In silico molecular interaction and energy profiling of the proteins of Cotton leaf curl Kokhran virus-Burewala strain and Tomato leaf curl New Delhi virus

Abstract

Begomoviruses (family Geminiviridae) are circular, single-stranded DNA (ssDNA) viruses having monopartite or bipartite genome. The genome is very small and comprises four to six ORFs. These viruses are economically important as they cause a number of diseases in plants, the most significant being Cotton leaf curl disease (CLCuD).. In plants more than one virus can exist at a particular time resulting in mixed infections. Mixed infections are common in nature and often result in causing disease severity in infected plants. Such infections are frequently observed in viruses of the genus Begomovirus, as they are transmitted by the ubiquitous whitefly Bemisia tabaci, a polyphagous insect that can infest multiple hundred plant species. In the present study, the coinfection of two Begomoviruses, Tomato leaf curl New Delhi virus (ToLCNDV) and Cotton leaf curl Kokhran Virus-Burewala strain (CLCuKoV-Bur) in relation to CLCuD by taking in account the interactions taking place between the proteins of the two viruses . By Adopting an in-silico approach, viral sequences were retrieved from GenBank viral proteins were modelled using homology modelling, threading and ab initio approaches. Structure assessment of the predicted structures was done using ERRTA, PROCHECK, and RAMPAGE and the most suitable models were docked using HADDOCK2.2 webserver. 56 interactions were performed by docking all the proteins of CLCuKoV-Bur with the proteins of TOLCNDV. All interactions exhibited a significant HADDOCK2.2 score, proving a strong interaction existed between the viruses. The most significant interaction of the proteins of CLCuKoV-Bur was seen between MP and NSP proteins of DNA-B of ToLCNDV. The interacting residues between the viruses were determined by PRODIGY webserver and important domains taking part in the interaction were determined, and interacting domains were identified. IX Based on the strong interaction existing between the proteins, and the domains taking part in the interaction control strategies maybe devised to limit the spread of the two viruses.