In-silico prediction and validation of Carica papaya protein domains interaction with the Papaya leaf curl virus and associated betasatellite encoded protein

Abstract

AbstractBegomovirus, the first-largest genus of plant viruses in family Geminiviridae, is a persistent menace to plants that causes millions of dollars’ worth of damage in a variety of vital crops around the world. One of the most important tropical fruit crops is Carica papaya, which has a wealth of pharmacological and bioactive components that are commonly used to treat a wide range of human illnesses, is infected by divergent begomovirus species. Here, we report the interacting regions of the one of the begomovirus species i.e. Papaya Leaf Curl Virus (PaLCuV and Papaya leaf betasatellite (PaLCuB) protein with papaya plant protein by using computational approaches. This includes primary sequence recognition, secondary structural assessment, 3D modelling, energy minimization, binding site prediction, protein–protein interaction, and interface analysis. Our results showed that papaya plant protein such as S-adenosyl methionine synthetase (SAMS), Proliferating cell nuclear antigen (PCNA), Cyclin-dependent kinases regulatory subunit 1 (CDK1), Adenosine kinase (ADK), and Calmodulin (CaM), an encoded protein of C. papaya, are involved in host–virus interaction. However, we find the best domain-level interactions based on the structural and interface analysis of the SAMS-CP, PCNA-Rep, CDK1-Rep, ADK-REn, CaM-PreCP, and PCNA-βC1 proteins of PaLCuV–PaLCuB. In this study, we attempted to understand the sequence–structure relationship and mode of the virus–host binding complex, which was verified and validated with integrative in silico approaches. Using several bioinformatics tools, our study has provided novel insights into the papaya protein–begomovirus protein binding mechanism. Thus, we anticipate that our findings from this study will be useful for the development of new therapeutic agents against the pathogen, paving the way for researchers to better control this destructive plant virus. This is the first in-silico investigation that combined the prediction and structural validation and interface analysis of the interaction between PaLCuV–PaLCuB and papaya proteins.