title: Use of eluted peptide sequence data to identify the binding characteristics of peptides to the insulin-dependent diabetes susceptibility allele HLA-DQ8 (DQ 3.2).
abstract: HLA-DQ8 (A1*0301, B1*0302) and -DQ2 (A1*0501, B1*0201) are both associated with diseases such as insulin-dependent diabetes mellitus and coeliac disease. We used the technique of pool sequencing to look at the requirements of peptides binding to HLA-DQ8, and combined these data with naturally sequenced ligands and in vitro binding assays to describe a novel motif for HLA-DQ8. The motif, which has the same basic format as many HLA-DR molecules, consists of four or five anchor regions, in the positions from the N-terminus of the binding core of n, n + 3, n + 5/6 and n + 8, i.e. P1, P4, P6/7 and P9. P1 and P9 require negative or polar residues, with mainly aliphatic residues at P4 and P6/7. The features of the HLA-DQ8 motif were then compared to a pool sequence of peptides eluted from HLA-DQ2. A consensus motif for the binding of a common peptide which may be involved in disease pathogenesis is described. Neither of the disease-associated alleles HLA-DQ2 and -DQ8 have Asp at position 57 of the beta-chain. This Asp, if present, may form a salt bridge with an Arg at position 79 of the alpha-chain and so alter the binding specificity of P9. HLA-DQ2 and -DQ8 both appear to prefer negatively charged amino acids at P9. In contrast, HLA-DQ7 (A1*0301, B1*0301), which is not associated with diabetes, has Asp at beta 57, allowing positively charged amino acids at P9. This analysis of the sequence features of DQ-binding peptides suggests molecular characteristics which may be useful to predict epitopes involved in disease pathogenesis.
authors.affiliation: Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK.
authors.forename: A
authors.initials: A
authors.lastname: Godkin
authors.forename: T
authors.initials: T
authors.lastname: Friede
authors.forename: M
authors.initials: M
authors.lastname: Davenport
authors.forename: S
authors.initials: S
authors.lastname: Stevanovic
authors.forename: A
authors.initials: A
authors.lastname: Willis
authors.forename: D
authors.initials: D
authors.lastname: Jewell
authors.forename: A
authors.initials: A
authors.lastname: Hill
authors.forename: H G
authors.initials: HG
authors.lastname: Rammensee
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D001402:B-Lymphocytes; D002461:Cell Line, Transformed; D003922:Diabetes Mellitus, Type 1 / Q000235:genetics* / Q000276:immunology*; D004198:Disease Susceptibility; D006683:HLA-DQ Antigens / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D004854:Herpesvirus 4, Human; D006801:Humans; D008024:Ligands; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000302:isolation & purification* / Q000378:metabolism; D011485:Protein Binding / Q000235:genetics / Q000276:immunology
chemical_list: D006683:HLA-DQ Antigens; C109756:HLA-DQ8 antigen; D008024:Ligands; D010455:Peptides