Rao2014 - Fatty acid beta-oxidation (reduced model)

  public model
Model Identifier
BIOMD0000000835
Short description 
This represents the reduced version of the "time course model" of Van Eunen et al (2013): Biochemical competition makes fatty-acid beta-oxidation vulnerable to substrate overload. The SBML was created from that of the original model and produces identical results when a time-course of 25 mins is run in COPASI
Format
SBML (L2V4)
Related Publication
  • A model reduction method for biochemical reaction networks.
  • Rao S, van der Schaft A, van Eunen K, Bakker BM, Jayawardhana B.
  • BMC Syst Biol 2014; 8: 52 , 1/ 2014 , Volume 8 , pages: 52 , PubMed ID: 24885656
  • 1Systems Biology Center for Energy Metabolism and Ageing, University of Groningen, ERIBA, Antonius Deusinglaan 1 9713 AV Groningen, Netherlands 2Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, P.O. Box 407, 9700 AK Groningen, Netherlands 3Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ, Groningen, Netherlands 4Institute of Technology and Management, Nijenborgh 4, University of Groningen, 9747 AG Groningen, Netherlands
  • BACKGROUND: In this paper we propose a model reduction method for biochemical reaction networks governed by a variety of reversible and irreversible enzyme kinetic rate laws, including reversible Michaelis-Menten and Hill kinetics. The method proceeds by a stepwise reduction in the number of complexes, defined as the left and right-hand sides of the reactions in the network. It is based on the Kron reduction of the weighted Laplacian matrix, which describes the graph structure of the complexes and reactions in the network. It does not rely on prior knowledge of the dynamic behaviour of the network and hence can be automated, as we demonstrate. The reduced network has fewer complexes, reactions, variables and parameters as compared to the original network, and yet the behaviour of a preselected set of significant metabolites in the reduced network resembles that of the original network. Moreover the reduced network largely retains the structure and kinetics of the original model. RESULTS: We apply our method to a yeast glycolysis model and a rat liver fatty acid beta-oxidation model. When the number of state variables in the yeast model is reduced from 12 to 7, the difference between metabolite concentrations in the reduced and the full model, averaged over time and species, is only 8%. Likewise, when the number of state variables in the rat-liver beta-oxidation model is reduced from 42 to 29, the difference between the reduced model and the full model is 7.5%. CONCLUSIONS: The method has improved our understanding of the dynamics of the two networks. We found that, contrary to the general disposition, the first few metabolites which were deleted from the network during our stepwise reduction approach, are not those with the shortest convergence times. It shows that our reduction approach performs differently from other approaches that are based on time-scale separation. The method can be used to facilitate fitting of the parameters or to embed a detailed model of interest in a more coarse-grained yet realistic environment.
Contributors
Submitter of the first revision: Shodhan Rao
Submitter of this revision: Mohammad Umer Sharif Shohan
Modellers: Shodhan Rao, Mohammad Umer Sharif Shohan

Metadata information

is (3 statements)
BioModels Database MODEL1403250000
BioModels Database BIOMD0000000835
BioModels Database MODEL1403250000

isDescribedBy (1 statement)
PubMed 24885656

hasTaxon (1 statement)
isVersionOf (1 statement)
occursIn (1 statement)
Brenda Tissue Ontology liver

Curation status
Curated
Tags

Connected external resources

SBGN view in Newt Editor

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Model files
Rao2014.xml SBML L2V4 representation of Rao2014 - Fatty acid beta-oxidation (reduced model) 355.39 KB Preview | Download

