Dynamic properties of MHC class II allotypes

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Proteins of the Major Histocompatibility Complex (MHC) are expressed as hundreds of different allelic variants (allotypes) across the human population. This polymorphic nature of the MHC gene locus and the corresponding expression of protein variants has the consequence that the immune peptidomes of individuals are distinct, and that the propensities to display pathogenic, autoimmune-related or tumor-associated antigens also differ. For the understanding of wanted and unwanted immune responses it is therefore essential to know the critical steps of peptide selection. Central for an understanding of antigen presentation by MHC class II molecules is the HLA-DM-catalyzed exchange of the placeholder CLIP (class II associated invariant chain peptide) against higher affine peptides. The understanding of the large differences in peptide exchange rates cannot be explained by static crystal structures alone, but requires an approach that captures the essential dynamic features of MHCII-peptide complexes. In this proposal we aim to (i) identify MHC-peptide complexes that strongly differ in their HLA-DM dependency, (ii) investigate the dynamic properties of these MHCII allotypes by NMR spectroscopy and to (iii) determine the enzymatic parameters of DM-catalyzed exchange. This will allow us to define the critical amino acids and molecular intermediates that determine HLA-DM susceptibility of individual MHCII-peptide complexes. In a second, initially independent part of the project we will delineate the cellular peptidomes of (iv) the MHCII peptide complexes investigated in Part 1 and (v) of tumor cell lines. Finally, the molecular mechanistic and cellular findings will be compared to define the impact of MHCII dynamics on cellular antigen presentation.