The capacity of purified I-Ad, I-Ed, I-Ak, and I-Ek to bind to protein derived peptides that have been previously reported to be T cell immunogens has been examined. For each of the 12 peptides studied strong binding to the relevant Ia restriction element was observed. All the peptides bound more than one Ia molecule; however, for 11 of 12 peptides, the dominant binding was to the restriction element, whereas in one instance the dominant binding was to a nonrestriction element. When the peptides were used to inhibit the presentation of antigen by prefixed accessory cells to T cells, an excellent correlation was found between the capacity of a peptide to inhibit the binding of an antigen to purified Ia and the capacity of the peptide to inhibit accessory cell presentation of the antigen. Thus, the binding of peptide to purified Ia is immunologically relevant, and Ia seems to be the only saturable molecule on the surface of the accessory cell involved in antigen presentation. Inhibition analysis also indicated that all peptides restricted to a particular Ia molecule competitively inhibited one another, suggesting that each Ia restriction element has a single binding site for antigen. Cross-linking of labeled peptides to Ia followed by electrophoretic analysis and autoradiography suggested that this single binding site is made up of portions of both alpha and beta chains of Ia.

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A detailed analysis of the residues within an immunogenic peptide that endow it with the capacity to interact with Ia and to be recognized by T cells is presented. Ia interacts with only a few of the peptide residues and overall exhibits a very broad specificity. Some residues appear to interact both with Ia and with T cells, leading to a model in which a peptide antigen is 'sandwiched' between Ia and the T-cell receptor.

We have previously experimentally analyzed the structural requirements for interaction between peptide antigens and mouse major histocompatibility complex (MHC) molecules of the d haplotype. We describe here two procedures devised to predict specifically the capacity of peptide molecules to interact with these MHC class II molecules (IAd and IEd). The accuracy of these procedures has been tested on a large panel of synthetic peptides of eukaryotic, prokaryotic, and viral origin, and also on a set of overlapping peptides encompassing the entire staphylococcal nuclease molecule. For both sets of peptides, IAd and 1Ed binding was successfully predicted in =75% of the cases. This suggests that definition of such sequence "motifs" could be of general use in predicting potentially immunogenic peptide regions within proteins.There is at present compelling evidence in support of the concept that T cells recognize a complex formed between major histocompatibility complex (MHC) molecules and "processed" antigen. The structural requirements for this interaction have been the object of intense investigation. In a previous study (1), the effect of a large number of single amino acid substitutions of an ovalbumin-derived peptide that binds strongly to ] on its capacity to bind purified IAd molecules was examined. Significant changes were only detected in a six-amino acid core region ] that had also been strongly implicated as crucial for binding by analysis of a set of N-and C-terminal truncated analogs. In a subsequent study (2), it was demonstrated that unrelated peptides that are good lAd binders contained regions ("motifs") that were structurally similar to each other and to . More recently, it was shown (A.S., L. Adorini, S.B., E.A., and H.M.G., unpublished data) that a different amino acid sequence pattern characterizes the interaction between peptide antigens and the other class II MHC molecule, lEd. The motif recognized by IEd molecules appears to be independent of the motif recognized by IAd and is defined by the presence of positively charged amino acids (refs. 3 and 4; A.S., L. Adorini, S.B., E.A., and H.M.G., unpublished data).In the present study, this information was used to derive a procedure that identifies motifs. Using a large panel of peptides, the presence of either an IAd or IEd motif as determined by this procedure was compared to the experimentally determined capacity of a given peptide to bind IAd and IEd. The peptide data base contained 62 peptides and, in addition, a set of peptides encompassing the entire staphylococcal nuclease molecule. In these sets ofpeptides, IAd and IEd binding was successfully predicted in ==75% of the cases, suggesting that similar procedures should be useful in selecting peptides capable of interacting with other MHC specificities, identify possible autoantigens in self molecules or specific blockers of autoimmune diseases, and because ofthe previously demonstrated strong correlation between MHC binding and immunogenicity (5) be useful in selecting potentially immun...