Master equation approach to protein folding and kinetic traps

被引:78
作者
Cieplak, M
Henkel, M
Karbowski, J
Banavar, JR
机构
[1] Polish Acad Sci, Inst Phys, PL-02668 Warsaw, Poland
[2] Univ Henri Poincare Nancy 1, Phys Mat Lab, F-54506 Vandoeuvre Nancy, France
[3] Boston Univ, Dept Phys, Ctr Polymer Studies, Boston, MA 02215 USA
[4] Penn State Univ, Dept Phys, University Pk, PA 16802 USA
[5] Penn State Univ, Ctr Phys Mat, University Pk, PA 16802 USA
关键词
D O I
10.1103/PhysRevLett.80.3654
中图分类号
O4 [物理学];
学科分类号
0702 ;
摘要
The master equation for 12-monomer lattice heteropolymers is solved numerically and the time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time follows the Arrhenius law and is governed by the longest relaxation time. For good folders significant kinetic traps appear in the folding funnel, whereas for bad folders the traps also occur in non-native energy valleys.
引用
收藏
页码:3654 / 3657
页数:4
相关论文
共 22 条
[11]  
DILL KA, 1995, PROTEIN SCI, V4, P561
[12]  
HENKEL M, 1998, CONFORMATL INVARIANC, pCH9
[13]   PROTEIN FOLDING FUNNELS - A KINETIC APPROACH TO THE SEQUENCE STRUCTURE RELATIONSHIP [J].
LEOPOLD, PE ;
MONTAL, M ;
ONUCHIC, JN .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1992, 89 (18) :8721-8725
[14]   Emergence of preferred structures in a simple model of protein folding [J].
Li, H ;
Helling, R ;
Tang, C ;
Wingreen, N .
SCIENCE, 1996, 273 (5275) :666-669
[15]   Universality and diversity of the protein folding scenarios: A comprehensive analysis with the aid of a lattice model [J].
Mirny, LA ;
Abkevich, V ;
Shakhnovich, EI .
FOLDING & DESIGN, 1996, 1 (02) :103-116
[16]   TOWARD AN OUTLINE OF THE TOPOGRAPHY OF A REALISTIC PROTEIN-FOLDING FUNNEL [J].
ONUCHIC, JN ;
WOLYNES, PG ;
LUTHEYSCHULTEN, Z ;
SOCCI, ND .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1995, 92 (08) :3626-3630
[17]   HOW DOES A PROTEIN FOLD [J].
SALI, A ;
SHAKHNOVICH, E ;
KARPLUS, M .
NATURE, 1994, 369 (6477) :248-251
[18]   NETWORK THEORY OF MICROSCOPIC AND MACROSCOPIC BEHAVIOR OF MASTER EQUATION SYSTEMS [J].
SCHNAKENBERG, J .
REVIEWS OF MODERN PHYSICS, 1976, 48 (04) :571-585
[19]   FOLDING KINETICS OF PROTEINLIKE HETEROPOLYMERS [J].
SOCCI, ND ;
ONUCHIC, JN .
JOURNAL OF CHEMICAL PHYSICS, 1994, 101 (02) :1519-1528
[20]  
van Kampen N.G, 1981, STOCHASTIC PROCESSES