Additional files
MODEL1403250000-biopax2.owl Auto-generated BioPAX (Level 2) 345.75 KB Preview | Download
MODEL1403250000-biopax3.owl Auto-generated BioPAX (Level 3) 493.34 KB Preview | Download
MODEL1403250000.m Auto-generated Octave file 87.19 KB Preview | Download
MODEL1403250000.pdf Auto-generated PDF file 650.53 KB Preview | Download
MODEL1403250000.png Auto-generated Reaction graph (PNG) 28.74 MB Preview | Download
MODEL1403250000.sci Auto-generated Scilab file 163.00 Bytes Preview | Download
MODEL1403250000.svg Auto-generated Reaction graph (SVG) 494.27 KB Preview | Download
MODEL1403250000.vcml Auto-generated VCML file 897.00 Bytes Preview | Download
MODEL1403250000.xpp Auto-generated XPP file 73.60 KB Preview | Download
MODEL1403250000_url-1.xml old xml file 396.61 KB Preview | Download
MODEL1403250000_urn.xml Auto-generated SBML file with URNs 396.31 KB Preview | Download
Rao2014.cps COPASI version 4.24 (Build 197) representation of Rao2014 - Fatty acid beta-oxidation (reduced model) 815.17 KB Preview | Download
Rao2014.sedml SEDML L1V2 representation of Rao2014 - Fatty acid beta-oxidation (reduced model) 1.01 KB Preview | Download

  • Model originally submitted by : Shodhan Rao
  • Submitted: Mar 25, 2014 12:08:43 PM
  • Last Modified: Oct 17, 2019 12:18:57 PM
Revisions
  • Version: 4 public model Download this version
    • Submitted on: Oct 17, 2019 12:18:57 PM
    • Submitted by: Mohammad Umer Sharif Shohan
    • With comment: Automatically added model identifier BIOMD0000000835
  • Version: 3 public model Download this version
    • Submitted on: Oct 17, 2019 11:55:42 AM
    • Submitted by: Mohammad Umer Sharif Shohan
    • With comment: Model has been curated
  • Version: 2 public model Download this version
    • Submitted on: Sep 3, 2014 5:10:59 PM
    • Submitted by: Shodhan Rao
    • With comment: Current version of Rao2014 - Fatty acid beta-oxidation (reduced model)
  • Version: 1 public model Download this version
    • Submitted on: Mar 25, 2014 12:08:43 PM
    • Submitted by: Shodhan Rao
    • With comment: Original import of vaneunen

