Dynamic simulation of protein complex formation on a genomic scale

Bioinformatics. 2005 Apr 15;21(8):1610-6. doi: 10.1093/bioinformatics/bti223. Epub 2004 Dec 14.


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 dynamic 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.

Contact: beyer@imb-jena.de

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

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • Gene Expression Regulation, Fungal / physiology*
  • Genomics / methods
  • Models, Biological*
  • Protein Binding
  • Protein Interaction Mapping / methods*
  • Proteome / metabolism*
  • Saccharomyces cerevisiae / physiology*
  • Saccharomyces cerevisiae Proteins / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Signal Transduction / physiology*


  • Proteome
  • Saccharomyces cerevisiae Proteins