Rule-based modeling for protein-protein interaction networks - the cyanobacterial circadian clock as a case study
Year: 2009
Type: conference-paper
Abstract: Rule-based modeling is a new approach to cope with the inherent combinatorial complexity in protein-protein interaction networks, such as cellular signaling pathways.In contrast to reactions that act on chemical species, rules can act on partially specified species.A single rule can thus account for multiple reactions and reflects the limited local context on which most protein-protein interaction events are conditioned on.The cyanobacterial circadian clock is purely protein-based and is centered around the cyclic phosphorylation of the hexameric KaiC protein.Its different phosphorylation states give rise to a combinatorial number of species that would be required for a traditional description.We give a detailed rule-based model, incorporating recent experimental findings of twosite phosphorylation and monomer exchange of the KaiC hexamer.Monte-Carlo sampling of kinetic parameters shows that monomer exchange alone may not be sufficient to synchronize the KaiC hexamers.
Authors: Heinz Koeppl, Marc Hafner, Vincent Danos
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W1914354126