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BIOMD0000000199 - Santolini2001_nNOS_Mechanism_Regulation

 

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Reference Publication
Publication ID: 11038356
Santolini J, Adak S, Curran CM, Stuehr DJ.
A kinetic simulation model that describes catalysis and regulation in nitric-oxide synthase.
J. Biol. Chem. 2001 Jan; 276(2): 1233-1243
Department of Immunology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.  [more]
Model
Original Model: DOQCS logo
Submitter: Sharat Vayttaden
Submission ID: MODEL4734733125
Submission Date: 10 Nov 2008 12:41:11 UTC
Last Modification Date: 16 May 2012 10:00:46 UTC
Creation Date: 14 Oct 2008 16:56:09 UTC
Encoders:  Lukas Endler
   Vijayalakshmi Chelliah
   Jérôme Santolini
set #1
bqbiol:occursIn Taxonomy Rattus norvegicus
bqbiol:isVersionOf Gene Ontology oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
Gene Ontology nitric-oxide synthase activity
bqbiol:hasVersion OMIM 163731
Notes
This is a model of neuronal Nitric Oxide Synthase expressed in Escherichia coli based on Santolini J. et al. J Biol Chem. (2001) 276(2):1233-43 .
Differing from the article, oxygen explicitly included in the reaction 2, 5 and 10 (numbers as in scheme 1 in the article). In the article the assumed oxygen concentration of 140 uM was included in the pseudo first order rate constant.
Fig 2E in the article shows different time courses for citrulline and NO than the ones produced by this model. Dr. Santolini, one of the authors of the article, wrote that the legends in fig. 2E might be mixed up and should rather denote NO and NO3 instead of citrulline and NO.

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.
For more information see the terms of use .
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Model
Publication ID: 11038356 Submission Date: 10 Nov 2008 12:41:11 UTC Last Modification Date: 16 May 2012 10:00:46 UTC Creation Date: 14 Oct 2008 16:56:09 UTC
Mathematical expressions
Reactions
r1 r2 r3 r4
r5 r6 rF rG
r9 r10    
Rules
Assignment Rule (variable: FeIII_t)      
Physical entities
Compartments Species
cytosol FeIII FeII FeII_O2
FeIII_star FeII_star FeII_star_O2
FeIII_NO FeII_NO NADPH
O2 citruline NO3
NO NADPplus FeIII_t
Global parameters
k1 k2 k3 k4
k5 k6 k7 k8
k9 k10    
Reactions (10)
 
 r1 [FeIII] + [NADPH] → [FeII] + [NADPplus];  
 
 r2 [FeII] + [O2] → [FeII_O2];  
 
 r3 [FeII_O2] → [FeIII_star];  
 
 r4 [FeIII_star] + 0.5 × [NADPH] → [FeII_star] + 0.5 × [NADPplus];  
 
 r5 [FeII_star] + [O2] → [FeII_star_O2];  
 
 r6 [FeII_star_O2] → [FeIII_NO] + [citruline];  
 
 rF [FeIII_NO] → [FeIII] + [NO];  
 
 rG [FeIII_NO] + 0.5 × [NADPH] → [FeII_NO] + 0.5 × [NADPplus];  
 
 r9 [FeII_NO] → [FeII] + [NO];  
 
 r10 [FeII_NO] + [O2] → [FeIII] + [NO3];  
 
Rules (1)
 
 Assignment Rule (name: FeIII_t) FeIII_t = FeIII+FeIII_star
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 FeIII
Compartment: cytosol
Initial concentration: 1.0
 
 FeII
Compartment: cytosol
Initial concentration: 0.0
 
 FeII_O2
Compartment: cytosol
Initial concentration: 0.0
 
 FeIII_star
Compartment: cytosol
Initial concentration: 0.0
 
 FeII_star
Compartment: cytosol
Initial concentration: 0.0
 
 FeII_star_O2
Compartment: cytosol
Initial concentration: 0.0
 
 FeIII_NO
Compartment: cytosol
Initial concentration: 0.0
 
 FeII_NO
Compartment: cytosol
Initial concentration: 0.0
 
 NADPH
Compartment: cytosol
Initial concentration: 40.0
 
 O2
Compartment: cytosol
Initial concentration: 140.0
 
 citruline
Compartment: cytosol
Initial concentration: 0.0
 
 NO3
Compartment: cytosol
Initial concentration: 0.0
 
 NO
Compartment: cytosol
Initial concentration: 0.0
 
 NADPplus
Compartment: cytosol
Initial concentration: 0.0
 
  FeIII_t
Compartment: cytosol
 
Global Parameters (10)
 
 k1
Value: 2.6   (Units: persec)
Constant
 
 k2
Value: 0.9   (Units: peruMpersec)
Constant
 
 k3
Value: 26.0   (Units: persec)
Constant
 
 k4
Value: 2.6   (Units: persec)
Constant
 
 k5
Value: 0.9   (Units: peruMpersec)
Constant
 
 k6
Value: 26.0   (Units: persec)
Constant
 
 k7
Value: 5.0   (Units: persec)
Constant
 
 k8
Value: 2.6   (Units: persec)
Constant
 
 k9
Value: 1.0E-4   (Units: persec)
Constant
 
 k10
Value: 0.0013   (Units: peruMpersec)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000199

Curator's comment: (updated: 10 Nov 2008 11:43:43 GMT)

Reproduction of results from teh original article using Copasi 4.4.27

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