Homology Modeling And Molecular Docking Studies Of CYP51from Penicillium Digitatum

Citrus green mold(Penicillium digitatum) is an important citrus diseases caused by pathogenic fungi. The disease results in a large number of citrus decay, causing huge losses to citrus production and economic interests of growers. Lanosterol14a-demethylase enzyme (CYP51) is a key enzyme in the fungal cell membrane for ergosterol synthesis process. Lacking of this kind of enzyme will result in the damage of synthesis of the fungal cell membrane, and lead to the loss of structure and function and the fungal death. So this enzyme has become an important target enzyme of common systemic fungicide such as triazole fungicides.In this paper, the homology modeling and molecular docking means are used to study the three-dimensional model structure of citrus green mold CYP51and the binding modes of its activate center with fungicides. The purpose of this study is to construct a three-dimensional structural model of citrus green mold CYP51at the molecular level, and to study different binding modes of fungicides in the active center of the PdCYP51. By analysis of fungicide molecules with citrus green mold CYP51through molecular docking studies, it can be used to clarify the citrus green mold CYP51activity center structural information, fungicides molecular interaction with the receptor sites, and the detailed mechanism. It will supply a reasonable explanation of the binding characteristics of four kinds of commercial fungicides on the spectral experiments of PdCYP51and bacterio static mechanism of citrus green mold.Homology modeling results of PdCYP51show that:human CYP51crystal (PDB ID:3LD6) could be as a reasonable template to build three-dimensional structure model of PdCYP51. The PdCYP51modeling structure includes twelve major a-helices, seven β-strands and other loops. After optimization by molecular dynamics simulation, the PdCYP51structure is evaluated by using PROCHECK and ERRAT program. The results indicate that the amino acid probability of PdCYP51structure in the reasonable region residues is as high as99.3%; the ERRAT-score value is77.186which is much larger than the standard threshold of50. Both aspects prove that modeling of the conformation of our PdCYP51modeling structure is reasonable. The PROSA program calculation results show that the Zscore value of PdCYP51modeling fall the range from the known better structural proteins. This indicates that the three-dimensional structure of PdCYP51is reasonable in view of the energy point.Molecular docking experiments results of the four commercialization fungicides show that:when diniconazole was docked into the citrus green mold CYP51active center, a pair of hydrogen bonds was formed between the T116amino acid residue with PdCYP51. There is a strong hydrophobic interaction and Van der Waals interactions between the ligand and receptor. When the other three fungicides molecular tebuconazole, triazole and triadimefon were docked into the active center of PdCYP51, although there was no formation of hydrogen bonds, but the formation of hydrophobic interaction and Van der Waals force with PdCYP51can still make these three compounds bind tightly with the active center of the PdCYP51. Y112, T116, Y126, F120, F219, M304and S309amino acid residues from the PdCYP51active center play an important role in the fungicides molecular recognition and binding process. They can be used as important factors in site-directed mutagenesis and designing new inhibitor molecules.Finally, through the discussion of formation of hydrogen bonds, hydrophobic and Van der Waals interaction of the PdCYP51active center with four fungicides by molecular docking, it could make a reasonable explanation for the antimicrobial activity of four fungicides and combined spectral differences. This could lay the foundation for the development of new antifungal inhibitors.