A computational approach/model to explore NMDA receptors functions (Keller et al 2017)

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Accession:235002
"... Here, we describe a general computational method aiming at developing kinetic Markov-chain based models of NMDARs subtypes capable of reproducing various experimental results. These models are then used to make predictions on additional (non-obvious) properties and on their role in synaptic function under various physiological and pharmacological conditions. For the purpose of this book chapter, we will focus on the method used to develop a NMDAR model that includes pharmacological site of action of different compounds. Notably, this elementary model can subsequently be included in a neuron model (not described in detail here) to explore the impact of their differential distribution on synaptic functions."
Reference:
1 . Keller AF, Bouteiller JC, Berger TW (2017) Development of a Computational Approach/Model to Explore NMDA Receptors Functions. Methods Mol Biol 1677:291-306 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Synapse;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s): NMDA;
Gene(s):
Transmitter(s):
Simulation Environment:
Model Concept(s): Ion Channel Kinetics;
Implementer(s):
Search NeuronDB for information about:  NMDA;
/
KellerEtAl2017
readme.txt
KELLER_Book_Chapter_figure3_NMDA_fct_Mg.py
NMDA8_v6_2L3.xml
                            
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Description: 
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Only contains the kinetic scheme. 
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Added all components to calculate current (Mg, perm_Ca, etc.)
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              <celldesigner:proteinReference>pr8</celldesigner:proteinReference>
            </celldesigner:speciesIdentity>
          </celldesigner:extension>
        </annotation>
      </species>
      <species metaid="s9" id="Glu" name="Glu" compartment="default" initialConcentration="0" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false">
        <annotation>
          <celldesigner:extension>
            <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
            <celldesigner:speciesIdentity>
              <celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
              <celldesigner:name>Glu</celldesigner:name>
            </celldesigner:speciesIdentity>
          </celldesigner:extension>
        </annotation>
      </species>
      <species metaid="Mg" id="Mg" name="Mg" compartment="default" initialAmount="1" substanceUnits="substance" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false">
        <annotation>
          <celldesigner:extension>
            <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
            <celldesigner:speciesIdentity>
              <celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
              <celldesigner:name>Mg</celldesigner:name>
            </celldesigner:speciesIdentity>
          </celldesigner:extension>
        </annotation>
      </species>
      <species metaid="Vm" id="Vm" name="Vm" compartment="default" initialAmount="-70" substanceUnits="substance" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false">
        <annotation>
          <celldesigner:extension>
            <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
            <celldesigner:speciesIdentity>
              <celldesigner:class>ION</celldesigner:class>
              <celldesigner:name>Vm</celldesigner:name>
            </celldesigner:speciesIdentity>
          </celldesigner:extension>
        </annotation>
      </species>
    </listOfSpecies>
    <listOfParameters>
      <parameter metaid="kon" id="kon" name="kon" value="31.6" units="per_mM_per_msec" constant="true" />
      <parameter metaid="koff" id="koff" name="koff" value="1.01" units="per_msec" constant="true" />
      <parameter metaid="kd1p" id="kd1p" name="kd1p" value="0.0851" units="per_msec" constant="true" />
      <parameter metaid="kd1m" id="kd1m" name="kd1m" value="0.0297" units="per_msec" constant="true" />
      <parameter metaid="kd2p" id="kd2p" name="kd2p" value="0.23" units="per_msec" constant="true" />
      <parameter metaid="kd2m" id="kd2m" name="kd2m" value="0.00101" units="per_msec" constant="true" />
      <parameter metaid="ksp" id="ksp" name="ksp" value="0.23" units="per_msec" constant="true" />
      <parameter metaid="ksm" id="ksm" name="ksm" value="0.178" units="per_msec" constant="true" />
      <parameter metaid="kfp" id="kfp" name="kfp" value="3.14" units="per_msec" constant="true" />
      <parameter metaid="kfm" id="kfm" name="kfm" value="0.174" units="pS" constant="true" />
      <parameter metaid="g1" id="g1" name="g1" value="40" units="pS" constant="true" />
      <parameter metaid="g2" id="g2" name="g2" value="247" units="pS" constant="true" />
      <parameter metaid="Vrev" id="Vrev" name="Vrev" value="-0.7" units="mV" constant="true" />
      <parameter metaid="alpha" id="alpha" name="alpha" value="0.01" units="dimensionless" constant="true" />
      <parameter metaid="cond" id="cond" name="cond" value="0" units="pS" constant="false" />
      <parameter metaid="Iunit" id="Iunit" name="Iunit" value="0" units="pA" constant="false" />
      <parameter metaid="I" id="I" name="I" value="0" units="pA" constant="false" />
      <parameter metaid="nbNMDAR" id="nbNMDAR" name="nbNMDAR" value="1" units="dimensionless" constant="true" />
      <parameter metaid="Omg" id="Omg" name="Omg" value="0" units="pS" constant="false" />
      <parameter metaid="Ica" id="Ica" name="Ica" value="0" units="pA" constant="false" />
      <parameter metaid="perm_Ca" id="perm_Ca" name="perm_Ca" value="0.1" units="dimensionless" constant="true" />
    </listOfParameters>
    <listOfRules>
      <assignmentRule metaid="CDMT00042" variable="Omg">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <divide />
