(E)-2-(乙酰胺亚甲基)琥珀酸水解酶与其催化底物相互作用的理论研究  

Theoretical investigation into the interaction between(E)-2-(Acetamidomethylene) succinate hydrolase and its catalysis substrate

作　　者：张红星[1] 张继龙[1] 郑清川[1] 

机构地区：[1]吉林大学理论化学研究所理论化学计算国家重点实验室,长春130023

出　　处：《黑龙江大学自然科学学报》2011年第5期655-659,675,共6页Journal of Natural Science of Heilongjiang University

基　　金：国家自然科学基金资助项目(20903045)

摘　　要：通过分子对接和分子动力学模拟等理论方法研究(E)-2-(乙酰胺亚甲基)琥珀酸(E-2AMS)水解酶与其水解底物E-2AMS的结合方式。MM-PBSA结合自由能计算结果和动力学轨迹的统计分析都表明,在E-2AMS与水解酶形成的复合结构中,底物酰胺键采取反式构型在能量上更有利。在这种结合方式中,水解酶活性位点处的关键残基Arg146、Arg167、Tyr168、Arg179和Tyr259与E-2AMS之间形成7条氢键,在催化反应中起到稳定底物的作用;而残基Ile41和Leu107的主链氨基形成"氧负离子洞",能够抵消催化过程中酰胺氧原子上积累的负电荷,有利于反应的顺利进行。Molecular docking,molecular dynamics（MD） simulation method were used to investigate the binding mode of（E）-2-（Acetamidomethylene）succinate（E-2AMS） hydrolase to its substrate.The results from MM-PBSA binding free energy calculation and the statistical analysis of the MD trajectories all show that the trans-amide configuration of E-2AMS is energetically favourable in the complex structure.In the binding mode,the key residues in the active site of hydrolase,Arg146,Arg167,Tyr168,Arg179 and Tyr259 form seven H-bonds with E-2AMS,which play an important role of stabilizing the substrate in the catalysis reaction.The main-chain amides of Ile41 and Leu107 form an oxyanion hole and offset the negative charge that builds up during catalysis,which is helpful for the catalysis process.

关 键 词：(E)-2-(乙酰胺亚甲基)琥珀酸 水解酶 分子对接 分子动力学模拟 MM-PBSA 

分 类 号：O629.8[理学—有机化学] Q55[理学—化学]