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A role for CH•••O interactions in protein-DNA recognition
被引:150
作者:
Mandel-Gutfreund, Y
[1
]
Margalit, H
[1
]
Jernigan, RL
[1
]
Zhurkin, VB
[1
]
机构:
[1] Hebrew Univ Jerusalem, Hadassah Med Sch, Dept Mol Genet & Biotechnol, IL-91120 Jerusalem, Israel
基金:
以色列科学基金会;
关键词:
protein-DNA recognition;
hydrogen bonds;
CH center dot center dot center dot O interactions;
electrostatics;
D O I:
10.1006/jmbi.1998.1660
中图分类号:
Q5 [生物化学];
Q7 [分子生物学];
学科分类号:
071010 ;
081704 ;
摘要:
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.
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页码:1129 / 1140
页数:12
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