Peptide folding kinetics from replica exchange molecular dynamics

被引:104
作者
Buchete, Nicolae-Viorel [1 ]
Hummer, Gerhard [1 ]
机构
[1] NIDDKD, Chem Phys Lab, NIH, Bethesda, MD 20892 USA
来源
PHYSICAL REVIEW E | 2008年 / 77卷 / 03期
关键词
D O I
10.1103/PhysRevE.77.030902
中图分类号
O35 [流体力学]; O53 [等离子体物理学];
学科分类号
070204 ; 080103 ; 080704 ;
摘要
We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica exchanges, we estimate short-time propagators in conformation space and use them to construct a master equation. For a helical peptide in explicit water, we determine the rates of transitions both locally between microscopic conformational states and globally for folding and unfolding. We show that accurate rates in the similar to 1/(100 ns) to similar to/(1 ns) range can be obtained from REMD with exchange times of 5 ps, in excellent agreement with results from long equilibrium molecular dynamics.
引用
收藏
页数:4
相关论文
共 30 条
[1]   Protein folding pathways from replica exchange simulations and a kinetic network model [J].
Andrec, M ;
Felts, AK ;
Gallicchio, E ;
Levy, RM .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (19) :6801-6806
[2]   The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics [J].
Becker, OM ;
Karplus, M .
JOURNAL OF CHEMICAL PHYSICS, 1997, 106 (04) :1495-1517
[3]   Ensemble of transition states for two-state protein folding from the eigenvectors of rate matrices [J].
Berezhkovskii, A ;
Szabo, A .
JOURNAL OF CHEMICAL PHYSICS, 2004, 121 (18) :9186-9187
[4]   Novel methods of sampling phase space in the simulation of biological systems [J].
Berne, BJ ;
Straub, JE .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 1997, 7 (02) :181-189
[5]   Diffusive model of protein folding dynamics with Kramers turnover in rate [J].
Best, RB ;
Hummer, G .
PHYSICAL REVIEW LETTERS, 2006, 96 (22)
[6]   Mean first-passage time calculations for the coil-to-helix transition: The active helix Ising model [J].
Buchete, NV ;
Straub, JE .
JOURNAL OF PHYSICAL CHEMISTRY B, 2001, 105 (28) :6684-6697
[7]  
BUCHETE NV, IN PRESS J PHYS CH B, P58302
[8]   Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics [J].
Chodera, John D. ;
Singhal, Nina ;
Pande, Vijay S. ;
Dill, Ken A. ;
Swope, William C. .
JOURNAL OF CHEMICAL PHYSICS, 2007, 126 (15)
[9]   Essential dynamics of reversible peptide folding:: Memory-free conformational dynamics governed by internal hydrogen bonds [J].
de Groot, BL ;
Daura, X ;
Mark, AE ;
Grubmüller, H .
JOURNAL OF MOLECULAR BIOLOGY, 2001, 309 (01) :299-313
[10]   On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction [J].
Fukunishi, H ;
Watanabe, O ;
Takada, S .
JOURNAL OF CHEMICAL PHYSICS, 2002, 116 (20) :9058-9067