Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis.
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 IEd binding was successfully predicted in approximately 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.
Sette
A
A
Cytel, La Jolla, CA 92037.
Buus
S
S
Appella
E
E
Smith
J A
JA
Chesnut
R
R
Miles
C
C
Colon
S M
SM
Grey
H M
HM
D000595:Amino Acid Sequence; D000818:Animals; D000941:Antigens / Q000276:immunology*; D001665:Binding Sites; D005057:Eukaryotic Cells; D006239:Haplotypes; D000949:Histocompatibility Antigens Class II / Q000276:immunology*; D051379:Mice; D008969:Molecular Sequence Data; D010047:Ovalbumin / Q000276:immunology; D011387:Prokaryotic Cells; D011506:Proteins / Q000276:immunology*; D014764:Viral Proteins / Q000276:immunology
D000941:Antigens; D000949:Histocompatibility Antigens Class II; D011506:Proteins; D014764:Viral Proteins; D010047:Ovalbumin