Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks

The modular architecture of protein-protein interaction (PPI) networks is evident in diverse species with a wide range of complexity. However, the molecular components that lead to the evolution of modularity in PPI networks have not been clearly identified. Here, we show that weak domain-linear mot...

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Bibliographic Details
Published in:PLoS computational biology 2014-10, Vol.10 (10), p.e1003881-e1003881
Main Authors: Kim, Inhae, Lee, Heetak, Han, Seong Kyu, Kim, Sanguk
Format: Article
Language:English
Subjects:
Analysis
Animals
Biological Evolution
Biology and Life Sciences
Computational Biology - methods
Genetic variation
Humans
Medical research
Mice
Models, Biological
Peptides
Phenotype
Protein Interaction Maps - physiology
Protein Structure, Tertiary
Protein-protein interactions
Proteins
Social networks
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Summary:The modular architecture of protein-protein interaction (PPI) networks is evident in diverse species with a wide range of complexity. However, the molecular components that lead to the evolution of modularity in PPI networks have not been clearly identified. Here, we show that weak domain-linear motif interactions (DLIs) are more likely to connect different biological modules than strong domain-domain interactions (DDIs). This molecular division of labor is essential for the evolution of modularity in the complex PPI networks of diverse eukaryotic species. In particular, DLIs may compensate for the reduction in module boundaries that originate from increased connections between different modules in complex PPI networks. In addition, we show that the identification of biological modules can be greatly improved by including molecular characteristics of protein interactions. Our findings suggest that transient interactions have played a unique role in shaping the architecture and modularity of biological networks over the course of evolution.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1003881