An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries.
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.
Udaka
K
K
Department of Biophysics, Kyoto University, Sakyo, Japan. keiko@molbio.biophys.kyoto-u.ac.jp
Wiesmüller
K H
KH
Kienle
S
S
Jung
G
G
Tamamura
H
H
Yamagishi
H
H
Okumura
K
K
Walden
P
P
Suto
T
T
Kawasaki
T
T
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
D018984:Epitopes, T-Lymphocyte; D006183:H-2 Antigens; D064532:Histocompatibility Antigen H-2D; D015395:Histocompatibility Antigens Class I; D019151:Peptide Library; D010455:Peptides