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Briefings in Functional Genomics and Proteomics Advance Access originally published online on February 12, 2008
Briefings in Functional Genomics and Proteomics 2008 7(1):17-26; doi:10.1093/bfgp/eln001
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© The Author 2008. Published by Oxford University Press. For permissions, please email: journals.permissions@oxfordjournals.org

Directional and quantitative phosphorylation networks

Claus Jørgensen and Rune Linding

Corresponding author. Rune Linding, Network & Systems Biology Team, Institute of Cancer Research, London, UK. E-mail: rune.linding{at}gmail.com

Directionality in protein signalling networks is due to modulated protein–protein interactions and is fundamental for proper signal progression and response to external and internal cues. This property is in part enabled by linear motifs embedding post-translational modification sites. These serve as recognition sites, guiding phosphorylation by kinases and subsequent binding of modular domains (e.g. SH2 and BRCT). Characterization of such modification-modulated interactions on a proteome-wide scale requires extensive computational and experimental analysis. Here, we review the latest advances in methods for unravelling phosphorylation-mediated cellular interaction networks. In particular, we will discuss how the combination of new quantitative mass-spectrometric technologies and computational algorithms together are enhancing mapping of these largely uncharted dynamic networks. By combining quantitative measurements of phosphorylation events with computational approaches, we argue that systems level models will help to decipher complex diseases through the ability to predict cellular systems trajectories.

Keywords: systems biology, mass spectrometry, network modelling, phosphorylation, quantitation, prediction


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