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BIOMD0000000166 - Zhu2007_TF_modulated_by_Calcium

 

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Reference Publication
Publication ID: 17560007
Zhu CL, Zheng Y, Jia Y.
A theoretical study on activation of transcription factor modulated by intracellular Ca2+ oscillations.
Biophys. Chem. 2007 Aug; 129(1): 49-55
Department of Physics, Jianghan University, Wuhan 430056, China.  [more]
Model
Original Model: BIOMD0000000166.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL8262954331
Submission Date: 25 Feb 2008 00:07:30 UTC
Last Modification Date: 27 May 2014 22:02:26 UTC
Creation Date: 21 Dec 2007 09:55:45 UTC
Encoders:  Harish Dharuri
set #1
bqmodel:isDerivedFrom BioModels Database Goldbeter1990_CalciumSpike_CICR
PubMed 9486144
set #2
bqbiol:hasTaxon Taxonomy cellular organisms
set #3
bqbiol:isVersionOf Gene Ontology calcium-mediated signaling
Notes

This a model from the article:
A theoretical study on activation of transcription factor modulated by intracellular Ca2+ oscillations.
Zhu CL, Zheng Y, Jia Y Biophys. Chem.[2007 Aug:129(1):49-55 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.

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.
For more information see the terms of use.
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M.(2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Model
Publication ID: 17560007 Submission Date: 25 Feb 2008 00:07:30 UTC Last Modification Date: 27 May 2014 22:02:26 UTC Creation Date: 21 Dec 2007 09:55:45 UTC
Mathematical expressions
Reactions
TF Synthesis TF degradation TF_synthesis_basal Calcium_Influx
Calcium Influx by stimulation Calcium Influx Calcium influx to cytoplasm Calcium Leakage
Leakage from cytoplasm      
Rules
Assignment Rule (variable: kf) Assignment Rule (variable: Kd)    
Physical entities
Compartments Species
cytoplasm TF_A Calcium in cytoplasm  
store Calcium in store    
Global parameters
kf Kd kf0 gamma
Ka Kb Kd0  
Reactions (9)
 
 TF Synthesis  ↔ [TF_A];  
 
 TF degradation [TF_A] ↔ ;  
 
 TF_synthesis_basal  ↔ [TF_A];  
 
 Calcium_Influx  ↔ [Calcium in cytoplasm];  
 
 Calcium Influx by stimulation  ↔ [Calcium in cytoplasm];  
 
 Calcium Influx [Calcium in cytoplasm] ↔ [Calcium in store];  
 
 Calcium influx to cytoplasm [Calcium in store] ↔ [Calcium in cytoplasm];  
 
 Calcium Leakage [Calcium in store] ↔ [Calcium in cytoplasm];  
 
 Leakage from cytoplasm [Calcium in cytoplasm] ↔ ;  
 
Rules (2)
 
 Assignment Rule (name: kf) kf = kf0*(1+gamma*Z^4/(Ka^4+Z^4))
 
 Assignment Rule (name: Kd) Kd = Kd0/(1+Z^4/Kb^4)
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
   TF_A
Compartment: cytoplasm
Initial concentration: 15.0
 
 Calcium in cytoplasm
Compartment: cytoplasm
Initial concentration: 0.25
 
   store Spatial dimensions: 3.0  Compartment size: 1.0
 
 Calcium in store
Compartment: store
Initial concentration: 0.0
 
Global Parameters (7)
 
   kf
Value: NaN
 
   Kd
Value: NaN
 
   kf0
Value: 6.0
Constant
 
   gamma
Value: 9.0
Constant
 
   Ka
Value: 0.5
Constant
 
   Kb
Value: 0.5
Constant
 
   Kd0
Value: 10.0
Constant
 
TF degradation (1)
 
   kd
Value: 1.0
Constant
 
TF_synthesis_basal (1)
 
   Rbas
Value: 0.1
Constant
 
Calcium_Influx (1)
 
   v0
Value: 1.0
Constant
 
Calcium Influx by stimulation (2)
 
   v1
Value: 5.7
Constant
 
   beta
Value: 0.3
Constant
 
Calcium Influx (3)
 
   Vm2
Value: 30.0
Constant
 
   K2
Value: 0.5
Constant
 
   n
Value: 2.0
Constant
 
Calcium influx to cytoplasm (5)
 
   Vm3
Value: 325.0
Constant
 
   Kr
Value: 1.7
Constant
 
   K_A
Value: 0.46
Constant
 
   m
Value: 2.0
Constant
 
   p
Value: 4.0
Constant
 
Calcium Leakage (1)
 
   k1
Value: 0.7
Constant
 
Leakage from cytoplasm (1)
 
   k
Value: 10.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000166

Curator's comment: (updated: 27 Aug 2009 17:39:05 BST)

The model reproduces Figure 3 of the reference publication. The model was integrated and simulated using Copasi v4.5 (Build 30).

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