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.
引用
收藏
页码:1129 / 1140
页数:12
相关论文
共 70 条
  • [1] RECOGNITION OF A DNA OPERATOR BY THE REPRESSOR OF PHAGE-434 - A VIEW AT HIGH-RESOLUTION
    AGGARWAL, AK
    RODGERS, DW
    DROTTAR, M
    PTASHNE, M
    HARRISON, SC
    [J]. SCIENCE, 1988, 242 (4880) : 899 - 907
  • [2] Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    Bahar, I
    Jernigan, RL
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1997, 266 (01) : 195 - 214
  • [3] REFINED 1.8 ANGSTROM CRYSTAL-STRUCTURE OF THE LAMBDA-REPRESSOR OPERATOR COMPLEX
    BEAMER, LJ
    PABO, CO
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1992, 227 (01) : 177 - 196
  • [4] Crystallographic evidence for C-alpha-H center dot center dot center dot O=C hydrogen bonds in a collagen triple helix
    Bella, J
    Berman, HM
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1996, 264 (04) : 734 - 742
  • [5] Inter-strand C-H center dot center dot center dot O hydrogen bonds stabilizing four-stranded intercalated molecules: Stereoelectronic effects of 04' in cytosine-rich DNA
    Berger, I
    Egli, M
    Rich, A
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1996, 93 (22) : 12116 - 12121
  • [6] THE NUCLEIC-ACID DATABASE - A COMPREHENSIVE RELATIONAL DATABASE OF 3-DIMENSIONAL STRUCTURES OF NUCLEIC-ACIDS
    BERMAN, HM
    OLSON, WK
    BEVERIDGE, DL
    WESTBROOK, J
    GELBIN, A
    DEMENY, T
    HSIEH, SH
    SRINIVASAN, AR
    SCHNEIDER, B
    [J]. BIOPHYSICAL JOURNAL, 1992, 63 (03) : 751 - 759
  • [7] STRUCTURE OF PVUII ENDONUCLEASE WITH COGNATE DNA
    CHENG, XD
    BALENDIRAN, K
    SCHILDKRAUT, I
    ANDERSON, JE
    [J]. EMBO JOURNAL, 1994, 13 (17) : 3927 - 3935
  • [8] CRYSTAL-STRUCTURE OF A P53 TUMOR-SUPPRESSOR DNA COMPLEX - UNDERSTANDING TUMORIGENIC MUTATIONS
    CHO, YJ
    GORINA, S
    JEFFREY, PD
    PAVLETICH, NP
    [J]. SCIENCE, 1994, 265 (5170) : 346 - 355
  • [9] SELECTION OF DNA-BINDING SITES FOR ZINC FINGERS USING RATIONALLY RANDOMIZED DNA REVEALS CODED INTERACTIONS
    CHOO, Y
    KLUG, A
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1994, 91 (23) : 11168 - 11172
  • [10] CO-CRYSTAL STRUCTURE OF THE HNF-3/FORK HEAD DNA-RECOGNITION MOTIF RESEMBLES HISTONE-H5
    CLARK, KL
    HALAY, ED
    LAI, ES
    BURLEY, SK
    [J]. NATURE, 1993, 364 (6436) : 412 - 420