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BIOMD0000000080 - Thomsen1989_AdenylateCyclase

 

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Reference Publication
Publication ID: 2574993
Thomsen WJ, Neubig RR.
Rapid kinetics of alpha 2-adrenergic inhibition of adenylate cyclase. Evidence for a distal rate-limiting step.
Biochemistry 1989 Oct; 28(22): 8778-8786
Department of Pharmacology, University of Michigan, Ann Arbor 48109-0626.  [more]
Model
Original Model: BIOMD0000000080.xml.origin
Submitter: Enuo He
Submission ID: MODEL1173806337
Submission Date: 27 Nov 2006 17:04:36 UTC
Last Modification Date: 12 Feb 2014 21:29:39 UTC
Creation Date: 27 Sep 2006 10:07:57 UTC
Encoders:  Enuo He
set #1
bqbiol:isVersionOf Gene Ontology heterotrimeric G-protein complex cycle
Gene Ontology negative regulation of adenylate cyclase activity
set #2
bqmodel:isDerivedFrom BioModels Database Thomsen1988_AdenylateCyclase_Inhibition
set #3
bqbiol:occursIn Taxonomy Homo sapiens
Notes

This model reproduces figure 5 and figure 4(B)of the paper, with Kinh represented by [G-GTP]. We arbitrarily chosed to set the initial concentration of D to 31 micorMolar based on legend of figure 4. [R] was not given anywhere in the paper and was chosen to calibrate the sigmoid response to an increased [GTP]. THe figure 5 in the model was successfully simulated on COPASI 4.0 ,the figure 4(B) was sucessfully simulated on both COPASI and SBML_odeSolver.

There are two curves for Kinh in the absence and presence of NaCl in the figure obtained from simulations of the model using parameters of set C and set D.Here in the model the initial value given is from set D.The parameters in set C :k7=0.5, k10=1.0,k5=0.1,the others are the same with set D.

Model
Publication ID: 2574993 Submission Date: 27 Nov 2006 17:04:36 UTC Last Modification Date: 12 Feb 2014 21:29:39 UTC Creation Date: 27 Sep 2006 10:07:57 UTC
Mathematical expressions
Reactions
Forming DR DR Binding with G_GDP produce DRG_GDP GDP Releasing GTP binding with DRG
G protein activation Hydrolysis of GTP to GDP    
Physical entities
Compartments Species
cell D DR DRG_GDP
G_GDP DRG GDP
DRG_GTP GTP G_GTP
R    
Reactions (6)
 
 Forming DR [D] + [R] ↔ [DR];  
 
 DR Binding with G_GDP produce DRG_GDP [DR] + [G_GDP] ↔ [DRG_GDP];  
 
 GDP Releasing [DRG_GDP] ↔ [GDP] + [DRG];  
 
 GTP binding with DRG [DRG] + [GTP] ↔ [DRG_GTP];  
 
 G protein activation [DRG_GTP] → [G_GTP] + [DR];  
 
 Hydrolysis of GTP to GDP [G_GTP] → [G_GDP];  
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 D
Compartment: cell
Initial concentration: 3.1E-5
 
 DR
Compartment: cell
Initial concentration: 0.0
 
 DRG_GDP
Compartment: cell
Initial concentration: 0.0
 
 G_GDP
Compartment: cell
Initial concentration: 1.0E-6
 
 DRG
Compartment: cell
Initial concentration: 0.0
 
 GDP
Compartment: cell
Initial concentration: 0.0
 
 DRG_GTP
Compartment: cell
Initial concentration: 0.0
 
 GTP
Compartment: cell
Initial concentration: 1.0E-5
 
 G_GTP
Compartment: cell
Initial concentration: 0.0
 
 R
Compartment: cell
Initial concentration: 1.0E-10
 
Forming DR (2)
 
   k1
Value: 5000000.0
Constant
 
   k7
Value: 10.0
Constant
 
DR Binding with G_GDP produce DRG_GDP (2)
 
   k2
Value: 1.0E8
Constant
 
   k8
Value: 0.1
Constant
 
GDP Releasing (2)
 
   k3
Value: 5.0
Constant
 
   k9
Value: 100000.0
Constant
 
GTP binding with DRG (2)
 
   k4
Value: 5000000.0
Constant
 
   k10
Value: 55.0
Constant
 
G protein activation (1)
 
   k5
Value: 1.0
Constant
 
Hydrolysis of GTP to GDP (1)
 
   k6
Value: 2.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000080

Curator's comment: (updated: 18 Oct 2006 13:19:20 BST)

Figure5 (dashed line) is reproduced.

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