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Advances in Bioinformatics
Volume 2011 (2011), Article ID 457578, 7 pages
http://dx.doi.org/10.1155/2011/457578
Research Article

Computational Design of a DNA- and Fc-Binding Fusion Protein

1Department of Bioinformatics, Center for Medical Biotechnology, University of Duisburg-Essen, Universitaetsstraβe 1-5, 45117 Essen, Germany
2Department of Electrical and Electronic Engineering, University of Cagliari, Piazza d'Armi, 09123 Cagliari, Italy

Received 29 April 2011; Revised 16 June 2011; Accepted 22 June 2011

Academic Editor: Shandar Ahmad

Copyright © 2011 Jonas Winkler 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

Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. In this work, we generated and optimized a new synthetic fusion protein using an evolutionary approach. The optimization was guided by directed evolution based on hydrophobicity scores, molecular weight, and secondary structure predictions. Several methods were used to refine the models built from the resulting sequences. We have successfully combined two unrelated naturally occurring binding sites, the immunoglobin Fc-binding site of the Z domain and the DNA-binding motif of MyoD bHLH, into a novel stable protein.