kowald1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000108) Biomodels 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. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.

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Alternative pathways as mechanism for the negative effects associated with overexpression of superoxide dismutase.

  • Axel Kowald
  • Hans Lehrach
  • Edda Klipp
J. Theor. Biol. 2006; 238 (4): 828-840
Abstract
One of the most important antioxidant enzymes is superoxide dismutase (SOD), which catalyses the dismutation of superoxide radicals to hydrogen peroxide. The enzyme plays an important role in diseases like trisomy 21 and also in theories of the mechanisms of aging. But instead of being beneficial, intensified oxidative stress is associated with the increased expression of SOD and also studies on bacteria and transgenic animals show that high levels of SOD actually lead to increased lipid peroxidation and hypersensitivity to oxidative stress. Using mathematical models we investigate the question how overexpression of SOD can lead to increased oxidative stress, although it is an antioxidant enzyme. We consider the following possibilities that have been proposed in the literature: (i) Reaction of H(2)O(2) with CuZnSOD leading to hydroxyl radical formation. (ii) Superoxide radicals might reduce membrane damage by acting as radical chain breaker. (iii) While detoxifying superoxide radicals SOD cycles between a reduced and oxidized state. At low superoxide levels the intermediates might interact with other redox partners and increase the superoxide reductase (SOR) activity of SOD. This short-circuiting of the SOD cycle could lead to an increased hydrogen peroxide production. We find that only one of the proposed mechanisms is under certain circumstances able to explain the increased oxidative stress caused by SOD. But furthermore we identified an additional mechanism that is of more general nature and might be a common basis for the experimental findings. We call it the alternative pathway mechanism.

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
Id Name Spatial dimensions Size
compartment_0000001 cell 3.0 1.0
Id Name Initial quantity Compartment Fixed
species_0000001 O2*- 0.0 compartment_0000001 (cell)
species_0000002 Cu(II)ZnSOD 0.000005 compartment_0000001 (cell)
species_0000006 H2O2 0.0 compartment_0000001 (cell)
species_0000007 LOO* 0.0 compartment_0000001 (cell)
species_0000008 HO* 0.0 compartment_0000001 (cell)
species_0000009 LOOH 0.0 compartment_0000001 (cell)
species_0000011 L* 0.0 compartment_0000001 (cell)
species_0000016 SODtotal 0.00001 compartment_0000001 (cell)
species_0000017 Cat 0.00001 compartment_0000001 (cell)

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
fast v16 species_0000001 = ∅

k10 * HO2star * compartment_0000001
reaction_0 v2 species_0000001 + species_0000002 > ∅

compartment_0000001 * k2 * species_0000001 * species_0000002
reaction_0000001 v1 ∅ > species_0000001

compartment_0000001 * k1
reaction_1 v3 species_0000001 > species_0000006 + species_0000002

compartment_0000001 * k3 * species_0000001 * Cu_I_ZnSOD
reaction_10 v13a ∅ > species_0000002

compartment_0000001 * k13a * Cu_I_ZnSOD
reaction_11 v13b species_0000002 > ∅

compartment_0000001 * k13b * species_0000002
reaction_12 v17 species_0000011 > species_0000007

compartment_0000001 * k17 * species_0000011
reaction_13 v18 species_0000007 > species_0000011 + species_0000009

compartment_0000001 * k18 * species_0000007
reaction_14 v19 {2.0}species_0000007 > ∅

compartment_0000001 * k19 * pow(species_0000007, 2)
reaction_2 v4 species_0000001 + species_0000007 > species_0000009

compartment_0000001 * k4 * species_0000001 * species_0000007
reaction_3 v5 species_0000001 + species_0000006 > {2.0}species_0000008

compartment_0000001 * k5 * species_0000001 * species_0000006
reaction_4 v6 species_0000006 > {2.0}species_0000008

compartment_0000001 * k6 * species_0000006 * species_0000002
reaction_5 v7 species_0000006 > ∅

compartment_0000001 * k7 * species_0000006 * species_0000017
reaction_6 v9 species_0000008 > ∅

compartment_0000001 * k9 * species_0000008
reaction_7 v10 ∅ > species_0000011 + species_0000006

compartment_0000001 * k10 * HO2star
reaction_8 v11 species_0000008 > species_0000011

compartment_0000001 * k11 * species_0000008
reaction_9 v12 species_0000009 > ∅

compartment_0000001 * k12 * species_0000009

Global parameters

Id Value
Cu_I_ZnSOD 0.0
HO2star 0.0
k1 0.00000066
k10 1000.0
k11 250000000.0
k12 0.38
k13a 0.0087
k13b 0.0087
k17 30000.0
k18 7.0
k19 88000.0
k2 1600000000.0
k3 1600000000.0
k4 100000.0
k5 20000.0
k6 1.0
k7 34000000.0
k9 1000000.0

Local parameters

Id Value Reaction

Assignment rules

Definition
Cu_I_ZnSOD = species_0000016 - species_0000002
HO2star = species_0000001 / 100.0

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments