Precise prediction of class II T-cell epitopes using a combinatorial peptide library approach

T-cell receptor (TCR) recognition of peptides bound to MHC-class II molecules has been shown to be highly degenerate at least in some CD4+ T cells. This feature has allowed us to use peptide mixtures composed of very large numbers of compounds (i.e. billions) to define T-cell recognition and identify the spectrum of stimulatory ligands for a given TCR. Here we define, using soluble combinatorial decapeptide libraries in the positional scanning format (PS-SCL), the recognition patterns of several human CD4+ T cell clones (TCC) specific for self and foreign antigens. Individual peptides were identified that stimulate the TCC at picomolar concentration. For myelin basic protein peptide 87-99 (MBP(87-99))-specific TCC we compared the proliferative response to a large set of single amino acid-modified peptides based on MBP(87-99) with the results obtained with PS-SCL. We demonstrate that (1) most of the TCC respond to peptide mixtures composed of large numbers of compounds and therefore can be studied using the PS-SCL approach; (2) the PS-SCL data precisely match the results obtained with single amino acid modified peptides. Furthermore, the observed responses of most TCC to complex peptide mixtures point out that degeneracy of antigen recognition is a common characteristic of TCR recognition and may be a key factor for thymic selection and peripheral survival of T cells.