In silico Prediction of Molecular Docking between Chicken BRD2 and Newcastle Disease Virus Matrix Protein to Elucidate Host-pathogen Interaction

Abstract

Background: Newcastle disease is one of the most contagious viral diseases caused by the Newcastle disease virus (NDV) which causes a huge loss in the terms of economy as well as mortality level in the poultry sector. The viral matrix protein is one of the proteins which helps in the attachment of virus, budding and assembly of progeny virions in the host cell. Host-pathogen interaction plays a very important role in the changeover of genetic diversity in organisms. Methods: The amino acid sequences of chicken BRD2 gene and matrix protein of NDV were used for structure prediction and visualization of protein-protein interaction between BRD2 and matrix protein by using Discovery Studio software. The nucleotide sequences of both genes were used for evolutionary analysis using MEGA7 software followed by selection pressure analysis using online Datamonkey server. Result: The results indicated that the ligand was attached with the matrix protein, which acts as a receptor on the virus surface. The purifying selection has been evident for the viral matrix protein gene. The docking of viral protein with host BRD2 protein has been detected in the study which further warrants experimental validation. In conclusion, the viral matrix protein interacts at amino acid position Tyrosine-148, Valine-339, Alanine-341 with ligand present on the chicken BRD2 protein. The evolutionary analysis revealed that the matrix protein of NDV R2B strain was the closest to that of Peacock, pigeon, duck and quail however, it exhibited maximum distance with the chicken NDV from Ireland, Vietnam and Haryana state of India.