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Rule-based modeling for protein-protein interaction networks - the Cyanobacterial circadian clock as a case studyproceedings

Hafner, M. and Danos, V. and Koeppl, H. (2009):
Rule-based modeling for protein-protein interaction networks - the Cyanobacterial circadian clock as a case studyproceedings.
Aarhus, Denmark, In: Proceedings of the International Workshop on Computational Systems Biology (WCSB), [Online-Edition: http://citeseerx.ist.psu.edu/viewdoc/summary;jsessionid=D87D...],
[Conference or Workshop Item]

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.

Item Type: Conference or Workshop Item
Erschienen: 2009
Creators: Hafner, M. and Danos, V. and Koeppl, H.
Title: Rule-based modeling for protein-protein interaction networks - the Cyanobacterial circadian clock as a case studyproceedings
Language: English
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.

Place of Publication: Aarhus, Denmark
Divisions: 18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications > Bioinspired Communication Systems
18 Department of Electrical Engineering and Information Technology
18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications
Event Title: Proceedings of the International Workshop on Computational Systems Biology (WCSB)
Date Deposited: 04 Apr 2014 13:06
Official URL: http://citeseerx.ist.psu.edu/viewdoc/summary;jsessionid=D87D...
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