Structural Basis of Cytochrome c Presentation by IEk

Abstract

The COOH-terminal peptides of pigeon and moth cytochrome c, bound to mouse IEk, are two of the most thoroughly studied T cell antigens. We have solved the crystal structures of the moth peptide and a weak agonist–antagonist variant of the pigeon peptide bound to IEk. The moth peptide and all other peptides whose structures have been solved bound to IEk, have a lysine filling the p9 pocket of IEk. However, the pigeon peptide has an alanine at p9 shifting the lysine to p10. Rather than kinking to place the lysine in the anchor pocket, the pigeon peptide takes the extended course through the binding groove, which is characteristic of all other peptides bound to major histocompatibility complex (MHC) class II. Thus, unlike MHC class I, in which peptides often kink to place optimally anchoring side chains, MHC class II imposes an extended peptide conformation even at the cost of a highly conserved anchor residue. The substitution of Ser for Thr at p8 in the variant pigeon peptide induces no detectable surface change other than the loss of the side chain methyl group, despite the dramatic change in recognition by T cells. Finally, these structures can be used to interpret the many published mutational studies of these ligands and the T cell receptors that recognize them.

Alternate interactions define the binding of peptides to the MHC molecule IAb

“…For example, peptide studies predicted the properties of the p1, p6, and p9 pockets of IE k (44)(45)(46). The structure of IE k with bound peptides confirmed these conclusions and determined the properties of the p4 pocket (12,23).…”

“…In nearly all MHCII structures the p7 amino acid points laterally toward the ␤-chain ␣-helix. In some cases, its contribution to MHC interaction is minimal because of a small side chain (12)(13)(14)23) or a rotamer that brings the side chain to the surface (12,16,20,21). In a few cases, the p7 rotamer buries a portion of the side chain with considerable ␤-chain interaction (11,15,17,18).…”

Cutting Edge: MHC Class II-Restricted Peptides Containing the Inflammation-Associated Marker 3-Nitrotyrosine Evade Central Tolerance and Elicit a Robust Cell-Mediated Immune Response

“…Although the loss of recognition of nMCC 88 -103 by the T cell hybridoma 2B4 constituted a negative result, this observation provided the first clear evidence that modification of tyrosine to nitrotyrosine could have an impact on the process of T cell recognition. Previous studies have indicated that Y97 of MCC 88 -103 is not involved in MHC binding (29); however, we wanted to eliminate the possibility that conversion of Y97 to (27,29). Furthermore, these results demonstrate unequivocally that conversion of tyrosine to nitrotyrosine has potentially profound consequences in terms of T cell recognition.…”

“…For this purpose we have used the well-established IE k -restricted peptide from the model Ag moth/pigeon cytochrome c (MCC 88 -103 ). The MCC 88 -103 peptide comprises one of the most extensively studied model systems for understanding MHC restriction and T cell recognition and continues to be widely used as a tool for understanding the processes of T cell tolerance and T cell activation (27,28). The IE k -restricted MCC 88 -103 peptide contains a single tyrosine residue (Y97) that is not involved in MHC binding, but is critically important for T cell recognition (27,29).…”

“…The MCC 88 -103 peptide comprises one of the most extensively studied model systems for understanding MHC restriction and T cell recognition and continues to be widely used as a tool for understanding the processes of T cell tolerance and T cell activation (27,28). The IE k -restricted MCC 88 -103 peptide contains a single tyrosine residue (Y97) that is not involved in MHC binding, but is critically important for T cell recognition (27,29). Using this system we formally demonstrate that conversion of tyrosine to nitrotyrosine has profound consequences in terms of immunological reactivity.…”