation of 14 Å, which corresponds to five layers of water. The way that dipole-bridge forms sensitively depends on the side-chain orientations and thereby explains the specificity in the solvent-mediated interactions between biomolecules.
机译:我们提出一个框架来描述液态水中的水分子和水溶液中的溶质分子的协同定向运动。通过分子动力学(MD)模拟,新量的“局部偶极子场”定义为通过每个空间位置的水分子的平均取向。在散装水的偶极子场中,我们发现了大小超过10Å的大型漩涡状结构。尽管单个分子的方向记忆很快消失,但这种相干模式仍保持300 ps以上。由两个氨基酸组成的系统的1-ns MD模拟表明,溶剂的位偶极子场的波动被固定在氨基酸周围,从而在氨基酸的侧链之间形成了稳定的偶极桥。即使在14Å的侧链分离中,偶极桥也明显形成,这相当于五层水。偶极桥灵敏地形成的方式取决于侧链的方向,从而解释了生物分子之间溶剂介导的相互作用的特异性。

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