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Bioinformatics Advance Access published online on December 14, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti223
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received October 10, 2004
Revised November 3, 2004
Accepted November 4, 2004

Article

Dynamic simulation of protein complex formation on a genomic scale

A. Beyer 1* and T. Wilhelm 1

1 Theoretical Systems Biology, Institute of Molecular Biotechnology, Beutenbergstr. 11, 07745 Jena, Germany

* To whom correspondence should be addressed.
A. Beyer, E-mail: beyer{at}imb-jena.de


  Abstract

Motivation: One of the central questions in the post-genomic era is the understanding of protein-protein interactions and of protein complex formation. It has been observed that protein complex size distributions of the yeast Saccharomyces cerevisiae decay exponentially. The shape of these size distributions reflects mechanisms of protein complex association and dissociation.

Results: We present the most simple dynamical model that is able to reproduce the observed protein complex size distribution for yeast. This protein association-dissociation model (PAD-model) simulates the dynamics of protein complex formation on a genomic scale for about 50 million protein molecules. By ruling out different model variants it is possible to elucidate fundamental features of the protein complex dynamics, e.g. complex association is independent of complex size. In addition, the PAD-model provides information about the complexity of the yeast proteome and it gives an idea of how many complexes could not be identified during the measurements.

Availability: All programs used for this publication are available on request from the authors.

Supplementary Information: Supplementary information about the model and its interpretation can be downloaded from http://www.imb-jena.de/tsb/pad.


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