Residues outside of the HLA-A2 peptide-binding groove can abrogate or enhance recognition of influenza virus matrix peptide pulsed cells by cytotoxic T lymphocytes.

An examination of the crystal structure of HLA-A2.1 reveals two classes of residues on the class I MHC molecule that could affect CTL recognition: (1) those predicted to interact with the TCR directly; and (2) those that interact with bound peptides. To examine the role of individual TCR contacting residues, as well as residues not predicted to interact with bound peptide or the TCR, a panel of 28 HLA-A2 variants that differ from each other by a single amino acid substitution in either the alpha 1- or alpha 2-domain was utilized. Peptide titration, time course and cold target inhibition analysis of these targets showed that only the substitution of position 62 in the alpha 1-domain had a significant effect on recognition of the MHC-peptide complex by influenza matrix protein M1 (57-68) peptide-specific, HLA-A2.1-restricted CTL. In contrast, substitutions at positions 154, 162 and 163 in the alpha 2-domain abolished recognition by the same CTL. Additionally, substitutions at position 138 in the alpha 2-domain and positions 107 and 127 on the loops connecting the beta-strand in the alpha 2-domain were recognized in a more efficient, heteroclitic fashion. Overall, there was no direct correlation between the level of peptide binding to the variants and the level of T cell recognition of the variants. These results indicate that residues in the alpha 2-domain may be more important than residues in the alpha 1-domain in controlling TCR binding to the class I MHC molecule and suggest that the "footprint" of the TCR may be more extensive than previously predicted and encompass a broad region that extends beyond the alpha 2-helix. These findings also imply that the class I MHC molecule may exist in a "tipped" orientation on the cell surface during T cell recognition.