<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
<model id="sod">
<notes>
 <body xmlns="http://www.w3.org/1999/xhtml">
   <p> This is the SOD model of Kowald et al, JTB 238 (2006) 828-840.  </p>
   <p> Below, L is lipid radical, SO is superoxide, OH=hydroxyl radical,  </p>
   <p> LOO is a radical, and LOOH is stable oxidized lipid.  </p>
   <p> SOD is the total SOD, SODII=metal oxidized, SODII=reduced.  </p>
   <p> HSO is protonated SO, a fast reaction; HSO neutral so it crosses membranes.  </p>
   <p> Catalase. T and SODT are externally manipulated boundary conditions (bc).  </p>
   <p> HSO and SODI are rule/algebraically determined. They are cloaked here as bc.  </p>
   <p> Units are all in molar (M) and in seconds.  </p>
 </body>
</notes>
<listOfCompartments>
   <compartment id="cell"  size="1" />
</listOfCompartments>
<listOfSpecies>
   <species id="SO"  initialConcentration="0"  compartment="cell" boundaryCondition="false"/>
   <species id="SODII"  initialConcentration="5e-06"  compartment="cell" boundaryCondition="false"/>
   <species id="H2O2"  initialConcentration="0"  compartment="cell" boundaryCondition="false"/>
   <species id="OH"  initialConcentration="0"  compartment="cell" boundaryCondition="false"/>
   <species id="L"  initialConcentration="0"  compartment="cell" boundaryCondition="false"/>
   <species id="LOO"  initialConcentration="0"  compartment="cell" boundaryCondition="false"/>
   <species id="LOOH"  initialConcentration="0"  compartment="cell" boundaryCondition="false"/>
   <species id="HSO"  initialConcentration="0"  compartment="cell" boundaryCondition="true"/>
   <species id="SODI"  initialConcentration="5e-06"  compartment="cell" boundaryCondition="true"/>
   <species id="SOD"  initialConcentration="1e-05"  compartment="cell" boundaryCondition="true"/>
   <species id="catalase"  initialConcentration="1e-05"  compartment="cell" boundaryCondition="true"/>
</listOfSpecies>
<listOfParameters>
   <parameter id="Keq"  value="100" />
</listOfParameters>
<listOfRules>
  <assignmentRule variable="HSO">
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <divide/>
 <ci>SO</ci>
 <ci>Keq</ci>
</apply>
    </math>
  </assignmentRule>
  <assignmentRule variable="SODI">
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <minus/>
 <ci>SOD</ci>
 <ci>SODII</ci>
</apply>
    </math>
  </assignmentRule>
</listOfRules>
<listOfReactions>
  <reaction id="etcV1"  reversible="false">
    <listOfProducts>
      <speciesReference species = "SO" />
    </listOfProducts>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <ci>k1</ci>
 <cn>1</cn>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k1" value = "6.6e-07"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="sooV2"  reversible="false">
    <listOfReactants>
      <speciesReference species = "SO" />
      <speciesReference species = "SODII" />
    </listOfReactants>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <apply>
  <times/>
  <ci>k2</ci>
  <ci>SO</ci>
 </apply>
 <ci>SODII</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k2" value = "1.6e+09"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="sorV3"  reversible="false">
    <listOfReactants>
      <speciesReference species = "SO" />
    </listOfReactants>
    <listOfProducts>
      <speciesReference species = "H2O2" />
      <speciesReference species = "SODII" />
    </listOfProducts>
    <listOfModifiers>
      <modifierSpeciesReference species = "SODI" />
    </listOfModifiers>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <apply>
  <times/>
  <ci>k3</ci>
  <ci>SO</ci>
 </apply>
 <ci>SODI</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k3" value = "1.6e+09"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="loorV4"  reversible="false">
    <listOfReactants>
      <speciesReference species = "SO" />
      <speciesReference species = "LOO" />
    </listOfReactants>
    <listOfProducts>
      <speciesReference species = "LOOH" />
    </listOfProducts>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <apply>
  <times/>
  <ci>k4</ci>
  <ci>SO</ci>
 </apply>
 <ci>LOO</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k4" value = "100000"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="habWeiV5"  reversible="false">
    <listOfReactants>
      <speciesReference species = "SO" />
      <speciesReference species = "H2O2" />
    </listOfReactants>
    <listOfProducts>
      <speciesReference species = "OH" />
    </listOfProducts>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <apply>
  <times/>
  <ci>k5</ci>
  <ci>SO</ci>
 </apply>
 <ci>H2O2</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k5" value = "20000"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="sodFenV6"  reversible="false">
