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BIOMD0000000085 - Maurya2005_GTPaseCycle_reducedOrder

 

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Reference Publication
Publication ID: 16986265
Maurya MR, Bornheimer SJ, Venkatasubramanian V, Subramaniam S.
Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module.
Syst Biol (Stevenage) 2005 Dec; 152(4): 229-242
San Diego Supercomputer Center, La Jolla, CA 92093, USA.  [more]
Model
Original Model: BIOMD0000000085.origin
Submitter: Sharat Vayttaden
Submission ID: MODEL5317679037
Submission Date: 11 Dec 2006 15:51:36 UTC
Last Modification Date: 13 Feb 2014 15:47:02 UTC
Creation Date: 29 Nov 2006 17:40:19 UTC
Encoders:  Enuo He
set #1
bqmodel:isDerivedFrom BioModels Database Bornheimer2004_GTPaseCycle
set #2
bqbiol:isVersionOf Gene Ontology regulation of G-protein coupled receptor protein signaling pathway
bqbiol:occursIn Taxonomy cellular organisms
Notes

This model is according to the paper Reduced-order modeling of biochemical networks: application to the GTPase-cycle signalling module by Maurya et al 2006.The figure 4c is reproduced by Copasi 4.0.19 (development) .It is three-dimensional logarithmic plots show the output of simulations of Z 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: 16986265 Submission Date: 11 Dec 2006 15:51:36 UTC Last Modification Date: 13 Feb 2014 15:47:02 UTC Creation Date: 29 Nov 2006 17:40:19 UTC
Mathematical expressions
Reactions
G protein binding GTP 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 G*AT hydrolysis GAD dissociation
GA binding Receptor RGA binding GTP RG*T binding GAP RG*AT hydrolysis
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 (17)
 
 G protein binding GTP [G] + [T] ↔ [G*T];  
 
 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];  
 
 G*AT hydrolysis [G*AT] ↔ [GAD] + [Pi];  
 
 GAD dissociation [GAD] ↔ [GA] + [D];  
 
 GA binding Receptor [GA] + [R] ↔ [RGA];  
 
 RGA binding GTP [RGA] + [T] ↔ [RG*AT];  
 
 RG*T binding GAP [RG*T] + [A] ↔ [RG*AT];  
 
 RG*AT hydrolysis [RG*AT] ↔ [RGAD] + [Pi];  
 
 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)/10E-9
 
 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-5
 
 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 GTP (2)
 
   k1
Value: 529000.0
Constant
 
   k2
Value: 8.38E-6
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
 
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
 
GA binding Receptor (2)
 
   k1
Value: 3.96E9
Constant
 
   k2
Value: 5.43E-5
Constant
 
RGA binding GTP (2)
 
   k1
Value: 1620000.0
Constant
 
   k2
Value: 0.00875
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
 
RGAD dissociation (2)
 
   k1
Value: 2.75
Constant
 
   k2
Value: 2940.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000085

Curator's comment: (updated: 11 Dec 2006 10:11:34 GMT)

Figure 5 C has been successfully reproduced.

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