Abstract

The 3D full-atom model of the whole-size CYP102A1 from Bacillus megaterium (cytochrome P450 BM3) has been constructed using molecular modeling methods. The structure model was constructed using crystal structures of the separate FAD-binding domain (PDB ID: 4DQK) and the complex of FMN-binding and monooxygenase domains (PDB ID: 1BVY). Modeling procedure included analysis of the domains’ surfaces to find the orientation with maximum inter-subunit contacts. The overall configuration of the obtained complex was optimized using molecular dynamics. The final full-atom structure model shows rather tight interactions between FAD- and FMN-binding domains due to 10 inter-domain hydrogen bonds and hydrophobic interactions between three pairs of amino acid residues. This 3D model can be used for structure-function studies and rational design of the enzyme as well as for construction of hybrid supramolecular structures of biocatalysts with cytochrome P450 BM3.

中文翻译：

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巨大芽孢杆菌三域单加氧酶CYP102A1ВМ3的完整结构建模

摘要

使用分子建模方法构建了巨大芽孢杆菌CYP102A1的3D全原子模型（细胞色素P450 BM3）。使用单独的FAD结合域（PDB ID：4DQK）和FMN结合和单加氧酶域（PDB ID：1BVY）的复合物的晶体结构构建结构模型。建模过程包括对区域表面的分析，以找到具有最大亚基间接触的方向。使用分子动力学对所得复合物的整体构型进行优化。最终的完整原子结构模型显示，由于10个域间氢键和三对氨基酸残基之间的疏水性相互作用，FAD和FMN结合域之间的相互作用非常紧密。