An independent method for the analysis of protein folding kinetics from all-atom molecular dynamics simulations

被引：1

作者：

Marianayagam, NJ ^{[1
]}

Brown, AG ^{[1
]}

Jackson, SE ^{[1
]}

机构：

[1] Univ Cambridge, Dept Chem, Cambridge CB2 1EW, England

来源：

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS | 2005年 / 23卷 / 01期

关键词：

D O I：

10.1080/07391102.2005.10507048

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：

We propose a method for extracting useful kinetic information from all-atom molecular I dynamics simulations of protein folding. By calculating the time correlation functions between the evolution of different structural properties during the course of the simulation we can determine the endpoint of the reaction and the mechanism by which it occurs. As a test of our method we use thermal denaturation simulations on a 76 residue protein, ubiquitin. The method we present should be used in combination with current techniques for analyzing molecular dynamics trajectories.

引用

页码：73 / 76

页数：4

共 13 条

[1]

Allen M. P., 2017, Computer Simulation of Liquids, VSecond, DOI [10.1093/oso/9780198803195.001.0001, DOI 10.1093/OSO/9780198803195.001.0001]

[2] A diagrammatic formulation of the kinetic theory of fluctuations in equilibrium classical fluids. I. The fluctuation basis and the cluster properties of associated functions [J].

Andersen, HC .

JOURNAL OF PHYSICAL CHEMISTRY B, 2002, 106 (33) :8326-8337

[3] Efficient viscosity estimation from molecular dynamics simulation via momentum impulse relaxation [J].

Arya, G ;

Maginn, EJ ;

Chang, HC .

JOURNAL OF CHEMICAL PHYSICS, 2000, 113 (06) :2079-2087

[4] Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography [J].

DePristo, MA ;

de Bakker, PIW ;

Blundell, TL .

STRUCTURE, 2004, 12 (05) :831-838

[5] Understanding hierarchical protein evolution from first principles [J].

Dokholyan, NV ;

Shakhnovich, EI .

JOURNAL OF MOLECULAR BIOLOGY, 2001, 312 (01) :289-307

[6] On the transition coordinate for protein folding [J].

Du, R ;

Pande, VS ;

Grosberg, AY ;

Tanaka, T ;

Shakhnovich, ES .

JOURNAL OF CHEMICAL PHYSICS, 1998, 108 (01) :334-350

[7] ''New view'' of protein folding reconciled with the old through multiple unfolding simulations [J].

Lazaridis, T ;

Karplus, M .

SCIENCE, 1997, 278 (5345) :1928-1931

[8] CHARACTERIZATION OF THE TRANSITION-STATE OF PROTEIN UNFOLDING BY USE OF MOLECULAR-DYNAMICS - CHYMOTRYPSIN INHIBITOR-2 [J].

LI, AJ ;

DAGGETT, V .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1994, 91 (22) :10430-10434

[9] The folding pathway of ubiquitin from all-atom molecular dynamics simulations [J].

Marianayagam, NJ ;

Jackson, SE .

BIOPHYSICAL CHEMISTRY, 2004, 111 (02) :159-171

[10] Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing [J].

Pande, VS ;

Baker, I ;

Chapman, J ;

Elmer, SP ;

Khaliq, S ;

Larson, SM ;

Rhee, YM ;

Shirts, MR ;

Snow, CD ;

Sorin, EJ ;

Zagrovic, B .

BIOPOLYMERS, 2003, 68 (01) :91-109

← 1 2 →