利用同源建模、分子模拟和分子对接技术分析家蚕中碳酸酐酶的结构和催化机制

Analysis of the Structure and Catalytic Mechanism of Carbonic Anhydrase in Silkworm by Homology Modeling, Molecular Simulation and Molecular Docking Techniques

摘要:

该研究以来源于家蚕的碳酸酐酶为研究对象，利用同源建模建立了家蚕碳酸酐酶的三维结构并预测了其潜在的活性区域。随后，利用Autodock-Vina对家蚕碳酸酐酶和底物进行分子对接，分析和评价了对接模型以及与乙酸对硝基苯酯底物对接过程中的相互作用。经分子动力学模拟和MM/PBSA，分析催化过程中家蚕碳酸酐酶的均方根偏差、溶剂可及面积以及径向分布函数。结果表明：建模所得的酶结构可靠性良好（完全允许区域为89.3%，允许区域10.3%，总和超过了99%）；家蚕碳酸酐酶与底物的对接结合能为-6.1 Kcal/mol；范德华力在家蚕碳酸酐酶和底物的结合中占主导地位，而极性溶剂化对结合有显著的反作用；家蚕碳酸酐酶与底物的相互作用的区域为：138L~150V和209L~217C；同源建模所得的家蚕碳酸酐酶结构稳定（模拟最后50 ns RMSD值约0.35 nm）。该研究对后续进一步理性设计和改造家蚕碳酸酐酶提供了一定的理论支持。

Abstract:

In this research, the carbonic anhydrase of Bombyxmori (BmCA) was used as the research object, the optimal three-dimensional structure of the carbonic anhydrase from the silkworm was established by homologous modeling, and its potential active sites were predicted. Subsequently, autodock-vina was used to perform molecular docking between BmCA and the substrate, then the docking model and the interaction with the substrate, 4-nitrophenyl acetate, during the docking process were analyzed and evaluated. The root mean square deviation, solvent accessible area and radial distribution function of BmCA in the catalytic process were analyzed though molecular dynamics simulation and MM/PBSA. The result indicated that the reliability of the enzyme structure obtained by modeling was good (fully allowable region: 89.30%; allowable region: 10.30%; the sum: more than 99%). The binding energy for docking BmCA and substrate was -6.1 Kcal/mol; Vander Waals force was dominant in the binding between the silkworm’s carbonic anhydrase and the substrate, the major contribution to binding was, whilst polar solvation antagonized strongly the binding; the regions where BmCA interacted with the substrate were 138L~150V and 209L~217C; The structure of BmCA obtained by homology modeling was stable (the RMSD value of the last 50 ns simulation was about 0.35 nm). This research provides certain theoretical support for further rational design and modification of BmCA.