Hafner, M. ; Danos, V. ; Koeppl, H. (2009)
Rule-based modeling for protein-protein interaction networks - the Cyanobacterial circadian clock as a case studyproceedings.
Proceedings of the International Workshop on Computational Systems Biology (WCSB).
Konferenzveröffentlichung, Bibliographie
Kurzbeschreibung (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.
| Typ des Eintrags: | Konferenzveröffentlichung |
|---|---|
| Erschienen: | 2009 |
| Autor(en): | Hafner, M. ; Danos, V. ; Koeppl, H. |
| Art des Eintrags: | Bibliographie |
| Titel: | Rule-based modeling for protein-protein interaction networks - the Cyanobacterial circadian clock as a case studyproceedings |
| Sprache: | Englisch |
| Publikationsjahr: | 2009 |
| Ort: | Aarhus, Denmark |
| Veranstaltungstitel: | Proceedings of the International Workshop on Computational Systems Biology (WCSB) |
| URL / URN: | http://citeseerx.ist.psu.edu/viewdoc/summary;jsessionid=D87D... |
| Kurzbeschreibung (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. |
| Fachbereich(e)/-gebiet(e): | 18 Fachbereich Elektrotechnik und Informationstechnik 18 Fachbereich Elektrotechnik und Informationstechnik > Institut für Nachrichtentechnik > Bioinspirierte Kommunikationssysteme 18 Fachbereich Elektrotechnik und Informationstechnik > Institut für Nachrichtentechnik |
| Hinterlegungsdatum: | 04 Apr 2014 13:06 |
| Letzte Änderung: | 23 Sep 2021 14:32 |
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