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BIOMD0000000100 - Rozi2003_GlycogenPhosphorylase_Activation

 

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Reference Publication
Publication ID: 14556891
Rozi A, Jia Y.
A theoretical study of effects of cytosolic Ca2+ oscillations on activation of glycogen phosphorylase.
Biophys. Chem. 2003 Dec; 106(3): 193-202
Department of Physics, Central China Normal University, Wuhan 430079, Hubei, PR China.  [more]
Model
Original Model: BIOMD0000000100.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL4589754842
Submission Date: 22 Mar 2007 22:54:48 UTC
Last Modification Date: 24 May 2014 17:51:59 UTC
Creation Date: 22 Mar 2007 10:28:32 UTC
Encoders:  Harish Dharuri
set #1
bqmodel:isDerivedFrom PubMed 17883229
PubMed 11093832
set #2
bqbiol:isVersionOf Gene Ontology calcium-mediated signaling
Gene Ontology inositol phosphate-mediated signaling
set #3
bqbiol:hasPart Gene Ontology phosphorylase kinase regulator activity
bqbiol:hasTaxon Taxonomy cellular organisms
set #4
bqbiol:hasPart KEGG Pathway hsa04020
Notes

The model reproduces the temporal evolution of Glycogen phosphorylase for a vale of Vm5=30 as depicted in Fig 1a of the paper. The model makes use of calcium oscillations from the Borghans model to stimulate the activation of glycogen phosphorylase. Hence, this is a simple extension of the Borghans model. The model was succesfully tested on MathSBML and Jarnac.


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 14556891 Submission Date: 22 Mar 2007 22:54:48 UTC Last Modification Date: 24 May 2014 17:51:59 UTC Creation Date: 22 Mar 2007 10:28:32 UTC
Mathematical expressions
Reactions
Calcium Influx Calcium transport to internal store Calcium transport to cytosol Calcium leak
Calcium efflux Agonist stimulated production of IP3 Ca-dependant IP3 degradation Ca independent IP3 degradation
Phosphorylase kinase activity Phosphatase activity    
Physical entities
Compartments Species
extracellular Extracellular Calcium    
cytosol Cytosolic Calcium IP3 Glycogen Phosphorylase
intravesicular Intravesicular Calcium    
Global parameters
v0 v1 beta Vm2
K2 Vm3 m Ka
Ky Kz Kf K
V4 Vm5 n K5
Kd epsilon Vpm1 gamma
Ka5 K1 Ka6 Vpm2
alpha G Ka1 Kp2
Ka2 p    
Reactions (10)
 
 Calcium Influx [Extracellular Calcium] → [Cytosolic Calcium];  
 
 Calcium transport to internal store [Cytosolic Calcium] → [Intravesicular Calcium];  
 
 Calcium transport to cytosol [Intravesicular Calcium] → [Cytosolic Calcium];   {IP3}
 
 Calcium leak [Intravesicular Calcium] → [Cytosolic Calcium];  
 
 Calcium efflux [Cytosolic Calcium] → [Extracellular Calcium];  
 
 Agonist stimulated production of IP3  → [IP3];  
 
 Ca-dependant IP3 degradation [IP3] → ;   {Cytosolic Calcium}
 
 Ca independent IP3 degradation [IP3] → ;  
 
 Phosphorylase kinase activity  → [Glycogen Phosphorylase];   {Cytosolic Calcium}
 
 Phosphatase activity [Glycogen Phosphorylase] → ;  
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Extracellular Calcium
Compartment: extracellular
Initial concentration: 1000.0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Cytosolic Calcium
Compartment: cytosol
Initial concentration: 0.0
 
 IP3
Compartment: cytosol
Initial concentration: 0.45
 
 Glycogen Phosphorylase
Compartment: cytosol
Initial concentration: 1.0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Intravesicular Calcium
Compartment: intravesicular
Initial concentration: 0.36
 
Global Parameters (30)
 
   v0
Value: 2.0   (Units: uM_per_min)
Constant
 
   v1
Value: 2.0   (Units: uM_per_min)
Constant
 
   beta
Value: 0.5   (Units: dimensionless)
Constant
 
   Vm2
Value: 6.0   (Units: uM_per_min)
Constant
 
   K2
Value: 0.1   (Units: uM)
Constant
 
   Vm3
Value: 20.0   (Units: uM_per_min)
Constant
 
   m
Value: 2.0   (Units: dimensionless)
Constant
 
   Ka
Value: 0.2   (Units: uM)
Constant
 
   Ky
Value: 0.2   (Units: uM)
Constant
 
   Kz
Value: 0.5   (Units: uM)
Constant
 
   Kf
Value: 1.0   (Units: min_inv)
Constant
 
   K
Value: 10.0   (Units: min_inv)
Constant
 
   V4
Value: 2.0   (Units: uM_per_min)
Constant
 
   Vm5
Value: 30.0   (Units: uM_per_min)
Constant
 
   n
Value: 4.0   (Units: dimensionless)
Constant
 
   K5
Value: 1.0   (Units: uM)
Constant
 
   Kd
Value: 0.4   (Units: uM)
Constant
 
   epsilon
Value: 0.1   (Units: min_inv)
Constant
 
   Vpm1
Value: 1.5   (Units: min_inv)
Constant
 
   gamma
Value: 9.0   (Units: dimensionless)
Constant
 
   Ka5
Value: 0.5   (Units: uM)
Constant
 
   K1
Value: 0.1
Constant
 
   Ka6
Value: 0.5   (Units: uM)
Constant
 
   Vpm2
Value: 0.6   (Units: min_inv)
Constant
 
   alpha
Value: 9.0   (Units: dimensionless)
Constant
 
   G
Value: 10000.0   (Units: uM)
Constant
 
   Ka1
Value: 10000.0   (Units: uM)
Constant
 
   Kp2
Value: 0.2
Constant
 
   Ka2
Value: 10000.0   (Units: uM)
Constant
 
   p
Value: 2.0   (Units: dimensionless)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000100

Curator's comment: (updated: 22 Mar 2007 19:00:01 GMT)

The model reproduces Fig 1a of the paper for Vm5=30. Simulation result shown, was generated by MathSBML.

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