Structural bases for MHC class I peptide selection and neoepitope formation

One task of the immune system is to distinguish between healthy cells and altered cells due to viruses or cancers. To achieve this CD8+ T-cells are constantly monitoring the Major histocompatibility class I (MHC-I) complexes expressed on all nucleated cells in the body. The MHC-I is basically a scaffold to hold and display a short (usually 8-10 amino acids) peptide. These peptides are selected by a complicated machinery from the total peptidome as formed by the proteolytic activity in the cells. The peptides derive from the proteome within the cells, which is degraded by the proteasome to peptides of various lengths. These are transported into the endoplasmic reticulum (ER) by the transporters associated with antigen processing (TAP). Inside the ER, the peptides can be further processed by the ER aminopeptidases (ERAP1 and ERAP 2) before being loaded into the MHC-I by the peptide loading complex (PLC). The peptide loading complex consists of tapasin, ERp57 and calreticulin. The peptide MHC-I complex (pMHC-I) is then transported to the cell surface where they can be presented to the T-Cells of the immune system. The T-cells express the highly variable T-cell Receptor (TCR) which are formed from recombining the V(D)J segment in the TCR gene. The T-cells are selected in the Thymus, where self-responding Tcells are killed and the remaining, with low affinity to self, continue into circulation. This ensures protection against autoimmunity, T-cell responses against healthy cells. Cancer-cell survival and proliferation require immune system escape and consequently many cancer cells have deficiencies in the processing system. In this thesis four studies are presented. The first concerns the mechanism of tapasin influence on the peptide selection and loading into the peptide binding cleft of the MHC-I. In this study, a leucine on a loop of tapasin is shown to be able to bind into the F-pocket of the peptide binding cleft, and influence the peptide loading of the MHC-I. The second study is about a neoepitope that is presented on TAP-deficient cancer cells. This peptide, Trh4, was the first identified TEIPP (T-cell epitopes associated with impaired peptide processing). As a murine H-2Db restricted peptide is has an unusual sequence, containing four sulphur containing residues of the total nine. Here, we show the formation and importance of sulphur-π interaction for complex stability and the unconventional methionine at peptide position 5 for the formation of TCR interaction. The third study is a follow-up on the second study, but here the immunogenicity of the peptide is in focus. While the wild-type Trh4 peptide displays low immunogenicity, the mutation of peptide position 3 to a proline significantly increase the immunogenicity of this epitope. However, the increased immunogenicity is surprisingly not related to increased stability of the pMHC-I complex. In the final paper, two virus-associated epitopes are studied due to their differences in immunogenicity and binding to MHC-I. Both peptides carry a glycosylation motif and are glycosylated in the source protein. Here we show the structural basis for the discrepancy between the peptides. The glycosylated residue in one peptide (GP92) is protruding from the peptide binding cleft free for interaction with a TCR, while for the other peptide (GP392), a glycosylation would hinder the utilisation of a dominant anchor residue of the peptide for peptide binding to the MHC-I