            <ci> RA2fs </ci>
            <apply>
              <plus />
              <cn type="integer"> 1 </cn>
              <apply>
                <divide />
                <apply>
                  <times />
                  <apply>
                    <exp />
                    <apply>
                      <times />
                      <cn type="integer"> -62 </cn>
                      <ci> Vm </ci>
                      <cn> 0.001 </cn>
                    </apply>
                  </apply>
                  <ci> Mg </ci>
                </apply>
                <cn> 3.57 </cn>
              </apply>
            </apply>
          </apply>
        </math>
      </assignmentRule>
      <assignmentRule metaid="CDMT00043" variable="cond">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <plus />
            <ci> g1 </ci>
            <apply>
              <divide />
              <apply>
                <minus />
                <ci> g2 </ci>
                <ci> g1 </ci>
              </apply>
              <apply>
                <plus />
                <cn type="integer"> 1 </cn>
                <apply>
                  <exp />
                  <apply>
                    <times />
                    <ci> alpha </ci>
                    <ci> Vm </ci>
                    <cn> 0.001 </cn>
                  </apply>
                </apply>
              </apply>
            </apply>
          </apply>
        </math>
      </assignmentRule>
      <assignmentRule metaid="CDMT00044" variable="Iunit">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <times />
            <ci> cond </ci>
            <apply>
              <minus />
              <ci> Vm </ci>
              <ci> Vrev </ci>
            </apply>
            <cn> 0.001 </cn>
            <ci> Omg </ci>
          </apply>
        </math>
      </assignmentRule>
      <assignmentRule metaid="CDMT00045" variable="I">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <times />
            <ci> Iunit </ci>
            <ci> nbNMDAR </ci>
          </apply>
        </math>
      </assignmentRule>
      <assignmentRule metaid="CDMT00046" variable="Ica">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <times />
            <ci> I </ci>
            <ci> perm_Ca </ci>
          </apply>
        </math>
      </assignmentRule>
    </listOfRules>
    <listOfReactions>
      <reaction metaid="re4" id="re4" reversible="true" fast="false">
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
            <celldesigner:baseReactants>
              <celldesigner:baseReactant species="R" alias="sa1">
                <celldesigner:linkAnchor position="E" />
              </celldesigner:baseReactant>
              <celldesigner:baseReactant species="Glu" alias="sa9">
                <celldesigner:linkAnchor position="S" />
              </celldesigner:baseReactant>
            </celldesigner:baseReactants>
            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="RA" alias="sa2">
                <celldesigner:linkAnchor position="W" />
              </celldesigner:baseProduct>
            </celldesigner:baseProducts>
            <celldesigner:connectScheme connectPolicy="direct">
              <celldesigner:listOfLineDirection>
                <celldesigner:lineDirection arm="0" index="0" value="unknown" />
                <celldesigner:lineDirection arm="1" index="0" value="unknown" />
                <celldesigner:lineDirection arm="2" index="0" value="unknown" />
              </celldesigner:listOfLineDirection>
            </celldesigner:connectScheme>
            <celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">0.015151515151512918,0.4392980437284233</celldesigner:editPoints>
            <celldesigner:line width="1.0" color="ff000000" />
          </celldesigner:extension>
        </annotation>
        <listOfReactants>
          <speciesReference metaid="CDMT00016" species="R" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa1</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
          <speciesReference metaid="CDMT00017" species="Glu" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa9</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="CDMT00018" species="RA" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa2</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfProducts>
        <kineticLaw metaid="CDMT00019">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus />
              <apply>
                <times />
                <cn type="integer"> 2 </cn>
                <ci> kon </ci>
                <ci> R </ci>
                <ci> Glu </ci>
              </apply>
              <apply>
                <times />
                <ci> RA </ci>
                <ci> koff </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction metaid="re5" id="re5" reversible="true" fast="false">
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
            <celldesigner:baseReactants>
              <celldesigner:baseReactant species="RA" alias="sa2">
                <celldesigner:linkAnchor position="E" />
              </celldesigner:baseReactant>
              <celldesigner:baseReactant species="Glu" alias="sa10">
                <celldesigner:linkAnchor position="S" />
              </celldesigner:baseReactant>
            </celldesigner:baseReactants>
            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="RA2" alias="sa3">
                <celldesigner:linkAnchor position="W" />
              </celldesigner:baseProduct>
            </celldesigner:baseProducts>
            <celldesigner:connectScheme connectPolicy="direct">
              <celldesigner:listOfLineDirection>
                <celldesigner:lineDirection arm="0" index="0" value="unknown" />
                <celldesigner:lineDirection arm="1" index="0" value="unknown" />
                <celldesigner:lineDirection arm="2" index="0" value="unknown" />
