A role for CH•••O interactions in protein-DNA recognition
A role for CH•••O interactions in protein-DNA recognition
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DOI：
10.1006/jmbi.1998.1660
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发表时间：
1998-04-17
影响因子：
5.6
通讯作者：
Zhurkin, VB
中科院分区：
文献类型：
--
作者：
Mandel-Gutfreund, Y;Margalit, H;Zhurkin, VB
关于CH…O氢键最近引起了人们极大的兴趣，许多报道表明这些非经典氢键在稳定核酸和蛋白质结构中的重要性。在这里，我们分析了CH…O在蛋白质-DNA界面的相互作用，基于43个蛋白质-DNA复合物的晶体结构。令人惊讶的是，我们发现，密切的分子间CH…涉及胸腺嘧啶甲基和胞嘧啶的C5位置的O接触与涉及氮和氧原子作为供体和受体的蛋白质-DNA氢键的数目相当。对这些密切接触者的几何形状的综合分析表明，它们与其他CH相似。在蛋白质和小分子中发现的O相互作用，以及经典的NH…O氢键。因此，我们认为胞嘧啶的C5和胸腺嘧啶的C5-Met形成相对较弱的CH。与Asp、Asn、Glu、Gln、Ser和Thr形成O氢键，有助于识别的特异性。包括这些相互作用，除了经典的蛋白质-DNA氢键，使简单的结构原理提取氨基酸-碱识别与静电的考虑一致。(C)出版社：Academic Press Limited。
The concept of CH ... O hydrogen bonds has recently gained much interest, with a number of reports indicating the significance of these non-classical hydrogen bonds in stabilizing nucleic acid and protein structures. Here, we analyze the CH ... O interactions in the protein-DNA interface, based on 43 crystal structures of protein-DNA complexes. Surprisingly, we find that the number of close intermolecular CH ... O contacts involving the thymine methyl group and position C5 of cytosine is comparable to the number of protein-DNA hydrogen bonds involving nitrogen and oxygen atoms as donors and acceptors. A comprehensive analysis of the geometries of these close contacts shows that they are similar to other CH ... O interactions found in proteins and small molecules, as well as to classical NH ... O hydrogen bonds. Thus, we suggest that C5 of cytosine and C5-Met of thymine form relatively weak CH ... O hydrogen bonds with Asp, Asn, Glu, Gin, Ser, and Thr, contributing to the specificity of recognition. Including these interactions, in addition to the classical protein-DNA hydrogen bonds, enables the extraction of simple structural principles for amino acid-base recognition consistent with electrostatic considerations. (C) 1998 Academic Press Limited.