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  <p>
      This a model from the article:
      <br/>
  <strong> Ultrasensitivity in the mitogen-activated protein kinase cascade. 
</strong>
  <br/>
Huang CY, Ferrell JE Jr 
      <em>Proc. Natl. Acad. Sci. U.S.A. </em>[1996:93(19):10078-83 
      <a href="http://www.ncbi.nlm.nih.gov/pubmed/8816754">8816754</a>,
      <br/>
  <strong>Abstract:</strong>
  <br/>
The mitogen-activated protein kinase (MAPK) cascade is a highly conserved series of three protein kinases implicated in diverse biological processes. Here we demonstrate that the cascade arrangement has unexpected consequences for the dynamics of MAPK signaling. We solved the rate equations for the cascade numerically and found that MAPK is predicted to behave like a highly cooperative enzyme, even though it was not assumed that any of the enzymes in the cascade were regulated cooperatively. Measurements of MAPK activation in Xenopus oocyte extracts confirmed this prediction. The stimulus/response curve of the MAPK was found to be as steep as that of a cooperative enzyme with a Hill coefficient of 4-5, well in excess of that of the classical allosteric protein hemoglobin. The shape of the MAPK stimulus/ response curve may make the cascade particularly appropriate for mediating processes like mitogenesis, cell fate induction, and oocyte maturation, where a cell switches from one discrete state to another.
   </p>
  <p>This model is automatically generated from the Model BIOMD0000000009 by using <a href="http://sbml.org/Software/libSBML" target="_blank">libsbml</a>. According to the <a href="http://www.ebi.ac.uk/biomodels//legal.html">terms of use</a>, this generated model is not related with Model BIOMD0000000009 any more. <br/>To retrieve the curated model, please visit <a href="http://www.ebi.ac.uk/biomodels/">BioModels Database</a>.</p>
  <p>This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.<br/>For more information see the <a href="http://www.ebi.ac.uk/biomodels/legal.html" target="_blank">terms of use</a>.<br/>To cite BioModels Database, please use <a href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&amp;pubmedid=16381960" target="_blank">Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.</a>
</p>
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          <Product metabolite="Metabolite_32" stoichiometry="1"/>
          <Product metabolite="Metabolite_35" stoichiometry="1"/>
        </ListOfProducts>
        <ListOfConstants>
          <Constant key="Parameter_463" name="k1" value="150"/>
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        <KineticLaw function="Function_13">
          <ListOfCallParameters>
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      </Reaction>
      <Reaction key="Reaction_36" name="binding PP-MAPKK and P-MAPK" reversible="true">
        <MiriamAnnotation>
<rdf:RDF
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        <ListOfSubstrates>
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        </ListOfSubstrates>
        <ListOfProducts>
          <Product metabolite="Metabolite_42" stoichiometry="1"/>
        </ListOfProducts>
        <ListOfConstants>
          <Constant key="Parameter_462" name="k1" value="1000"/>
          <Constant key="Parameter_461" name="k2" value="150"/>
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        <KineticLaw function="Function_14">
          <ListOfCallParameters>
            <CallParameter functionParameter="FunctionParameter_62">
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            <CallParameter functionParameter="FunctionParameter_71">
              <SourceParameter reference="Metabolite_42"/>
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      <Reaction key="Reaction_37" name="phosphorylation of P-MAPK" reversible="false">
        <MiriamAnnotation>
