蛋白质-DNA复合物结合区的柔性以及界面水的结构和有序性。,Journal of Chemical Information and Modeling

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蛋白质-DNA复合物结合区的柔性以及界面水的结构和有序性。
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2019-10-15 , DOI: 10.1021/acs.jcim.9b00685
Sandip Mondal , Sanjoy Bandyopadhyay

蛋白质和DNA之间的非共价相互作用对于理解生物体中的不同生物活性非常重要。一个重要的问题是蛋白质如何识别靶标DNA以及所得的蛋白质-DNA复合物对其周围水合环境的影响。在这项研究中，我们已经对由λ阻遏蛋白的α-螺旋N端结构域及其操纵子DNA的二聚体形式形成的蛋白质-DNA复合物进行了原子分子动力学模拟。已详细研究了蛋白质残基和结合中涉及的DNA成分的局部异质灵活性以及围绕这些残基的水的微观结构和有序性。计算表明界面处同时存在高度有序和无序的水分子。发现一部分双配位水分子在界面处表现出高度的有序性，而无规取向的水分子则与三个水分子配位。已经发现这种作用更多地围绕着以复合状态接触的蛋白质和DNA残基。我们认为，这种高度有序的二配位水分子很可能充当粘合剂，促进蛋白质-DNA复合物的形成并保持其结构稳定性。

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Flexibility of the Binding Regions of a Protein-DNA Complex and the Structure and Ordering of Interfacial Water.

Noncovalent interactions between protein and DNA are important to comprehend different biological activities in living organisms. One important issue is how the protein identifies the target DNA and the influence of the resulting protein-DNA complex on the hydration environment around it. In this study, we have carried out atomistic molecular dynamics simulations of the protein-DNA complex formed by the dimeric form of the α-helical N-terminal domain of the λ-repressor protein with its operator DNA. Local heterogeneous flexibilities of the residues of the protein and the DNA components that are involved in binding and the microscopic structure and ordering of water around those have been investigated in detail. The calculations revealed concurrent existence of highly ordered as well as disordered water molecules at the interface. It is found that a fraction of doubly coordinated water molecules exhibit high degree of ordering at the interface, while the randomly oriented ones are coordinated with three water molecules. The effect has been found to be more around the protein and DNA residues that are in contact in the complexed state. We believe that such highly ordered two-coordinated water molecules are likely to act as an adhesive to facilitate the formation of a protein-DNA complex and maintain its structural stability.

更新日期：2019-10-16

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