DICP OpenIR
Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations
Zhang, Yuxin1,2,3; Huang, Xiaoqin2; Han, Keli1; Zheng, Fang2,3; Zhan, Chang-Guo2,3
关键词Esterase Cocaine Binding Process Energy Barrier
刊名CHEMICO-BIOLOGICAL INTERACTIONS
2016-11-25
DOI10.1016/j.cbi.2016.05.011
259页:142-147
收录类别SCI ; ISTP
文章类型Article
WOS标题词Science & Technology ; Life Sciences & Biomedicine
类目[WOS]Biochemistry & Molecular Biology ; Pharmacology & Pharmacy ; Toxicology
关键词[WOS]HIGH-ACTIVITY MUTANTS ; BUTYRYLCHOLINESTERASE-CATALYZED HYDROLYSIS ; FUNDAMENTAL REACTION-MECHANISM ; PARTICLE-MESH EWALD ; TRANSITION-STATES ; PERTURBATION SIMULATION ; (-)-COCAINE HYDROLYSIS ; COMPUTATIONAL DESIGN ; REACTION PATHWAY ; HYDROLASE
英文摘要The combined molecular dynamics (MD) and potential of mean force (PMF) simulations have been performed to determine the free energy profile of the CocE)-(+)-cocaine binding process in comparison with that of the corresponding CocE-(-)-cocaine binding process. According to the MD simulations, the equilibrium CocE-(+)-cocaine binding mode is similar to the CocE-(-)-cocaine binding mode. However, based on the simulated free energy profiles, a significant free energy barrier (similar to 5 kcal/mol) exists in the CocE-(+)-cocaine binding process whereas no obvious free energy barrier exists in the CocE-(-)-cocaine binding process, although the free energy barrier of similar to 5 kcal/mol is not high enough to really slow down the CocE-(+)-cocaine binding process. In addition, the obtained free energy profiles also demonstrate that (+)-cocaine and (-)-cocaine have very close binding free energies with CocE, with a negligible difference (similar to 0.2 kcal/mol), which is qualitatively consistent with the nearly same experimental K-M values of the CocE enzyme for (+)-cocaine and (-)-cocaine. The consistency between the computational results and available experimental data suggests that the mechanistic insights obtained from this study are reasonable. (C) 2016 Elsevier Ireland Ltd. All rights reserved.
语种英语
WOS记录号WOS:000388843500014
引用统计
文献类型期刊论文
条目标识符http://cas-ir.dicp.ac.cn/handle/321008/150421
专题中国科学院大连化学物理研究所
作者单位1.Chinese Acad Sci, State Key Lab Mol React Dynam, Dalian Inst Chem Phys, Zhongshan Rd 457, Dalian 116023, Peoples R China
2.Univ Kentucky, Coll Pharm, Mol Modeling & Biopharmaceut Ctr, 789 South Limestone St, Lexington, KY 40536 USA
3.Univ Kentucky, Coll Pharm, Dept Pharmaceut Sci, 789 South Limestone St, Lexington, KY 40536 USA
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Zhang, Yuxin,Huang, Xiaoqin,Han, Keli,et al. Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations[J]. CHEMICO-BIOLOGICAL INTERACTIONS,2016,259:142-147.
APA Zhang, Yuxin,Huang, Xiaoqin,Han, Keli,Zheng, Fang,&Zhan, Chang-Guo.(2016).Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations.CHEMICO-BIOLOGICAL INTERACTIONS,259,142-147.
MLA Zhang, Yuxin,et al."Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations".CHEMICO-BIOLOGICAL INTERACTIONS 259(2016):142-147.
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