In Silico Characterization of the Coat Protein of Whitefly-transmitted Geminiviruses

Abstract

This analysis was conducted from September, 2025 to June, 2026 at the Applied Microbiology and Plant Pathology Laboratory, University Department of Botany, TMBU, Bhagalpur, Bihar and the Plant Virology Laboratory, Department of Plant Pathology, BAU, Sabour, Bhagalpur, Bihar, India where computational approaches were used to assess the coat proteins of some well-characterized members of the family Geminiviridae. A comprehensive sequence analysis was performed to identify conserved regions within the protein sequences, followed by phylogenetic analysis, secondary structure prediction, homology modelling, and functional annotation to understand their structural and functional features. The tertiary structures of the six selected begomovirus coat proteins revealed a highly conserved eight-stranded antiparallel β-barrel core, indicating a high degree of structural conservation that may be important for capsid assembly and stability. In contrast, variations in surface-exposed loops and terminal regions produced subtle differences in sequence, charge, and flexibility, which may contribute to differences in host adaptation, vector transmission, and intracellular trafficking. The predicted structural models provided valuable insights into the spatial organization of the coat protein and suggested potential mechanisms underlying their multifunctional roles during viral infection. The Ramachandran plot showed good stereochemical quality and reliable backbone geometry, with most residues falling in the favoured regions, suggesting that the coat protein structures are reliable and suitable for further structural analysis. Overall, this study provided computational insights into the structural and functional characteristics of begomovirus coat proteins and highlighted their potential significance as targets for the development of antiviral strategies, diagnostic approaches, and improved crop disease management.