Force Distribution Analysis on MetJ Based on All-atom MD Simulation
作者单位：College of Chemistry and Molecular Engineering Peking University
会议名称：《2019中国化学会第十五届全国计算（机）化学学术会议》
会议日期：2019年
学科分类：081704[工学-应用化学] 07[理学] 08[工学] 0817[工学-化学工程与技术] 070303[理学-有机化学] 0703[理学-化学]
关 键 词：Force distribution analysis Molecular Dynamic simulation Elastic Network Model Methionine repressor Allosteric regulation
摘 要：The forces between atoms(or molecules) have important influence on protein properties. They cause conformational change when a protein binds with ligands, and thus affect the protein activity and are closely related to mechanisms of protein regulation in cells. In the past studies, people have paid much attention to the structure of proteins, but less attention has been paid to the forces. In this study, the force properties of MetJ, a methionine inhibitor, were investigated by means of all-atom Molecular Dynamics(MD) simulation and theoretical analysis. The decomposition of multi-body forces are analyzed, and a scheme was proposed where three-body and four-body forces can be decomposed into a sum of the pairwise forces along inter-atomic direction. An anisotropic network model(ANM) was used to calculate the residual force F and position fluctuation △R in Met J, which were shown to negatively correlated with each other and satisfy a universal relationship of