Nazaret2008_Dynnik1980_CarbohydrateEnergyMetabolism

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Model Identifier
MODEL1202170000
Short description

This model is from the article:
An old paper revisited: ‘‘A mathematical model of carbohydrate energy metabolism. Interaction between glycolysis, the Krebs cycle and the H-transporting shuttles at varying ATPases load’’ by V.V. Dynnik, R. Heinrich and E.E. Sel’kov
Nazaret C, Mazat JP. J Theor Biol 2008 Jun;252(3):520-9. 18304584 ,
Abstract:
We revisit an old Russian paper by V.V. Dynnik, R. Heinrich and E.E. Sel’kov (1980a, b) describing: ‘‘A mathematical model of carbohydrate energy metabolism. Interaction between glycolysis, the Krebs cycle and the H-transporting shuttles at varying ATPases load’’. We analyse the model mathematically and calculate the control coefficients as a function of ATPase loads. We also evaluate the structure of the metabolic network in terms of elementary flux modes. We show how this model can respond to an ATPase load as well as to the glucose supply. We also show how this simple model can help in understanding the articulation between the major blocks of energetic metabolism, i.e. glycolysis, the Krebs cycle and the H-transporting shuttles.

Note: "dynnik_v1.xml":

  • created directly from "heinrich.sci" model file provided by Christine Nazaret
  • IDs changed to as per the paper
  • initial conditions set to steady state
  • results of Fig. 3 may be reproduced by running a a parameter scan over b15 in COPASI

"dynnik_v2.xml":

  • rescaled species such as s2_e1 = s2 * e1 are introduced whose evolution may be described through reaction participation, rather than via ODEs
  • original variables are retained as global parameters

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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Format
SBML (L2V4)
Related Publication
  • An old paper revisited: "a mathematical model of carbohydrate energy metabolism. Interaction between glycolysis, the Krebs cycle and the H-transporting shuttles at varying ATPases load" by V.V. Dynnik, R. Heinrich and E.E. Sel'kov.
  • Nazaret C, Mazat JP
  • Journal of theoretical biology , 6/ 2008 , Volume 252 , pages: 520-529 , PubMed ID: 18304584
  • IMB, Université de Bordeaux 2, 146 Rue Léo-Saignat, F 33076 Bordeaux-cedex, France. nazaret@sm.u-bordeaux2.fr
  • We revisit an old Russian paper by V.V. Dynnik, R. Heinrich and E.E. Sel'kov (1980a,b) describing: "A mathematical model of carbohydrate energy metabolism. Interaction between glycolysis, the Krebs cycle and the H-transporting shuttles at varying ATPases load". We analyse the model mathematically and calculate the control coefficients as a function of ATPase loads. We also evaluate the structure of the metabolic network in terms of elementary flux modes. We show how this model can respond to an ATPase load as well as to the glucose supply. We also show how this simple model can help in understanding the articulation between the major blocks of energetic metabolism, i.e. glycolysis, the Krebs cycle and the H-transporting shuttles.
Contributors
Submitter of the first revision: Kieran Smallbone
Submitter of this revision: Kieran Smallbone
Modellers: Kieran Smallbone

Metadata information

is (2 statements)
BioModels Database MODEL1202170000
Taxonomy Homo sapiens

isDescribedBy (2 statements)
PubMed 6445762
PubMed 18304584

hasTaxon (1 statement)
Taxonomy Eukaryota

isVersionOf (1 statement)
Gene Ontology energy homeostasis

hasProperty (1 statement)
Mathematical Modelling Ontology Ordinary differential equation model


Curation status
Non-curated


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Model files

MODEL1202170000_url.xml SBML L2V4 representation of Nazaret2008_Dynnik1980_CarbohydrateEnergyMetabolism 51.32 KB Preview | Download

Additional files

MODEL1202170000-biopax2.owl Auto-generated BioPAX (Level 2) 24.66 KB Preview | Download
MODEL1202170000-biopax3.owl Auto-generated BioPAX (Level 3) 515.00 Bytes Preview | Download
MODEL1202170000.m Auto-generated Octave file 9.97 KB Preview | Download
MODEL1202170000.pdf Auto-generated PDF file 2.80 KB Preview | Download
MODEL1202170000.png Auto-generated Reaction graph (PNG) 226.54 KB Preview | Download
MODEL1202170000.sci Auto-generated Scilab file 154.00 Bytes Preview | Download
MODEL1202170000.svg Auto-generated Reaction graph (SVG) 42.26 KB Preview | Download
MODEL1202170000.vcml Auto-generated VCML file 605.00 Bytes Preview | Download
MODEL1202170000.xpp Auto-generated XPP file 7.23 KB Preview | Download
MODEL1202170000_urn.xml Auto-generated SBML file with URNs 56.50 KB Preview | Download

  • Model originally submitted by : Kieran Smallbone
  • Submitted: Feb 17, 2012 11:11:05 AM
  • Last Modified: May 11, 2012 2:05:24 PM
Revisions
  • Version: 2 public model Download this version
    • Submitted on: May 11, 2012 2:05:24 PM
    • Submitted by: Kieran Smallbone
    • With comment: Current version of Nazaret2008_Dynnik1980_CarbohydrateEnergyMetabolism
  • Version: 1 public model Download this version
    • Submitted on: Feb 17, 2012 11:11:05 AM
    • Submitted by: Kieran Smallbone
    • With comment: Original import of dynnik

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