Structural Characterization and Validation of Crimean-Congo Haemorrhagic Fever Virus Nucleoprotein Using Bioinformatics Approaches

Abstract

Crimean-Congo haemorrhagic fever virus (CCHFV) is an important viral pathogen, and characterization of its structural proteins contributes to a better understanding of viral molecular features. In this study, the CCHFV nucleoprotein was subjected to sequence analysis, three-dimensional structure modelling, structural validation, and physicochemical characterization. The nucleoprotein sequence consisting of 482 amino acids was retrieved from the NCBI database and used for homology-based structural modelling. The predicted model was generated using the CCHFV nucleoprotein X-ray crystallographic structure (template: 4aqf.2.A), showing 100% query coverage, 97.03% sequence similarity, and a Global Model Quality Estimate (GMQE) score of 0.93. Structural validation demonstrated the reliability of the model, with 97.03% residues present in the Ramachandran favoured region and 0.00% residues identified as outliers. The model quality assessment further showed a MolProbity score of 2.03, clash score of 2.55, and QMEANDisCo global score of 0.87 ± 0.05, indicating good structural agreement with the template structure. Physicochemical analysis revealed that the nucleoprotein has a molecular weight of 53,891.36 Da, theoretical isoelectric point of 8.47, positive overall charge, instability index of 31.44, aliphatic index of 76.33, and GRAVY value of −0.414. The obtained structural model and characterization data provide a foundation for further investigations of CCHFV nucleoprotein structure and function.