Figure 1.
Results from analyzing T1D association with HLA-DRB1. A: Results from analyzing DRB1 association with T1D. The logarithmic P values (black line) were computed from the likelihood χ2 test over successive ROR steps, at each of which the numbers of amino acids (AAs) were gradually deleted and the number of unique alleles reduced; comparable P values for incremental change (red line) were also computed. B: Results from analyzing DRB1 association with T1D, visually displaying how specific AAs were deleted throughout the ROR procedure. Color intensity corresponds to the logarithmic P values. C: A typical HLA-DR molecule (DRB1*01:01, bound to native peptide from HLA-A, 1AQD.pdb) showing the interactions of key residues in the bottom side of the β-sheet floor of the α1β1 domain (below the antigen-binding groove). In the majority of alleles, β14 is a Glu, while β25 is an Arg. The two interact extensively with each other as well as with neighboring residues β31Phe, β36Glu, β39Arg, β41Asp, and β43Asp, mostly through electrostatic interactions and weaker cation-π interactions involving β31Phe and β39Arg. This set of interactions is seen in essentially all crystal structures of HLA-DR molecules known to date. Water molecules documented in the crystal structure and bridging interactions between polar side chains are not shown for clarity. The antigenic peptide is in the gray ribbon above the β-sheet floor: N indicates its amino terminus, while C indicates its carboxy terminus. D: The crystal structure of the heterodimer HLA-DRα/HLA-DRB1:04:01 in complex with an antigenic peptide showing mostly the antigenic peptide-binding domains α1β1 (2seb.pdb) as well as the 11 AAs identified by ROR and located within the binding grove (nine residues) or right below (two residues). The MHC II molecule is shown in line ribbons colored according to secondary structure (red, α-helix; turquoise, β-sheet; green, random coil), with the β1-helix at the bottom of the picture and the α1-helix at the top. The antigenic peptide backbone is shown in gray, with its amino terminus labeled as N and its carboxy terminus labeled as C. The 11 residues revealed by ROR to play a role in the pathogenesis of T1D within HLA-DRB1 alleles are shown in stick form (red, oxygen; blue, nitrogen; gray, carbon; no hydrogens shown). Residues β14Glu and β25Arg are located below the β-sheet floor, and the entire network of interactions is shown in greater detail in panel C. The entire HLA-DRB1*04:01 complex has been tilted with respect to the conventional TCR view (shown in Supplementary Video for a simulated DRB1*04:01 complex tilted toward the reader so that all 11 residues, so-revealed by the ROR process, could be exposed to view). PDB, Protein Data Bank.