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-2Kb. Peptide sequence design was accomplished by a combination of an ant colony optimization algorithm with artificial neural network classifiers. Experimental tests yielded nine H-2Kb 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.

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Author:Joanna Marta WisniewskaGND, Natalie Jäger, Anja Freier, Florian O. Losch, Karl-Heinz Wiesmüller, Peter WaldenORCiDGND, Paul WredeORCiDGND, Gisbert SchneiderORCiDGND, Jan Alexander HißORCiDGND
Parent Title (English):Journal of biomedicine and biotechnology
Place of publication:New York, NY
Document Type:Article
Date of Publication (online):2010/09/23
Year of first Publication:2010
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2010/09/23
Issue:Article ID 396847
Page Number:9
First Page:1
Last Page:9
Copyright © 2010 Joanna M.Wisniewska et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Institutes:Biochemie, Chemie und Pharmazie / Biochemie und Chemie
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Sammlung Biologie / Sondersammelgebiets-Volltexte
Licence (German):License LogoCreative Commons - Namensnennung 3.0