An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

被引:411
作者
Kortemme, T
Morozov, AV
Baker, D
机构
[1] Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA
[2] Univ Washington, Dept Biochem, Seattle, WA 98195 USA
[3] Univ Washington, Dept Phys, Seattle, WA 98195 USA
基金
美国国家卫生研究院;
关键词
hydrogen bond; electrostatics; protein docking; protein design; free energy function;
D O I
10.1016/S0022-2836(03)00021-4
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
Hydrogen bonding is a key contributor to the specificity of intramolecular and intermolecular interactions in biological systems. Here, we develop an orientation-dependent hydrogen bonding potential based on the geometric characteristics of hydrogen bonds in high-resolution protein crystal structures, and evaluate it using four tests related to the prediction and design of protein structures and protein-protein complexes. The new potential is superior to the widely used Coulomb model of hydrogen bonding in prediction of the sequences of proteins and protein-protein interfaces from their structures, and improves discrimination of correctly docked protein-protein complexes from large sets of alternative structures. (C) 2003 Elsevier Science Ltd. All rights reserved.
引用
收藏
页码:1239 / 1259
页数:21
相关论文
共 65 条
[1]   PRINCIPLES THAT GOVERN FOLDING OF PROTEIN CHAINS [J].
ANFINSEN, CB .
SCIENCE, 1973, 181 (4096) :223-230
[2]   HYDROGEN-BONDING IN GLOBULAR-PROTEINS [J].
BAKER, EN ;
HUBBARD, RE .
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 1984, 44 (02) :97-179
[3]  
Bonneau R, 2001, PROTEINS, P119
[4]   CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS [J].
BROOKS, BR ;
BRUCCOLERI, RE ;
OLAFSON, BD ;
STATES, DJ ;
SWAMINATHAN, S ;
KARPLUS, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) :187-217
[5]   POLAR HYDROGEN POSITIONS IN PROTEINS - EMPIRICAL ENERGY PLACEMENT AND NEUTRON-DIFFRACTION COMPARISON [J].
BRUNGER, AT ;
KARPLUS, M .
PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1988, 4 (02) :148-156
[6]   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
[7]   Protein docking along smooth association pathways [J].
Camacho, CJ ;
Vajda, S .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (19) :10636-10641
[8]   Design, activity, and structure of a highly specific artificial endonuclease [J].
Chevalier, BS ;
Kortemme, T ;
Chadsey, MS ;
Baker, D ;
Monnat, RJ ;
Stoddard, BL .
MOLECULAR CELL, 2002, 10 (04) :895-905
[9]   A 2ND GENERATION FORCE-FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC-ACIDS, AND ORGANIC-MOLECULES [J].
CORNELL, WD ;
CIEPLAK, P ;
BAYLY, CI ;
GOULD, IR ;
MERZ, KM ;
FERGUSON, DM ;
SPELLMEYER, DC ;
FOX, T ;
CALDWELL, JW ;
KOLLMAN, PA .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (19) :5179-5197
[10]   Automated design of the surface positions of protein helices [J].
Dahiyat, BI ;
Gordon, DB ;
Mayo, SL .
PROTEIN SCIENCE, 1997, 6 (06) :1333-1337