Naturally processed HLA class I bound peptides from c-myc-transfected cells reveal allele-specific motifs.

Naturally processed peptides, bound to HLA-A2, A68, B40 molecules, were isolated from a c-myc transfected lymphoblastoid B cell lines for sequence analysis. Forty-three sequences of bound peptides could be grouped into three structural motifs. One of the peptide sequences obtained, SLLPAIVEL, was identical to a previously reported peptide bound to HLA-A2.1 and was used for grouping HLA-A2-bound peptides. A second motif, identical to that previously reported for HLA-A68-bound peptides, was also observed. A distinct third motif, consistent with the structure of the HLA-B40 "45 pocket," was observed. The peptides within this group contained glutamate in position 2, usually followed by a hydrophobic residue in positions 3 and 9. Within this motif group of peptides bound to MHC class I molecules, one peptide, HEETPPTTS, was 100% homologous to residues 243-251 of the c-myc protein.