Theoretical Modeling of Replication Association Protein of Indian Cassava Mosaic Virus and its docking with N-Acetyl D-Glucosamine

Abstract

The Bean golden mosaic virus (BGMV), also known as the Begomovirus, belongs to the family Geminiviridae and is transmitted through the whitefly. One of the forms of it is Indian cassava mosaic virus (ICMV) which adversely affects the yields of tomatoes, guavas, green chillies, potatoes, etc. ICMV has been modelled theoretically in the present work with the help of tools of homology modelling. The latter is concerned with insilico approaches to build, predict and analyse the 3-D structure of proteins (for which the crystal structure is unavailable). The closest homologue of Association Protein of Tomato was 1L2M_A, with the highest sequence identity. Both consensus and chimera models were made and studied. The best one was then used for the docking studies. Thereafter, the putative binding sites to be attacked by various inhibitors were located and then docked with N-Acetyl-D-glucosamine (NAG). NAG was optimized using B3LYP/6-31G(d,p) methods and its properties are studies. The docking scores of NAG on the active sites of Replication Association Protein of Indian Cassava Mosaic Virus were checked and it was found that NAG proves to be an effective inhibitor for ICMV. This study will now be tried in the wet lab to check the efficiency of our theoretical findings.