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models


Species
Species Initial Concentration/Amount
C12AcylCarCYT 0.11 μmol
C16EnoylCoAMAT 0.0 μmol
C10AcylCarMAT 0.0 μmol
C6AcylCoAMAT 0.0 μmol
C4AcylCarMAT 0.0 μmol
C4AcylCoAMAT 0.0 μmol
FADHMAT 0.46 μmol
NADHMAT 16.0 μmol
species 1 234.0 μmol
C16AcylCarMAT 0.0 μmol
Reactions
Reactions Rate Parameters
C12AcylCarCYT => C12AcylCarMAT; CarMAT, CarCYT, C12AcylCarCYT, C12AcylCarMAT Vfcact*(C12AcylCarCYT*CarMAT-C12AcylCarMAT*CarCYT/Keqcact)/(C12AcylCarCYT*CarMAT+KmcactCarMAT*C12AcylCarCYT+KmcactC12AcylCarCYT*CarMAT*(1+CarCYT/KicactCarCYT)+Vfcact/(Vrcact*Keqcact)*(KmcactCarCYT*C12AcylCarMAT*(1+C12AcylCarCYT/KicactC12AcylCarCYT)+CarCYT*(KmcactC12AcylCarMAT+C12AcylCarMAT))) KicactC12AcylCarCYT=56.0; KmcactCarMAT = 130.0; KmcactCarCYT = 130.0; Vfcact = 0.42; Keqcact = 1.0; KicactCarCYT = 200.0; Vrcact = 0.42; KmcactC12AcylCarMAT=15.0; KmcactC12AcylCarCYT=15.0
C16EnoylCoAMAT => C14AcylCoAMAT + AcetylCoAMAT + NADHMAT; C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C8EnoylCoAMAT, NADtMAT, CoAMAT, C16AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, C4AcetoacylCoAMAT, AcetylCoAMAT, C14AcylCoAMAT, C16EnoylCoAMAT, NADHMAT VMAT*sfmtpC16*Vmtp*(C16EnoylCoAMAT*(NADtMAT-NADHMAT)*CoAMAT/(KmmtpC16EnoylCoAMAT*KmmtpNADMAT*KmmtpCoAMAT)-C14AcylCoAMAT*NADHMAT*AcetylCoAMAT/(KmmtpC16EnoylCoAMAT*KmmtpNADMAT*KmmtpCoAMAT*Keqmtp))/((1+C16EnoylCoAMAT/KmmtpC16EnoylCoAMAT+C14AcylCoAMAT/KmmtpC14AcylCoAMAT+C14EnoylCoAMAT/KmmtpC14EnoylCoAMAT+C16AcylCoAMAT/KmmtpC16AcylCoAMAT+C12EnoylCoAMAT/KmmtpC12EnoylCoAMAT+C12AcylCoAMAT/KmmtpC12AcylCoAMAT+C10EnoylCoAMAT/KmmtpC10EnoylCoAMAT+C10AcylCoAMAT/KmmtpC10AcylCoAMAT+C8EnoylCoAMAT/KmmtpC8EnoylCoAMAT+C8AcylCoAMAT/KmmtpC8AcylCoAMAT+C6AcylCoAMAT/KmmtpC6AcylCoAMAT+C4AcetoacylCoAMAT/KicrotC4AcetoacylCoA)*(1+(NADtMAT-NADHMAT)/KmmtpNADMAT+NADHMAT/KmmtpNADHMAT)*(1+CoAMAT/KmmtpCoAMAT+AcetylCoAMAT/KmmtpAcetylCoAMAT))/VMAT KmmtpC6AcylCoAMAT = 13.83; Keqmtp = 0.71; KmmtpC14EnoylCoAMAT = 25.0; KmmtpC10AcylCoAMAT = 13.83; KmmtpC12AcylCoAMAT = 13.83; KmmtpAcetylCoAMAT = 30.0; KmmtpC8AcylCoAMAT = 13.83; KmmtpC16EnoylCoAMAT = 25.0; KmmtpC14AcylCoAMAT = 13.83; KmmtpC10EnoylCoAMAT = 25.0; sfmtpC16=1.0; KicrotC4AcetoacylCoA = 1.6; KmmtpCoAMAT = 30.0; Vmtp = 2.84; KmmtpC12EnoylCoAMAT = 25.0; KmmtpNADMAT = 60.0; KmmtpC16AcylCoAMAT = 13.83; KmmtpC8EnoylCoAMAT = 25.0; KmmtpNADHMAT = 50.0
