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arXiv · 0711.4512

Eliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch

M. J. Morelli·R. J. Allen·S. Tanase-Nicola·P. R. ten Wolde
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Abstract

In many stochastic simulations of biochemical reaction networks, it is desirable to ``coarse-grain'' the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed, but it remains unclear which methods are reliable and which reactions can safely be eliminated. We address these issues for a model gene regulatory network that is particularly sensitive to dynamical fluctuations: a bistable genetic switch. We remove protein-DNA and/or protein-protein association-dissociation reactions from the reaction set, using various coarse-graining strategies. We determine the effects on the steady-state probability distribution function and on the rate of fluctuation-driven switch flipping transitions. We find that protein-protein interactions may be safely eliminated from the reaction set, but protein-DNA interactions may not. We also find that it is important to use the chemical master equation rather than macroscopic rate equations to compute effective propensity functions for the coarse-grained reactions.

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M. J. Morelli, R. J. Allen, S. Tanase-Nicola, P. R. ten Wolde. 2007-11-28. Eliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch. https://doi.org/10.1063/1.2821957

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