title: Truncation variants of peptides isolated from MHC class II molecules suggest sequence motifs.
abstract: T cells recognize foreign protein antigens in the form of peptide fragments bound tightly to the outer aspect of molecules encoded by the major histocompatibility complex (MHC). Most of the amino-acid differences that distinguish MHC allelic variants line the peptide-binding cleft, and different allelic forms of MHC molecules bind distinct peptides. It has been demonstrated that peptide-binding to MHC class I involves anchor residues in certain positions and that antigenic peptides associated with MHC class I exhibit allele-specific structural motifs. We have previously reported an analysis of MHC class II-associated peptide sequences. Here we extend this analysis and show that certain amino-acid residues occur at particular positions in the sequence of peptides binding to a given MHC class II molecule. These sequence motifs require the amino terminus to be shifted one or two positions to obtain alignment; such shifts occur naturally for a single peptide sequence without qualitatively altering CD4 T-cell recognition.
authors.affiliation: ImmuLogic Pharmaceutical Corporation, Palo Alto, California 94304.
authors.lastname: Rudensky AYu
authors.forename: P
authors.initials: P
authors.lastname: Preston-Hurlburt
authors.forename: B K
authors.initials: BK
authors.lastname: al-Ramadi
authors.forename: J
authors.initials: J
authors.lastname: Rothbard
authors.forename: C A
authors.initials: CA
authors.lastname: Janeway
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000937:Antigen-Antibody Reactions; D001426:Bacterial Proteins / Q000502:physiology*; D001666:Binding Sites, Antibody; D002460:Cell Line; D002851:Chromatography, High Pressure Liquid; D000949:Histocompatibility Antigens Class II / Q000276:immunology*; D007074:Immunoglobulin G / Q000737:chemistry / Q000276:immunology; D007143:Immunoglobulin Heavy Chains / Q000737:chemistry / Q000276:immunology; D007135:Immunoglobulin Variable Region / Q000737:chemistry / Q000276:immunology; D051379:Mice; D008810:Mice, Inbred C57BL; D008969:Molecular Sequence Data; D010446:Peptide Fragments; D011990:Receptors, Transferrin / Q000737:chemistry; D012097:Repressor Proteins / Q000502:physiology*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013601:T-Lymphocytes / Q000276:immunology; D014759:Viral Envelope Proteins / Q000737:chemistry / Q000276:immunology
chemical_list: D001426:Bacterial Proteins; D000949:Histocompatibility Antigens Class II; C024138:I-E-antigen; D007074:Immunoglobulin G; D007143:Immunoglobulin Heavy Chains; D007135:Immunoglobulin Variable Region; D010446:Peptide Fragments; D011990:Receptors, Transferrin; D012097:Repressor Proteins; D014759:Viral Envelope Proteins; C060486:methionine repressor protein, Bacteria