Substitution of aspartic acid at β57 with alanine alters MHC class II peptide binding activity but not protein stability: HLA-DQ (α1*0201, β1*0302) and (α1*0201, β1*0303)

In class II major histocompatibility complex (MHC) proteins, residue β57 is usually aspartic acid. Alleles carrying serine, valine, or alanine at this position are strongly correlated with the development of insulin-dependent diabetes mellitus (IDDM). Aspβ57 participates in a conserved salt bridge that bridges the α and β subunits in the peptide-binding site. It has been proposed that the correlation between IDDM and MHC alleles lacking Aspβ57 may be due to an instability of the protein caused by loss of this salt bridge. Using a pair of HLA-DQ proteins (α1*0201, β1*0302) and (α1*0201, β1*0303) differing only in having aspartic acid or alanine at position β57, we show that the polymorphism does not have a significant effect on protein stability for either the empty or peptide-loaded forms. However, the circular dichroism spectra indicate that empty and peptide-loaded Alaβ57 proteins display slightly different secondary structures relative to their Aspβ57 counterparts. A set of three peptides shows different binding affinities for DQ(α1*0201, β1*0302) relative to DQ(α1*0201, β1*0303). We propose that substitution of Aspβ57 residue causes a local rearrangement within the DQ peptide-binding site that alters the peptide-binding specificity. This rearrangement may help to explain the previously observed differences in SDS stability between Asp and non-Aspβ57 DQ proteins.