Homology modeling, binding site identification and docking in flavone hydroxylase CYP105P2 in Streptomyces peucetius ATCC 27952

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• 作者：Bashistha Kumar Kanth ; Kwangkyoung Liou ; Jae Kyung Sohng
• 关键词：Cytochrome P450 ; Homology modeling ; Molecular dynamics simulation ; Molecular docking ; Flavone ; Ligand-binding site
• 刊名：Computational Biology and Chemistry
• 出版年：2010
• 出版时间：August 2010
• 年：2010
• 卷：34
• 期：4
• 页码：226-231
• 全文大小：772 K

文摘

Homology models of cytochrome P450 105P2 (CYP105P2) were constructed using four P450 structures, CYP105A1, CYP105, CYP165B3 and CYP107L1, as templates for the model building. Using Accelrys Discovery Studio 2.1 software, the lowest energy CYP105P2 model was then assessed for stereochemical quality and side-chain environment. Further active site optimization of the CYP105P2 model built using these templates was performed by molecular dynamics to generate the final CYP105P2 model. The substrates, flavone, flavanone, quercetin and naringenin, were docked into the model. The model-flavone complex was used to validate the active site architecture, and structurally and functionally important residues were identified by subsequent characterization of the secondary structure.