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        <ListOfSubstrates>
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        <ListOfProducts>
          <Product metabolite="Metabolite_31" stoichiometry="1"/>
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      </Reaction>
      <Reaction key="Reaction_38" name="binding MAPK-Pase and PP-MAPK" reversible="true">
        <MiriamAnnotation>
<rdf:RDF
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          <Substrate metabolite="Metabolite_34" stoichiometry="1"/>
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        <ListOfProducts>
          <Product metabolite="Metabolite_45" stoichiometry="1"/>
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        <ListOfConstants>
          <Constant key="Parameter_459" name="k1" value="1000"/>
          <Constant key="Parameter_458" name="k2" value="150"/>
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        <KineticLaw function="Function_14">
          <ListOfCallParameters>
            <CallParameter functionParameter="FunctionParameter_62">
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        <ListOfProducts>
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      <StateTemplateVariable objectReference="Metabolite_31"/>
      <StateTemplateVariable objectReference="Metabolite_35"/>
      <StateTemplateVariable objectReference="Metabolite_36"/>
      <StateTemplateVariable objectReference="Metabolite_33"/>
      <StateTemplateVariable objectReference="Metabolite_30"/>
      <StateTemplateVariable objectReference="Metabolite_27"/>
      <StateTemplateVariable objectReference="Metabolite_39"/>
      <StateTemplateVariable objectReference="Metabolite_34"/>
      <StateTemplateVariable objectReference="Metabolite_26"/>
      <StateTemplateVariable objectReference="Metabolite_41"/>
      <StateTemplateVariable objectReference="Metabolite_43"/>
      <StateTemplateVariable objectReference="Metabolite_45"/>
      <StateTemplateVariable objectReference="Metabolite_25"/>
      <StateTemplateVariable objectReference="Metabolite_29"/>
      <StateTemplateVariable objectReference="Metabolite_42"/>
      <StateTemplateVariable objectReference="Metabolite_40"/>
      <StateTemplateVariable objectReference="Metabolite_32"/>
      <StateTemplateVariable objectReference="Metabolite_37"/>
      <StateTemplateVariable objectReference="Metabolite_44"/>
      <StateTemplateVariable objectReference="Metabolite_38"/>
      <StateTemplateVariable objectReference="Metabolite_46"/>
      <StateTemplateVariable objectReference="Metabolite_47"/>
      <StateTemplateVariable objectReference="Metabolite_48"/>
      <StateTemplateVariable objectReference="Metabolite_49"/>
      <StateTemplateVariable objectReference="Compartment_1"/>
    </StateTemplate>
    <InitialState type="initialState">
      0 0 0 289062.7919999999 722.6569799999999 0 0 7226.569799999998 0 0 722.6569799999999 0 0 0 72.265698 2890627.92 0 0 2890627.92 0 0 0 0 0 0 0 4e-012 
    </InitialState>
  </Model>
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      <Report reference="Report_7" target="" append="1"/>
      <Problem>
        <Parameter name="JacobianRequested" type="bool" value="1"/>
        <Parameter name="StabilityAnalysisRequested" type="bool" value="1"/>
      </Problem>
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        <Parameter name="Derivation Factor" type="unsignedFloat" value="0.001"/>
        <Parameter name="Use Newton" type="bool" value="1"/>
        <Parameter name="Use Integration" type="bool" value="1"/>
        <Parameter name="Use Back Integration" type="bool" value="1"/>
        <Parameter name="Accept Negative Concentrations" type="bool" value="0"/>
        <Parameter name="Iteration Limit" type="unsignedInteger" value="50"/>
        <Parameter name="Maximum duration for forward integration" type="unsignedFloat" value="1e+009"/>
