Monte Carlo study of the effect of beta 2-microglobulin on the binding cleft of the HLA-A2 complex

Peptide recognition by class I products of the major histocompatibility complex requires association of the class I heavy chain with beta 2-microglobulin. We present results of Monte Carlo simulations of the beta-pleated sheet floor of the human class I MHC molecule, HLA-A2, with and without beta 2-microglobulin. We find a significant effect of beta 2-microglobulin on the side chains of residues near a region that would accommodate the C-terminus of a bound peptide. By modeling simultaneously each loop and its neighboring strand at either end of the class I cleft, we find that beta 2-microglobulin restricts the conformational space of residues that are central to binding peptides. The effect is most pronounced for R97 and H114 and somewhat less important for Y99 and Y116, the latter forming strong hydrogen bonds with neighboring residues in the heavy chain itself.