Mandel-Gutfreund Y, Margalit H, Jernigan R L, Zhurkin V B
Department of Molecular Genetics and Biotechnology, The Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel.
J Mol Biol. 1998 Apr 17;277(5):1129-40. doi: 10.1006/jmbi.1998.1660.
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, Gln, 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.
CH...O氢键的概念最近备受关注，大量报告表明这些非经典氢键在稳定核酸和蛋白质结构方面具有重要意义。在此，我们基于43个蛋白质-DNA复合物的晶体结构，分析了蛋白质-DNA界面中的CH...O相互作用。令人惊讶的是，我们发现涉及胸腺嘧啶甲基和胞嘧啶C5位的紧密分子间CH...O接触的数量，与涉及氮和氧原子作为供体和受体的蛋白质-DNA氢键数量相当。对这些紧密接触的几何结构进行全面分析表明，它们与蛋白质和小分子中发现的其他CH...O相互作用以及经典的NH...O氢键相似。因此，我们认为胞嘧啶的C5位和胸腺嘧啶的C5-甲基与天冬氨酸、天冬酰胺、谷氨酸、谷氨酰胺、丝氨酸和苏氨酸形成相对较弱的CH...O氢键，这有助于识别的特异性。除了经典的蛋白质-DNA氢键外，纳入这些相互作用能够提取出与静电考虑相一致的氨基酸-碱基识别的简单结构原则。
