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