Epitope-based immunoinformatics study of a novel PilQ380–706-PilA fusion protein from Pseudomonas aeruginosa

Abstract

Infections with Pseudomonas aeruginosa (P. aeruginosa) have been a long-standing challenge for clinical therapy, because of the complexity of pathogenesis and its widespread resistance to antibiotics. The main aim of the present study was to design and analyze a novel PilQ380–706-PilA fusion protein as a vaccine candidate using immunoinformatics tools. The potential antigenic B and T-cell epitopes were determined. Hydrophobicity, hydrophilicity, flexibility, and surface accessibility of the protein were assessed by online algorithm tools. Allergenicity of the protein was analyzed for the safety concern. Most promising T cell epitopes were selected based on their binding efficiency with commonly occurring MHC class II alleles. The 3D structure model of the fusion protein was generated using RaptorX and I-TASSER servers and validated by Ramachandran plot using RAMPAGE server. Among 19 antigenic epitopes, 12 of them demonstrated the hydrophilic property. Two potential continuous B-cell epitopes were found in the sequence positions 20–41 and 95–152. Based on the prediction tools, the PilQ-PilA was not determined as an allergenic protein. Five epitopes were found to interact with the H2-IAd allele, and also five epitopes with H2-IAb. Among them, it was found that “IPVRQVMIEARIVEA”, “PVRQVMIEARIVEAN” and “VRQVMIEARIVEANV” were potential T-cell epitopes as they interacted with mouse MHC class-II alleles. Ramachandran plot showed about 93.2% residues were present in the favored region. Based on the present study, it could be concluded that these predicted epitopes may be efficient for recognition by B and T-cells to generate a specific immune response.