        <Parameter name="Maximum duration for backward integration" type="unsignedFloat" value="1e+006"/>
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    </Task>
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        <Parameter name="StepSize" type="float" value="0.01"/>
        <Parameter name="Duration" type="float" value="1"/>
        <Parameter name="TimeSeriesRequested" type="bool" value="1"/>
        <Parameter name="OutputStartTime" type="float" value="0"/>
      </Problem>
      <Method name="Deterministic (LSODA)" type="Deterministic(LSODA)">
        <Parameter name="Integrate Reduced Model" type="bool" value="0"/>
        <Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-006"/>
        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-012"/>
        <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
      </Method>
    </Task>
    <Task key="Task_8" name="Scan" type="scan" scheduled="false" updateModel="false">
      <Problem>
        <Parameter name="Subtask" type="unsignedInteger" value="0"/>
        <ParameterGroup name="ScanItems">
          <ParameterGroup name="ScanItem">
            <Parameter name="Number of steps" type="unsignedInteger" value="100"/>
            <Parameter name="Type" type="unsignedInteger" value="1"/>
            <Parameter name="Object" type="cn" value="CN=Root,Model=Huang1996_MAPK_ultrasens,Vector=Compartments[compartment],Vector=Metabolites[MAPKKK activator],Reference=InitialConcentration"/>
            <Parameter name="Minimum" type="float" value="1e-006"/>
            <Parameter name="Maximum" type="float" value="0.1"/>
            <Parameter name="log" type="bool" value="1"/>
          </ParameterGroup>
        </ParameterGroup>
        <Parameter name="Output in subtask" type="bool" value="0"/>
        <Parameter name="Adjust initial conditions" type="bool" value="0"/>
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      <Method name="Scan Framework" type="ScanFramework">
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      <Method name="Bit Pattern Tree Algorithm" type="EFMBitPatternTreeMethod">
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        <ParameterText name="ObjectiveExpression" type="expression">
          
        </ParameterText>
        <Parameter name="Maximize" type="bool" value="0"/>
        <ParameterGroup name="OptimizationItemList">
        </ParameterGroup>
        <ParameterGroup name="OptimizationConstraintList">
        </ParameterGroup>
      </Problem>
      <Method name="Random Search" type="RandomSearch">
        <Parameter name="Number of Iterations" type="unsignedInteger" value="100000"/>
        <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
        <Parameter name="Seed" type="unsignedInteger" value="0"/>
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        <Parameter name="Steady-State" type="cn" value="CN=Root,Vector=TaskList[Steady-State]"/>
        <Parameter name="Time-Course" type="cn" value="CN=Root,Vector=TaskList[Time-Course]"/>
        <ParameterGroup name="Experiment Set">
        </ParameterGroup>
      </Problem>
      <Method name="Evolutionary Programming" type="EvolutionaryProgram">
        <Parameter name="Number of Generations" type="unsignedInteger" value="200"/>
        <Parameter name="Population Size" type="unsignedInteger" value="20"/>
        <Parameter name="Random Number Generator" type="unsignedInteger" value="1"/>
        <Parameter name="Seed" type="unsignedInteger" value="0"/>
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    </Task>
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        <Parameter name="Steady-State" type="key" value="Task_0"/>
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      <Method name="MCA Method (Reder)" type="MCAMethod(Reder)">
        <Parameter name="Modulation Factor" type="unsignedFloat" value="1e-009"/>
