In-silico prediction of coat protein structure of Indian citrus ringspot virus and their interactions with the Argonaut2/DCL4 proteins

Abstract

The RNA silencing mechanism is a crucial regulatory system in plants, particularly in antiviral defense. However, most of the plant viruses encode a specific protein called RNA silencing suppressor protein that suppress the RNA silencing mechanism of host. This study employs the bioinformatics tools, including SWISS homology model and I-TASSER, to predict the coat protein (CP) tertiary structure of Indian citrus ringspot virus (ICRSV). Then, five protein-protein docking servers (GRAMM, pyDockWEB, HawkDock, ZDOCK and ClusPro) were utilized to investigate interactions of CP of ICRSV with Argonaut2/Dicer-Like (DCL4) protein 4 of RNA silencing pathway of host. In blind docking experiments, the CP consistently engaged in docking interactions with DCL4, while with AGO2, it interacted near the PIWI and MID domains. The AGO2-CP cluster demonstrated 4 salt bridges, 30 hydrogen bonds, and 328 non-bonded contacts, with interface areas spanning 2529 in AGO2 and 2424 in CP, involving 50 and 51 interface residues, respectively. Similarly, the DCL4-CP cluster showed 5 hydrogen bonds and 122 non-bonded contacts, with interface areas spanning 965 in DCL4 and 987 in CP, involving 16 and 19 interface residues, respectively. The established phenomenon of CP interaction with AGO2/DCL4, may resulting in the inhibition of the RNA silencing mechanism and shedding light on the suppression mechanisms of host defense responses.

Supplementary information: The online version contains supplementary material available at 10.1007/s13337-024-00904-8.

Keywords: Coat protein; ICRSV; In-silico; RISCs; RNA silencing.