title: An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries.
abstract: Specificities of three mouse major histocompatibility complex (MHC) class I molecules, Kb, Db, and Ld, were analyzed by positional scanning using combinatorial peptide libraries. The result of the analysis was used to create a scoring program to predict MHC-binding peptides in proteins. The capacity of the scoring was then challenged with a number of peptides by comparing the prediction with the experimental binding. The score and the experimental binding exhibited a linear correlation but with substantial deviations of data points. Statistically, for approximately 80% of randomly chosen peptides, MHC-binding capacity could be predicted within one log concentration of peptides for a half-maximal binding. Known cytotoxic T-lymphocyte epitope peptides could be predicted, with a few exceptions. In addition, frequent findings of MHC-binding peptides with incomplete or no anchor amino acid(s) suggested a substantial bias introduced by natural antigen processing in peptide selection by MHC class I molecules.
authors.affiliation: Department of Biophysics, Kyoto University, Sakyo, Japan. keiko@molbio.biophys.kyoto-u.ac.jp
authors.forename: K
authors.initials: K
authors.lastname: Udaka
authors.forename: K H
authors.initials: KH
authors.lastname: Wiesmüller
authors.forename: S
authors.initials: S
authors.lastname: Kienle
authors.forename: G
authors.initials: G
authors.lastname: Jung
authors.forename: H
authors.initials: H
authors.lastname: Tamamura
authors.forename: H
authors.initials: H
authors.lastname: Yamagishi
authors.forename: K
authors.initials: K
authors.lastname: Okumura
authors.forename: P
authors.initials: P
authors.lastname: Walden
authors.forename: T
authors.initials: T
authors.lastname: Suto
authors.forename: T
authors.initials: T
authors.lastname: Kawasaki
mesh_terms: D000818:Animals; D017951:Antigen Presentation / Q000276:immunology*; D001331:Automation; D001665:Binding Sites; D002460:Cell Line; D018984:Epitopes, T-Lymphocyte / Q000276:immunology; D006183:H-2 Antigens / Q000276:immunology; D064532:Histocompatibility Antigen H-2D; D015395:Histocompatibility Antigens Class I / Q000276:immunology* / Q000378:metabolism; D008285:Major Histocompatibility Complex / Q000276:immunology*; D051379:Mice; D019151:Peptide Library; D010455:Peptides / Q000276:immunology* / Q000378:metabolism
chemical_list: D018984:Epitopes, T-Lymphocyte; D006183:H-2 Antigens; D064532:Histocompatibility Antigen H-2D; D015395:Histocompatibility Antigens Class I; D019151:Peptide Library; D010455:Peptides