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BIOMD0000000086 - Bornheimer2004_GTPaseCycle

 

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Reference Publication
Publication ID: 15520372
Bornheimer SJ, Maurya MR, Farquhar MG, Subramaniam S.
Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction.
Proc. Natl. Acad. Sci. U.S.A. 2004 Nov; 101(45): 15899-15904
Departments of Chemistry and Biochemistry, Cellular and Molecular Medicine, and Bioengineering and San Diego Supercomputer Center, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.  [more]
Model
Original Model: BIOMD0000000086.origin
Submitter: Enuo He
Submission ID: MODEL4822989369
Submission Date: 11 Dec 2006 15:52:06 UTC
Last Modification Date: 05 Jul 2012 15:49:52 UTC
Creation Date: 29 Nov 2006 17:40:19 UTC
Encoders:  Enuo He
set #1
bqbiol:isVersionOf Gene Ontology regulation of G-protein coupled receptor protein signaling pathway
bqbiol:hasTaxon Taxonomy cellular organisms
Notes

This model is according to the paper Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction by Bornheimer et al 2004.The figure 3 is reproduced by Copasi 4.0.19 (development) .It is three-dimensional logarithmic plots show the output of simulations of Z and v at various concentrations of R and GAP.


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: 15520372 Submission Date: 11 Dec 2006 15:52:06 UTC Last Modification Date: 05 Jul 2012 15:49:52 UTC Creation Date: 29 Nov 2006 17:40:19 UTC
Mathematical expressions
Reactions
G protein binding GAP G protein binding GTP G binding Receptor G*T hydrolysis
GD dissociation RG binding GTP G*T binding Receptor G*T binding GAP
GD binding GAP GD binding Receptor RG*T hydrolysis RGD dissociation
GA binding GTP G*AT hydrolysis GAD dissociation RG binding GAP
GA binding Receptor RGA binding GTP G*AT binding Receptor RG*T binding GAP
RG*AT hydrolysis RGD binding GAP GAD binding Receptor RGAD dissociation
Rules
Assignment Rule (variable: Z) Assignment Rule (variable: v)    
Physical entities
Compartments Species
cell A G GA
T R G*T
GD Pi D
RG RG*T G*AT
GAD RGD RGA
RG*AT RGAD  
Global parameters
Z v    
Reactions (24)
 
 G protein binding GAP [G] + [A] ↔ [GA];  
 
 G protein binding GTP [G] + [T] ↔ [G*T];  
 
 G binding Receptor [G] + [R] ↔ [RG];  
 
 G*T hydrolysis [G*T] ↔ [GD] + [Pi];  
 
 GD dissociation [GD] ↔ [G] + [D];  
 
 RG binding GTP [RG] + [T] ↔ [RG*T];  
 
 G*T binding Receptor [G*T] + [R] ↔ [RG*T];  
 
 G*T binding GAP [G*T] + [A] ↔ [G*AT];  
 
 GD binding GAP [GD] + [A] ↔ [GAD];  
 
 GD binding Receptor [GD] + [R] ↔ [RGD];  
 
 RG*T hydrolysis [RG*T] ↔ [RGD] + [Pi];  
 
 RGD dissociation [RGD] ↔ [RG] + [D];  
 
 GA binding GTP [GA] + [T] ↔ [G*AT];  
 
 G*AT hydrolysis [G*AT] ↔ [GAD] + [Pi];  
 
 GAD dissociation [GAD] ↔ [GA] + [D];  
 
 RG binding GAP [RG] + [A] ↔ [RGA];  
 
 GA binding Receptor [GA] + [R] ↔ [RGA];  
 
 RGA binding GTP [RGA] + [T] ↔ [RG*AT];  
 
 G*AT binding Receptor [G*AT] + [R] ↔ [RG*AT];  
 
 RG*T binding GAP [RG*T] + [A] ↔ [RG*AT];  
 
 RG*AT hydrolysis [RG*AT] ↔ [RGAD] + [Pi];  
 
 RGD binding GAP [RGD] + [A] ↔ [RGAD];  
 
 GAD binding Receptor [GAD] + [R] ↔ [RGAD];  
 
 RGAD dissociation [RGAD] ↔ [RGA] + [D];  
 
Rules (2)
 
 Assignment Rule (name: parameter_0) Z = (species_5+species_10+species_15+species_11)/1E-8
 
 Assignment Rule (name: parameter_1) v = (25*species_15+25*species_11+0.013*species_10+0.013*species_5)/1E-8
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 A
Compartment: cell
Initial concentration: 0.0
 
