RELATIVE IMPLICATION OF PEPTIDE RESIDUES IN BINDING TO MAJOR HISTOCOMPATIBILITY COMPLEX CLASS-I H-2D(B) - APPLICATION TO THE DESIGN OF HIGH-AFFINITY, ALLELE-SPECIFIC PEPTIDES

The H-2D(b) peptide sequence SMIENLEYM was manipulated (N-and C-termin us truncation and alanine substitution) to determine the role of struc tural elements (peptide ends and residue side chains) in binding to H- 2D(b). We found that good binding affinity could be obtained by compen sating the minimal binding condition for one element by the optimal co ndition of the other element. In particular, we showed, that although the minimal binding sequence could be as short as a heptamer (deletion of positions 1 and 2), it needed the presence of optimal amino acids at other positions (IENLEYM). Conversely, the structurally minimal pep tide would accept multiple alanine residues, but required the optimal nonameric length (AAAENAEAA). Positions 1, 2, 3, 4, 5, 7 and 9, but no t 6 and 8, were involved in the H-2D(b)-peptide interaction. Most resi dues interacted directly with the MHC molecule via their main chain (a mino and carboxyl) atoms (positions 1 and 2), their side chains (posit ions 3 and 5), or both (position 9). Positions 4 and 7 were found to p lay an indirect role, probably by influencing the secondary structure. At the C-terminus, the presence of a residue at position 9, but not t he hydrophobic nature of its side chain, was mandatory for binding. At the N-terminus, the role of the residue at position 1 was of either m inor or critical importance depending on the presence or not of a stro ng auxiliary anchor at position 3. The indirect contribution of residu e side chains at positions 4 and 7 reflected the importance of dynamic components in the binding process. Based on these results, we designe d a series of high-affinity, H-2D(b) selective peptides derived from t he sequence X(1) AIX(4)NAEAL, where X(1) = Y or K and X(4) = E or K. A fter radioiodination or fluorescent (FITC) labelling, these peptides b ound strongly and specifically to the surface of viable H-2D(b)-expres sing cells. Rationally designed synthetic peptides, either alone or in a stable complex with MHC, might be of value for controlling CTL acti vity.