MHC I stabilizing potential of computer-designed octapeptides.
Experimental results are presented for 180 in silico designed octapeptide sequences and their stabilizing effects on the major histocompatibility class I molecule H-2K(b). Peptide sequence design was accomplished by a combination of an ant colony optimization algorithm with artificial neural network classifiers. Experimental tests yielded nine H-2K(b) stabilizing and 171 nonstabilizing peptides. 28 among the nonstabilizing octapeptides contain canonical motif residues known to be favorable for MHC I stabilization. For characterization of the area covered by stabilizing and non-stabilizing octapeptides in sequence space, we visualized the distribution of 100,603 octapeptides using a self-organizing map. The experimental results present evidence that the canonical sequence motives of the SYFPEITHI database on their own are insufficient for predicting MHC I protein stabilization.
Wisniewska
Joanna M
JM
Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Siesmayerstrasse. 70, 60323 Frankfurt am Main, Germany.
Jäger
Natalie
N
Freier
Anja
A
Losch
Florian O
FO
Wiesmüller
Karl-Heinz
KH
Walden
Peter
P
Wrede
Paul
P
Schneider
Gisbert
G
Hiss
Jan A
JA