Interaction between bound water molecules and local protein structures: A statistical analysis of the hydrogen bond structures around bound water molecules
Interaction between bound water molecules and local protein structures: A statistical analysis of the hydrogen bond structures around bound water molecules
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DOI：
10.1002/prot.24953
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发表时间：
2016-01-01
影响因子：
2.9
通讯作者：
Kim, Dongsup
中科院分区：
文献类型：
--
作者：
Hong, Seungpyo;Kim, Dongsup
水分子通过与蛋白质的结构关联，在蛋白质折叠和蛋白质相互作用中发挥重要作用。这种结构关联的例子可以在蛋白质晶体结构中找到，并且通常可以在结构的背景下解释蛋白质的功能。本文报道了蛋白质与水分子相互作用的局部结构的系统分析，以及它们的几何特征的表征。我们首先通过比较水分子在蛋白质-蛋白质相互作用（PPI）界面、晶体接触（CC）界面和非界面区域的偏好，研究了水分子与大的局部相互作用环境的相互作用。发现水分子对PPI和CC界面有较高的偏好。此外，PPI界面上的结合水更有利于与复杂的相互作用结构相结合，这意味着这种水介导的结构可能参与了PPI界面的形成。然后研究了水介导的两两相互作用，并推导了水介导的残渣相互作用势。随后，分析了水分子周围的极性原子类型，并观察了氢键受体的偏好。此外，分析了蛋白质与水相互作用的几何结构，发现蛋白质表面的主要结构呈现平面几何而不是四面体几何。本研究揭示了水-蛋白相互作用的一些以前未被发现的特征，并有望更好地了解蛋白质的结构和功能。蛋白质2016;84:43-51。(c) 2015 Wiley期刊公司
Water molecules play an important role in protein folding and protein interactions through their structural association with proteins. Examples of such structural association can be found in protein crystal structures, and can often explain protein functionality in the context of structure. We herein report the systematic analysis of the local structures of proteins interacting with water molecules, and the characterization of their geometric features. We first examined the interaction of water molecules with a large local interaction environment by comparing the preference of water molecules in three regions, namely, the protein-protein interaction (PPI) interfaces, the crystal contact (CC) interfaces, and the non-interfacial regions. High preference of water molecules to the PPI and CC interfaces was found. In addition, the bound water on the PPI interface was more favorably associated with the complex interaction structure, implying that such water-mediated structures may participate in the shaping of the PPI interface. The pairwise water-mediated interaction was then investigated, and the water-mediated residue-residue interaction potential was derived. Subsequently, the types of polar atoms surrounding the water molecules were analyzed, and the preference of the hydrogen bond acceptor was observed. Furthermore, the geometries of the structures interacting with water were analyzed, and it was found that the major structure on the protein surface exhibited planar geometry rather than tetrahedral geometry. Several previously undiscovered characteristics of water-protein interactions were unfolded in this study, and are expected to lead to a better understanding of protein structure and function. Proteins 2016; 84:43-51. (c) 2015 Wiley Periodicals, Inc.