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BIOMD0000000054 - Ataullahkhanov1996_Adenylate

 

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Reference Publication
Publication ID: 8733433
Ataullakhanov FI, Komarova SV, Vitvitsky VM.
A possible role of adenylate metabolism in human erythrocytes: simple mathematical model.
J. Theor. Biol. 1996 Mar; 179(1): 75-86
National Research Center for Hematology, Moscow, Russia.  [more]
Model
Original Model: BIOMD0000000054.origin
Submitter: Harish Dharuri
Submission ID: MODEL4770526315
Submission Date: 12 Apr 2006 22:04:58 UTC
Last Modification Date: 05 Jul 2012 14:43:25 UTC
Creation Date: 12 Apr 2006 22:04:58 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:hasPart Gene Ontology regulation of glycolytic process
Gene Ontology AMP biosynthetic process
Gene Ontology regulation of sodium ion transport
bqbiol:hasTaxon Taxonomy Homo sapiens
Notes

The model reproduces ion and adenylate pool concentration corresponding to line 2 of Fig 3 of the publication. This model was tested successfully on Jarnac


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: 8733433 Submission Date: 12 Apr 2006 22:04:58 UTC Last Modification Date: 05 Jul 2012 14:43:25 UTC Creation Date: 12 Apr 2006 22:04:58 UTC
Mathematical expressions
Reactions
Passive ion influx ATP consumption by ion pump ATP from glycolysis AMP synthesis de novo
Adenylate pool      
Rules
Assignment Rule (variable: ATP) Assignment Rule (variable: AMP)    
Physical entities
Compartments Species
Erythrocyte Ions Energy pool Adenylate pool
Global parameters
ATP AMP Membrane permeability Extracellular ion concentration
Ion pump activity Glycolytic activity de novo AMP synthesis AMP degradation
Dependence of AMP degradation on ATP Dependence of AMP degradation on AMP    
Reactions (5)
 
 Passive ion influx  → [Ions];  
 
 ATP consumption by ion pump 3.0 × [Ions] + [Energy pool] → ;  
 
 ATP from glycolysis  → [Energy pool];  
 
 AMP synthesis de novo [Energy pool] → ;  
 
 Adenylate pool  → [Adenylate pool];  
 
Rules (2)
 
 Assignment Rule (name: T) ATP = ((A+3*E)-((6*A*E-3*E^2)+A^2)^0.5)/6
 
 Assignment Rule (name: M) AMP = ((7*A-3*E)-((6*A*E-3*E^2)+A^2)^0.5)/6
 
 Erythrocyte Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ions
Compartment: Erythrocyte
Initial concentration: 10.0
 
 Energy pool
Compartment: Erythrocyte
Initial concentration: 2.1
 
 Adenylate pool
Compartment: Erythrocyte
Initial concentration: 1.11
 
Global Parameters (10)
 
   ATP
Value: 1.0
 
   AMP
Value: 0.01
 
   Membrane permeability
Value: 0.121
Constant
 
   Extracellular ion concentration
Value: 100.0
Constant
 
   Ion pump activity
Value: 0.2
Constant
 
   Glycolytic activity
Value: 13.48
Constant
 
   de novo AMP synthesis
Value: 0.02
Constant
 
   AMP degradation
Value: 0.01
Constant
 
   Dependence of AMP degradation on ATP
Value: 1.2
Constant
 
   Dependence of AMP degradation on AMP
Value: -1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000054

Curator's comment: (updated: 18 Dec 2006 21:56:08 GMT)

The plots here correspond to line 2 of Ion concentration and adenylate pool shown in Fig 3. Simulation result obtained with Jarnac.

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