Identification of a putative motif for binding of peptides to HLA-DQ2

To understand the rules determining peptide binding to the celiacdisease and type 1 diabetes mellitus associated HLA-DQ2 molecule,we have studied in detail the binding of a peptide OVA 258–276Y(IINFEKLTEWTSSNVMEERY) which exhibitsstrong binding to DQ2.First we tested a set of N- and C-terminal truncated variants,and found the core binding region to comprise residues 267–276Y.Single alanine substitution analysis of the OVA 267–276Ypeptide revealed thatreplacements of V₂₇₂, E₂₇₅ and the C-terminalY had negative effects whereas the substitution of N₂₇₁ hada positive effect. A polyalanine analogue of the OVA 267–276Ypeptide with V₂₇₂, E₂₇₅ and a C-terminal Y bound at least aswell as the original peptide. A variant peptide with a deletionof R₂₇₆ displayed decreased binding, suggesting that the anchorresidues were out of frame in this analogue. To further characterizethe residues playing a role in the binding of the OVA 267–276Ypeptide to DQ2 we tested the binding ofseveral analogues withsubstitutions for V₂₇₂, E₂₇₅ and the C-terminal Y residue. Ourresults indicate that peptides binding to DQ2 have anchor residuesin relative positions 4, 7 and 9 (P4, P7 and P9). Residues withnegatively charged or hydrophobic aliphatic but not positivelycharged side chains are preferred in P4 and P7, whereas residueswith bulky hydrophobic side chains are preferred in P9.