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BIOMD0000000046 - Olsen2003_peroxidase

 

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Reference Publication
Publication ID: 12823550
Olsen LF, Hauser MJ, Kummer U.
Mechanism of protection of peroxidase activity by oscillatory dynamics.
Eur. J. Biochem. 2003 Jul; 270(13): 2796-2804
European Media Laboratory, Heidelberg, Germany. lfo@bmb.sdu.dk  [more]
Model
Original Model: JWS logo
Submitter: Nicolas Le Novère
Submission ID: MODEL6623265463
Submission Date: 13 Sep 2005 14:54:50 UTC
Last Modification Date: 12 Feb 2014 14:14:00 UTC
Creation Date: 22 Aug 2005 22:49:18 UTC
Encoders:  Nicolas Le Novère
   Jacky L Snoep
set #1
bqbiol:occursIn Taxonomy Armoracia rusticana
bqbiol:isVersionOf Gene Ontology NADH peroxidase activity
set #2
bqmodel:isDerivedFrom PubMed 11901676
Notes

Notes of the BioModels curators:

The current model reproduce the figure 7, panel B of the paper. Note that there is a typo in the figure. The ordinates represent the concentration of peroxyde, as stated in the legend, and not of oxygen. The model has been tested in COPASI (http://www.copasi.org/, build 13).

Notes of the original version of the SBML file:

SBML level 2 code generated for the JWS Online project by Jacky Snoep using PySCeS
Run this model online at http://jjj.biochem.sun.ac.za
To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based modelling using JWS Online , Bioinformatics, 20:2143-2144


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: 12823550 Submission Date: 13 Sep 2005 14:54:50 UTC Last Modification Date: 12 Feb 2014 14:14:00 UTC Creation Date: 22 Aug 2005 22:49:18 UTC
Mathematical expressions
Reactions
v1 v2 v3 v4
v5 v6 v7 v8
v9 v10 v11 v12
v131 v132 v14  
Physical entities
Compartments Species
compartment NADH O2 H2O2
per3 coI ArH
coII Ar NADrad
super coIII per2
NAD2 NAD O2g
NADHres    
Reactions (15)
 
 v1 [NADH] + [O2] → [H2O2] + [NAD];  
 
 v2 [per3] + [H2O2] → [coI];  
 
 v3 [ArH] + [coI] → [Ar] + [coII];  
 
 v4 [coII] + [ArH] → [per3] + [Ar];  
 
 v5 [NADrad] + [O2] → [NAD] + [super];  
 
 v6 [per3] + [super] → [coIII];  
 
 v7 2.0 × [super] → [H2O2] + [O2];  
 
 v8 [NADrad] + [coIII] → [NAD] + [coI];  
 
 v9 2.0 × [NADrad] → [NAD2];  
 
 v10 [per3] + [NADrad] → [per2] + [NAD];  
 
 v11 [per2] + [O2] → [coIII];  
 
 v12 [NADHres] → [NADH];  
 
 v131 [O2g] → [O2];  
 
 v132 [O2] → [O2g];  
 
 v14 [NADH] + [Ar] → [NADrad] + [ArH];  
 
   Spatial dimensions: 3.0  Compartment size: 1.0
 
 NADH
Compartment: compartment
Initial concentration: 0.0
 
 O2
Compartment: compartment
Initial concentration: 0.0
 
 H2O2
Compartment: compartment
Initial concentration: 0.0
 
 per3
Compartment: compartment
Initial concentration: 1.4
 
 coI
Compartment: compartment
Initial concentration: 0.0
 
 ArH
Compartment: compartment
Initial concentration: 500.0
 
 coII
Compartment: compartment
Initial concentration: 0.0
 
 Ar
Compartment: compartment
Initial concentration: 0.0
 
 NADrad
Compartment: compartment
Initial concentration: 0.0
 
 super
Compartment: compartment
Initial concentration: 0.0
 
 coIII
Compartment: compartment
Initial concentration: 0.0
 
 per2
Compartment: compartment
Initial concentration: 0.0
 
 NAD2
Compartment: compartment
Initial concentration: 0.0
 
 NAD
Compartment: compartment
Initial concentration: 0.0
 
 O2g
Compartment: compartment
Initial concentration: 12.0
 
 NADHres
Compartment: compartment
Initial concentration: 0.0
 
v1 (1)
 
   k1
Value: 3.0E-6
Constant
 
v2 (1)
 
   k2
Value: 18.0
Constant
 
v3 (1)
 
   k3
Value: 0.15
Constant
 
v4 (1)
 
   k4
Value: 0.0052
Constant
 
v5 (1)
 
   k5
Value: 20.0
Constant
 
v6 (1)
 
   k6
Value: 17.0
Constant
 
v7 (1)
 
   k7
Value: 20.0
Constant
 
v8 (1)
 
   k8
Value: 40.0
Constant
 
v9 (1)
 
   k9
Value: 60.0
Constant
 
v10 (1)
 
   k10
Value: 1.8
Constant
 
v11 (1)
 
   k11
Value: 0.1
Constant
 
v12 (1)
 
   k12
Value: 0.08
Constant
 
v131 (1)
 
   k13f
Value: 0.0060
Constant
 
v132 (1)
 
   k13b
Value: 0.0060
Constant
 
v14 (1)
 
   k14
Value: 0.7
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000046

Curator's comment: (updated: 29 Dec 2006 23:20:19 GMT)

Figure 7B reproduced in COPASI v4.0 build 19

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