Homology modeling and docking analysis of ßC1 protein encoded by Cotton leaf curl Multan betasatellite with different plant flavonoids

Abstract Cotton leaf curl Multan virus (CLCuMuV) belonging to begomoviruses (Family Geminiviridae ) can infect cotton and many other agricultural crops. Betasatellite associated with CLCuMuV i.e., cotton leaf curl Multan betasatellite (CLCuMuB) is a small circular single-stranded deoxyribose nucleic acid (ssDNA) molecule that is essential for CLCuMuV to induce disease symptoms. Betasatellite molecule contains a sC1 gene encoding for a pathogenicity determinant multifunctional protein, which extensively interacts with host plant machinery to cause virus infection. In this study the interaction of sC1 with selected plant flavonoids has been studied. The study was focused on sequence analysis, three-dimensional structural modeling and docking analysis of sC1 protein of CLCuMuB. Sequence analysis and physicochemical properties showed that sC1 is negatively charged protein having more hydrophilic regions and is not very stable. Three-dimensional model of this protein revealed three helical, four beta pleated sheets and four coiled regions. The score of docking experiments using flavonoids as ligand indicated that plant flavonoids robinetinidol-(4alpha,8)-gallocatechin, quercetin 7-O-beta-D-glucoside, swertianolin, 3′,4′,5-trihydroxy-3-methoxyflavon-7-olate, agathisflavone, catiguanin B, 3′,4′,5,6-tetrahydroxy-3,7-dimethoxyflavone, quercetin-7-O-[alpha-L-rhamnopyranosyl(1->6)-beta-D-galactopyranoside], prunin 6″-O-gallate and luteolin 7-O-beta-D-glucosiduronic acid have strong binding with active site of sC1 protein. The results obtained from this study clearly indicate that flavonoids are involved in defense against the virus infection, as these molecules binds to the active site of sC1 protein. This information might be interesting to study plant defense mechanism based on the special compounds produced by the plants.