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.
pp. 87-90, Aarhus, Denmark, Proceedings of the International Workshop on Computational Systems Biology (WCSB), [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... |
Export: | |
Suche nach Titel in: | TUfind oder in Google |
![]() |
Send an inquiry |
Options (only for editors)
![]() |
Show editorial Details |