Pocket mutations of HLA-B27 show that anchor residues act cumulatively to stabilize peptide binding

Major histocompatibility complex (MHC) class I molecules bind endogenously synthesized peptides for presentation to cytotoxic T-cells. The human class I molecule HLA-B27 consists of a trimolecular complex containing the HLA-B27 heavy chain, a peptide that is usually nine amino acid residues (aa) long, and beta 2-microglobulin (beta 2m). The key interactions for peptide selectivity are between Glu-45, which forms a salt bridge with the Arg at P2 of the peptide, and Asp-116 which favors the binding of peptides containing a Lys or Arg at P9. The t1/2 of dissociation of [125I]beta 2m was measured for peptide-specific HLA-B27 wild-type (wt) and mutant complexes. HLA-B27 wt and HLA-B27 D116F formed relatively stable complexes, with a t1/2 of dissociation on the scale of hours, with appropriate peptides that contained Arg at P2, whereas HLA-B27 E45T required a Gln at P2. Similarly, kinetically stable D116F complexes were formed only with peptides that contained a Leu or Val at P9 instead of Arg or Lys. The [125I]beta 2m dissociation rate data were fit to a set of equations in order to calculate relative binding coefficients for each anchor residue at P2 and P9. The P2 coefficients were sensitive to the E45T mutation but not the D116F mutation, whereas the P9 coefficients were sensitive only to the D116F mutation. Thus, drastic structural changes in one subsite do not affect the other subsite, indicating that the dominant anchor residues at P2 and P9 independently contribute to stabilizing the class I/peptide complex.