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    <Task key="Task_3" name="Lyapunov Exponents" type="lyapunovExponents" scheduled="false" updateModel="false">
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        <Parameter name="ExponentNumber" type="unsignedInteger" value="3"/>
        <Parameter name="DivergenceRequested" type="bool" value="1"/>
        <Parameter name="TransientTime" type="float" value="0"/>
      </Problem>
      <Method name="Wolf Method" type="WolfMethod">
        <Parameter name="Orthonormalization Interval" type="unsignedFloat" value="1"/>
        <Parameter name="Overall time" type="unsignedFloat" value="1000"/>
        <Parameter name="Relative Tolerance" type="unsignedFloat" value="1e-006"/>
        <Parameter name="Absolute Tolerance" type="unsignedFloat" value="1e-012"/>
        <Parameter name="Max Internal Steps" type="unsignedInteger" value="10000"/>
      </Method>
    </Task>
    <Task key="Task_2" name="Time Scale Separation Analysis" type="timeScaleSeparationAnalysis" scheduled="false" updateModel="false">
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      <Problem>
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        <Parameter name="OutputStartTime" type="float" value="0"/>
      </Problem>
      <Method name="ILDM (LSODA,Deuflhard)" type="TimeScaleSeparation(ILDM,Deuflhard)">
        <Parameter name="Deuflhard Tolerance" type="unsignedFloat" value="1e-006"/>
      </Method>
    </Task>
    <Task key="Task_1" name="Sensitivities" type="sensitivities" scheduled="false" updateModel="false">
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      <Problem>
        <Parameter name="SubtaskType" type="unsignedInteger" value="1"/>
        <ParameterGroup name="TargetFunctions">
          <Parameter name="SingleObject" type="cn" value=""/>
          <Parameter name="ObjectListType" type="unsignedInteger" value="7"/>
        </ParameterGroup>
        <ParameterGroup name="ListOfVariables">
          <ParameterGroup name="Variables">
            <Parameter name="SingleObject" type="cn" value=""/>
            <Parameter name="ObjectListType" type="unsignedInteger" value="41"/>
          </ParameterGroup>
        </ParameterGroup>
      </Problem>
      <Method name="Sensitivities Method" type="SensitivitiesMethod">
        <Parameter name="Delta factor" type="unsignedFloat" value="0.001"/>
        <Parameter name="Delta minimum" type="unsignedFloat" value="1e-012"/>
      </Method>
    </Task>
    <Task key="Task_10" name="Moieties" type="moieties" scheduled="false" updateModel="false">
      <Problem>
      </Problem>
      <Method name="Householder Reduction" type="Householder">
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    </Task>
  </ListOfTasks>
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        <Object cn="String=&#x0a;"/>
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  </ListOfReports>
  <ListOfPlots>
    <PlotSpecification name="Dose-response" type="Plot2D" active="1">
      <Parameter name="log X" type="bool" value="1"/>
      <Parameter name="log Y" type="bool" value="0"/>
      <ListOfPlotItems>
        <PlotItem name="[KKK_P_norm]|[&quot;MAPKKK activator&quot;]_0" type="Curve2D">
          <Parameter name="Line type" type="unsignedInteger" value="0"/>
          <Parameter name="Recording Activity" type="string" value="during"/>
          <ListOfChannels>
            <ChannelSpec cn="CN=Root,Model=Huang1996_MAPK_ultrasens,Vector=Compartments[compartment],Vector=Metabolites[MAPKKK activator],Reference=InitialConcentration"/>
            <ChannelSpec cn="CN=Root,Model=Huang1996_MAPK_ultrasens,Vector=Compartments[compartment],Vector=Metabolites[KKK_P_norm],Reference=Concentration"/>
          </ListOfChannels>
        </PlotItem>
        <PlotItem name="[KK_PP_norm]|[&quot;MAPKKK activator&quot;]_0" type="Curve2D">
