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MHC I stabilizing potential of computer-designed octapeptides.

ABSTRACT: 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.

SUBMITTER: Wisniewska JM

PROVIDER: S-EPMC2876253 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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MHC I stabilizing potential of computer-designed octapeptides.

Wisniewska Joanna M JM 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

Journal of biomedicine & biotechnology 20100525

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 M ...[more]

PMID: 20508831

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