A pattern search method for putative anchor residues in T cell epitopes

摘要: The binding affinity between an antigenic peptide and its particular major histocompatibility complex (MHC) molecule seems to be largely determined by only a few residues. These residues have been called “anchors” because of their property fitting into “pockets” inside the groove MHC molecule. To predict natural epitopes within longer sequence, it therefore appears important know motif or pattern describing anchors, i.e. anchors amino acid residue preference distance anchor residues. A large set class I-restricted peptides has described. Peptide sequences vary in length lack obvious common sequence motif. For list belonging one type I molecule, we describe method find most prominent with at least two Briefly, are aligned, positions searched for, where all share high similarity. alignments scored according similarity We show that motifs predicted for alleles A2.1, B27, Kb, Kd, Db substantial agreement experimental data. derive HLA-A1, All, B8, B14, H-2Ld II I-Ab I-As. In some cases, higher scores were obtained allowing slight variation number anchors. Therefore, support view is not uniform. This can used short epitope Anchor search regions infectious viruses, bacteria parasites.