In silico analysis of coinfection of the proteins of Tomato leaf curl Palampur virus and Zucchini yellow mosaic virus

Abstract

Begomoviruses and potyviruses are among the most economically important plant viruses, causing significant losses in crop yields and quality worldwide. The coinfection of begomoviruses and potyviruses has been reported in several crop plants, leading to severe yield losses. Understanding the mechanisms of their interactions can help to develop strategies to mitigate their impact on agriculture. Our study provides insights into the potential for coinfection between ToLCPV and ZYMV, two important plant viruses in the begomovirus and potyvirus families, respectively. In this study, we adopted in-silico methods to investigate the potential for coinfection between these two viruses. The viral protein sequences were retrieved through Uniprot and processed by using BLASTp. All the 18 proteins were modelled using homology modelling, threading and ab-initio approaches. Their structures were further assessed by ERRAT, QMEAN and Ramachandran Analysis. The suitable and selected protein models were simulated dynamically using GROMACS and again analyzed for their structural stability. The most stable and suitable structures were docked, and 80 interactions were performed using HADDOCK webserver. Through which we found that the proteins of both viruses have structural compatibility and can interact with each other. Specifically, we identified the Rep protein and nuclear shuttle protein of ToLCPV to have strong interactions with the proteins of ZYMV. And the cylindrical inclusion (CI) and HC-Pro proteins of ZYMV as potential targets for interaction. The interacting residues of these proteins were determined using PRODIGY webserver. These findings can inform future research on the mechanisms of coinfection between plant viruses and aid in the development of effective viral control measures.