HLA CLASS-I BINDING MOTIFS DERIVED FROM RANDOM PEPTIDE LIBRARIES DIFFER AT THE COOH TERMINUS FROM THOSE OF ELUTED PEPTIDES

Recombinant HLA-A2, HLA-B8, or HLA-B53 heavy chain produced in Escheri chia call was combined with recombinant beta(2)-microglobulin (beta(2) m) and a pool of randomly synthesised nonamer peptides. This mixture w as allowed to refold to form stable major histocompatability complex ( MHC) class I complexes, which were then purified by gel filtration chr omatography. The peptides bound to the MHC class I molecules were subs equently eluted and sequenced as a pool. Peptide binding motifs for th ese three MHC class I molecules were derived and compared with previou sly described motifs derived ti-om analysis of naturally processed pep tides eluted from the surface of cells. This comparison indicated that the peptides bound by the recombinant MHC class I molecules showed a similar motif to naturally processed and presented peptides, with the exception of the peptide COOH terminus. Whereas the motifs derived fro m naturally processed peptides eluted from HLA-A2 and HLA-B8 indicated a strong preference for hydrophobic amino acids at the COOH terminus, this preference was not observed in our studies. We propose that this difference reflects the effects of processing or transport on the pep tide repertoire available for binding to MHC class I molecules in vivo .