Eliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch.
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.
Morelli
Marco J
MJ
FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands.
Allen
Rosalind J
RJ
Tănase-Nicola
Sorin
S
ten Wolde
Pieter Rein
PR
D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D011336:Probability; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013269:Stochastic Processes; D013997:Time Factors
D011506:Proteins; D004247:DNA