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Figure 2 | BMC Systems Biology

Figure 2

From: Modeling the evolution of a classic genetic switch

Figure 2

Simulation algorithm and results. a. The deterministic part models galactose transport and protein-protein/galactose interactions. Steady-state concentrations are used to update the system's components but, regardless of the time taken to reach equilibrium, simulation time is not advanced. The state of the system ([Gal4p], and [Gal4-80p], in particular) is then used to update the stochastic propensity functions for protein synthesis via the statistical-mechanical promoter models. The Gillespie algorithm selects a reaction channel and a time, τ containing no protein synthesis or degradation reactions, which is used to update the simulation time. The system's components are updated according to the selected reaction, and the algorithm re-iterates. b. Typical time-series data from a single simulation of the GAL network in S. cerevisiae in very low galactose (10 -7 M). c. Gal1p equilibrium protein distributions obtained from 100 simulations of the S. cerevisiae GAL network in very low galactose. d. Induction-response curves were constructed from equilibrium protein distributions in increasing concentrations of galactose. Bars indicate +/- standard deviation. Prior to the WGD, the bi-functional Gal1/3p molecule served as the network's co-inducer and galactokinase.

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