Hydrogen bonds in protein-DNA complexes: Where geometry meets plasticity

被引：75

作者：

Coulocheri, Stavroula A. ^{[1
]}

Pigis, Diomidis G. ^{[1
]}

Papavassiliou, Kostas A. ^{[1
]}

Papavassiliou, Athanasios G. ^{[1
]}

机构：

[1] Univ Athens, Sch Med, Dept Biol Chem, GR-11527 Athens, Greece

来源：

BIOCHIMIE | 2007年 / 89卷 / 11期

关键词：

hydrogen bond (H-bond); protein-DNA recognition; hydrogen-bonding patterns; specificity; recognition code;

D O I：

10.1016/j.biochi.2007.07.020

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：

Recognition of a DNA sequence by a protein is achieved by interface-coupled chemical and shape complementation. This complementation between the two Molecules is clearly directional and is determined by the specific chemical contacts including mainly hydrogen bonds. Directionality is an instrumental property of hydrogen bonding as it influences molecular conformations, which also affects DNA-protein recognition. The prominent elements in the recognition of a particular DNA sequence by a protein are the hydrogen-bond donors and acceptors of the base pairs into the grooves of the DNA that must interact with complementary moieties of the protein partner. Protein side chains make most of the crucial contacts through bidentate and complex hydrogen-bonding interactions with DNA base edges hence conferring remarkable specificity. (C) 2007 Elsevier Masson SAS. All rights reserved.

引用

页码：1291 / 1303

页数：13

共 68 条

[1] Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information [J].

Ahmad, S ;

Gromiha, MM ;

Sarai, A .

BIOINFORMATICS, 2004, 20 (04) :477-486

[2] Is there a code for protein-DNA recognition? Probab(ilistical)ly ... [J].

Benos, PV ;

Lapedes, AS ;

Stormo, GD .

BIOESSAYS, 2002, 24 (05) :466-475

[3] Stair motifs at protein-DNA interfaces:: Nonadditivity of H-bond, stacking, and cation-π interactions [J].

Biot, C ;

Wintjens, R ;

Rooman, M .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2004, 126 (20) :6220-6221

[4] Hydrogen bond energetics:: A simulation and statistical analysis of N-methyl acetamide (NMA), water, and human lysozyme [J].

Buck, M ;

Karplus, M .

JOURNAL OF PHYSICAL CHEMISTRY B, 2001, 105 (44) :11000-11015

[5] A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys [J].

Chen, Y ;

Kortemme, T ;

Robertson, T ;

Baker, D ;

Varani, G .

NUCLEIC ACIDS RESEARCH, 2004, 32 (17) :5147-5162

[6] Physical basis of a protein-DNA recognition code [J].

Choo, Y ;

Klug, A .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 1997, 7 (01) :117-125

[7]

Coulson C. A., 1957, RESEARCH, V10, P149

[8] THE OCCURRENCE OF C-H-CENTER-DOT-CENTER-DOT-CENTER-DOT-O HYDROGEN-BONDS IN PROTEINS [J].

DEREWENDA, ZS ;

LEE, L ;

DEREWENDA, U .

JOURNAL OF MOLECULAR BIOLOGY, 1995, 252 (02) :248-262

[9] THE C-H...O HYDROGEN-BOND IN CRYSTALS - WHAT IS IT [J].

DESIRAJU, GR .

ACCOUNTS OF CHEMICAL RESEARCH, 1991, 24 (10) :290-296

[10]

DONOHUE J, 1938, STRUCTURAL CHEM MOL, P443

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