Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods

Abstract

In silico prediction of epitopes is a potentially time-saving alternative to experimental epitopeidentifcation but is often subject to misidentifcation of epitopes and may not be useful for proteinsfrom archaeal microorganisms. In this study, we mapped B- and T-cell epitopes of a model antigefrom the methanogen Methanobrevibacter ruminantium M1, the Big_1 domain (AdLP-D1, amino acids 19–198) of an adhesin-like protein. A series of 17 overlapping 20-mer peptides was selected to cove the Big_1 domain. Peptide-specifc antibodies were produced in mice and measured by ELISA, while an in vitro splenocyte re-stimulation assay determined specifc T-cell responses. Overall, fve peptide of the 17 peptides were shown to be major immunogenic epitopes of AdLP-D1. These immunogenic regions were examined for their localization in a homology-based model of AdLP-D1. Validate epitopes were found in the outside region of the protein, with loop like secondary structures refecting their fexibility. The empirical data were compared with epitope predictions made by programmes based on a range of algorithms. In general, the epitopes identifed by in silico predictions were not comparable to those determined empirically.