C10AcylCarMAT => C10AcylCoAMAT; C16AcylCarMAT, C14AcylCarMAT, C12AcylCarMAT, C8AcylCarMAT, C6AcylCarMAT, C4AcylCarMAT, CoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, C4AcylCoAMAT, CarMAT, C10AcylCarMAT, C10AcylCoAMAT VMAT*sfcpt2C10*Vcpt2*(C10AcylCarMAT*CoAMAT/(Kmcpt2C10AcylCarMAT*Kmcpt2CoAMAT)-C10AcylCoAMAT*CarMAT/(Kmcpt2C10AcylCarMAT*Kmcpt2CoAMAT*Keqcpt2))/((1+C10AcylCarMAT/Kmcpt2C10AcylCarMAT+C10AcylCoAMAT/Kmcpt2C10AcylCoAMAT+C16AcylCarMAT/Kmcpt2C16AcylCarMAT+C16AcylCoAMAT/Kmcpt2C16AcylCoAMAT+C14AcylCarMAT/Kmcpt2C14AcylCarMAT+C14AcylCoAMAT/Kmcpt2C14AcylCoAMAT+C12AcylCarMAT/Kmcpt2C12AcylCarMAT+C12AcylCoAMAT/Kmcpt2C12AcylCoAMAT+C8AcylCarMAT/Kmcpt2C8AcylCarMAT+C8AcylCoAMAT/Kmcpt2C8AcylCoAMAT+C6AcylCarMAT/Kmcpt2C6AcylCarMAT+C6AcylCoAMAT/Kmcpt2C6AcylCoAMAT+C4AcylCarMAT/Kmcpt2C4AcylCarMAT+C4AcylCoAMAT/Kmcpt2C4AcylCoAMAT)*(1+CoAMAT/Kmcpt2CoAMAT+CarMAT/Kmcpt2CarMAT))/VMAT Kmcpt2C10AcylCarMAT = 51.0; Keqcpt2 = 2.22; sfcpt2C10=0.95; Kmcpt2C12AcylCarMAT = 51.0; Kmcpt2C16AcylCoAMAT = 38.0; Vcpt2 = 0.391; Kmcpt2C12AcylCoAMAT = 38.0; Kmcpt2C10AcylCoAMAT = 38.0; Kmcpt2C16AcylCarMAT = 51.0; Kmcpt2C14AcylCoAMAT = 38.0; Kmcpt2C14AcylCarMAT = 51.0; Kmcpt2CoAMAT = 30.0; Kmcpt2C6AcylCoAMAT = 1000.0; Kmcpt2C4AcylCoAMAT = 1000000.0; Kmcpt2C8AcylCoAMAT = 38.0; Kmcpt2C8AcylCarMAT = 51.0; Kmcpt2C4AcylCarMAT = 51.0; Kmcpt2C6AcylCarMAT = 51.0; Kmcpt2CarMAT = 350.0
C6AcylCoAMAT => C6EnoylCoAMAT + FADHMAT; C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C4AcylCoAMAT, FADtMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C8EnoylCoAMAT, C4EnoylCoAMAT, C6AcylCoAMAT, C6EnoylCoAMAT, FADHMAT VMAT*sfmcadC6*Vmcad*(C6AcylCoAMAT*(FADtMAT-FADHMAT)/(KmmcadC6AcylCoAMAT*KmmcadFAD)-C6EnoylCoAMAT*FADHMAT/(KmmcadC6AcylCoAMAT*KmmcadFAD*Keqmcad))/((1+C6AcylCoAMAT/KmmcadC6AcylCoAMAT+C6EnoylCoAMAT/KmmcadC6EnoylCoAMAT+C12AcylCoAMAT/KmmcadC12AcylCoAMAT+C12EnoylCoAMAT/KmmcadC12EnoylCoAMAT+C10AcylCoAMAT/KmmcadC10AcylCoAMAT+C10EnoylCoAMAT/KmmcadC10EnoylCoAMAT+C8AcylCoAMAT/KmmcadC8AcylCoAMAT+C8EnoylCoAMAT/KmmcadC8EnoylCoAMAT+C4AcylCoAMAT/KmmcadC4AcylCoAMAT+C4EnoylCoAMAT/KmmcadC4EnoylCoAMAT)*(1+(FADtMAT-FADHMAT)/KmmcadFAD+FADHMAT/KmmcadFADH))/VMAT KmmcadC12EnoylCoAMAT = 1.08; KmmcadC8AcylCoAMAT = 4.0; KmmcadC6EnoylCoAMAT = 1.08; sfmcadC6=1.0; KmmcadC6AcylCoAMAT = 9.4; KmmcadC12AcylCoAMAT = 5.7; KmmcadC4AcylCoAMAT = 135.0; Vmcad = 0.081; Keqmcad = 6.0; KmmcadFADH = 24.2; KmmcadC10AcylCoAMAT = 5.4; KmmcadFAD = 0.12; KmmcadC10EnoylCoAMAT = 1.08; KmmcadC4EnoylCoAMAT = 1.08; KmmcadC8EnoylCoAMAT = 1.08
