Accelerated molecular dynamics simulations of protein folding.
Accelerated molecular dynamics simulations of protein folding.
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DOI：
10.1002/jcc.23964
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发表时间：
2015-07-30
影响因子：
3
通讯作者：
McCammon, J. Andrew
中科院分区：
文献类型：
--
作者：
Miao, Yinglong;Feixas, Ferran;Eun, Changsun;McCammon, J. Andrew
Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2–2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the 2nd order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies.
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影响因子：
5.5
作者：
Hess, Berk;Kutzner, Carsten;Lindahl, Erik
通讯作者：
Lindahl, Erik
影响因子：
5.5
作者：
Goetz, Andreas W.;Williamson, Mark J.;Xu, Dong;Poole, Duncan;Le Grand, Scott;Walker, Ross C.
通讯作者：
Walker, Ross C.
影响因子：
5.5
作者：
Doshi, Urmi;Hamelberg, Donald
通讯作者：
Hamelberg, Donald
DOI：
10.1021/jp401962k
发表时间：
2013-10-24
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Deng NJ;Dai W;Levy RM
通讯作者：
Levy RM
影响因子：
5.5
作者：
Cino, Elio A.;Choy, Wing-Yiu;Karttunen, Mikko
通讯作者：
Karttunen, Mikko