          <Parameter name="Line type" type="unsignedInteger" value="0"/>
          <Parameter name="Recording Activity" type="string" value="during"/>
          <ListOfChannels>
            <ChannelSpec cn="CN=Root,Model=Huang1996_MAPK_ultrasens,Vector=Compartments[compartment],Vector=Metabolites[MAPKKK activator],Reference=InitialConcentration"/>
            <ChannelSpec cn="CN=Root,Model=Huang1996_MAPK_ultrasens,Vector=Compartments[compartment],Vector=Metabolites[KK_PP_norm],Reference=Concentration"/>
          </ListOfChannels>
        </PlotItem>
        <PlotItem name="[K_PP_norm]|[&quot;MAPKKK activator&quot;]_0" type="Curve2D">
          <Parameter name="Line type" type="unsignedInteger" value="0"/>
          <Parameter name="Recording Activity" type="string" value="during"/>
          <ListOfChannels>
            <ChannelSpec cn="CN=Root,Model=Huang1996_MAPK_ultrasens,Vector=Compartments[compartment],Vector=Metabolites[MAPKKK activator],Reference=InitialConcentration"/>
            <ChannelSpec cn="CN=Root,Model=Huang1996_MAPK_ultrasens,Vector=Compartments[compartment],Vector=Metabolites[K_PP_norm],Reference=Concentration"/>
          </ListOfChannels>
        </PlotItem>
      </ListOfPlotItems>
    </PlotSpecification>
  </ListOfPlots>
  <GUI>
  </GUI>
  <SBMLReference file="BIOMD0000000009.xml">
    <SBMLMap SBMLid="E1" COPASIkey="Metabolite_25"/>
    <SBMLMap SBMLid="E1_KKK" COPASIkey="Metabolite_37"/>
    <SBMLMap SBMLid="E2" COPASIkey="Metabolite_26"/>
    <SBMLMap SBMLid="E2_P_KKK" COPASIkey="Metabolite_38"/>
    <SBMLMap SBMLid="K" COPASIkey="Metabolite_32"/>
    <SBMLMap SBMLid="KK" COPASIkey="Metabolite_29"/>
    <SBMLMap SBMLid="KKK" COPASIkey="Metabolite_27"/>
    <SBMLMap SBMLid="KKK_P_norm" COPASIkey="Metabolite_49"/>
    <SBMLMap SBMLid="KKPase" COPASIkey="Metabolite_36"/>
    <SBMLMap SBMLid="KKPase_PP_KK" COPASIkey="Metabolite_43"/>
    <SBMLMap SBMLid="KKPase_P_KK" COPASIkey="Metabolite_44"/>
    <SBMLMap SBMLid="KK_PP_norm" COPASIkey="Metabolite_48"/>
    <SBMLMap SBMLid="KPase" COPASIkey="Metabolite_35"/>
    <SBMLMap SBMLid="KPase_PP_K" COPASIkey="Metabolite_45"/>
    <SBMLMap SBMLid="KPase_P_K" COPASIkey="Metabolite_46"/>
    <SBMLMap SBMLid="K_PP_norm" COPASIkey="Metabolite_47"/>
    <SBMLMap SBMLid="PP_K" COPASIkey="Metabolite_34"/>
    <SBMLMap SBMLid="PP_KK" COPASIkey="Metabolite_31"/>
    <SBMLMap SBMLid="PP_KK_K" COPASIkey="Metabolite_41"/>
    <SBMLMap SBMLid="PP_KK_P_K" COPASIkey="Metabolite_42"/>
    <SBMLMap SBMLid="P_K" COPASIkey="Metabolite_33"/>
    <SBMLMap SBMLid="P_KK" COPASIkey="Metabolite_30"/>
    <SBMLMap SBMLid="P_KKK" COPASIkey="Metabolite_28"/>
    <SBMLMap SBMLid="P_KKK_KK" COPASIkey="Metabolite_39"/>
    <SBMLMap SBMLid="P_KKK_P_KK" COPASIkey="Metabolite_40"/>
    <SBMLMap SBMLid="compartment" COPASIkey="Compartment_1"/>
    <SBMLMap SBMLid="r10a" COPASIkey="Reaction_38"/>
    <SBMLMap SBMLid="r10b" COPASIkey="Reaction_39"/>
    <SBMLMap SBMLid="r1a" COPASIkey="Reaction_20"/>
    <SBMLMap SBMLid="r1b" COPASIkey="Reaction_21"/>
    <SBMLMap SBMLid="r2a" COPASIkey="Reaction_22"/>
    <SBMLMap SBMLid="r2b" COPASIkey="Reaction_23"/>
    <SBMLMap SBMLid="r3a" COPASIkey="Reaction_24"/>
    <SBMLMap SBMLid="r3b" COPASIkey="Reaction_25"/>
    <SBMLMap SBMLid="r4a" COPASIkey="Reaction_26"/>
    <SBMLMap SBMLid="r4b" COPASIkey="Reaction_27"/>
    <SBMLMap SBMLid="r5a" COPASIkey="Reaction_28"/>
    <SBMLMap SBMLid="r5b" COPASIkey="Reaction_29"/>
    <SBMLMap SBMLid="r6a" COPASIkey="Reaction_30"/>
    <SBMLMap SBMLid="r6b" COPASIkey="Reaction_31"/>
    <SBMLMap SBMLid="r7a" COPASIkey="Reaction_32"/>
    <SBMLMap SBMLid="r7b" COPASIkey="Reaction_33"/>
    <SBMLMap SBMLid="r8a" COPASIkey="Reaction_34"/>
    <SBMLMap SBMLid="r8b" COPASIkey="Reaction_35"/>
    <SBMLMap SBMLid="r9a" COPASIkey="Reaction_36"/>
    <SBMLMap SBMLid="r9b" COPASIkey="Reaction_37"/>
  </SBMLReference>
</COPASI>
