- Author:
- pmr2.import <nobody@models.cellml.org>
- Date:
- 2009-06-17 15:07:12+12:00
- Desc:
- committing version01 of martinov_vitvitsky_mosharov_banerjee_ataullakhanov_2000
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/martinov_vitvitsky_mosharov_banerjee_ataullakhanov_2000/rawfile/e7ea96fe028581706e4e1c29b1b365b041bcad4b/martinov_vitvitsky_mosharov_banerjee_ataullakhanov_2000.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : martinov_model_2000.xml
CREATED : 7th November 2003
LAST MODIFIED : 27th November 2003
AUTHOR : Catherine Lloyd
Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.0 Specification released on
10th August 2001, and the 16/1/02 CellML Metadata 1.0 Specification.
DESCRIPTION : This file contains a CellML description of Martinov et al.'s mathematical model of substrate switching as a form of regulation in the methionine metabolic pathway.
CHANGES:
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" cmeta:id="martinov_vitvitsky_mosharov_banerjee_ataullakhanov_2000_version01" name="martinov_vitvitsky_mosharov_banerjee_ataullakhanov_2000_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>A Substrate Switch: A New Mode of Regulation in the Methionine Metabolic Pathway</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This is the original unchecked version of the model imported from the previous
CellML model repository, 24-Jan-2006.
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
The methionine pathway serves three important functions in cellular metabolism:
</para>
<itemizedlist>
<listitem>
<para>It regulates between the amino acids methionine and cysteine for protein synthesis;</para>
</listitem>
<listitem>
<para>It provides the substrate for polyamine synthesis; and</para>
</listitem>
<listitem>
<para>It provides the mechanism by which methyl groups are transferred from 5-methyltetrahydrofolate to a wide range of substrates, and it represents the main mechanism for transmethylation reactions in mammals.</para>
</listitem>
</itemizedlist>
<para>
Abnormalities in methionine metabolism are associated with cardiovascular disease, liver disease, neural tube defects, and cancer.
</para>
<para>
Due to its essential role in cellular metabolism, the methionine pathway has been the subject of many experimental studies. These studies have revealed a high complexity of the cycle, in part due to the fact that enzymes in the cycle are activated and inhibited by intermediates of the cycle. In 2000, Martinov <emphasis>et al.</emphasis> developed a mathematical model of the methionine pathway in order to try to better understand the molecular mechanisms underlying the complexity of the methionine cycle. This model has been described in CellML and can be downloaded in various formats as explained in <xref linkend="sec_download_this_model"/> below. The model structure is also outlined in <xref linkend="fig_reaction_diagram"/> below.
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
<ulink url="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WMD-45CWWXP-4Y&_user=140507&_coverDate=06%2F21%2F2000&_alid=130687516&_rdoc=1&_fmt=summary&_orig=search&_qd=1&_cdi=6932&_sort=d&_docanchor=&view=c&_acct=C000011498&_version=1&_urlVersion=0&_userid=140507&md5=629a6e8f7eac87db9f76def118fe8aa5">A Substrate Switch: A New Mode of Regulation in the Methionine Metabolic Pathway</ulink>, Michael V. Martinov, Victor M. Vitvitsky, Eugene V. Mosharov, Ruma Banerjee, and Fazoil I. Ataullakhanov, 2000, <ulink url="http://www.sciencedirect.com/science?_ob=JournalURL&_cdi=6932&_auth=y&_acct=C000011498&_version=1&_urlVersion=0&_userid=140507&md5=c8e64d20ff203cda2255f4b6b7affe4f">
<emphasis>Journal of Theoretical Biology</emphasis>
</ulink>, 204, 521-532. (A PDF version of the article is available on the <emphasis>Journal of Theoretical Biology</emphasis> website.) <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10833353&dopt=Abstract">PubMed ID: 10833353</ulink>
</para>
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>reaction diagram</title>
</objectinfo>
<imagedata fileref="martinov_2000.png"/>
</imageobject>
</mediaobject>
<caption>Simplified pathway of methionine metabolism in liver cells employed for modelling in the study described here. The main metabolites are shown in blue boxes and the enzymes in red boxes.</caption>
</informalfigure>
<para>
Model simulations revealed that S-adenosylmethionine (AdoMet) metabolism can operate under two different modes:
</para>
<itemizedlist>
<listitem>
<para>The first, with a low metabolic rate and a low AdoMet concentration, serves predominantly to supply the cell with AdoMet, the substrate for various methylation reactions.</para>
</listitem>
<listitem>
<para>The second, with a high metabolic rate and high AdoMet concentration serves as an opportunity for cleavage of excess methionine and can also serve as a source of cysteine when its increased synthesis is necessary.</para>
</listitem>
</itemizedlist>
<para>
The switch that triggers interconversion between the two modes is methionine concentration. This kinetic behaviour results from the kinetic properties of i) the two isozymes of AdoMet synthetase, MATI and MATIII; one is inhibited by AdoMet, while the other is activated by it, and ii) glycine-N-methyltransferase (GNMT) that displays highly cooperative kinetics.