    <listOfReactants>
      <speciesReference species = "H2O2" />
    </listOfReactants>
    <listOfProducts>
      <speciesReference species = "OH" />
      <speciesReference species = "OH" />
    </listOfProducts>
    <listOfModifiers>
      <modifierSpeciesReference species = "SODII" />
    </listOfModifiers>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <apply>
  <times/>
  <ci>k6</ci>
  <ci>H2O2</ci>
 </apply>
 <ci>SODII</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k6" value = "1"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="catGpxV7"  reversible="false">
    <listOfReactants>
      <speciesReference species = "H2O2" />
    </listOfReactants>
    <listOfModifiers>
      <modifierSpeciesReference species = "catalase" />
    </listOfModifiers>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <apply>
  <times/>
  <ci>k7</ci>
  <ci>H2O2</ci>
 </apply>
 <ci>catalase</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k7" value = "3.4e+07"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="ohSinkV9"  reversible="false">
    <listOfReactants>
      <speciesReference species = "OH" />
    </listOfReactants>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <ci>k9</ci>
 <ci>OH</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k9" value = "1e+06"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="hsoLipPeroxV10"  reversible="false">
    <listOfProducts>
      <speciesReference species = "L" />
      <speciesReference species = "H2O2" />
    </listOfProducts>
    <listOfModifiers>
      <modifierSpeciesReference species = "HSO" />
    </listOfModifiers>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <ci>k10</ci>
 <ci>HSO</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k10" value = "1000"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="hoLipPeroxV11"  reversible="false">
    <listOfReactants>
      <speciesReference species = "OH" />
    </listOfReactants>
    <listOfProducts>
      <speciesReference species = "L" />
    </listOfProducts>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <ci>k11</ci>
 <ci>OH</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k11" value = "2.5e+08"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="loohDeOxV12"  reversible="false">
    <listOfReactants>
      <speciesReference species = "LOOH" />
    </listOfReactants>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <ci>k12</ci>
 <ci>LOOH</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k12" value = "0.38"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="sodoV13a"  reversible="false">
    <listOfProducts>
      <speciesReference species = "SODII" />
    </listOfProducts>
    <listOfModifiers>
      <modifierSpeciesReference species = "SODI" />
    </listOfModifiers>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <ci>k13a</ci>
 <ci>SODI</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k13a" value = "0.0087"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="sodrV13b"  reversible="false">
    <listOfReactants>
      <speciesReference species = "SODII" />
    </listOfReactants>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <ci>k13b</ci>
 <ci>SODII</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k13b" value = "0.0087"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="lipRadOxV17"  reversible="false">
    <listOfReactants>
      <speciesReference species = "L" />
    </listOfReactants>
    <listOfProducts>
      <speciesReference species = "LOO" />
    </listOfProducts>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <ci>k17</ci>
 <ci>L</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k17" value = "30000"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="chainRxV18"  reversible="false">
    <listOfReactants>
      <speciesReference species = "LOO" />
    </listOfReactants>
    <listOfProducts>
      <speciesReference species = "L" />
      <speciesReference species = "LOOH" />
    </listOfProducts>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <ci>k18</ci>
 <ci>LOO</ci>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k18" value = "7"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
  <reaction id="looSelfV19"  reversible="false">
    <listOfReactants>
      <speciesReference species = "LOO" />
      <speciesReference species = "LOO" />
    </listOfReactants>
  <kineticLaw>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
 <times/>
 <ci>k19</ci>
 <apply>
  <power/>
  <ci>LOO</ci>
  <cn>2</cn>
 </apply>
</apply>
    </math>
    <listOfParameters>
      <parameter id = "k19" value = "88000"/>
    </listOfParameters>
    </kineticLaw>
  </reaction>
</listOfReactions>
</model>
</sbml>
