首页|期刊导航|南京大学学报(自然科学版)|Characterization of the dissociation pathways of dichloromethane and glutathione in dichloromethane dehalogenase

Characterization of the dissociation pathways of dichloromethane and glutathione in dichloromethane dehalogenaseOA北大核心CSTPCD

中文摘要

Dichloromethane(DCM)dehalogenase stands as a crucial enzyme implicated in the degradation of methylene chloride across diverse environmental and biological contexts.However,the unbinding pathways of ligands from DCM dehalogenase remain unexplored.In order to gain a deeper understanding of the binding sites and dissociation pathways of dichloromethane(DCM)and glutathione(GSH)from the DCM dehalogenase,random accelerated molecular dynamics(RAMD)simulations were performed,in which DCM and GSH were forced to leave the active site.The protein structure was predicted using Alphafold2,and the conformations of GSH and DCM in the binding pocket were predicted by docking.A long equilibrium simulation was conducted to validate the structure of the complex.The results show that GSH is most commonly observed in three main pathways,one of which is more important than the other two.In addition,DCM was observed to escape along a unique pathway.The key residues and protein helices of each pathway were identified.The results can provide a theoretical foundation for the subsequent dissociation mechanism of DCM dehalogenase.

Gao Xudan;Zhang Huizhu;Mei Ye;

State Key Laboratory of Precision Spectroscopy,School of Physics and Electronic Science,East China Normal University,Shanghai200241,ChinaState Key Laboratory of Precision Spectroscopy,School of Physics and Electronic Science,East China Normal University,Shanghai200241,China NYU-ECNU Center for Computational Chemistry at NYU Shanghai,Shanghai200062,China Collaborative Innovation Center of Extreme Optics,Shanxi University,Taiyuan,030006,China

化学

DCM dehalogenaseGSHAlphafold2RAMDunbinding pathways

《南京大学学报(自然科学版)》 2024 (004)

P.651-660 / 10

National Natural Science Foundation of China(22073030);the Oriental Scholars of Shanghai Universities。

10.13232/j.cnki.jnju.2024.04.012

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