</para>
<para>
Finally, the authors concluded that their mathematical model provides an explanation for how different cellular needs are met by regulation of the methionine pathway. In addition, the model also identifies a critical role for GNMT in depleting excess methionine in the high rate, high concentration mode, thus avoiding the toxicity associated with accumulation of this amino acid.
</para>
</sect1>
</article>
</documentation>
<units name="micromolar">
<unit units="mole" prefix="micro"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="hour">
<unit units="second" multiplier="3600.0"/>
</units>
<units name="flux">
<unit units="micromolar"/>
<unit units="hour" exponent="-1"/>
</units>
<units name="first_order_rate_constant">
<unit units="hour" exponent="-1"/>
</units>
<component name="environment">
<variable units="hour" public_interface="out" name="time"/>
</component>
<component cmeta:id="Ado" name="Ado">
<rdf:RDF>
<rdf:Description rdf:about="AdoMet">
<dc:title>AdoMet</dc:title>
<dcterms:alternative>adenosine</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="Ado" initial_value="1.0"/>
</component>
<component cmeta:id="Met" name="Met">
<rdf:RDF>
<rdf:Description rdf:about="MetMet">
<dc:title>MetMet</dc:title>
<dcterms:alternative>methionine</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="Met" initial_value="45.0"/>
</component>
<component cmeta:id="Hcy" name="Hcy">
<rdf:RDF>
<rdf:Description rdf:about="HcyMet">
<dc:title>HcyMet</dc:title>
<dcterms:alternative>homocysteine</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="Hcy" initial_value="0.3"/>
<variable units="micromolar" public_interface="in" name="AdoHcy"/>
<variable units="micromolar" public_interface="in" name="Ado"/>
<variable units="micromolar" public_interface="in" name="K_AHC"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Hcy</ci>
<apply>
<times/>
<ci>AdoHcy</ci>
<apply>
<divide/>
<ci>K_AHC</ci>
<ci>Ado</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="K_AHC">
<variable units="micromolar" public_interface="out" name="K_AHC" initial_value="0.1"/>
<variable units="micromolar" public_interface="in" name="AdoHcy"/>
<variable units="micromolar" public_interface="in" name="Ado"/>
<variable units="micromolar" public_interface="in" name="Hcy"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>K_AHC</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>Ado</ci>
<ci>Hcy</ci>
</apply>
<ci>AdoHcy</ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="AdoMet" name="AdoMet">
<rdf:RDF>
<rdf:Description rdf:about="AdoMet">
<dc:title>AdoMet</dc:title>
<dcterms:alternative>S-adenosylmethionine</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="AdoMet" initial_value="60.0"/>
<variable units="flux" public_interface="in" name="V_MET"/>
<variable units="flux" public_interface="in" name="V_GNMT"/>
<variable units="flux" public_interface="in" name="V_MATI"/>
<variable units="flux" public_interface="in" name="V_MATIII"/>
<variable units="hour" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>AdoMet</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>V_MATI</ci>
<ci>V_MATIII</ci>
</apply>
<apply>
<plus/>
<ci>V_MET</ci>
<ci>V_GNMT</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="AdoHcy" name="AdoHcy">
<rdf:RDF>
<rdf:Description rdf:about="AdoHcy">
<dc:title>AdoHcy</dc:title>
<dcterms:alternative>S-adenosylhomocysteine</dcterms:alternative>
</rdf:Description>
</rdf:RDF>
<variable units="micromolar" public_interface="out" name="AdoHcy" initial_value="3.0"/>
<variable units="flux" public_interface="in" name="V_MET"/>
<variable units="flux" public_interface="in" name="V_GNMT"/>
<variable units="flux" public_interface="in" name="V_D"/>
<variable units="micromolar" public_interface="in" name="Ado"/>
<variable units="micromolar" public_interface="in" name="K_AHC"/>
<variable units="hour" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>AdoHcy</ci>
