期刊
STRUCTURE
卷 16, 期 7, 页码 1010-1018出版社
CELL PRESS
DOI: 10.1016/j.str.2008.03.013
关键词
-
资金
- NIDA NIH HHS [R41 DA032293] Funding Source: Medline
- NIDCR NIH HHS [U01 DE017018] Funding Source: Medline
- NIGMS NIH HHS [R01 GM080742-01A2, R01 GM080742, R01GM080742] Funding Source: Medline
Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. We performed folding simulations of six small proteins (20-60 residues) with distinct native structures by the replica exchange method. In all cases, native or near-native states were reached in simulations. For three small proteins, multiple folding transitions are observed, and the computationally characterized thermodynamics are in qualitative agreement with experiments. The predictive power of all-atom DMD highlights the importance of environment-dependent hydrogen bond interactions in modeling protein folding. The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes and applied to protein engineering and design of protein-protein interactions.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据