C4AcylCarMAT => C4AcylCoAMAT; C16AcylCarMAT, C14AcylCarMAT, C12AcylCarMAT, C10AcylCarMAT, C8AcylCarMAT, C6AcylCarMAT, CoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, CarMAT, C4AcylCarMAT, C4AcylCoAMAT VMAT*sfcpt2C4*Vcpt2*(C4AcylCarMAT*CoAMAT/(Kmcpt2C4AcylCarMAT*Kmcpt2CoAMAT)-C4AcylCoAMAT*CarMAT/(Kmcpt2C4AcylCarMAT*Kmcpt2CoAMAT*Keqcpt2))/((1+C4AcylCarMAT/Kmcpt2C4AcylCarMAT+C4AcylCoAMAT/Kmcpt2C4AcylCoAMAT+C16AcylCarMAT/Kmcpt2C16AcylCarMAT+C16AcylCoAMAT/Kmcpt2C16AcylCoAMAT+C14AcylCarMAT/Kmcpt2C14AcylCarMAT+C14AcylCoAMAT/Kmcpt2C14AcylCoAMAT+C12AcylCarMAT/Kmcpt2C12AcylCarMAT+C12AcylCoAMAT/Kmcpt2C12AcylCoAMAT+C10AcylCarMAT/Kmcpt2C10AcylCarMAT+C10AcylCoAMAT/Kmcpt2C10AcylCoAMAT+C8AcylCarMAT/Kmcpt2C8AcylCarMAT+C8AcylCoAMAT/Kmcpt2C8AcylCoAMAT+C6AcylCarMAT/Kmcpt2C6AcylCarMAT+C6AcylCoAMAT/Kmcpt2C6AcylCoAMAT)*(1+CoAMAT/Kmcpt2CoAMAT+CarMAT/Kmcpt2CarMAT))/VMAT Kmcpt2C10AcylCarMAT = 51.0; Keqcpt2 = 2.22; Kmcpt2C12AcylCarMAT = 51.0; Kmcpt2C16AcylCoAMAT = 38.0; Vcpt2 = 0.391; Kmcpt2C12AcylCoAMAT = 38.0; sfcpt2C4=0.01; Kmcpt2C10AcylCoAMAT = 38.0; Kmcpt2C16AcylCarMAT = 51.0; Kmcpt2C14AcylCoAMAT = 38.0; Kmcpt2C14AcylCarMAT = 51.0; Kmcpt2CoAMAT = 30.0; Kmcpt2C6AcylCoAMAT = 1000.0; Kmcpt2C4AcylCoAMAT = 1000000.0; Kmcpt2C8AcylCoAMAT = 38.0; Kmcpt2C8AcylCarMAT = 51.0; Kmcpt2C4AcylCarMAT = 51.0; Kmcpt2C6AcylCarMAT = 51.0; Kmcpt2CarMAT = 350.0
C4AcylCoAMAT => C4EnoylCoAMAT + FADHMAT; C6AcylCoAMAT, FADtMAT, C6EnoylCoAMAT, C4AcylCoAMAT, C4EnoylCoAMAT, FADHMAT VMAT*sfscadC4*Vscad*(C4AcylCoAMAT*(FADtMAT-FADHMAT)/(KmscadC4AcylCoAMAT*KmscadFAD)-C4EnoylCoAMAT*FADHMAT/(KmscadC4AcylCoAMAT*KmscadFAD*Keqscad))/((1+C4AcylCoAMAT/KmscadC4AcylCoAMAT+C4EnoylCoAMAT/KmscadC4EnoylCoAMAT+C6AcylCoAMAT/KmscadC6AcylCoAMAT+C6EnoylCoAMAT/KmscadC6EnoylCoAMAT)*(1+(FADtMAT-FADHMAT)/KmscadFAD+FADHMAT/KmscadFADH))/VMAT KmscadC4EnoylCoAMAT = 1.08; KmscadC6AcylCoAMAT = 285.0; KmscadC6EnoylCoAMAT = 1.08; KmscadFAD = 0.12; Keqscad = 6.0; Vscad = 0.081; KmscadFADH = 24.2; sfscadC4=1.0; KmscadC4AcylCoAMAT = 10.7
