goldbeter4

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000098) Biomodels notes: The model reproduces the time profile of cytosolic and intracellular calcium as depicted in the upper panel of Fig 2 in the paper. The model was successfully tested on MathSBML and Jarnac. 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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Minimal model for signal-induced Ca2+ oscillations and for their frequency encoding through protein phosphorylation.

  • Albert Goldbeter
  • G Dupont
  • MJ Berridge
Proc. Natl. Acad. Sci. U.S.A. 1990; 87 (4): 1461-1465
Abstract
In a variety of cells, hormonal or neurotransmitter signals elicit a train of intracellular Ca2+ spikes. The analysis of a minimal model based on Ca2(+)-induced Ca2+ release from intracellular stores shows how sustained oscillations of cytosolic Ca2+ may develop as a result of a rise in inositol 1,4,5-trisphosphate (InsP3) triggered by external stimulation. This rise elicits the release of a certain amount of Ca2+ from an InsP3-sensitive intracellular store. The subsequent rise in cytosolic Ca2+ in turn triggers the release of Ca2+ from a second store insensitive to InsP3. In contrast to the model proposed by Meyer and Stryer [Meyer, T. & Stryer, L. (1988) Proc. Natl. Acad. Sci. USA 85, 5051-5055], the present model, which contains only two variables, predicts the occurrence of periodic Ca2+ spikes in the absence of InsP3 oscillations. Such results indicate that repetitive Ca2+ spikes evoked by external stimuli do not necessarily require the concomitant, periodic variation of InsP3. The model is closely related to that proposed by Kuba and Takeshita [Kuba, K. & Takeshita, S. (1981) J. Theor. Biol. 93, 1009-1031] for Ca2+ oscillations in sympathetic neurones, based on Ca2(+)-induced Ca2+ release. We extend their results by showing the minimal conditions in which the latter process gives rise to periodic behavior and take into account the role of the rise in InsP3 caused by external stimulation. The analysis further shows how signal-induced Ca2+ oscillations might be effectively encoded in terms of their frequency through the phosphorylation of a cellular substrate by a protein kinase activated by cytosolic Ca2+.

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
1e-06 mole
1e-06 mole litre^(-1.0) second^(-1.0)
1.0 second^(-1.0)
1e-06 mole litre^(-1.0)
1.0 dimensionless
Id Name Spatial dimensions Size
cytosol cytosol 3.0 1.0
store store 3.0 1.0
Id Name Initial quantity Compartment Fixed
Y 1.6 store (store)
Z 0.15 cytosol (cytosol)

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
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
R0 Ca influx ∅ > Z

cytosol * v0
R1 InsP3 dependent Ca influx ∅ > Z

cytosol * v1 * beta
R2 ATP driven Ca pumping into store Z > Y

cytosol * (Vm2 * pow(Z, n) / (pow(K2, n) + pow(Z, n)))
R3 ATP driven pumping into cytosol Y > Z

store * (Vm3 * pow(Y, m) * pow(Z, p) / ((pow(Kr, m) + pow(Y, m)) * (pow(Ka, p) + pow(Z, p))))
R_eff Ca efflux Z > ∅

cytosol * k * Z
Rf Ca leak Y > Z

store * kf * Y

Global parameters

Id Value
K2 1.0 uM
Ka 0.9 uM
Kr 2.0 uM
Vm2 65.0 uM_per_sec
Vm3 500.0 uM_per_sec
beta 0.301 dimensionless
k 10.0 sec_inv
kf 1.0 sec_inv
m 2.0 dimensionless
n 2.0 dimensionless
p 4.0 dimensionless
v0 1.0 uM_per_sec
v1 7.3 uM_per_sec

Local parameters

Id Value Reaction

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments