All-Atom Direct Folding Simulation for Proteins Using the Accelerated Molecular Dynamics in Implicit Solvent Model

We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. I...

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Published inChinese physics letters Vol. 32; no. 11; pp. 169 - 172
Main Author 李宗超 段莉莉 冯国强 张庆刚
Format Journal Article
LanguageEnglish
Published 01.11.2015
Subjects
Computer simulation
Deviation
Folding
Free energy
Molecular dynamics
Molecular structure
Proteins
Solvents
分子动力学方法
分子模拟
原子
模型
溶剂
蛋白质折叠
计算机辅助药物设计
隐式
Online AccessGet full text
ISSN0256-307X
1741-3540
DOI10.1088/0256-307X/32/11/118701

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Summary:We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.
Bibliography:We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.
LI Zong-Chao, DUAN Li-Li, FENG Guo-Qiang, ZHANG Qing-Gang（ School of Physics and Electronics, Shandong Normal University, Jinan 250014）
11-1959/O4
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SourceType-Scholarly Journals-1
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ISSN:0256-307X
1741-3540
DOI:10.1088/0256-307X/32/11/118701