Calcium_Influx
Calcium_Influx
∅ = Z
Calcium_Influx_stimulation
Calcium Influx by stimulation
∅ = Z
Calcium_into_cytoplasm
Calcium influx to cytoplasm
Y = Z
Calcium_into_store
Calcium Influx
Z = Y
Leakage
Calcium Leakage
Y = Z
Leakage_from_cytoplasm
Leakage from cytoplasm
Z = ∅
TF_degradation
TF degradation
X = ∅
TF_synthesis
TF Synthesis
∅ = X
TF_synthesis_basal
TF_synthesis_basal
∅ = X
Assignment rules
Kd = Kd0 / (1.0 + pow(Z, 4.0) / pow(Kb, 4.0))
kf = kf0 * (1.0 + gamma * pow(Z, 4.0) / (pow(Ka, 4.0) + pow(Z, 4.0)))
Function definitions
Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.
A theoretical study on activation of transcription factor modulated by intracellular Ca2+ oscillations.
Biophys. Chem. 2007;
129
(1):
49
- PubMed: 17560007
- DOI: 10.1016/j.bpc.2007.05.006
- ISSN: 0301-4622
- URL: https://ncbi.nlm.nih.gov/pubmed/17560007
Abstract
This work presents both deterministic and stochastic models of genetic expression modulated by intracellular calcium (Ca2+) oscillations, based on macroscopic differential equations and chemical Langevin equations, respectively. In deterministic case, the oscillations of intracellular Ca2+ decrease the effective Ca2+ threshold for the activation of transcriptional activator (TF-A). The average activation of TF-A increases with the increase of the average amplitude of intracellular Ca2+ oscillations, but decreases with the increase of the period of intracellular Ca2+ oscillations, which are qualitatively consistent with the experimental results on the gene expression in lymphocytes. In stochastic case, it is found that a large internal fluctuation of the biochemical reaction can enhance gene expression efficiency specifically at a low level of external stimulations or at a small rate of TF-A dimer phosphorylation activated by Ca2+, which reduces the threshold of the average intracellular Ca2+ concentration for gene expression.
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000166).
Biomodels notes: "The model reproduces Figure 3 of the reference publication. The model was integrated and simulated using Copasi v4.5 (Build 30)."
JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.