Characterization of the dissociation pathways of dichloromethane and glutathione in dichloromethane dehalogenase

二氯甲烷脱卤酶中二氯甲烷和谷胱甘肽解离途径的表征

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.

二氯甲烷(DCM)脱卤酶是在多种环境和生物背景下参与二氯甲烷降解的关键酶.然而,对DCM脱卤酶的配体解结合途径的研究尚不清楚.为了深入地了解DCM和谷胱甘肽(GSH)在DCM脱卤酶中的结合位点和解离途径,采用随机加速分子动力学(RAMD)模拟,驱动DCM和GSH离开活性部位.利用Alphafold2预测蛋白结构,通过对接预测GSH和DCM在结合口袋中的构象.通过长时间的平衡模拟验证该蛋白配体复合物的结构.结果表明,GSH在三种主要途径中最常见,其中一种比另外两种更重要.此外,模拟观察到DCM有一条独特的逃逸途径,鉴定了每个通路的关键残基和蛋白螺旋.该结果可为后续研究DCM脱卤酶解离机理提供理论基础.