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Journal of Biomedicine and Biotechnology
Volume 2010, Article ID 396847, 9 pages
http://dx.doi.org/10.1155/2010/396847
Research Article

MHC I Stabilizing Potential of Computer-Designed Octapeptides

1Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Siesmayerstraße. 70, 60323 Frankfurt am Main, Germany
2Clinical Research Group Tumor Immunologie, Skin Cancer Center Charité, Clinic of Dermatology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
3Institut für Organische Chemie, Universität Tübingen, Auf der Morgenstelle 18, 74076 Tübingen, Germany
4Institute of Molecular Biology and Bioinformatics, Charité-Universitätsmedizin Berlin, Arnimallee 22, 14195 Berlin, Germany
5Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Street. 10, 8093 Zürich, Switzerland

Received 28 September 2009; Revised 27 January 2010; Accepted 8 March 2010

Academic Editor: Yongqun Oliver He

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.

Abstract

Experimental results are presented for 180 in silico designed octapeptide sequences and their stabilizing effects on the major histocompatibility class I molecule H - 2 K 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 - 2 K 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.