决明查尔酮合成酶的同源模建和分子模拟对接

Homology Modeling and Molecular Simulation Docking on Chalcone Synthase from Senna tora

查尔酮合成酶(chalcone synthase,CHS)是植物中类黄酮生物合成途径的关键酶,其催化对-香豆酰辅酶A和丙二酸单酰辅酶A发生缩合反应。本研究以苜蓿CHS的晶体为模板,利用同源建模构建决明CHS的三维模型。经过动力学优化后,决明CHS的三维模型与苜蓿CHS的结构极为相似,主要由α-螺旋和β-折叠构成,其中有13个α螺旋,占32.82%,15个β折叠,占19.23%,无规则卷曲占47.95%。模型验证结果表明决明CHS的三维模型具有合理的立体化学性质与氨基酸相容性。决明CHS含有两个重要的结构域:对-香豆酰辅酶A结合域与丙二酸单酰辅酶A结合域。决明CHS与对-香豆酰辅酶A、丙二酸单酰辅酶A的结合主要通过氢键与范德华力。决明CHS中Cys164、His303与活性中心的H_2O能够形成电子传递体系,参与对-香豆酰辅酶A形成CHS-对-香豆酰基中间产物。本研究结果为利用此类CHS三维模型研究其催化机理和分子工程改造奠定基础。

Chalcone synthase （CHS） is a key enzyme of the flavonoid biosynthesis pathway in plants. The reaction cata- lyzed by CHS involves the condensation of p-coumaroyl-CoA and malonyl-CoA molecules. In this study, a three dimen- sional model of CHS from Senna tora was constructed by homology modeling using the crystal structure of CHS from Medicago sativa as a template. The three dimensional structure of CHS from Senna tora,which was mainly composed of α-helices and some B-sheets,was similar to that of CHS from M. sativa. After validation,the stereochemistry and internal consistency of the CHS model were reasonable. CHS model had two individual domains ： one was responsible for the bind- ing of p-coumaroyl-CoA and another one took charge of the binding of malonyl-CoA. The binding between CHS model and ligands depended on mainly hydrogen bonds and van der Waals interactions. It was proposed that the formation of p- coumaroyl-enzyme intermediate involved His303, Cys164 residues and water molecules. An electron was transferred from water molecules within the reaction center to the imidazole ring of His303, and further to Cys164 giving rise to the forma- tion of CHS-ligands complex. Such results would lay a foundation of the catalytic mechanism and molecular reforming.