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Energy transport pathway in proteins: Insights from non-equilibrium molecular dynamics with elastic network model

文献类型： 外文期刊

作者： Wang, Wei Bu 1 ; Liang, Yu 2 ; Zhang, Jing 2 ; Wu, Yi Dong 1 ; Du, Jian Jun 3 ; Li, Qi Ming 2 ; Zhu, Jian Zhuo 1 ; Su, Ji 1 ;

作者机构： 1.Yanshan Univ, Coll Sci, Key Lab Microstruct Mat Phys Hebei Prov, Qinhuangdao 066004, Peoples R China

2.Beijing Inst Biol Prod Co Ltd, Beijing 101111, Peoples R China

3.Beijing Res Ctr Informat Technol Agr, Beijing Key Lab Digital Plant, Beijing 100097, Peoples R China

期刊名称：SCIENTIFIC REPORTS （ 影响因子：4.379； 五年影响因子：5.133 ）

ISSN： 2045-2322

年卷期： 2018 年 8 卷

页码：

收录情况： SCI

摘要： Intra-molecular energy transport between distant functional sites plays important roles in allosterically regulating the biochemical activity of proteins. How to identify the specific intra-molecular signaling pathway from protein tertiary structure remains a challenging problem. In the present work, a nonequilibrium dynamics method based on the elastic network model (ENM) was proposed to simulate the energy propagation process and identify the specific signaling pathways within proteins. In this method, a given residue was perturbed and the propagation of energy was simulated by nonequilibrium dynamics in the normal modes space of ENM. After that, the simulation results were transformed from the normal modes space to the Cartesian coordinate space to identify the intraprotein energy transduction pathways. The proposed method was applied to myosin and the third PDZ domain (PDZ3) of PSD-95 as case studies. For myosin, two signaling pathways were identified, which mediate the energy transductions form the nucleotide binding site to the 50 kDa cleft and the converter subdomain, respectively. For PDZ3, one specific signaling pathway was identified, through which the intra-protein energy was transduced from ligand binding site to the distant opposite side of the protein. It is also found that comparing with the commonly used cross-correlation analysis method, the proposed method can identify the anisotropic energy transduction pathways more effectively.

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