PEPTIDE LENGTH PREFERENCES FOR RAT AND MOUSE MHC CLASS-I MOLECULES USING RANDOM PEPTIDE LIBRARIES

MHC class I molecules bind short peptides for presentation to CD8(+) T cells. The determination of the three-dimensional structure of variou s MHC class I complexes has revealed that both ends of the peptide bin ding site are composed of polar residues conserved among all human and murine MHC class I sequences, which act to lock the ends of the pepti de into the groove. In the rat, however, differences in these importan t residues occur, suggesting the possibility that certain rat MHC clas s I molecules may be able to bind and present longer peptides. Here we have studied the peptide length preferences elf two rat MHC class la molecules expressed in the TAP2-deficient, mouse cell line RMA-S: RT1- A1 degrees, which carries unusual key residues at both ends of the gro ove, and RT1.A(a) which carries the canonical residues. Temperature-de pendent peptide stabilization assays were performed using synthetic ra ndom peptide libraries of different lengths (7-15 amino acids) and suc cessful stabilization was determined by FAGS analysis. Results for two naturally expressed mouse MHC class I molecules revealed different le ngth preferences (H2-K-b, 8-13-mer and H2-D-b, 9-15-mer peptides). The rat MHC class la molecule, RT1-A(a), revealed a preference for 9-15-m er peptides, whereas RT1-A1 degrees showed a more stringent preference for 9-12-mer peptides, thereby ruling out the hypothesis that unusual residues in rat MHC molecules allow binding of longer peptides.