Kim Inhae, Lee Heetak, Han Seong Kyu, Kim Sanguk
Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea.
Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea.
PLoS Comput Biol. 2014 Oct 9;10(10):e1003881. doi: 10.1371/journal.pcbi.1003881. eCollection 2014 Oct.
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.
蛋白质-蛋白质相互作用（PPI）网络的模块化架构在具有广泛复杂性的多种物种中都很明显。然而，导致PPI网络模块化进化的分子成分尚未被明确识别。在这里，我们表明，与强结构域-结构域相互作用（DDI）相比，弱结构域-线性基序相互作用（DLI）更有可能连接不同的生物模块。这种分子层面的分工对于多种真核生物复杂PPI网络中模块化的进化至关重要。特别是，DLI可能补偿了复杂PPI网络中不同模块之间连接增加所导致的模块边界减少。此外，我们表明，通过纳入蛋白质相互作用的分子特征，可以大大改善生物模块的识别。我们的研究结果表明，在进化过程中，瞬时相互作用在塑造生物网络的架构和模块化方面发挥了独特作用。