 G
Compartment: cell
Initial concentration: 1.0E-8
 
 GA
Compartment: cell
Initial concentration: 0.0
 
 T
Compartment: cell
Initial concentration: 4.68E-4
 
 R
Compartment: cell
Initial concentration: 1.0E-6
 
 G*T
Compartment: cell
Initial concentration: 0.0
 
 GD
Compartment: cell
Initial concentration: 0.0
 
 Pi
Compartment: cell
Initial concentration: 0.0044
 
 D
Compartment: cell
Initial concentration: 1.49E-4
 
 RG
Compartment: cell
Initial concentration: 0.0
 
 RG*T
Compartment: cell
Initial concentration: 0.0
 
 G*AT
Compartment: cell
Initial concentration: 0.0
 
 GAD
Compartment: cell
Initial concentration: 0.0
 
 RGD
Compartment: cell
Initial concentration: 0.0
 
 RGA
Compartment: cell
Initial concentration: 0.0
 
 RG*AT
Compartment: cell
Initial concentration: 0.0
 
 RGAD
Compartment: cell
Initial concentration: 0.0
 
Global Parameters (2)
 
  Z  
 
  v  
 
G protein binding GAP (2)
 
   k1
Value: 8780000.0
Constant
 
   k2
Value: 8.0
Constant
 
G protein binding GTP (2)
 
   k1
Value: 529000.0
Constant
 
   k2
Value: 8.38E-6
Constant
 
G binding Receptor (2)
 
   k1
Value: 6.36E8
Constant
 
   k2
Value: 0.0179
Constant
 
G*T hydrolysis (2)
 
   k1
Value: 0.013
Constant
 
   k2
Value: 9.03E-7
Constant
 
GD dissociation (2)
 
   k1
Value: 1.0E-4
Constant
 
   k2
Value: 62.3
Constant
 
RG binding GTP (2)
 
   k1
Value: 853000.0
Constant
 
   k2
Value: 0.00468
Constant
 
G*T binding Receptor (2)
 
   k1
Value: 1.32E8
Constant
 
   k2
Value: 1.28
Constant
 
G*T binding GAP (2)
 
   k1
Value: 386000.0
Constant
 
   k2
Value: 0.0408
Constant
 
GD binding GAP (2)
 
   k1
Value: 64100.0
Constant
 
   k2
Value: 0.95
Constant
 
GD binding Receptor (2)
 
   k1
Value: 9.47E7
Constant
 
   k2
Value: 0.00227
Constant
 
RG*T hydrolysis (2)
 
   k1
Value: 0.013
Constant
 
   k2
Value: 2.22E-9
Constant
 
RGD dissociation (2)
 
   k1
Value: 2.0
Constant
 
   k2
Value: 1470000.0
Constant
 
GA binding GTP (2)
 
   k1
Value: 44700.0
Constant
 
   k2
Value: 8.32E-8
Constant
 
G*AT hydrolysis (2)
 
   k1
Value: 25.0
Constant
 
   k2
Value: 0.244
Constant
 
GAD dissociation (2)
 
   k1
Value: 1.0E-4
Constant
 
   k2
Value: 3.83
Constant
 
RG binding GAP (2)
 
   k1
Value: 74300.0
Constant
 
   k2
Value: 0.00572
Constant
 
GA binding Receptor (2)
 
   k1
Value: 2.28E7
Constant
 
   k2
Value: 5.43E-5
Constant
 
RGA binding GTP (2)
 
   k1
Value: 1620000.0
Constant
 
   k2
Value: 0.00875
Constant
 
G*AT binding Receptor (2)
 
   k1
Value: 6200000.0
Constant
 
   k2
Value: 0.0433
Constant
 
RG*T binding GAP (2)
 
   k1
Value: 6300000.0
Constant
 
   k2
Value: 0.478
Constant
 
RG*AT hydrolysis (2)
 
   k1
Value: 25.0
Constant
 
   k2
Value: 0.00297
Constant
 
RGD binding GAP (2)
 
   k1
Value: 13000.0
Constant
 
   k2
Value: 0.685
Constant
 
GAD binding Receptor (2)
 
   k1
Value: 4.94E7
Constant
 
   k2
Value: 0.00421
Constant
 
RGAD dissociation (2)
 
   k1
Value: 2.75
Constant
 
   k2
Value: 2940.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000086

Curator's comment: (updated: 01 Mar 2008 19:19:53 GMT)

Figure 3A. Simulations were done in COPASI 4, and plotted with Gnuplot.

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