</apply>
<apply>
<divide/>
<apply>
<minus/>
<apply>
<plus/>
<ci>V_MET</ci>
<ci>V_GNMT</ci>
</apply>
<ci>V_D</ci>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci>K_AHC</ci>
<ci>Ado</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_MATI">
<variable units="flux" public_interface="out" name="V_MATI" initial_value="200.0"/>
<variable units="micromolar" public_interface="in" name="Met"/>
<variable units="micromolar" public_interface="in" name="AdoMet"/>
<variable units="flux" name="V_MATImax" initial_value="561.0"/>
<variable units="micromolar" name="Km_MATI" initial_value="41.0"/>
<variable units="micromolar" name="Ki_MATI" initial_value="50.0"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_MATI_calculation">
<eq/>
<ci> V_MATI </ci>
<apply>
<divide/>
<ci> V_MATImax </ci>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<times/>
<apply>
<divide/>
<ci> Km_MATI </ci>
<ci> Met </ci>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> AdoMet </ci>
<ci> Ki_MATI </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_MATIII">
<variable units="flux" public_interface="out" name="V_MATIII" initial_value="200.0"/>
<variable units="micromolar" public_interface="in" name="AdoMet"/>
<variable units="micromolar" public_interface="in" name="Met"/>
<variable units="flux" name="V_MATIIImax" initial_value="22870.0"/>
<variable units="micromolar" name="Km1_MATIII"/>
<variable units="micromolar" name="Km2_MATIII" initial_value="21.1"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_MATIII_calculation">
<eq/>
<ci> V_MATIII </ci>
<apply>
<divide/>
<ci> V_MATIIImax </ci>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<apply>
<times/>
<ci> Km1_MATIII </ci>
<ci> Km2_MATIII </ci>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> Met </ci>
<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
<apply>
<times/>
<ci> Met </ci>
<ci> Km2_MATIII </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply id="Km1_MATIII_calculation">
<eq/>
<ci> Km1_MATIII </ci>
<apply>
<divide/>
<cn cellml:units="micromolar"> 20000.0 </cn>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<times/>
<cn cellml:units="dimensionless"> 5.7 </cn>
<apply>
<power/>
<apply>
<divide/>
<ci> AdoMet </ci>
<apply>
<plus/>
<ci> AdoMet </ci>
<cn cellml:units="micromolar"> 600.0 </cn>
</apply>
</apply>
<cn cellml:units="dimensionless"> 2.0 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_MET">
<variable units="flux" public_interface="out" name="V_MET" initial_value="399.7"/>
<variable units="micromolar" public_interface="in" name="AdoMet"/>
<variable units="micromolar" public_interface="in" name="AdoHcy"/>
<variable units="flux" name="V_METmax" initial_value="4544.0"/>
<variable units="micromolar" name="Km1_MET"/>
<variable units="dimensionless" name="Km2_MET_A" initial_value="0.1"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_MET_calculation">
<eq/>
<ci> V_MET </ci>
<apply>
<divide/>
<ci> V_METmax </ci>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> Km1_MET </ci>
<ci> AdoMet </ci>
</apply>
<ci> Km2_MET_A </ci>
<apply>
<times/>
<ci> Km2_MET_A </ci>
<apply>
<divide/>
<ci> Km1_MET </ci>
<ci> AdoMet </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply id="Km1_MET_calculation">
<eq/>
<ci> Km1_MET </ci>
<apply>
<times/>
<cn cellml:units="micromolar"> 10.0 </cn>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> AdoHcy </ci>
<cn cellml:units="micromolar"> 4.0 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_GNMT">
<variable units="flux" public_interface="out" name="V_GNMT" initial_value="0.3"/>
<variable units="micromolar" public_interface="in" name="AdoMet"/>
<variable units="micromolar" public_interface="in" name="AdoHcy"/>
<variable units="flux" name="V_GNMTmax" initial_value="10600.0"/>
<variable units="micromolar" name="Km_GNMT" initial_value="4500.0"/>
<variable units="micromolar" name="Ki_GNMT" initial_value="20.0"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_GNMT_calculation">
