基于分子对接研究甘油脱氢酶的催化多功能性
Enzyme Promiscuity Study of Glycerol Dehydrogenase Based on Molecular Docking

作者: 王世珍 , 任 红 , 张永辉 , 李红春 , 王媛菁 , 方柏山 :厦门大学化学化工学院,化工与生物化工系,福建 厦门;

关键词: 甘油脱氢酶酶催化多功能性分子对接手性化合物Glycerol Dehydrogenase Enzyme Promiscuity Molecular Docking Chiral Chemicals

摘要:
基于生物信息学的方法研究甘油脱氢酶的催化多功能性。通过Brenda数据库搜索,查找、归纳甘油脱氢酶(EC1.1.1.6,Glycerol dehydrogenase,GDH)的底物谱。利用分子模拟对接的方法,研究甘油脱氢酶和手性对映体R-1-氨基-2-丙醇和S-1-氨基-2-丙醇的结合模式,获得酶与底物结合的关键氨基酸残基位点为ASP123,THR177,SER243和GLU180。通过比较结合能,研究手性对映体与酶结合的差异性,阐明甘油脱氢酶对R-1-氨基-2-丙醇,S-1-氨基-2-丙醇选择性的来源。分子对接可以反映酶对手性化合物的识别能力,可用作研究甘油脱氢酶的催化多功能性的手性底物谱的初步筛选手段,节省研究时间和成本。

Abstract: Enzyme promiscuity of glycerol dehydrogenase (GDH) was studied based on bioinformatics methods. Substrate specificity of glycerol dehydrogenase (EC1.1.1.6) was profiled by searching and analyzing Brenda data base. R-1-amino-2-propanol and S-amino-2-propanol were docked with glycerol dehydrogenase by Autodock 4.0, respectively. The docking mode was studied. The key amino acid residues identified as ASP123, THR177, SER243 and GLU180. By comparing the binding energy of both enantiomers, the effects of chiral conformation on the combination were analyzed to real the catalytic selectivity of GDH to the enantiomers. These results indicate that molecular docking can be applied as a primary method for exploring the substrate specificity of glycerol dehydrogenase for enzyme promiscuity study which is saving time and costs.

文章引用: 王世珍 , 任 红 , 张永辉 , 李红春 , 王媛菁 , 方柏山 (2015) 基于分子对接研究甘油脱氢酶的催化多功能性。 生物物理学, 3, 18-24. doi: 10.12677/BIPHY.2015.31003

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