Theoretical & Computational Neuroscience | Neuronal Signaling Mechanisms | Theory & Simulation
Modelling Ca 2+ -dependent proteins in the spine – challenges and solutions
Melanie I Stefan*, Shirley Pepke, Stefan Mihalas, Thomas Bartol, Terrence Sejnowski, Mary B Kennedy
*Corresponding author: Melanie I Stefan
Biology Division, California Institute of Technology, Pasadena, CA, USA
F1000Posters 2012, 3: 1454 (poster) [English]
Poster [15.30 MB]
Neuroinformatics 2012, 5 - 7 Sep 2012, P56
International Neuroinformatics Coordinating Facility (INCF)
Modelling post-synaptic proteins poses three technical problems: small absolute molecule numbers, large numbers of possible states, and the complex geometry of the spine, which is not a well-mixed compartment. Computational approaches are needed that solve all three of these problems.
Stochastic simulation methods can be used for systems with small molecule numbers, agent-based methods to represent multi-state molecules, and spatial methods to simulate events in complex geometries. We used the agent-based spatial stochastic simulator MCell to model the Ca 2+-dependent activation of calmodulin and Ca 2+/calmodulin-dependent kinase II (CaMKII) in the spine.
Next steps will include the extension of our model to include more interaction partners, and to represent some of the regulation events in more detail.
Figure 1 was reproduced with kind permission from Kennedy et al (2005) Nat Rev Neurosci 6(6):423-34.
Figure 8 was reproduced with kind permission from Endler et al (2012) Computational Systems Neurobiology Le Novere N (Ed.), Springer.
No relevant competing interests disclosed.
NIH/NSF Collaborative Research in Neurosciences (CRCNS), DA030749
European Molecular Biology Organisation (EMBO), Post-doctoral fellowship
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