Structural basis for HLA-DQ2-mediated presentation of gluten epitopes in celiac disease

Abstract

Celiac disease, also known as celiac sprue, is a gluten-induced autoimmune-like disorder of the small intestine, which is strongly associated with HLA-DQ2. The structure of DQ2 complexed with an immunogenic epitope from gluten, QLQPFPQPELPY, has been determined to 2.2-A resolution by x-ray crystallography. The glutamate at P6, which is formed by tissue transglutaminase-catalyzed deamidation, is an important anchor residue as it participates in an extensive hydrogen-bonding network involving Lys-beta71 of DQ2. The gluten peptide-DQ2 complex retains critical hydrogen bonds between the MHC and the peptide backbone despite the presence of many proline residues in the peptide that are unable to participate in amide-mediated hydrogen bonds. Positioning of proline residues such that they do not interfere with backbone hydrogen bonding results in a reduction in the number of registers available for gluten peptides to bind to MHC class II molecules and presumably impairs the likelihood of establishing favorable side-chain interactions. The HLA association in celiac disease can be explained by a superior ability of DQ2 to bind the biased repertoire of proline-rich gluten peptides that have survived gastrointestinal digestion and that have been deamidated by tissue transglutaminase. Finally, surface-exposed proline residues in the proteolytically resistant ligand were replaced with functionalized analogs, thereby providing a starting point for the design of orally active agents for blocking gluten-induced toxicity.

Fig. 1.

(A) Difference electron density map calculated with Fourier coefficients |F_o| – |F_c| and phases derived from the final model less the αI-gliadin peptide and solvent molecules. Map is contoured at 2.8 σ. There are extra amino acids on either side of the P2–P9 residues of the peptide–DQ2 construct that are not modeled because of a lack of electron density. (B) grasp (25) generated the electrostatic potential surface of HLA-DQ2 (red region, negative; blue region, positive) with the bound αI-gliadin peptide (C, white; N, blue; O, red). (C) Putative hydrogen-bonding network in the DQ2–αI-gliadin complex (shown as red dashes). αI-gliadin is shown in yellow (C, yellow; N, blue; O, red). Backbone structure of HLA-DQ α- and β-chains are shown in green and blue ribbon plots, respectively, and side chains engaged in hydrogen bonding are shown in gray (C, gray; N, blue; O, red). Gray spheres represent water molecules.

Fig. 2.

Hydrogen-bonding network in the epitope-binding site of DQ2. αI-gliadin is shown in yellow (C, yellow; N, blue; O, red), and HLA-DQ2 α- and β-chains are shown in gray (C, gray; N, blue; O, red). Gray spheres represent water molecules. Atom-to-atom distances are given in Å.

Fig. 3.

(A) Binding of a peptide that does not contain any Pro residues to HLA-DQ2. A number of peptide main-chain NH groups form hydrogen bonds in the peptide binding site. Several peptide side-chains dock into binding pockets (P1, P4, P6, P7, P9) of the HLA molecule, providing additional binding energy and serving as a selectivity filter. (B) Binding of a Pro-rich peptide (such as the αI-gliadin) to HLA-DQ2 in a favorable register. Hydrogen-bond interactions involving peptide main-chain NH groups are still established, although there is significantly less main-chain NH groups available. (C) The same peptide in a shifted register cannot form such hydrogen bonds. Similarly, peptides that have Pro at unfavorable locations cannot form such hydrogen bonds, thereby limiting the registers available for binding.