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montanez1

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montanez1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000191). Biomodels notes: "Time courses and steady states for the model, calculated using SBMLODESolver. The time courses differ from the ones in fig. 3A of the article, but the authors confirmed that they are correct. The differences seem to be due to different time steps used for the creation of fig 3 B." JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.

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Manuscript information

In silico analysis of arginine catabolism as a source of nitric oxide or polyamines in endothelial cells.

  • R Montañez
  • C Rodríguez-Caso
  • F Sánchez-Jiménez
  • MA Medina
Amino Acids 2008; 34 (2): 223-229
Abstract
We use a modeling and simulation approach to carry out an in silico analysis of the metabolic pathways involving arginine as a precursor of nitric oxide or polyamines in aorta endothelial cells. Our model predicts conditions of physiological steady state, as well as the response of the system to changes in the control parameter, external arginine concentration. Metabolic flux control analysis allowed us to predict the values of flux control coefficients for all the transporters and enzymes included in the model. This analysis fulfills the flux control coefficient summation theorem and shows that both the low affinity transporter and arginase share the control of the fluxes through these metabolic pathways.

Unit definitions 4

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
— 60.0 second
— 1e-06 mole
— 1e-06 mole litre^(-1.0)
— 1.6666666666666667e-08 mole litre^(-1.0) second^(-1.0)

Compartments 2

Id Name Spatial dimensions Size
cytosol cytosol 3.0 1.0
extracellular extracellular 3.0 1.0

Species 3

Id Name Initial quantity Compartment Fixed
ARGex Arginine ex 330.0 extracellular (extracellular) ✔
ARGin Arginine in 1.0 cytosol (cytosol) ✘
ORN Ornithine 1.0 cytosol (cytosol) ✘

Initial assignments 0

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Reactions 5
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
Arginase Arginase ARGin > ORN

cytosol * (Vmaxarg * ARGin / (Kmarg * (1 + ORN / Kioarg) + ARGin))
Arginine_transport Arginine transport ARGex > ARGin

extracellular * (ARGex / (Kmhat + ARGex) * (Vmaxhat / (1 + ORN / Kiornhat + ARGin / Kmhat)) + ARGex / (Kmlat + ARGex) * (Vmaxlat / (1 + ORN / Kiornhat + ARGin / Kmlat)))
NOS Nitric oxide synthase ARGin > ∅

cytosol * (Vmaxnos1 * ARGin / (Kmnos1 + ARGin))
ODC Ornithine decarboxylase ORN > ∅

cytosol * (Vmaxodc * ORN / (Kmodc + ORN))
Ornithine_efflux Ornithine efflux ORN > ∅

cytosol * (Vmaxefflhat / (1 + ARGex / Kmhat) * (ORN / (Kiornhat * (1 + ARGin / Kmhat) + ORN)) + Vmaxeffllat / (1 + ARGex / Kmlat) * (ORN / (Kmeffllat * (1 + ARGin / Kmlat) + ORN)))

Parameters 18   0

Global parameters

Id Value

Local parameters

Id Value Reaction
Vmaxarg 110.0 microMpermin Arginase (Arginase)
Kmarg 1500.0 microM Arginase (Arginase)
Kioarg 1000.0 microM Arginase (Arginase)
Kmhat 70.0 microM Arginine_transport (Arginine transport)
Vmaxhat 160.5 microM Arginine_transport (Arginine transport)
Kmlat 847.0 microM Arginine_transport (Arginine transport)
Vmaxlat 420.0 microMpermin Arginine_transport (Arginine transport)
Kiornhat 360.0 microM Arginine_transport (Arginine transport)
Kmhat 70.0 microM Ornithine_efflux (Ornithine efflux)
Kmlat 847.0 microM Ornithine_efflux (Ornithine efflux)
Vmaxefflhat 160.5 microMpermin Ornithine_efflux (Ornithine efflux)
Vmaxeffllat 420.0 microMpermin Ornithine_efflux (Ornithine efflux)
Kmeffllat 847.0 microM Ornithine_efflux (Ornithine efflux)
Kiornhat 360.0 microM Ornithine_efflux (Ornithine efflux)
Vmaxnos1 1.33 microMpermin NOS (Nitric oxide synthase)
Kmnos1 16.0 microM NOS (Nitric oxide synthase)
Vmaxodc 0.013 microMpermin ODC (Ornithine decarboxylase)
Kmodc 90.0 microM ODC (Ornithine decarboxylase)

Rules 0   0   0

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition

Events 0

Trigger Assignments