              </celldesigner:listOfLineDirection>
            </celldesigner:connectScheme>
            <celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">0.01580180449628621,0.4333781965006729</celldesigner:editPoints>
            <celldesigner:line width="1.0" color="ff000000" />
          </celldesigner:extension>
        </annotation>
        <listOfReactants>
          <speciesReference metaid="CDMT00020" species="RA" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa2</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
          <speciesReference metaid="CDMT00021" species="Glu" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa10</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="CDMT00022" species="RA2" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa3</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfProducts>
        <kineticLaw metaid="CDMT00035">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus />
              <apply>
                <times />
                <ci> RA </ci>
                <ci> Glu </ci>
                <ci> kon </ci>
              </apply>
              <apply>
                <times />
                <ci> RA2 </ci>
                <cn type="integer"> 2 </cn>
                <ci> koff </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction metaid="re6" id="re6" reversible="true" fast="false">
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
            <celldesigner:baseReactants>
              <celldesigner:baseReactant species="RA2" alias="sa3">
                <celldesigner:linkAnchor position="N" />
              </celldesigner:baseReactant>
            </celldesigner:baseReactants>
            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="D1" alias="sa4">
                <celldesigner:linkAnchor position="S" />
              </celldesigner:baseProduct>
            </celldesigner:baseProducts>
            <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
              <celldesigner:listOfLineDirection>
                <celldesigner:lineDirection index="0" value="unknown" />
              </celldesigner:listOfLineDirection>
            </celldesigner:connectScheme>
            <celldesigner:line width="1.0" color="ff000000" />
          </celldesigner:extension>
        </annotation>
        <listOfReactants>
          <speciesReference metaid="CDMT00023" species="RA2" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa3</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="CDMT00024" species="D1" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa4</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfProducts>
        <kineticLaw metaid="CDMT00036">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus />
              <apply>
                <times />
                <ci> RA2 </ci>
                <ci> kd1m </ci>
              </apply>
              <apply>
                <times />
                <ci> D1 </ci>
                <ci> kd1p </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction metaid="re7" id="re7" reversible="true" fast="false">
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
            <celldesigner:baseReactants>
              <celldesigner:baseReactant species="RA2" alias="sa3">
                <celldesigner:linkAnchor position="S" />
              </celldesigner:baseReactant>
            </celldesigner:baseReactants>
            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="D2" alias="sa5">
                <celldesigner:linkAnchor position="N" />
              </celldesigner:baseProduct>
            </celldesigner:baseProducts>
            <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
              <celldesigner:listOfLineDirection>
                <celldesigner:lineDirection index="0" value="unknown" />
              </celldesigner:listOfLineDirection>
            </celldesigner:connectScheme>
            <celldesigner:line width="1.0" color="ff000000" />
          </celldesigner:extension>
        </annotation>
        <listOfReactants>
          <speciesReference metaid="CDMT00025" species="RA2" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa3</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="CDMT00026" species="D2" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa5</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfProducts>
        <kineticLaw metaid="CDMT00037">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus />
              <apply>
                <times />
                <ci> RA2 </ci>
                <ci> kd2p </ci>
              </apply>
              <apply>
                <times />
                <ci> D2 </ci>
                <ci> kd2m </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction metaid="re8" id="re8" reversible="true" fast="false">
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
            <celldesigner:baseReactants>
              <celldesigner:baseReactant species="RA2" alias="sa3">
                <celldesigner:linkAnchor position="ENE" />
              </celldesigner:baseReactant>
            </celldesigner:baseReactants>
            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="RA2f" alias="sa6">
                <celldesigner:linkAnchor position="WSW" />
              </celldesigner:baseProduct>
            </celldesigner:baseProducts>
            <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
              <celldesigner:listOfLineDirection>
                <celldesigner:lineDirection index="0" value="unknown" />
              </celldesigner:listOfLineDirection>
            </celldesigner:connectScheme>
            <celldesigner:line width="1.0" color="ff000000" />
          </celldesigner:extension>
        </annotation>
        <listOfReactants>
