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Structural features for peptides binding the class I molecules

Examination of the MHC crystal structures indicate that key peptide binding positions are defined pockets within the groove of a particular allele of class I molecules; for example, for H-2Kb, the high-affinity binding of ovalbumin peptide SIINFEKL requires P5 to be occupied F/Y, and P8 to have L/I, and other peptides that lack these anchoring amino acids would bind with such a low affinity that would be unable to induce, or be effective targets for CTLs. Using MUC1 8 or 9mers as model peptides, we were able to demonstrate the following: (1) these bind with low affinity; (2) the binding is unusual and the peptides loop out of the groove - indeed, the 9mer loops out so much it can be detected by monoclonal anti-MUC1 peptide antibody; and (3) crystallization structures of Kb with the 8mer (SAPDTRPA) demonstrates that MUC1 and SIINFEKL have an identical shape within the groove, the only difference being imposed by the side chains, which are selectively recognized by T-cell receptor. The amino acids occupied in the specific anchoring pockets are small hydrophobic, rather than long/large hydrophobic F/Y or L/I residues, thus the low affinity of the MUC1 peptide. The implication of the studies is that the rules for high-affinity binding in generation of CTL hold, but that these are not fixed rules: low-affinity peptides bind, and indeed with the same general conformation and shape as high-affinity peptides in one dimension; in another they are clearly more 'flexible'.

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McKenzie, I., Apostolopoulos, V., Mu, Y. et al. Structural features for peptides binding the class I molecules. Breast Cancer Res 3 (Suppl 1), A40 (2001).

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