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<model metaid="metaid_0000002" id="Fung2005_Metabolator" name="Fung2005_Metabolic_Oscillator">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<h1>A Synthetic Gene-Metabolic Oscillator </h1>
<b>Reference:</b>
<a href="http://www.nature.com/nature/journal/v435/n7038/abs/nature03508.html">
<i>Fung et al; Nature (2005) 435:118-122</i>
</a>
<br/>
<table border="0" cellpadding="2" cellspacing="0">
<thead>
<tr>
<th align="left" bgcolor="#eeeeee" valign="middle">Name of kinetic law</th>
<th align="left" bgcolor="#eeeeee" valign="middle">Reaction</th>
</tr>
</thead>
<tbody>
<tr>
<td>Glycolytic flux, V_gly:</td>
<td>nil -> AcCoA;</td>
</tr>
<tr>
<td>Flux to TCA cycle/ETOH, V_TCA:</td>
<td>AcCoA -> TCA/EtOH;</td>
</tr>
<tr>
<td>HOAc ex/import,reversible, V_out:</td>
<td> HOAc -> HOAc_E</td>
</tr>
<tr>
<td>V_Pta:</td>
<td>AcCoA + Pi -> AcP + CoA</td>
</tr>
<tr>
<td>reversible, V_Ack:</td>
<td>AcP + ADP -> OAc + ATP</td>
</tr>
<tr>
<td>V_Acs:</td>
<td>OAC + ATP -> AcCoA +PPi</td>
</tr>
<tr>
<td>Acetic acid-base equillibrium, reversible, V_Ace:</td>
<td>OAC + H -> HOAc</td>
</tr>
<tr>
<td>Expression of LacI, R_LacI:</td>
<td>nil -> LacI</td>
</tr>
<tr>
<td>Expression of Acs, R_Acs:</td>
<td>nil -> Acs</td>
</tr>
<tr>
<td>Expression of Pta, R_Pta:</td>
<td> nil -> Pta</td>
</tr>
<tr>
<td>LacI degradation, R_dLacI:</td>
<td>LacI -> nil</td>
</tr>
<tr>
<td>Acs degradation, R_dAcs:</td>
<td>Acs -> nil</td>
</tr>
<tr>
<td>Pta degradation, R_dPta:</td>
<td>Pta -> nil</td>
</tr>
</tbody>
</table>
<p>For this model the differential equation for V_Ace was changed from:
<br/>
C*(AcP*H-K_eq*OAC) with C = 100 in the supplemental material
<br/>
to C*(OAc*H-K_eq*HOAc) with C = 100, as in
<a href="http://www.pnas.org/cgi/content/abstract/101/8/2299">
<i>Bulter et. al; PNAS(2004),101,2299-2304</i>
</a>, and a value for K_eq of 5*10^-4 after communication with the authors.</p>
<p>
<font size="2">translated to SBML by:
<br/>
Lukas Endler(luen at tbi.univie.ac.at), Christoph Flamm (xtof at tbi.univie.ac.at)</font>
</p>
<p>
<u> Biomodels Curation </u> The model reproduces 3a of the paper for glycolytic flux Vgly = 0.5. The authors have agreed that the values on Y-axis are marked wrong and hence there is a discrepancy between model simulation results and the figure. Also, note that the values of concentration and time are in dimensionless units. The model was successfully tested on MathSBML and Jarnac.
</p>
<p>This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2008 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>.</p>
</body>
</notes>
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<ci> compartment </ci>
<ci> k2 </ci>
<ci> Acs </ci>
<ci> OAc </ci>
</apply>
<apply>
<plus/>
<ci> KM2 </ci>
<ci> OAc </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
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</listOfReactants>
<listOfProducts>
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</listOfProducts>
<kineticLaw>
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<apply>
<times/>
<ci> compartment </ci>
<ci> C </ci>
<apply>
<minus/>
<apply>
<times/>
<ci> OAc </ci>
<ci> H </ci>
</apply>
<apply>
<times/>
<ci> Keq </ci>
<ci> HOAc </ci>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
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</rdf:RDF>
</annotation>
<listOfProducts>
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</listOfProducts>
<listOfModifiers>
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</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> compartment </ci>
<apply>
<plus/>
<apply>
<divide/>
<apply>
<times/>
<ci> alpha1 </ci>
<apply>
<power/>
<apply>
<divide/>
<ci> AcP </ci>
<ci> Kg1 </ci>
</apply>
<ci> n </ci>
</apply>
</apply>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<power/>
<apply>
<divide/>
<ci> AcP </ci>
<ci> Kg1 </ci>
</apply>
<ci> n </ci>
</apply>
</apply>
</apply>
<ci> alpha0 </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
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<rdf:Description rdf:about="#metaid_0000041">
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</annotation>
<listOfProducts>
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<listOfModifiers>
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<kineticLaw>
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<apply>
<times/>
<ci> compartment </ci>
<apply>
<plus/>
<apply>
<divide/>
<apply>
<times/>
<ci> alpha2 </ci>
<apply>
<power/>
<apply>
<divide/>
<ci> AcP </ci>
<ci> Kg2 </ci>
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<ci> n </ci>
</apply>
</apply>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<power/>
<apply>
<divide/>
<ci> AcP </ci>
<ci> Kg2 </ci>
</apply>
<ci> n </ci>
</apply>
</apply>
</apply>
<ci> alpha0 </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="metaid_0000042" id="R_Pta" name="Phosphate acetyl transferase synthase" reversible="false">
<annotation>
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<rdf:Description rdf:about="#metaid_0000042">
<bqbiol:hasPart>
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<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0006350"/>
<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0043037"/>
</rdf:Bag>
</bqbiol:hasPart>
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</annotation>
<listOfProducts>
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</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="LacI"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<apply>
<divide/>
<ci> alpha3 </ci>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<power/>
<apply>
<divide/>
<ci> LacI </ci>
<ci> Kg3 </ci>
</apply>
<ci> n </ci>
</apply>
</apply>
</apply>
<ci> alpha0 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="metaid_0000043" id="R_dLacI" name="LacI degradation" reversible="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_0000043">
<bqbiol:isVersionOf>
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<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0030163"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="LacI"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> compartment </ci>
<ci> kd </ci>
<ci> LacI </ci>
</apply>
</math>
</kineticLaw>
</reaction>
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<annotation>
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<rdf:Description rdf:about="#metaid_0000044">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0030163"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="Acs"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> compartment </ci>
<ci> kd </ci>
<ci> Acs </ci>
</apply>
</math>
</kineticLaw>
</reaction>
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<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#metaid_0000045">
<bqbiol:isVersionOf>
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<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0030163"/>
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</bqbiol:isVersionOf>
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</rdf:RDF>
</annotation>
<listOfReactants>
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</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> compartment </ci>
<ci> kd </ci>
<ci> Pta </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>