Natural peptides selected by diabetogenic DQ8 and murine I-Ag7 molecules show common sequence specificity

Abstract

In this study, a large number of naturally processed peptides was isolated and identified from the human diabetes-susceptible class II MHC molecules HLA-DQ8 (DQA1*0301,DQB1*0302) and from murine I-A g7 species, both of which are expressed in genetically identical APC lines. The peptides presented during the processing of autologous proteins were highly selective in showing sequence specificity, mainly consisting of 1 or more acidic residues at their C terminus. Testing for binding to the MHC molecules revealed that the position 9 (P9) acidic residues of the peptides contributed decisively to binding. For HLA-DQ8, the P1 residue, which was also an acidic amino acid, influenced binding positively. Both HLA-DQ8 and I-A g7 selected for common peptides that bound in the same register. There was no evidence for selection of peptides having nonspecific or promiscuous binding. Thus, diabetogenic class II MHC molecules are highly selective in terms of the peptides presented by their APCs, and this is governed by the features of their P9 anchor pocket. These results are in striking contrast to those from studies examining synthetic peptide or phage display libraries, in which many peptides were shown to bind.

The peptide-binding motif of HLA-DR8 shares important structural features with other type 1 diabetes-associated alleles

“…12 As for I-A g7 and DQ8, this pocket also accepted Gln, Asn and Gly. 12,27 The decrease of Arg, Lys and Pro at P9 confirmed previous the data for non-Asp b57 alleles, 27 suggesting that these amino acids at P9 would negatively interfere with the peptide binding to DR8. An interesting result concerned the positions P4 and P6, with a clear preference for Lys: 46% of the peptides had Lys at P4 or P6.…”

“…9 The absence of Asp at b57 is related to the preference of these alleles for the binding of acid residues in the P9 pocket. [10][11][12][13] This common feature, known to be involved in clinical disease 14,15 is also found in HLA-DR8, with Ser at b57, but not in the DQ4 (DQA1*0401/DQB1*0402), molecule of the DR8 haplotype that has an Asp at b57.…”

“…16), DQ8 (ref. 17) and DQ2, 18 together with peptide-binding data and studies of naturally processed peptides selected by these T1D-associated molecules 12,19 permitted the description of the peptide-binding motifs for these alleles. However, the HLA-DR8 peptide repertoire has only been partially described 20 and the binding motif remains unknown.…”

Do the peptide-binding properties of diabetogenic class II molecules explain autoreactivity?

“…Since I-A g7 and DQ8 were noticeably SDS-unstable it was proposed that they must bind promiscuously and to low affinity peptides [16]. However, mass-spectrometry based identification of naturally processed peptides selected by I-A g7 and DQ8 generated very different results: both the murine and human alleles selected for similar peptides with a very well defined binding motif characterized by multiple C-termini acidic amino acids [17,[24][25][26].…”

“…Binding studies demonstrated that the acidic amino acids interacted with the P9 pocket and contributed significantly towards binding affinity [24,25]. And moreover, the specificity of the P9 pocket, composed of the non-Asp β57 residue, was crucial in determining selection of peptides [24,26].…”