Binding of alanine-substituted peptides to the MHC class I protein, K^d

Peptides eluted from the native MHC class I molecule, K^d, are generally nonamers that display a strong preference for Tyr in position 2. We investigated the molecular basis for this 'consensus motif' by synthesizing a virally derived peptide, NP 147-155, that is known to be presented by K^d on living cells, and peptide variants of NP 147-155 in which the amino acids in the different positions were sequentially replaced by Ala. All of the peptides bound to purified K^d molecules in vitro with high affinity, except for the peptide in which Tyr² was replaced by Ala, for which the affinity for K^d decreased at least 100-fold. These results confirm the interpretation of the in vivo studies; namely, that Tyr² is a critical anchor residue. for binding to K^d.