          <speciesReference metaid="CDMT00027" species="RA2" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa3</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="CDMT00028" species="RA2f" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa6</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfProducts>
        <kineticLaw metaid="CDMT00038">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus />
              <apply>
                <times />
                <ci> RA2 </ci>
                <ci> kfp </ci>
              </apply>
              <apply>
                <times />
                <ci> RA2f </ci>
                <ci> kfm </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction metaid="re9" id="re9" reversible="true" fast="false">
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
            <celldesigner:baseReactants>
              <celldesigner:baseReactant species="RA2" alias="sa3">
                <celldesigner:linkAnchor position="ESE" />
              </celldesigner:baseReactant>
            </celldesigner:baseReactants>
            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="RA2s" alias="sa7">
                <celldesigner:linkAnchor position="WNW" />
              </celldesigner:baseProduct>
            </celldesigner:baseProducts>
            <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
              <celldesigner:listOfLineDirection>
                <celldesigner:lineDirection index="0" value="unknown" />
              </celldesigner:listOfLineDirection>
            </celldesigner:connectScheme>
            <celldesigner:line width="1.0" color="ff000000" />
          </celldesigner:extension>
        </annotation>
        <listOfReactants>
          <speciesReference metaid="CDMT00029" species="RA2" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa3</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="CDMT00030" species="RA2s" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa7</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfProducts>
        <kineticLaw metaid="CDMT00039">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus />
              <apply>
                <times />
                <ci> RA2 </ci>
                <ci> ksp </ci>
              </apply>
              <apply>
                <times />
                <ci> RA2s </ci>
                <ci> ksm </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction metaid="re10" id="re10" reversible="true" fast="false">
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
            <celldesigner:baseReactants>
              <celldesigner:baseReactant species="RA2s" alias="sa7">
                <celldesigner:linkAnchor position="ENE" />
              </celldesigner:baseReactant>
            </celldesigner:baseReactants>
            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="RA2fs" alias="sa8">
                <celldesigner:linkAnchor position="WSW" />
              </celldesigner:baseProduct>
            </celldesigner:baseProducts>
            <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
              <celldesigner:listOfLineDirection>
                <celldesigner:lineDirection index="0" value="unknown" />
              </celldesigner:listOfLineDirection>
            </celldesigner:connectScheme>
            <celldesigner:line width="1.0" color="ff000000" />
          </celldesigner:extension>
        </annotation>
        <listOfReactants>
          <speciesReference metaid="CDMT00031" species="RA2s" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa7</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="CDMT00032" species="RA2fs" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa8</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfProducts>
        <kineticLaw metaid="CDMT00040">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus />
              <apply>
                <times />
                <ci> RA2s </ci>
                <ci> kfp </ci>
              </apply>
              <apply>
                <times />
                <ci> RA2fs </ci>
                <ci> kfm </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction metaid="re11" id="re11" reversible="true" fast="false">
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
            <celldesigner:baseReactants>
              <celldesigner:baseReactant species="RA2f" alias="sa6">
                <celldesigner:linkAnchor position="ESE" />
              </celldesigner:baseReactant>
            </celldesigner:baseReactants>
            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="RA2fs" alias="sa8">
                <celldesigner:linkAnchor position="WNW" />
              </celldesigner:baseProduct>
            </celldesigner:baseProducts>
            <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
              <celldesigner:listOfLineDirection>
                <celldesigner:lineDirection index="0" value="unknown" />
              </celldesigner:listOfLineDirection>
            </celldesigner:connectScheme>
            <celldesigner:line width="1.0" color="ff000000" />
          </celldesigner:extension>
        </annotation>
        <listOfReactants>
          <speciesReference metaid="CDMT00033" species="RA2f" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa6</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfReactants>
        <listOfProducts>
          <speciesReference metaid="CDMT00034" species="RA2fs" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa8</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
        </listOfProducts>
        <kineticLaw metaid="CDMT00041">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus />
              <apply>
                <times />
                <ci> RA2f </ci>
                <ci> ksp </ci>
              </apply>
              <apply>
                <times />
                <ci> RA2fs </ci>
                <ci> ksm </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>

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