Modelling Ca2+ -dependent proteins in the spine - challenges and solutions
2012
Background / Purpose:
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.
Main conclusion:
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 Ca2+-dependent activation of calmodulin and Ca2+/calmodulin-dependent kinase II (CaMKII) in the spine.
Next steps:
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.
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