The role of water in protein-DNA recognition

被引:178
作者
Jayaram, B
Jain, T
机构
[1] Indian Inst Technol, Dept Chem, New Delhi 110016, India
[2] Indian Inst Technol, Supercomp Facil Bioinformat & Computat Biol, New Delhi 110016, India
来源
ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE | 2004年 / 33卷
关键词
hydrogen bonds; water-mediated recognition; electrostatic screening; packing densities; thermodynamic view; protein-DNA interactions;
D O I
10.1146/annurev.biophys.33.110502.140414
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
Is it by design or by default that water molecules are observed at the interfaces of some protein-DNA complexes? Both experimental and theoretical studies on the thermodynamics of protein-DNA binding overwhelmingly support the extended hydrophobic view that water release from interfaces favors binding. Structural and energy analyses indicate that the waters that remain at the interfaces of protein-DNA complexes ensure liquid-state packing densities, screen the electrostatic repulsions between like charges (which seems to be by design), and in a few cases act as linkers between complementary charges on the biomolecules (which may well be by default). This review presents a survey of the current literature on water in protein-DNA complexes and a critique of various interpretations of the data in the context of the role of water in protein-DNA binding and principles of protein-DNA recognition in general.
引用
收藏
页码:343 / 361
页数:21
相关论文
共 149 条
[1]   POLY-ELECTROLYTE THEORIES AND THEIR APPLICATIONS TO DNA [J].
ANDERSON, CF ;
RECORD, MT .
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, 1982, 33 :191-222
[2]   Hydration of DNA [J].
Berman, Helen M. .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 1991, 1 (03) :423-427
[3]   HYDRATION OF DNA - TAKE 2 [J].
BERMAN, HM .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 1994, 4 (03) :345-350
[4]   The Protein Data Bank [J].
Berman, HM ;
Westbrook, J ;
Feng, Z ;
Gilliland, G ;
Bhat, TN ;
Weissig, H ;
Shindyalov, IN ;
Bourne, PE .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242
[5]  
BERMAN HM, 1998, HDB NUCL ACID STRUCT, P295
[6]   PROTEIN DATA BANK - COMPUTER-BASED ARCHIVAL FILE FOR MACROMOLECULAR STRUCTURES [J].
BERNSTEIN, FC ;
KOETZLE, TF ;
WILLIAMS, GJB ;
MEYER, EF ;
BRICE, MD ;
RODGERS, JR ;
KENNARD, O ;
SHIMANOUCHI, T ;
TASUMI, M .
JOURNAL OF MOLECULAR BIOLOGY, 1977, 112 (03) :535-542
[7]  
BEVERIDGE DL, 1993, WATER BIOL MACROMOLE, V17, P165
[8]   BOUND WATER-MOLECULES AND CONFORMATIONAL STABILIZATION HELP MEDIATE AN ANTIGEN-ANTIBODY ASSOCIATION [J].
BHAT, TN ;
BENTLEY, GA ;
BOULOT, G ;
GREENE, MI ;
TELLO, D ;
DALLACQUA, W ;
SOUCHON, H ;
SCHWARZ, FP ;
MARIUZZA, RA ;
POLJAK, RJ .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1994, 91 (03) :1089-1093
[9]   Binding of proteins to the minor groove of DNA: What are the structural and energetic determinants for kinking a basepair step? [J].
Bosch, D ;
Campillo, M ;
Pardo, L .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2003, 24 (06) :682-691
[10]   Features of a Smad3 MH1-DNA complex -: Roles of water and zinc in DNA binding [J].
Chai, JJ ;
Wu, JW ;
Yan, N ;
Massagué, J ;
Pavletich, NP ;
Shi, YG .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2003, 278 (22) :20327-20331