物理化学学报2017，Vol.33Issue(4)：691-708,18.DOI:10.3866/PKU.WHXB201612191
酶催化过程的全程模拟
Global Simulations of Enzymatic Catalysis
摘要
Abstract
Enzymatic catalytic processes generally involve substrate delivery,selective catalytic reaction,and product release.Owing to the complex protein environment effect,any nonchemical or chemical step may determine the enzyme activity.Herein,to comprehensively understand enzymatic activity,extensive combined quantum mechanics/molecular mechanics (QM/MM) and molecular mechanics (MM) molecular dynamics (MD) simulations were carried out on several kinds of enzymes.Possible reaction mechanisms,roles of the conserved residues,and effects of the protein environment on the whole enzymatic process are discussed in detail,which will enrich the knowledge of reactivity in proteins.With the improvement and development of multiscale models and computational methods,it is expected that global simulations of extremely large and complicated enzymes will enable and lend support to enzyme engineering.关键词
酶催化/底物输运/自由能计算/QM/MM MD模拟/随机加速动力学模拟Key words
Enzymatic catalysis/Substrate delivery/Free energy calculations/QM/MM MD simulation/Random acceleration molecular dynamics (DAMD) simulation分类
化学化工引用本文复制引用
赵媛,曹泽星..酶催化过程的全程模拟[J].物理化学学报,2017,33(4):691-708,18.基金项目
The project was supported by the National Natural Science Foundation of China (21133007,21373164,21172053).国家自然科学基金(21133007,21373164,21172053)资助项目 （21133007,21373164,21172053）
