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Open Access Research article

Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs

Zhongyang Liu1, Qijun Liu12, Hanchang Sun13, Lin Hou14, Hao Guo1, Yunping Zhu1*, Dong Li1* and Fuchu He15*

Author Affiliations

1 State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China

2 Department of Chemistry and Biology, College of Science, National University of Defense Technology, 109 Deya Road, Changsha 410073, China

3 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, 109 Deya Road, Changsha 410073, China

4 School of Mathematical Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China

5 Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, Shanghai 200032, China

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BMC Evolutionary Biology 2011, 11:133  doi:10.1186/1471-2148-11-133

Published: 20 May 2011

Abstract

Background

High-throughput screens have revealed large-scale protein interaction networks defining most cellular functions. How the proteins were added to the protein interaction network during its growth is a basic and important issue. Network motifs represent the simplest building blocks of cellular machines and are of biological significance.

Results

Here we study the evolution of protein interaction networks from the perspective of network motifs. We find that in current protein interaction networks, proteins of the same age class tend to form motifs and such co-origins of motif constituents are affected by their topologies and biological functions. Further, we find that the proteins within motifs whose constituents are of the same age class tend to be densely interconnected, co-evolve and share the same biological functions, and these motifs tend to be within protein complexes.

Conclusions

Our findings provide novel evidence for the hypothesis of the additions of clustered interacting nodes and point out network motifs, especially the motifs with the dense topology and specific function may play important roles during this process. Our results suggest functional constraints may be the underlying driving force for such additions of clustered interacting nodes.