Intermediate Structure and Slow Hydration Water Dynamics in Protein Folding Process
Intermediate Structure and Slow Hydration Water Dynamics in Protein Folding Process
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蛋白质折叠过程中的中间结构和缓慢水合水动力学
DOI：
10.3866/pku.whxb20100733
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发表时间：
2010-07-01
影响因子：
10.9
通讯作者：
Zhu Huai-Qiu
中科院分区：
文献类型：
--
作者：
Gao Meng;Yao Xin-Qiu;Zhu Huai-Qiu
长期以来，人们一直认为水合水的缓慢动力学是蛋白质稳定性、功能和折叠的主要决定因素。然而，关于水合水缓慢动力学的起源及其与蛋白质折叠的关系，目前尚缺乏原子水平的机制。使用40个100-ns。以Trp-cage微型蛋白的原子分子动力学模拟为例，分析了蛋白质折叠过程中水合水的动力学，详细探讨了水合水慢动力学的起源。在折叠过程中，即使蛋白质的拓扑结构发生了很大的变化，也存在一定的中间蛋白质结构，其中水合水表现出缓慢的动力学。通过提供丰富的氢键连接和凸拓扑结构的优势，这些结构可以长时间奴役水分子，我们将其称为“居住中心”。居住中心可能是水合作用缓慢的起源。此外，居住中心的分布与折叠过程密切相关。在折叠轨迹中，疏水核周围的残基形成一个主要的驻留中心。这些结果有助于解释蛋白质表面慢水动力学的起源，并可能为进一步的实验研究提供一些见解，通过捕获慢水合水动力学来探测蛋白质折叠过程中重要的中间结构。
The slow dynamics of hydration water has long been recognized as a major determinant of protein stability, function, and folding. However, an atomic level mechanism is still lacking on the origin of the slow dynamics of hydration water and how it is involved in protein folding. Using forty 100-ns all. atom molecular dynamics simulations of the Trp-cage mini-protein as a case study, we analyzed the dynamics of hydration water in the protein folding process to explore the origin of the slow dynamics of hydration water in detail. During the folding process, even if the topological structure of the protein changed greatly, there were certain intermediate protein structures where the hydration water showed slow dynamics. By providing rich hydrogen bond connections and the advantage of a convex topology these structures enslave water molecules for very long time and we refer to these as "residence centers". Residence centers are the possible origin of the slow dynamics of hydration water. Additionally, the distribution of residence centers is closely related to the folding process. In folded trajectories, the residues around the hydrophobic core form a main residence center. These results are helpful in explaining the origin of the slow water dynamics on protein surfaces and may provide some insight into further experimental study to probe important intermediate structures during the process of protein folding by capturing slow hydration water dynamics.