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BIOMD0000000072 - Yi2003_GproteinCycle

 

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Reference Publication
Publication ID: 12960402
Yi TM, Kitano H, Simon MI.
A quantitative characterization of the yeast heterotrimeric G protein cycle.
Proc. Natl. Acad. Sci. U.S.A. 2003 Sep; 100(19): 10764-10769
Systems Biology Group, Exploratory Research for Advanced Technology Kitano Symbiotic Systems Project, Japan Science and Technology Corporation, Shibuya, Tokyo, Japan.  [more]
Model
Original Model: BIOMD0000000072.xml.origin
Submitter: Enuo He
Submission ID: MODEL9468910329
Submission Date: 17 Oct 2006 15:12:36 UTC
Last Modification Date: 05 Jul 2012 14:41:34 UTC
Creation Date: 17 Oct 2006 15:12:36 UTC
Encoders:  Enuo He
set #1
bqbiol:occursIn Taxonomy Saccharomyces cerevisiae
bqbiol:isVersionOf Gene Ontology G-protein coupled receptor signaling pathway
Gene Ontology heterotrimeric G-protein complex cycle
Notes

The paper describes both wild-type and mutant cells of G protein cycle by using different values of G protein deactivation. We chosed the wild-type, k=0.11 s-1.

The unit of the concentration for the proteins are numbers of molecules per cell.

Figure5(A) was reproduced with COPASI 4.0 (Build 18) and SBML_odeSolver. Figure5(B) was reproduced with COPASI 4.0 (Build 18).


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: 12960402 Submission Date: 17 Oct 2006 15:12:36 UTC Last Modification Date: 05 Jul 2012 14:41:34 UTC Creation Date: 17 Oct 2006 15:12:36 UTC
Mathematical expressions
Reactions
Ligand-Receptor Association Receptor Synthesis Receptor Degradation Heterotrimeric G-Protein Formation
G-protein Activation Receptor-Ligand Degradation G-protein Inactivation  
Physical entities
Compartments Species
cell Ligand Receptor Inactive heterotrimeric G-protein
Free levels of G-beta-gamma G-alpha-GDP G-alpha-GTP
Receptor-Ligand    
Reactions (7)
 
 Ligand-Receptor Association [Ligand] + [Receptor] ↔ [Receptor-Ligand];  
 
 Receptor Synthesis  → [Receptor];  
 
 Receptor Degradation [Receptor] → ;  
 
 Heterotrimeric G-Protein Formation [G-alpha-GDP] + [Free levels of G-beta-gamma] → [Inactive heterotrimeric G-protein];  
 
 G-protein Activation [Inactive heterotrimeric G-protein] → [G-alpha-GTP] + [Free levels of G-beta-gamma];   {Receptor-Ligand}
 
 Receptor-Ligand Degradation [Receptor-Ligand] → ;  
 
 G-protein Inactivation [G-alpha-GTP] → [G-alpha-GDP];  
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ligand
Compartment: cell
Initial concentration: 6.02E17
 
 Receptor
Compartment: cell
Initial concentration: 10000.0
 
 Inactive heterotrimeric G-protein
Compartment: cell
Initial concentration: 7000.0
 
 Free levels of G-beta-gamma
Compartment: cell
Initial concentration: 3000.0
 
 G-alpha-GDP
Compartment: cell
Initial concentration: 3000.0
 
 G-alpha-GTP
Compartment: cell
Initial concentration: 0.0
 
 Receptor-Ligand
Compartment: cell
Initial concentration: 0.0
 
Ligand-Receptor Association (2)
 
   k1
Value: 3.32E-18
Constant
 
   k2
Value: 0.01
Constant
 
Receptor Synthesis (1)
 
   v
Value: 4.0
Constant
 
Receptor Degradation (1)
 
   k1
Value: 4.0E-4
Constant
 
Heterotrimeric G-Protein Formation (1)
 
   k1
Value: 1.0
Constant
 
G-protein Activation (1)
 
   k1
Value: 1.0E-5
Constant
 
Receptor-Ligand Degradation (1)
 
   k1
Value: 0.0040
Constant
 
G-protein Inactivation (1)
 
   k1
Value: 0.11
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000072

Curator's comment: (updated: 17 Oct 2006 10:58:25 BST)

Figure 5B reproduced with COPASI v4 build 18

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