Structural Analysis and Docking of Stilbene Synthase Protein from Chinese Grape Vine Vitis pseudoreticulata

Abstract

Aims: The present work aims to perform the molecular modeling of stilbene synthase protein from Chinese grape vine Vitis pseudoreticulata. Place and Duration of Study: The study has been performed in the Department of Biotechnology, GITAM Institute of Technology, GITAM University, Visakhapatnam, India for a period of 8 months. Methodology: The sequence of Vitis STS protein was obtained by BLAST search from DFCI web server using Arabidopsis Stilbene synthase sequence. To read the amino acid pattern among these sequences, Multiple Sequence alignment have been performed using clustal W. The secondary and 3D structures were predicted for the protein and the stability of the structures was determined through Ramachandran plot and PROSA analysis. 3D structure obtained using Swiss model workspace was utilized for docking studies. Results: In the multiple sequence alignment except Gossypium and Ipomea remaining sequences were aligning well. The secondary structure of the protein is possessing helices, coils and sheets respectively and most of the protein structure is coiled. The predicted model was subjected to evaluation by PROSA with a Z score of -10.1. Ramachandran plot revealed that the predicted that 96.6% residues were in favoured region, 2.6% were in allowed region and 0.8% were in outlier region proving that the predicted model is acceptable. Docking STS protein with secondary metabolite ligands elucidated that anethole, ascorbic acid and arbutin have good binding affinity. Conclusion: The structural model of Vitis pseudoreticulata stilbene synthase has been determined, and in silico docking studies have elucidated that this protein has docked with some of the essential secondary metabolites like anethole, ascorbic acid and arbutin which might enhance the performance when they enter into a biological system.