Eur. Phys. J. B 41, 113-121 (2004)
https://doi.org/10.1140/epjb/e2004-00301-0

Investigation of a protein complex network

¹ Institute of Biochemistry and Biophysics, P.O. Box 13145-1384, Tehran, Iran and School of Medicine, Tehran University, P.O. Box 14155-6447, Tehran, Iran
² Department of Physics, Sharif University of Technology, P.O. Box 11365-9161, Tehran, Iran

Corresponding authors: ^a mashaghi@ibb.ut.ac.ir - ^b ramzanpour@mehr.sharif.edu - ^b vahid@sharif.edu

Received: 8 December 2003
Revised: 21 April 2004
Published online: 30 September 2004

Abstract

The budding yeast Saccharomyces cerevisiae is the first eukaryote whose genome has been completely sequenced. It is also the first eukaryotic cell whose proteome (the set of all proteins) and interactome (the network of all mutual interactions between proteins) has been analyzed. In this paper we study the structure of the yeast protein complex network in which weighted edges between complexes represent the number of shared proteins. It is found that the network of protein complexes is a small world network with scale free behavior for many of its distributions. However we find that there are no strong correlations between the weights and degrees of neighboring complexes. To reveal non-random features of the network we also compare it with a null model in which the complexes randomly select their proteins. Finally we propose a simple evolutionary model based on duplication and divergence of proteins.