In silico Characterization of Coat Protein of PVS-Bitlis isolate and Docking Analysis with Host Protein

Abstract

Potato virus S (PVS) is one of the common viruses worldwide and usually produces moderate symptoms in potato plants. The interactions of viral proteins with their hosts are very important in establishing a successful infection and ensuring systemic spread. In this study, the interaction between the PVS coat protein (CP) and the PSH-RGH6 protein in the defense system encoded by the potato plant was investigated using homology modeling and protein-protein docking approach. The CP gene of the PVS-Bitlis isolate was amplified by RT-PCR using gene-specific primers. The gene of interest was cloned into the pGEM-T Easy vector and the plasmid carrying the PVS-Bitlis CP gene was sequenced. By using the amino subsequence of the obtained sequence, I-TASSER program created a protein model based on homology. For the PSH-RGH6 protein, a model of the protein was created using the Swiss-model program. The interaction among both proteins was investigated with the AutoDock approach in Chimera 1.15 program. According to the docking results, the existence of interaction between PVS-Bitlis CP and PSH-RGH6 proteins has been determined and this interaction needs to be confirmed with further analysis.