Investigation of a Protein Complex Network

TL;DR

This paper analyzes the structure of the yeast protein complex network, revealing its small-world and scale-free properties, and introduces an evolutionary model based on protein duplication and divergence.

Contribution

It provides the first detailed analysis of the yeast protein complex network's topology and proposes a simple evolutionary model explaining its features.

Findings

The network exhibits small-world and scale-free characteristics.

No strong correlation between weights and degrees of neighboring complexes.

Comparison with a null model highlights non-random network features.

Abstract

The budding yeast {\it 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.