基于分子动力学模拟的VmoLac非特异性底物催化活性的理论研究  

Theoretical Study of the Catalytic Activity of VmoLac Non-specific Substrates Based on Molecular Dynamics Simulations

作　　者：李聪聪 刘明皓 韩佳睿 朱镜璇 韩葳葳[1] 李婉南[1] LI Congcong;LIU Minghao;HAN Jiarui;ZHU Jingxuan;HAN Weiwei;LI Wannan(Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education,School of Life Science,Jilin University,Changchun 130012,China)

机构地区：[1]吉林大学分子酶学工程教育部重点实验室,生命科学学院,长春130012

出　　处：《高等学校化学学报》2021年第8期2518-2528,共11页Chemical Journal of Chinese Universities

基　　金：吉林省科技发展计划项目批准号资助~。

摘　　要：采用分子动力学模拟方法研究了VmoLac的非特异性底物催化活性,模拟了VmoLac/3-oxo-C10-AHL,VmoLac/3-oxo-C6-AHL,VmoLac/γ-nonalacton和VmoLac/ethyl-paraoxon 4个复合物.分析了分子动力学模拟过程中不同底物结合引起VmoLac构象变化的主要原因.结果表明,3-oxo-C10-AHL和γ-nonalacton的结合会使VmoLac活性口袋附近的Loop8结构域运动明显,利于底物结合在Loop8疏水通道外侧进而引起催化反应;VmoLac活性口袋周围的门控残基W264和Y230之间距离的变化会影响底物的结合;Y98与长链内酯、壬内酯的羰基碳之间形成的进攻距离较小,而与短链内酯的羰基碳以及对氧磷的磷原子之间形成的进攻距离较大,短的距离更有利于发生亲核进攻反应;D257是引发VmoLac催化反应的关键残基;当VmoLac催化3-oxo-C10-AHL和γ-nonalacton时,D257与极化水以及底物形成更多的氢键,使底物与酶更容易结合.从理论催化机制角度解释了VmoLac催化长链内酯(3-oxo-C10-AHL)比短链内酯(3-oxo-C6-AHL)的能力强,催化壬内酯(γ-nonalacton)比对氧磷(ethyl-paraoxon)能力强的原因,为实验结果提供了理论证明.The molecular dynamics simulation method was used to study the catalytic activity of VmoLac non-specific substrates.Four systems of VmoLac/3-oxo-C10-AHL,VmoLac/3-oxo-C6-AHL,VmoLac/γ-nonalacton and VmoLac/ethyl-paraoxon complexs were simulated.The main reasons for the conformational changes caused by the binding of different substrates to VmoLac were analyzed.The analysis results show that the 3-oxo-C10-AHL andγ-nonalacton combination can make the active pocket near Loop8 structure domain motion obviously.The flexible conformation made it easier for the substrate to bind to the outside of the hydrophobic channel of Loop8,which was conducive to the catalytic reaction.VmoLac activity around the pocket gating residues W264 and Y230 changes will affect the distance between the combination of the substrate.The distance between Y98 and the carbonyl carbon of long-chain lactone and nonolactone was relatively small,while the distance between Y98 and the carbonyl carbon of short-chain lactone and the phosphorus atom of phosphorus oxide was relatively large.Shorter distance was more conducive to the occurrence of nucleophilic offensive reaction.D257 was the key residue that initiated the VmoLac catalytic reaction.When VmoLac catalyzed 3-oxo-C10-AHL orγ-nonalacton,D257 formed more hydrogen bonds with polarized water and substrate,which made the substrate more easily bind to the enzyme.VmoLac had a stronger ability to catalyze long-chain lactones than short-chain lactones,and a stronger ability to catalyze long-chain lactones than phosphorus oxides from the perspective of theoretical catalytic mechanism,which provides theoretical proof for the experimental structure.

关 键 词：嗜热磷酸三酯酶样内酯酶 VmoLac 分子对接 分子动力学模拟 

分 类 号：O641[理学—物理化学]