Complexes generated by the binding of free peptides to class II MHC molecules are antigenically diverse compared with those generated by intracellular processing.

We investigated the specificity of T cell hybridomas isolated from mice immunized with synthetic peptides identical in sequence with the dominant, naturally processed, I-Ak-restricted peptides of hen egg lysozyme (HEL). Surprisingly, the majority of hybridomas showed little or no recognition of intact HEL after processing by different APCs. This was not an artifact caused by the use of synthetic peptides since the peptide-specific hybridomas responded to a tryptic digest of HEL or to naturally processed HEL peptides extracted from I-Ak. Thus, the interaction of free peptides with class II MHC molecules can generate complexes that are antigenically dissimilar to those resulting from intracellular processing of intact Ag. This has important implications both for the interpretation of experimental studies that involve peptide immunization and for the efficacy of peptide vaccination as a strategy for intervention in human disease.