Similarity between segments in protein conformational epitopes and MHC II peptides

In immune response, major histocompatibility complex class II (MHC II) molecules bind peptides derived from antigens and present them. The formation of MHC II-peptide complexes was a critical signal in inducing of antibodies production of B cells. In this research, we tried to investigate whether there was a similarity or relationship between the segments in B cell conformational epitopes and MHC II peptides. All the segments from the conformational epitopes and MHC II peptides were extracted and the relationship between them was analysed. From current results, it can be hinted that the epitope segments have a higher similarity to the known MHC II peptides. Furthermore, the majority of known conformational epitopes were found to contain at least one segment identical or similar to a MHC II peptide. Such results may not only facilitate the study of antigen information processing but also help to improve the conformational epitope prediction algorithm.