IDENTIFICATION OF AN HLA-DQ2 PEPTIDE BINDING MOTIF AND HLA-DPW3-BOUNDSELF-PEPTIDE BY POOL SEQUENCING

Molecules of the major histocompatibility complex (MHC) present antige nic peptides to T cells. Sequencing peptide pools eluted from MHC clas s I molecules has established allele-specific peptide binding motifs. We applied pool sequencing to analyze human MHC class II-bound peptide s and found that HLA-DQ2-eluted peptides predominantly contained lysin e, isoleucine, and phenylalanine at relative position i, i + 3 and i 8, respectively. These residues putatively represent anchor residues for MHC binding. Analysis of a heterogeneous HLA-DPw3/DPw4-eluted pept ide pool yielded a sequence matching an epitope from the endogeneous e nzyme glyceraldehyde-3-phosphate dehydrogenase. This self-peptide and a partially identical, known allo-epitope bound specifically to DPw3 a nd DR13 molecules, suggesting the sharing of a binding motif. In parti cular, the presence of an arginine at relative position 3 appeared imp ortant for binding to these HLA class II specificities. Thus, pool seq uencing is applicable for the analysis of MHC class II-eluted peptides .