C16AcylCoAMAT => C16EnoylCoAMAT + FADHMAT; C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, FADtMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C8EnoylCoAMAT, C16AcylCoAMAT, C16EnoylCoAMAT, FADHMAT VMAT*sflcadC16*Vlcad*(C16AcylCoAMAT*(FADtMAT-FADHMAT)/(KmlcadC16AcylCoAMAT*KmlcadFAD)-C16EnoylCoAMAT*FADHMAT/(KmlcadC16AcylCoAMAT*KmlcadFAD*Keqlcad))/((1+C16AcylCoAMAT/KmlcadC16AcylCoAMAT+C16EnoylCoAMAT/KmlcadC16EnoylCoAMAT+C14AcylCoAMAT/KmlcadC14AcylCoAMAT+C14EnoylCoAMAT/KmlcadC14EnoylCoAMAT+C12AcylCoAMAT/KmlcadC12AcylCoAMAT+C12EnoylCoAMAT/KmlcadC12EnoylCoAMAT+C10AcylCoAMAT/KmlcadC10AcylCoAMAT+C10EnoylCoAMAT/KmlcadC10EnoylCoAMAT+C8AcylCoAMAT/KmlcadC8AcylCoAMAT+C8EnoylCoAMAT/KmlcadC8EnoylCoAMAT)*(1+(FADtMAT-FADHMAT)/KmlcadFAD+FADHMAT/KmlcadFADH))/VMAT KmlcadC10EnoylCoAMAT = 1.08; KmlcadC14AcylCoAMAT = 7.4; Keqlcad = 6.0; sflcadC16=0.9; KmlcadFADH = 24.2; KmlcadC12AcylCoAMAT = 9.0; KmlcadFAD = 0.12; KmlcadC12EnoylCoAMAT = 1.08; KmlcadC10AcylCoAMAT = 24.3; KmlcadC16EnoylCoAMAT = 1.08; Vlcad = 0.01; KmlcadC16AcylCoAMAT = 2.5; KmlcadC8AcylCoAMAT = 123.0; KmlcadC8EnoylCoAMAT = 1.08; KmlcadC14EnoylCoAMAT = 1.08
C4EnoylCoAMAT + species_1 => C4AcetoacylCoAMAT + NADHMAT; C6KetoacylCoAMAT, C6EnoylCoAMAT, C4EnoylCoAMAT, species_1, C4AcetoacylCoAMAT, NADHMAT VMAT*sfcrotC4*Vcrot*sfmschadC4*Vmschad*(C4EnoylCoAMAT*species_1/(KmcrotC4EnoylCoAMAT*KmmschadC4HydroxyacylCoAMAT*KmmschadNADMAT)-C4AcetoacylCoAMAT*NADHMAT/(KmcrotC4EnoylCoAMAT*KmmschadC4HydroxyacylCoAMAT*KmmschadNADMAT*Keqcrot*Keqmschad))/(sfcrotC4*Vcrot*(1+C4AcetoacylCoAMAT/KmmschadC4AcetoacylCoAMAT+C6KetoacylCoAMAT/KmmschadC6KetoacylCoAMAT)*(1+species_1/KmmschadNADMAT+NADHMAT/KmmschadNADHMAT)/(KmcrotC4EnoylCoAMAT*Keqcrot)+sfmschadC4*Vmschad*species_1*(1+C4EnoylCoAMAT/KmcrotC4EnoylCoAMAT+C6EnoylCoAMAT/KmcrotC6EnoylCoAMAT+C4AcetoacylCoAMAT/KicrotC4AcetoacylCoA)/(KmmschadC4HydroxyacylCoAMAT*KmmschadNADMAT))/VMAT sfcrotC4=1.0; KmcrotC6EnoylCoAMAT = 25.0; Keqmschad = 2.17E-4; sfmschadC4=0.67; Vcrot = 3.6; Keqcrot = 3.13; KmmschadC4AcetoacylCoAMAT = 16.9; KicrotC4AcetoacylCoA = 1.6; Vmschad = 1.0; KmmschadNADMAT = 58.5; KmmschadC4HydroxyacylCoAMAT = 69.9; KmmschadNADHMAT = 5.4; KmmschadC6KetoacylCoAMAT = 5.8; KmcrotC4EnoylCoAMAT = 40.0
C6EnoylCoAMAT + species_1 => C6KetoacylCoAMAT + NADHMAT; C4AcetoacylCoAMAT, C4EnoylCoAMAT, C6EnoylCoAMAT, species_1, C6KetoacylCoAMAT, NADHMAT