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

Marco J. Morelli, Rosalind J. Allen, Sorin Tanase-Nicola, Pieter Rein ten Wolde

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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. (C) 2008 American Institute of Physics.

Original languageEnglish
Article number045105
Pages (from-to)-
Number of pages13
JournalThe Journal of Chemical Physics
Volume128
Issue number4
DOIs
Publication statusPublished - 28 Jan 2008

Keywords / Materials (for Non-textual outputs)

  • COUPLED CHEMICAL-REACTIONS
  • REPRESSOR
  • EQUILIBRIUM
  • ALGORITHM
  • KINETICS
  • SYSTEMS
  • MODELS

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