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BIOMD0000000084 - Hornberg2005_ERKcascade

 

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Reference Publication
Publication ID: 15634347
Hornberg JJ, Bruggeman FJ, Binder B, Geest CR, de Vaate AJ, Lankelma J, Heinrich R, Westerhoff HV.
Principles behind the multifarious control of signal transduction. ERK phosphorylation and kinase/phosphatase control.
FEBS J. 2005 Jan; 272(1): 244-258
Department of Molecular Cell Physiology, Institute for Molecular Cell Biology, BioCentrum Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands.  [more]
Model
Original Model: JWS logo
Submitter: Nicolas Le Novère
Submission ID: MODEL6623610941
Submission Date: 11 Dec 2006 10:48:55 UTC
Last Modification Date: 14 May 2012 12:15:35 UTC
Creation Date: 11 Dec 2006 10:48:55 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:hasPart KEGG Pathway rno04010
set #2
bqbiol:is Gene Ontology MAPK cascade
Gene Ontology epidermal growth factor receptor signaling pathway
set #3
bqbiol:occursIn Taxonomy Mammalia
Notes

SBML level 2 code generated for the JWS Online project by Jacky Snoep using PySCeS
Run this model online at http://jjj.biochem.sun.ac.za
To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based modelling using JWS Online , Bioinformatics, 20:2143-2144

Biomodels Curation The model reproduces the time series depicted in Fig 2 of the paper. Also, by varying the values of Vmax for the second kinase (k5) the time series of X3P as shown in Fig3 can be reproduced. The model was successfully tested on MathSBML and Jarnac.

Model
Publication ID: 15634347 Submission Date: 11 Dec 2006 10:48:55 UTC Last Modification Date: 14 May 2012 12:15:35 UTC Creation Date: 11 Dec 2006 10:48:55 UTC
Mathematical expressions
Reactions
Receptor inactivation Receptor activation Kinase-1 activation Kinase-1 inactivation
Kinase-2 activation Kinase-2 inactivation Kinase-3 activation Kinase-3 inactivation
Physical entities
Compartments Species
Cytosol R Rin x1
x1p x2 x2p
x3 x3p  
Reactions (8)
 
 Receptor inactivation [R] ↔ [Rin];  
 
 Receptor activation [Rin] ↔ [R];  
 
 Kinase-1 activation [x1] ↔ [x1p];   {R}
 
 Kinase-1 inactivation [x1p] ↔ [x1];  
 
 Kinase-2 activation [x2] ↔ [x2p];   {x1p}
 
 Kinase-2 inactivation [x2p] ↔ [x2];  
 
 Kinase-3 activation [x3] ↔ [x3p];   {x2p}
 
 Kinase-3 inactivation [x3p] ↔ [x3];  
 
 Cytosol Spatial dimensions: 3.0  Compartment size: 1.0
 
 R
Compartment: Cytosol
Initial amount: 0.5
 
 Rin
Compartment: Cytosol
Initial amount: 0.0
 
 x1
Compartment: Cytosol
Initial amount: 1.0
 
 x1p
Compartment: Cytosol
Initial amount: 0.0
 
 x2
Compartment: Cytosol
Initial amount: 1.0
 
 x2p
Compartment: Cytosol
Initial amount: 0.0
 
 x3
Compartment: Cytosol
Initial amount: 1.0
 
 x3p
Compartment: Cytosol
Initial amount: 0.0
 
Receptor inactivation (2)
 
   Vm1
Value: 1.0
Constant
 
   Km1
Value: 0.1
Constant
 
Receptor activation (2)
 
   Vm2
Value: 0.01
Constant
 
   Km2
Value: 0.1
Constant
 
Kinase-1 activation (2)
 
   k3
Value: 1.0
Constant
 
   Km3
Value: 0.1
Constant
 
Kinase-1 inactivation (2)
 
   Vm4
Value: 0.3
Constant
 
   Km4
Value: 1.0
Constant
 
Kinase-2 activation (2)
 
   k5
Value: 1.0
Constant
 
   Km5
Value: 0.1
Constant
 
Kinase-2 inactivation (2)
 
   Vm6
Value: 0.3
Constant
 
   Km6
Value: 1.0
Constant
 
Kinase-3 activation (2)
 
   k7
Value: 1.0
Constant
 
   Km7
Value: 0.1
Constant
 
Kinase-3 inactivation (4)
 
   Vm8
Value: 0.3
Constant
 
   Km8
Value: 1.0
Constant
 
   Inh
Constant
 
   Ki8
Value: 1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000084

Curator's comment: (updated: 19 Dec 2006 00:36:45 GMT)

The plot corresponds to Fig 2 of the paper. Simulation results obtained with MathSBML.

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