T-cell epitope frequency in ordered and disordered protein regions

Abstract

Frequently asked question in immunology is whether the immunodominance of T-cell epitopes is dependent to their localization in the antigen 3D structure or epitope-intrinsic. Using epitope prediction algorithms we have found that both HLA-I and HLA-II epitope frequencies were higher in ordered protein regions, for all analysed taxonomic categories (archaea, bacteria, eukarya, and viridae) and that epitopes appertaining to ordered protein regions were prevalently hydrophobic. Epitope frequency in disordered protein regions of various lengths was constant while in ordered regions had shown a rising trend with prolonging region length. The comparison between predicted and experimentally evaluated epitopes of several tumor associated antigens of cancer/testis antigen group, revealed that majority of epitopes presented by HLA-I and HLA-II molecules were localized in ordered protein regions.