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BIOMD0000000231 - Valero2006_Adenine_TernaryCycle

 

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Reference Publication
Publication ID: 16884499
Valero E, Varón R, García-Carmona F.
A kinetic study of a ternary cycle between adenine nucleotides.
FEBS J. 2006 Aug; 273(15): 3598-3613
Departamento de Química-Física, Escuela Politécnica Superior de Albacete, Universidad de Castilla-La Mancha, Albacete, Spain. Edelmira.Valero@uclm.es  [more]
Model
Original Model: JWS logo
Submitter: Lukas Endler
Submission ID: MODEL5952687775
Submission Date: 25 Jun 2009 18:58:10 UTC
Last Modification Date: 09 Mar 2012 11:40:35 UTC
Creation Date: 19 Aug 2009 16:30:30 UTC
Encoders:  Vijayalakshmi Chelliah
   Edelmira Valero
set #1
bqbiol:isVersionOf Gene Ontology adenosine metabolic process
set #2
bqbiol:isVersionOf Reactome REACT_2124
set #3
bqbiol:hasTaxon Taxonomy Bos taurus
Notes

This a model from the article:
A kinetic study of a ternary cycle between adenine nucleotides.
Valero E, Varón R, García-Carmona F FEBS J. [2006 Aug;273(15):3598-613 16884499 ,
Abstract:
In the present paper, a kinetic study is made of the behavior of a moiety-conserved ternary cycle between the adenine nucleotides. The system contains the enzymes S-acetyl coenzyme A synthetase, adenylate kinase and pyruvate kinase, and converts ATP into AMP, then into ADP and finally back to ATP. L-Lactate dehydrogenase is added to the system to enable continuous monitoring of the progress of the reaction. The cycle cannot work when the only recycling substrate in the reaction medium is AMP. A mathematical model is proposed whose kinetic behavior has been analyzed both numerically by integration of the nonlinear differential equations describing the kinetics of the reactions involved, and analytically under steady-state conditions, with good agreement with the experimental results being obtained. The data obtained showed that there is a threshold value of the S-acetyl coenzyme A synthetase/adenylate kinase ratio, above which the cycle stops because all the recycling substrate has been accumulated as AMP, never reaching the steady state. In addition, the concept of adenylate energy charge has been applied to the system, obtaining the enabled values of the rate constants for a fixed adenylate energy charge value and vice versa.

Model
Publication ID: 16884499 Submission Date: 25 Jun 2009 18:58:10 UTC Last Modification Date: 09 Mar 2012 11:40:35 UTC Creation Date: 19 Aug 2009 16:30:30 UTC
Mathematical expressions
Reactions
v1 v2 v3 v4
Physical entities
Compartments Species
compartment ATP AMP ADP
Pyr NADH Lac
Global parameters
Vmapp1 Kmapp1 Vm2 Km2ATP
Km2AMP K Vmapp3 Kmapp3
k4      
Reactions (4)
 
 v1 [ATP] ↔ [AMP];  
 
 v2 [ATP] + [AMP] ↔ 2.0 × [ADP];  
 
 v3 [ADP] ↔ [ATP] + [Pyr];  
 
 v4 [Pyr] + [NADH] ↔ [Lac];  
 
   compartment Spatial dimensions: 3.0  Compartment size: 1.0
 
 ATP
Compartment: compartment
Initial concentration: 16.3
 
 AMP
Compartment: compartment
Initial concentration: 0.0
 
 ADP
Compartment: compartment
Initial concentration: 0.0
 
 Pyr
Compartment: compartment
Initial concentration: 0.0
 
 NADH
Compartment: compartment
Initial concentration: 256.0
 
 Lac
Compartment: compartment
Initial concentration: 0.0
Constant
 
Global Parameters (9)
 
   Vmapp1
Value: 2.3
Constant
 
   Kmapp1
Value: 700.0
Constant
 
   Vm2
Value: 170.0
Constant
 
   Km2ATP
Value: 25.0
Constant
 
   Km2AMP
Value: 110.0
Constant
 
   K
Value: 71000.0
Constant
 
   Vmapp3
Value: 65.0
Constant
 
   Kmapp3
Value: 260.0
Constant
 
   k4
Value: 5.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000231

Curator's comment: (updated: 19 Aug 2009 18:32:11 BST)

The model reproduces figures 1A and 1B, of the reference publication. Figure 1B is obtained using Vmapp1=33microMolar/sec. The model was integrated and curated using Copasi v4.5 (Build 30)

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