Nucleotide sequence characterization, amino acid variations and 3D structural analysis of HN protein of the NDV VIId genotype

Abstract

Abstract Background Haemagglutinin–neuraminidase (HN) is one of the membrane proteins of Newcastle disease virus (NDV) that plays a significant role during host viral infection. Therefore, antibodies against HN are vital for the host's ability to protect itself against NDV infection due to their critical functions in viral infection. As a result, HN has been a candidate protein in vaccine development against the Newcastle disease virus. Methods This report used the full‐length sequence of the HN protein of NDV isolated in Iran (VIId subgenotype). We characterize and identify amino acid substitutions in comparison to other more prevalent NDV genotypes, VII subgenotypes and vaccine strains. Furthermore, bioinformatics tools were applied to determine the three‐dimensional structure, molecular dynamics simulation and prediction of B‐cell antigenic epitopes. Results The results showed that the antigenic regions of our isolate are quite comparable to the other VII subgenotypes of NDV isolated from different geographical places. Moreover, by employing the final 3D structure of our HN protein, the amino acid residues are proposed as a B‐cell epitope by epitope prediction servers, which leads to the introduction of linear and conformational antigenic sites. Conclusions Immunoinformatic vaccine design principles currently exhibit tremendous potential for developing a new generation of candidate vaccines quickly and economically to eradicate infectious viruses, including the NDV. In order to accomplish this, focus is directed on residues that might be considered antigenic.

Keywords

• antigenic regions
• bioinformatics
• haemagglutinin–neuraminidase protein
• Newcastle disease virus
• substitutions
• VIId subgenotype