Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation  

作　　者：Yong-Shun Song Xin Zhou Wei-Mou Zheng Yan-Ting Wang 宋永顺;周昕;郑伟谋;王延颋(School of Physical Sciences, University of Chinese Academy of Sciences;Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences)

机构地区：[1]School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China [2]Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China

出　　处：《Communications in Theoretical Physics》2017年第7期137-148,共12页理论物理通讯（英文版）

基　　金：Supported by the National Basic Research Program of China under Grant No.2013CB932804;the National Natural Science Foundation of China under Grant No.11421063;the CAS Biophysics Interdisciplinary Innovation Team Project

摘　　要：To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics （MD） simulation in aqueous solution four fragments cut out of a protein G, including one a-helix （seqB： KVFKQYAN）, two -turns （seqA： LNGKTLKG and seqC： YDDATKTF）, and one -strand （seqD： DGEWTYDD）. The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-#s equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics.

关 键 词：protein folding molecular dynamics simulation structure prediction 

分 类 号：Q51[生物学—生物化学] TG111.4[金属学及工艺—物理冶金]