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Identification of key residues in protein functional movements by using molecular dynamics simulations combined with a perturbation-response scanning method

Identification of key residues in protein functional movements by using molecular dynamics simulations combined with a perturbation-response scanning method

作     者:Jun-Bao Ma Wei-Bu Wang Ji-Guo Su 马君宝;王韦卜;苏计国

作者机构:Key Laboratory for Microstructural Material Physics of Hebei ProvinceSchool of ScienceYanshan UniversityQinhuangdao 066004China 

出 版 物:《Chinese Physics B》 (中国物理B(英文版))

年 卷 期:2021年第30卷第10期

页      面:665-672页

核心收录:

学科分类:0710[理学-生物学] 071010[理学-生物化学与分子生物学] 081704[工学-应用化学] 07[理学] 08[工学] 0817[工学-化学工程与技术] 

主  题:protein functional movements molecular dynamics simulations perturbation-response scanning method 

摘      要:The realization of protein functional movement is usually accompanied by specific conformational changes,and there exist some key residues that mediate and control the functional motions of proteins in the allosteric *** the present work,the perturbation-response scanning method developed by our group was combined with the molecular dynamics(MD)simulation to identify the key residues controlling the functional movement of *** our method,a physical quantity that is directly related to protein specific function was introduced,and then based on the MD simulation trajectories,the perturbation-response scanning method was used to identify the key residues for functional motions,in which the residues that highly correlated with the fluctuation of the function-related quantity were identified as the key residues controlling the specific functional motions of the *** protein systems,i.e.,the heat shock protein 70 and glutamine binding protein,were selected as case studies to validate the effectiveness of our *** calculated results are in good agreement with the experimental *** location of the key residues in the two proteins are similar,indicating the similar mechanisms behind the performance of their biological functions.

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