<eq/>
<ci> V_GNMT </ci>
<apply>
<times/>
<apply>
<divide/>
<ci> V_GNMTmax </ci>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<power/>
<apply>
<divide/>
<ci> Km_GNMT </ci>
<ci> AdoMet </ci>
</apply>
<cn cellml:units="dimensionless"> 2.3 </cn>
</apply>
</apply>
</apply>
<apply>
<divide/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<ci> AdoHcy </ci>
<ci> Ki_GNMT </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="V_D">
<variable units="flux" public_interface="out" name="V_D" initial_value="400.0"/>
<variable units="first_order_rate_constant" name="alphad" initial_value="1333.0"/>
<variable units="micromolar" public_interface="in" name="Hcy"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="V_D_calculation">
<eq/>
<ci> V_D </ci>
<apply>
<times/>
<ci> alphad </ci>
<ci> Hcy </ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_2="V_MATI" component_1="AdoMet"/>
<map_variables variable_2="AdoMet" variable_1="AdoMet"/>
<map_variables variable_2="V_MATI" variable_1="V_MATI"/>
</connection>
<connection>
<map_components component_2="V_MATIII" component_1="AdoMet"/>
<map_variables variable_2="AdoMet" variable_1="AdoMet"/>
<map_variables variable_2="V_MATIII" variable_1="V_MATIII"/>
</connection>
<connection>
<map_components component_2="V_GNMT" component_1="AdoMet"/>
<map_variables variable_2="AdoMet" variable_1="AdoMet"/>
<map_variables variable_2="V_GNMT" variable_1="V_GNMT"/>
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<map_variables variable_2="V_MET" variable_1="V_MET"/>
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<connection>
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<map_variables variable_2="V_GNMT" variable_1="V_GNMT"/>
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<map_variables variable_2="AdoHcy" variable_1="AdoHcy"/>
<map_variables variable_2="V_MET" variable_1="V_MET"/>
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<connection>
<map_components component_2="V_MATI" component_1="Met"/>
<map_variables variable_2="Met" variable_1="Met"/>
</connection>
<connection>
<map_components component_2="V_MATIII" component_1="Met"/>
<map_variables variable_2="Met" variable_1="Met"/>
</connection>
<connection>
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<map_variables variable_2="AdoHcy" variable_1="AdoHcy"/>
<map_variables variable_2="K_AHC" variable_1="K_AHC"/>
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<connection>
<map_components component_2="Ado" component_1="K_AHC"/>
<map_variables variable_2="Ado" variable_1="Ado"/>
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<map_components component_2="Hcy" component_1="K_AHC"/>
<map_variables variable_2="Hcy" variable_1="Hcy"/>
<map_variables variable_2="K_AHC" variable_1="K_AHC"/>
</connection>
<connection>
<map_components component_2="AdoHcy" component_1="Ado"/>
<map_variables variable_2="Ado" variable_1="Ado"/>
</connection>
<connection>
<map_components component_2="AdoHcy" component_1="Hcy"/>
<map_variables variable_2="AdoHcy" variable_1="AdoHcy"/>
</connection>
<connection>
<map_components component_2="Ado" component_1="Hcy"/>
<map_variables variable_2="Ado" variable_1="Ado"/>
</connection>
<connection>
<map_components component_2="environment" component_1="AdoMet"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="AdoHcy"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="V_D" component_1="Hcy"/>
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A Substrate Switch: A New Mode of Regulation in the Methionine
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The University of Auckland, Bioengineering Institute
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Martinov et al.'s mathematical model of substrate switching as a form of regulation in the methionine metabolic pathway.
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