VMAT*sfcrotC6*Vcrot*sfmschadC6*Vmschad*(C6EnoylCoAMAT*species_1/(KmcrotC6EnoylCoAMAT*KmmschadC6HydroxyacylCoAMAT*KmmschadNADMAT)-C6KetoacylCoAMAT*NADHMAT/(KmcrotC6EnoylCoAMAT*KmmschadC6HydroxyacylCoAMAT*KmmschadNADMAT*Keqcrot*Keqmschad))/(sfcrotC6*Vcrot*(1+C6KetoacylCoAMAT/KmmschadC6KetoacylCoAMAT+C4AcetoacylCoAMAT/KmmschadC4AcetoacylCoAMAT)*(1+species_1/KmmschadNADMAT+NADHMAT/KmmschadNADHMAT)/(KmcrotC6EnoylCoAMAT*Keqcrot)+sfmschadC6*Vmschad*species_1*(1+C6EnoylCoAMAT/KmcrotC6EnoylCoAMAT+C4EnoylCoAMAT/KmcrotC4EnoylCoAMAT+C4AcetoacylCoAMAT/KicrotC4AcetoacylCoA)/(KmmschadC6HydroxyacylCoAMAT*KmmschadNADMAT))/VMAT KmcrotC6EnoylCoAMAT = 25.0; Keqmschad = 2.17E-4; Vcrot = 3.6; KmmschadC6HydroxyacylCoAMAT = 28.6; Keqcrot = 3.13; KmmschadC4AcetoacylCoAMAT = 16.9; KicrotC4AcetoacylCoA = 1.6; Vmschad = 1.0; sfcrotC6=0.83; KmmschadNADMAT = 58.5; KmmschadNADHMAT = 5.4; KmmschadC6KetoacylCoAMAT = 5.8; sfmschadC6=1.0; KmcrotC4EnoylCoAMAT = 40.0
C16AcylCarMAT => C16AcylCoAMAT; C14AcylCarMAT, C12AcylCarMAT, C10AcylCarMAT, C8AcylCarMAT, C6AcylCarMAT, C4AcylCarMAT, CoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, C4AcylCoAMAT, CarMAT, C16AcylCarMAT, C16AcylCoAMAT VMAT*sfcpt2C16*Vcpt2*(C16AcylCarMAT*CoAMAT/(Kmcpt2C16AcylCarMAT*Kmcpt2CoAMAT)-C16AcylCoAMAT*CarMAT/(Kmcpt2C16AcylCarMAT*Kmcpt2CoAMAT*Keqcpt2))/((1+C16AcylCarMAT/Kmcpt2C16AcylCarMAT+C16AcylCoAMAT/Kmcpt2C16AcylCoAMAT+C14AcylCarMAT/Kmcpt2C14AcylCarMAT+C14AcylCoAMAT/Kmcpt2C14AcylCoAMAT+C12AcylCarMAT/Kmcpt2C12AcylCarMAT+C12AcylCoAMAT/Kmcpt2C12AcylCoAMAT+C10AcylCarMAT/Kmcpt2C10AcylCarMAT+C10AcylCoAMAT/Kmcpt2C10AcylCoAMAT+C8AcylCarMAT/Kmcpt2C8AcylCarMAT+C8AcylCoAMAT/Kmcpt2C8AcylCoAMAT+C6AcylCarMAT/Kmcpt2C6AcylCarMAT+C6AcylCoAMAT/Kmcpt2C6AcylCoAMAT+C4AcylCarMAT/Kmcpt2C4AcylCarMAT+C4AcylCoAMAT/Kmcpt2C4AcylCoAMAT)*(1+CoAMAT/Kmcpt2CoAMAT+CarMAT/Kmcpt2CarMAT))/VMAT Kmcpt2C10AcylCarMAT = 51.0; Keqcpt2 = 2.22; Kmcpt2C12AcylCarMAT = 51.0; Kmcpt2C16AcylCoAMAT = 38.0; Vcpt2 = 0.391; Kmcpt2C12AcylCoAMAT = 38.0; Kmcpt2C10AcylCoAMAT = 38.0; Kmcpt2C16AcylCarMAT = 51.0; Kmcpt2C14AcylCoAMAT = 38.0; Kmcpt2C14AcylCarMAT = 51.0; Kmcpt2CoAMAT = 30.0; Kmcpt2C6AcylCoAMAT = 1000.0; sfcpt2C16=0.85; Kmcpt2C4AcylCoAMAT = 1000000.0; Kmcpt2C8AcylCoAMAT = 38.0; Kmcpt2C8AcylCarMAT = 51.0; Kmcpt2C4AcylCarMAT = 51.0; Kmcpt2C6AcylCarMAT = 51.0; Kmcpt2CarMAT = 350.0
Curator's comment:
(added: 17 Oct 2019, 12:18:35, updated: 17 Oct 2019, 12:18:35)
Model is encoded in COPASI 4.24 (Build 197) and plots are generated using R ggplot package. Model simulation time is 25 min. Figure 8 (middle) figure has been reproduced and the figure is exact to that presented in the paper