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BIOMD0000000108 - Kowald2006_SOD

 

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Reference Publication
Publication ID: 16085106
Kowald A, Lehrach H, Klipp E.
Alternative pathways as mechanism for the negative effects associated with overexpression of superoxide dismutase.
J. Theor. Biol. 2006 Feb; 238(4): 828-840
Kinetic Modelling Group, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany. kowald@molgen.mpg.de  [more]
Model
Original Model: BIOMD0000000108.xml.origin
Submitter: Enuo He
Submission ID: MODEL5128825728
Submission Date: 09 Apr 2007 19:30:35 UTC
Last Modification Date: 06 Apr 2014 23:54:04 UTC
Creation Date: 28 Mar 2007 12:43:05 UTC
Encoders:  Enuo He
set #1
bqbiol:hasTaxon Taxonomy cellular organisms
bqbiol:isVersionOf Gene Ontology regulation of superoxide metabolic process
Gene Ontology superoxide dismutase activity
Notes

This model is according to the paper from Axel Kowald Alternative pathways as mechanism for the negative effects associated with overexpression of superoxide dismutase.

Reactions from 1 to 17 are listed in the paper, note that for clarity species whose concentrations are assumed to be constant (e.g.water, oxygen,protons, metal ions) are omitted from the diagram. In the paper, v16 is a fast reaction, but we do not use fast reaction in the model.

Figure2 has been reproduced by both SBMLodeSolver and Copasi4.0.20(development) . Figure 3 has been obtained with Copasi4.0.20(development) using parameter scan.

The steady-state of [LOO*] a little bit lower than showed on the paper, I guess it may be the simulation method used in the paper use fast reaction and also the reaction (5) listed on Page 831 on the paper is slightly different from equation (2) on Page 832. The rest of them are the quite the same.


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: 16085106 Submission Date: 09 Apr 2007 19:30:35 UTC Last Modification Date: 06 Apr 2014 23:54:04 UTC Creation Date: 28 Mar 2007 12:43:05 UTC
Mathematical expressions
Reactions
v1 v2 v3 v4
v5 v6 v7 v9
v10 v11 v12 v13a
v13b v17 v18 v19
v16      
Rules
Assignment Rule (variable: HO2*) Assignment Rule (variable: Cu(I)ZnSOD)    
Physical entities
Compartments Species
cell O2*- Cu(II)ZnSOD H2O2
LOO* HO* LOOH
L* SODtotal Cat
Global parameters
k1 k2 k3 k4
k5 k6 k7 k9
k10 k11 k12 k13a
k13b k17 k18 k19
HO2* Cu(I)ZnSOD    
Reactions (17)
 
 v1  → [O2*-];  
 
 v2 [O2*-] + [Cu(II)ZnSOD] → ;  
 
 v3 [O2*-] → [H2O2] + [Cu(II)ZnSOD];  
 
 v4 [O2*-] + [LOO*] → [LOOH];  
 
 v5 [O2*-] + [H2O2] → 2.0 × [HO*];  
 
 v6 [H2O2] → 2.0 × [HO*];   {Cu(II)ZnSOD}
 
 v7 [H2O2] → ;   {Cat}
 
 v9 [HO*] → ;  
 
 v10  → [L*] + [H2O2];  
 
 v11 [HO*] → [L*];  
 
 v12 [LOOH] → ;  
 
 v13a  → [Cu(II)ZnSOD];  
 
 v13b [Cu(II)ZnSOD] → ;  
 
 v17 [L*] → [LOO*];  
 
 v18 [LOO*] → [L*] + [LOOH];  
 
 v19 2.0 × [LOO*] → ;  
 
 v16 [O2*-] ↔ ;  
 
Rules (2)
 
 Assignment Rule (name: HO2star) HO2* = species_0000001/100
 
 Assignment Rule (name: Cu_I_ZnSOD) Cu(I)ZnSOD = species_0000016-species_0000002
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 O2*-
Compartment: cell
Initial concentration: 0.0
 
 Cu(II)ZnSOD
Compartment: cell
Initial concentration: 5.0E-6
 
 H2O2
Compartment: cell
Initial concentration: 0.0
 
   LOO*
Compartment: cell
Initial concentration: 0.0
 
 HO*
Compartment: cell
Initial concentration: 0.0
 
 LOOH
Compartment: cell
Initial concentration: 0.0
 
 L*
Compartment: cell
Initial concentration: 0.0
 
 SODtotal
Compartment: cell
Initial concentration: 1.0E-5
Constant
 
 Cat
Compartment: cell
Initial concentration: 1.0E-5
Constant
 
Global Parameters (18)
 
   k1
Value: 6.6E-7
Constant
 
   k2
Value: 1.6E9
Constant
 
   k3
Value: 1.6E9
Constant
 
   k4
Value: 100000.0
Constant
 
   k5
Value: 20000.0
Constant
 
   k6
Value: 1.0
Constant
 
   k7
Value: 3.4E7
Constant
 
   k9
Value: 1000000.0
Constant
 
   k10
Value: 1000.0
Constant
 
   k11
Value: 2.5E8
Constant
 
   k12
Value: 0.38
Constant
 
   k13a
Value: 0.0087
Constant
 
   k13b
Value: 0.0087
Constant
 
   k17
Value: 30000.0
Constant
 
   k18
Value: 7.0
Constant
 
   k19
Value: 88000.0
Constant
 
   HO2*  
 
   Cu(I)ZnSOD  
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000108

Curator's comment: (updated: 29 Mar 2007 01:45:06 BST)

Figure2 has been reproduced by both SBMLodeSolver and Copasi4.0.20(development). Because the absolute concentrations of the different variables vary by several orders of magnitude, different scales and axes are used. Not all the species are displayed on the figure.

The steady-state of [LOO*] a little bit lower than showed on the paper

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