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BIOMD0000000191 - Montañez2008_Arginine_catabolism

 

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Reference Publication
Publication ID: 17520329
Montañez R, Rodríguez-Caso C, Sánchez-Jiménez F, Medina MA.
In silico analysis of arginine catabolism as a source of nitric oxide or polyamines in endothelial cells.
Amino Acids 2008 Feb; 34(2): 223-229
Procel Group, Department of Molecular Biology and Biochemistry, University of Málaga, and CIBERER, Málaga, Spain.  [more]
Model
Original Model: BIOMD0000000191.origin
Submitter: Armando Reyes-Palomares
Submission ID: MODEL7416883636
Submission Date: 10 Sep 2008 16:48:31 UTC
Last Modification Date: 08 Apr 2016 15:45:31 UTC
Creation Date: 27 Nov 2008 11:36:17 UTC
Encoders:  Lukas Endler
   Armando Reyes-Palomares
   Carlos Rodríguez-Caso
   Raul Montañez
   Francisca Sánchez-Jiménez
   Miguel A. Medina
set #1
bqbiol:hasVersion Gene Ontology nitric oxide biosynthetic process
Gene Ontology ornithine metabolic process
bqbiol:isPartOf KEGG Pathway Arginine and proline metabolism
Gene Ontology arginine catabolic process
bqbiol:occursIn Taxonomy Mammalia
Notes

SBML creators: Armando Reyes-Palomares * , Raul Montañez *, Carlos Rodriguez-Caso +, Francisca Sanchez-Jimenez * , Miguel A. Medina *

* ProCel Group, Department of Molecular Biology and Biochemistry, Faculty of Sciences, Campus de Teatinos, University of Malaga and CIBER de Enfermedades Raras (CIBER-ER). + Complex Systems Lab (ICREA-UPF), Barcelona Biomedical Research Park (PRBB-GRIB).

http://asp.uma.es

In silico analysis of arginine catabolism as a source of nitric oxide or polyamines in endothelial cells.
Montañez, R et al.: Amino Acids. 2008 Feb;34(2):223-9.
The model reproduces the dynamical behavior of the arginine catabolism and transport in relation to the nitric oxide production. In this model there are some additions and corrections to the publication. All perturbations and analysis have produced results very close to the published experiments. The model was successfully tested on CoPaSi v.4.4 (build 26).

Erratum: parameters values modificated respect to the publication to reach the steady-state:

Kmodc=90 µM (60 µM in the paper)

Kiornhat (is equivalent to the parameter Kmefflhat Eq ) = 360 µM (380 µM in the paper)


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: 17520329 Submission Date: 10 Sep 2008 16:48:31 UTC Last Modification Date: 08 Apr 2016 15:45:31 UTC Creation Date: 27 Nov 2008 11:36:17 UTC
Mathematical expressions
Reactions
Arginase Arginine transport Ornithine efflux Nitric oxide synthase
Ornithine decarboxylase      
Physical entities
Compartments Species
extracellular Arginine ex    
cytosol Ornithine Arginine in  
 extracellular Spatial dimensions: 3.0  Compartment size: 1.0
 
 Arginine ex
Compartment: extracellular
Initial concentration: 330.0
Constant
 
 cytosol Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ornithine
Compartment: cytosol
Initial concentration: 1.0
 
 Arginine in
Compartment: cytosol
Initial concentration: 1.0
 
Arginase (3)
 
 Vmaxarg
Value: 110.0   (Units: microMpermin)
Constant
 
 Kmarg
Value: 1500.0   (Units: microM)
Constant
 
 Kioarg
Value: 1000.0   (Units: microM)
Constant
 
Arginine transport (5)
 
 Kmhat
Value: 70.0   (Units: microM)
Constant
 
 Vmaxhat
Value: 160.5   (Units: microM)
Constant
 
 Kmlat
Value: 847.0   (Units: microM)
Constant
 
 Vmaxlat
Value: 420.0   (Units: microMpermin)
Constant
 
 Kiornhat
Value: 360.0   (Units: microM)
Constant
 
Ornithine efflux (6)
 
 Kmhat
Value: 70.0   (Units: microM)
Constant
 
 Kmlat
Value: 847.0   (Units: microM)
Constant
 
 Vmaxefflhat
Value: 160.5   (Units: microMpermin)
Constant
 
 Vmaxeffllat
Value: 420.0   (Units: microMpermin)
Constant
 
 Kmeffllat
Value: 847.0   (Units: microM)
Constant
 
 Kiornhat
Value: 360.0   (Units: microM)
Constant
 
Nitric oxide synthase (2)
 
 Vmaxnos1
Value: 1.33   (Units: microMpermin)
Constant
 
   Kmnos1
Value: 16.0   (Units: microM)
Constant
 
Ornithine decarboxylase (2)
 
 Vmaxodc
Value: 0.013   (Units: microMpermin)
Constant
 
 Kmodc
Value: 90.0   (Units: microM)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000191

Curator's comment: (updated: 10 Sep 2008 15:55:01 BST)

Steady state concentrations and time courses calculated using SBML ODESolver (20080507)

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