Peptide length variants p2Ca and QL9 present distinct conformations to Ld-specific T cells

Recent advances have provided insights into how the TCR interacts with MHC/peptide complexes and a rationale to predict optimal epitopes for MHC binding and T cell recognition. For example, peptides of nine residues are predicted to be optimal for binding to H2-L-d, although 8 mer epitopes have also been identified. It has been predicted that 8 mer and 9 mer length variant peptides bound to Ld present identical epitopes to T cells. However, in contrast to this prediction, we demonstrate here that the 8 mer peptide p2Ca and its 9 mer length variant QL9, extended by an N-terminal glutamine, assume distinct conformations when bound to L-d. We generated self-L-d -restricted CTL clones specific for p2Ca that recognize L-d/QL9 poorly if at all. This result is in sharp contrast to what has been observed with L-d-alloreactive T cells that possess a much higher affinity for L-d/QL9 than for L-d /p2Ca. Alanine substitutions of the N-terminal residues of the QL9 peptide rescue detection by these self-L-d/p2Ca-specific T cells, but decrease recognition by the L-d-alloreactive 2C T cell clone. In addition, 2C T cell recognition of the p2Ca peptide is affected by different alanine substitutions compared with 2C T cell recognition of the QI,9 peptide. These data clearly demonstrate that the p2Ca and QL9 peptides assume distinct conformations when bound to L-d and, furthermore, demonstrate that there is flexibility in peptide binding within the MHC class I cleft.