How well can simulation predict protein folding kinetics and thermodynamics?

被引:199
作者
Snow, CD [1 ]
Sorin, EJ
Rhee, YM
Pande, VS
机构
[1] Stanford Univ, Biophys Program, Stanford, CA 94305 USA
[2] Stanford Univ, Dept Chem, Stanford, CA 94305 USA
来源
ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE | 2005年 / 34卷
关键词
folding rate; molecular dynamics; transition state ensemble; P(fold) reaction coordinate;
D O I
10.1146/annurev.biophys.34.040204.144447
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
Simulation of protein folding has come a long way in five years. Notably, new quantitative comparisons with experiments for small, rapidly folding proteins have become possible. As the only way to validate simulation methodology, this achievement marks a significant advance. Here, we detail these recent achievements and ask whether simulations have indeed rendered quantitative predictions in several areas, including protein folding kinetics, thermodynamics, and physics-based methods for structure prediction. We conclude by looking to the future of such comparisons between simulations and experiments.
引用
收藏
页码:43 / 69
页数:27
相关论文
共 122 条
[101]   Mathematical analysis of coupled parallel simulations [J].
Shirts, MR ;
Pande, VS .
PHYSICAL REVIEW LETTERS, 2001, 86 (22) :4983-4987
[102]   All-atom structure prediction and folding simulations of a stable protein [J].
Simmerling, C ;
Strockbine, B ;
Roitberg, AE .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2002, 124 (38) :11258-11259
[103]   Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin [J].
Singhal, N ;
Snow, CD ;
Pande, VS .
JOURNAL OF CHEMICAL PHYSICS, 2004, 121 (01) :415-425
[104]   Absolute comparison of simulated and experimental protein-folding dynamics [J].
Snow, CD ;
Nguyen, N ;
Pande, VS ;
Gruebele, M .
NATURE, 2002, 420 (6911) :102-106
[105]   Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy [J].
Snow, CD ;
Qiu, LL ;
Du, DG ;
Gai, F ;
Hagen, SJ ;
Pande, VS .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (12) :4077-4082
[106]   Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations [J].
Sorin, EJ ;
Rhee, YM ;
Nakatani, BJ ;
Pande, VS .
BIOPHYSICAL JOURNAL, 2003, 85 (02) :790-803
[107]  
SORIN EJ, 2005, IN PRESS BIOPHYS J
[108]   Multidimensional replica-exchange method for free-energy calculations [J].
Sugita, Y ;
Kitao, A ;
Okamoto, Y .
JOURNAL OF CHEMICAL PHYSICS, 2000, 113 (15) :6042-6051
[109]   Replica-exchange molecular dynamics method for protein folding [J].
Sugita, Y ;
Okamoto, Y .
CHEMICAL PHYSICS LETTERS, 1999, 314 (1-2) :141-151
[110]   Describing protein folding kinetics by molecular dynamics simulations.: 2.: Example applications to alanine dipeptide and β-hairpin peptide [J].
Swope, WC ;
Pitera, JW ;
Suits, F ;
Pitman, M ;
Eleftheriou, M ;
Fitch, BG ;
Germain, RS ;
Rayshubski, A ;
Ward, TJC ;
Zhestkov, Y ;
Zhou, R .
JOURNAL OF PHYSICAL CHEMISTRY B, 2004, 108 (21) :6582-6594