Molecular Dynamics Study of the Hydrogen-Bond Kinetics of Protein Hydration Water

水分子驻留在生物分子表面的寿命根据水合作用部位的不同而不同。是什么决定了生命的多样性？尽管以前有许多研究，但仍然没有统一的图像定量解释这一现象。本文计算了一种特殊水化模式——水桥的寿命，结果表明水桥寿命在1到~300 ps之间变化。我们发现它遵循1/k(V_<step>)Pm，其中Pm和V_<step>是两个关键因素，即形成一个超过一个给体原子参与的特定氢键的概率，以及水化位点的结构波动。这一关系提供了一幅氢键动力学的原子细节图，并表明当一个特定的氢键模式出现时，氢键转换发生。氢键转换速率常数k可以描述为水化位点结构波动的函数。

The lifetime during which a water molecule resides at the surface of a biomolecule varies according to the hydration site. What determines this variety of lifetimes? Despite many previous studies, there is still no uniform picture quantitatively explaining this phenomenon. Here we calculate the lifetime for a particular hydration pattern, the water bridge, to show that the water-bridge lifetime varies from 1 to ~300 ps. We find that it follows 1/k(V_<step>)Pm, where Pm and V_<step> are two crucial factors, namely the probability of forming a specific hydrogen bond in which more than one donor atom participates, and the structural fluctuation of the hydration site, respectively. This relationship provides a picture of the hydrogen bond kinetics with atomistic detail and shows that hydrogen bond switching occurs when a particular hydrogen-bonding pattern appears. The rate constant of hydrogen bond switching k can be described as a function of the structural fluctuations of the hydration site.