Coarse-Grained Brownian Dynamics Simulation of Rule-Based Models

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2013
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Klann, Michael
Paulevé, Loïc
Koeppl, Heinz
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GUPTA, Ashutosh, ed. and others. Computational methods in systems biology : 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013, proceedings. Berlin: Springer, 2013, pp. 64-77. Lecture Notes in Bioinformatics. 8130. ISSN 0302-9743. eISSN 1611-3349. ISBN 978-3-642-40707-9. Available under: doi: 10.1007/978-3-642-40708-6_6
Zusammenfassung

Studying spatial effects in signal transduction, such as colocalization along scaffold molecules, comes at a cost of complexity. In this paper, we propose a coarse-grained, particle-based spatial simulator, suited for large signal transduction models. Our approach is to combine the particle-based reaction and diffusion method, and (non-spatial) rulebased modeling: the location of each molecular complex is abstracted by a spheric particle, while its internal structure in terms of a site-graph is maintained explicit. The particles diffuse inside the cellular compartment and the colliding complexes stochastically interact according to a rulebased scheme. Since rules operate over molecular motifs (instead of full complexes), the rule set compactly describes a combinatorial or even infinite number of reactions. The method is tested on a model of Mitogen Activated Protein Kinase (MAPK) cascade of yeast pheromone response signaling. Results demonstrate that the molecules of the MAPK cascade co-localize along scaffold molecules, while the scaffold binds to a plasma membrane bound upstream component, localizing the whole signaling complex to the plasma membrane. Especially we show, how rings stabilize the resulting molecular complexes and derive the effective dissociation rate constant for it.

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11th International Conference, CMSB 2013, 22. Sept. 2013 - 24. Sept. 2013, Klosterneuburg, Austria
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ISO 690KLANN, Michael, Loïc PAULEVÉ, Tatjana PETROV, Heinz KOEPPL, 2013. Coarse-Grained Brownian Dynamics Simulation of Rule-Based Models. 11th International Conference, CMSB 2013. Klosterneuburg, Austria, 22. Sept. 2013 - 24. Sept. 2013. In: GUPTA, Ashutosh, ed. and others. Computational methods in systems biology : 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013, proceedings. Berlin: Springer, 2013, pp. 64-77. Lecture Notes in Bioinformatics. 8130. ISSN 0302-9743. eISSN 1611-3349. ISBN 978-3-642-40707-9. Available under: doi: 10.1007/978-3-642-40708-6_6
BibTex
@inproceedings{Klann2013Coars-42426,
  year={2013},
  doi={10.1007/978-3-642-40708-6_6},
  title={Coarse-Grained Brownian Dynamics Simulation of Rule-Based Models},
  number={8130},
  isbn={978-3-642-40707-9},
  issn={0302-9743},
  publisher={Springer},
  address={Berlin},
  series={Lecture Notes in Bioinformatics},
  booktitle={Computational methods in systems biology : 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013, proceedings},
  pages={64--77},
  editor={Gupta, Ashutosh},
  author={Klann, Michael and Paulevé, Loïc and Petrov, Tatjana and Koeppl, Heinz}
}
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