title: Comparison of actual and random-positioning-model distributions of peptide scavenging and T cell-presented sites in antigenic proteins.
abstract: In a peptide with a T cell-presented epitope (T site), a folded structure with a hydrophobic surface, 'the scavenger (S) site', may regulate transfer to major histocompatibility complex class II molecules. Three procedures which were proposed to identify T sites selected for amphipathic helical patterns but not T sites. In testing whether S sites lay in or near T sites, we found their linkage was not greater than that generated by a model in which segments of equal length and number to the S and T sites for each protein were distributed at random. This study establishes criteria for evaluation of schemes to predict functional motifs in antigenic proteins.
authors.affiliation: Department of Pharmacology, University of Massachusetts Medical School, North Worcester 01655.
authors.forename: M
authors.initials: M
authors.lastname: Salomon
authors.forename: S
authors.initials: S
authors.lastname: Adams
authors.forename: A
authors.initials: A
authors.lastname: Pardanani
authors.forename: S
authors.initials: S
authors.lastname: Vazquez
authors.forename: R E
authors.initials: RE
authors.lastname: Humphreys
authors.forename: R A
authors.initials: RA
authors.lastname: Lew
mesh_terms: D000595:Amino Acid Sequence; D000941:Antigens / Q000737:chemistry*; D000939:Epitopes; D000949:Histocompatibility Antigens Class II / Q000378:metabolism; D008969:Molecular Sequence Data; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013601:T-Lymphocytes / Q000276:immunology*
chemical_list: D000941:Antigens; D000939:Epitopes; D000949:Histocompatibility Antigens Class II