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voit1

voit1

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Parameters

Global parameters

Fixed species

Initial values

Functions and Rules

Assignment rules

flux_X5_in = 11.06 * pow(X2, 0.04) * pow(X3, 0.32) * pow(X4, 0.16) * pow(X14, 0.6) * pow(X15f, 0.4)

flux_X3_out = 76.434 * pow(X2, -0.412) * pow(X3, 0.593) * pow(X12r, 0.718) * pow(X13, 0.18) * pow(X15f, 0.103)

flux_X2_out = 30.12 * pow(X1, -0.00333) * pow(X2, 0.575) * pow(X3, -0.17) * pow(X4, 0.00333) * pow(X10, 0.5111) * pow(X11, 0.0667) * pow(X12f, 0.411) * pow(X17, 0.0111)

flux_X1_in = 31.912 * pow(X0, 0.968) * pow(X2, -0.194) * pow(X7, 0.00968) * pow(X8, 0.968) * pow(X19, 0.0323)

flux_X1_out = 89.935 * pow(X1, 0.75) * pow(X6, -0.4) * X9

flux_X2_in = 142.72 * pow(X1, 0.517) * pow(X2, -0.179) * pow(X3, 0.183) * pow(X6, -0.276) * pow(X9, 0.689) * pow(X12r, 0.311)

flux_X3_in = 7.8819 * pow(X2, 0.394) * pow(X3, -0.392) * pow(X4, -0.01) * pow(X5, 0.0128) * pow(X12f, 0.949) * pow(X15r, 0.0513)

flux_X4_in = 11.07 * pow(X3, 0.5) * X13

flux_X4_out = 3.4556 * pow(X1, -0.0429) * pow(X2, 0.214) * pow(X4, 0.386) * pow(X14, 0.857) * pow(X17, 0.143)

flux_X5_out = 4.929 * pow(X2, -0.04) * pow(X4, -0.04) * pow(X5, 0.25) * pow(X15r, 0.2) * pow(X16, 0.8)

flux_X6_in = 0.19424 * pow(X1, -0.3) * pow(X2, 0.3) * pow(X4, 0.3) * X17

flux_X6_out = 1.0939 * pow(X6, 0.2) * X18

flux_X7_in = 1.0939 * pow(X6, 0.2) * X18

flux_X7_out = 1.2288 * pow(X7, 0.3) * X19

X8 = piecewise(8.0, eq(heat_shock, 1.0), 1.0)

X9 = piecewise(1.0, eq(heat_shock, 8.0), 1.0)

X10 = piecewise(1.0, eq(heat_shock, 1.0), 1.0)

X11 = piecewise(1.0, eq(heat_shock, 6.0), 1.0)

X12f = piecewise(1.0, eq(heat_shock, 16.0), 1.0)

X12r = piecewise(16.0, eq(heat_shock, 1.0), 1.0)

X13 = piecewise(16.0, eq(heat_shock, 1.0), 1.0)

X14 = piecewise(1.0, eq(heat_shock, 16.0), 1.0)

X15f = piecewise(1.0, eq(heat_shock, 50.0), 1.0)

X15r = piecewise(50.0, eq(heat_shock, 1.0), 1.0)

X16 = piecewise(16.0, eq(heat_shock, 1.0), 1.0)

X17 = piecewise(1.0, eq(heat_shock, 12.0), 1.0)

X18 = piecewise(18.0, eq(heat_shock, 1.0), 1.0)

X19 = piecewise(1.0, eq(heat_shock, 6.0), 1.0)

Function definitions

Events

Constraints

Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.


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Biochemical and genomic regulation of the trehalose cycle in yeast: review of observations and canonical model analysis.

  • Eberhard O Voit
J. Theor. Biol. 2003; 223 (1): 55
Abstract
The physiological hallmark of heat-shock response in yeast is a rapid, enormous increase in the concentration of trehalose. Normally found in growing yeast cells and other organisms only as traces, trehalose becomes a crucial protector of proteins and membranes against a variety of stresses, including heat, cold, starvation, desiccation, osmotic or oxidative stress, and exposure to toxicants. Trehalose is produced from glucose 6-phosphate and uridine diphosphate glucose in a two-step process, and recycled to glucose by trehalases. Even though the trehalose cycle consists of only a few metabolites and enzymatic steps, its regulatory structure and operation are surprisingly complex. The article begins with a review of experimental observations on the regulation of the trehalose cycle in yeast and proposes a canonical model for its analysis. The first part of this analysis demonstrates the benefits of the various regulatory features by means of controlled comparisons with models of otherwise equivalent pathways lacking these features. The second part elucidates the significance of the expression pattern of the trehalose cycle genes in response to heat shock. Interestingly, the genes contributing to trehalose formation are up-regulated to very different degrees, and even the trehalose degrading trehalases show drastically increased activity during heat-shock response. Again using the method of controlled comparisons, the model provides rationale for the observed pattern of gene expression and reveals benefits of the counterintuitive trehalase up-regulation.
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000266) Biomodels notes: Table of steady state concentrations and fluxes of the model with and without heat shock. The calculations were performed using Copasi. The article does not give much quantitative data for the behavior under heat shock, the approximate fold changes of steady state concentrations can be found in section 5.2.1. "Biochemical consequences of heat shock" of the article. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.