Theory of Free Energy and Entropy in Noncovalent Binding

被引:303
作者
Zhou, Huan-Xiang [1 ,2 ]
Gilson, Michael K. [3 ]
机构
[1] Florida State Univ, Dept Phys, Tallahassee, FL 32306 USA
[2] Florida State Univ, Inst Mol Biophys, Tallahassee, FL 32306 USA
[3] Univ Maryland, Maryland Biotechnol Inst, Ctr Adv Res Biotechnol, Rockville, MD 20850 USA
关键词
MOLECULAR-DYNAMICS SIMULATIONS; STRUCTURE-BASED DESIGN; NMR ORDER PARAMETERS; CONFIGURATIONAL ENTROPY; CONFORMATIONAL ENTROPY; TRANSLATIONAL ENTROPY; FLEXIBLE DOCKING; BIOMOLECULAR SIMULATIONS; VIBRATIONAL ENTROPY; PROTEIN ASSOCIATION;
D O I
10.1021/cr800551w
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
The theory of noncovalent binding was formulated and interpreted in a number of different ways so as to provide a unified rigorous review of the developed material for intermolecular and intramolecular multivalent binding to bring out important physical implications. The study aims to support the development of well-founded models of binding and the meaningful interpretation of experimental data, that include the changes in translation and other entropy components on binding, the implications of correlation for entropy, and multivalency and the relationship between intramolecular and intermolecular binding. The experiment revealed that the entropy is a property of the whole system that may be partioned in useful and rigorous ways through conditional probability distributions that enables the definition of configurational and solvation entropies.
引用
收藏
页码:4092 / 4107
页数:16
相关论文
共 124 条
[1]   NMR ORDER PARAMETERS AND FREE-ENERGY - AN ANALYTICAL APPROACH AND ITS APPLICATION TO COOPERATIVE CA2+ BINDING BY CALBINDIN-D(9K) [J].
AKKE, M ;
BRUSCHWEILER, R ;
PALMER, AG .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993, 115 (21) :9832-9833
[2]   Performance characteristics of biomolecular simulations on high-end systems with multi-core processors [J].
Alam, Sadaf R. ;
Agarwal, Pratul K. ;
Vetter, Jeffrey S. .
PARALLEL COMPUTING, 2008, 34 (11) :640-651
[3]   Energy landscape and transition state of protein-protein association [J].
Alsallaq, Ramzi ;
Zhou, Huan-Xiang .
BIOPHYSICAL JOURNAL, 2007, 92 (05) :1486-1502
[4]  
Amzel LM, 1997, PROTEINS, V28, P144
[5]   On the calculation of entropy from covariance matrices of the atomic fluctuations [J].
Andricioaei, I ;
Karplus, M .
JOURNAL OF CHEMICAL PHYSICS, 2001, 115 (14) :6289-6292
[6]   Polarizable empirical force field for the primary and secondary alcohol series based on the classical drude model [J].
Anisimov, Victor M. ;
Vorobyov, Igor V. ;
Roux, Benoit ;
MacKerell, Alexander D., Jr. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2007, 3 (06) :1927-1946
[7]   Information content of signals using correlation function expansions of the entropy [J].
Attard, P ;
Jepps, OG ;
Marcelja, S .
PHYSICAL REVIEW E, 1997, 56 (04) :4052-4067
[8]   Direct determination of vibrational density of states change on ligand binding to a protein [J].
Balog, E ;
Becker, T ;
Oettl, M ;
Lechner, R ;
Daniel, R ;
Finney, J ;
Smith, JC .
PHYSICAL REVIEW LETTERS, 2004, 93 (02) :028103-1
[9]   Conformational heterogeneity and low-frequency vibrational modes of proteins [J].
Balog, Erika ;
Smith, Jeremy C. ;
Perahia, David .
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2006, 8 (47) :5543-5548
[10]   Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling [J].
Bastug, Turgut ;
Chen, Po-Chia ;
Patra, Swarna M. ;
Kuyucak, Serdar .
JOURNAL OF CHEMICAL PHYSICS, 2008, 128 (15)