vanEunen2013 - Network dynamics of fatty acid β-oxidation (steady-state model)

  public model
Model Identifier
BIOMD0000000505
Short description
vanEunen2013 - Network dynamics of fatty acid β-oxidation (steady-state model)

Lipid metabolism plays an important role in the development of metabolic syndrome, a major risk factor for cardiovascular disease and diabetes. This model gives insights into the response of lipid oxidation to dietart and medical interventions. The model predicts the rate of lipid oxidation and the time course of most acyl carnitines. There are two models described in the paper, (i) steady-state model [ BIOMD0000000505 ], (ii) time-course model [ BIOMD0000000506 ]. This model corresponds to the steady-state model.

This model is described in the article:

van Eunen K, Simons SM, Gerding A, Bleeker A, den Besten G, Touw CM, Houten SM, Groen BK, Krab K, Reijngoud DJ, Bakker BM.
PLoS Comput Biol. 2013;9(8):e1003186.

Abstract:

Fatty-acid metabolism plays a key role in acquired and inborn metabolic diseases. To obtain insight into the network dynamics of fatty-acid β-oxidation, we constructed a detailed computational model of the pathway and subjected it to a fat overload condition. The model contains reversible and saturable enzyme-kinetic equations and experimentally determined parameters for rat-liver enzymes. It was validated by adding palmitoyl CoA or palmitoyl carnitine to isolated rat-liver mitochondria: without refitting of measured parameters, the model correctly predicted the β-oxidation flux as well as the time profiles of most acyl-carnitine concentrations. Subsequently, we simulated the condition of obesity by increasing the palmitoyl-CoA concentration. At a high concentration of palmitoyl CoA the β-oxidation became overloaded: the flux dropped and metabolites accumulated. This behavior originated from the competition between acyl CoAs of different chain lengths for a set of acyl-CoA dehydrogenases with overlapping substrate specificity. This effectively induced competitive feedforward inhibition and thereby led to accumulation of CoA-ester intermediates and depletion of free CoA (CoASH). The mitochondrial [NAD⁺]/[NADH] ratio modulated the sensitivity to substrate overload, revealing a tight interplay between regulation of β-oxidation and mitochondrial respiration.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Format
SBML (L2V4)
Related Publication
  • Biochemical competition makes fatty-acid β-oxidation vulnerable to substrate overload.
  • van Eunen K, Simons SM, Gerding A, Bleeker A, den Besten G, Touw CM, Houten SM, Groen BK, Krab K, Reijngoud DJ, Bakker BM
  • PLoS computational biology , 0/ 2013 , Volume 9 , pages: e1003186 , PubMed ID: 23966849
  • Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
  • Fatty-acid metabolism plays a key role in acquired and inborn metabolic diseases. To obtain insight into the network dynamics of fatty-acid β-oxidation, we constructed a detailed computational model of the pathway and subjected it to a fat overload condition. The model contains reversible and saturable enzyme-kinetic equations and experimentally determined parameters for rat-liver enzymes. It was validated by adding palmitoyl CoA or palmitoyl carnitine to isolated rat-liver mitochondria: without refitting of measured parameters, the model correctly predicted the β-oxidation flux as well as the time profiles of most acyl-carnitine concentrations. Subsequently, we simulated the condition of obesity by increasing the palmitoyl-CoA concentration. At a high concentration of palmitoyl CoA the β-oxidation became overloaded: the flux dropped and metabolites accumulated. This behavior originated from the competition between acyl CoAs of different chain lengths for a set of acyl-CoA dehydrogenases with overlapping substrate specificity. This effectively induced competitive feedforward inhibition and thereby led to accumulation of CoA-ester intermediates and depletion of free CoA (CoASH). The mitochondrial [NAD⁺]/[NADH] ratio modulated the sensitivity to substrate overload, revealing a tight interplay between regulation of β-oxidation and mitochondrial respiration.
Contributors
Kieran Smallbone

Metadata information

is
BioModels Database MODEL1312040000
BioModels Database BIOMD0000000505
isDescribedBy
PubMed 23966849
hasTaxon
Taxonomy Rattus
isVersionOf
Gene Ontology fatty acid oxidation
occursIn
Gene Ontology mitochondrion
Brenda Tissue Ontology liver
hasProperty
Mathematical Modelling Ontology Ordinary differential equation model

Curation status
Curated


Tags
Name Description Size Actions

Model files

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  • Model originally submitted by : Kieran Smallbone
  • Submitted: 04-Dec-2013 17:23:23
  • Last Modified: 04-Mar-2014 11:24:24
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 04-Mar-2014 11:24:24
    • Submitted by: Kieran Smallbone
    • With comment: Current version of vanEunen2013 - Network dynamics of fatty acid β-oxidation (steady-state model)
  • Version: 1 public model Download this version
    • Submitted on: 04-Dec-2013 17:23:23
    • Submitted by: Kieran Smallbone
    • 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
C8AcylCoAMAT

fatty acyl-CoA
0.0 μmol
C8EnoylCoAMAT

cis-2-enoyl-CoA
0.0 μmol
AcetylCoAMAT

acetyl-CoA
70.0 μmol
C6AcylCarCYT

O-acylcarnitine
0.0 μmol
C6AcylCarMAT

O-acylcarnitine
0.0 μmol
FADHMAT

FADH(.)
0.46 μmol
Reactions
Reactions Rate Parameters
C8AcylCoAMAT => C8EnoylCoAMAT + FADHMAT; C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, FADtMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C8AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, FADtMAT, C8EnoylCoAMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, FADHMAT, C8AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, FADtMAT, C8EnoylCoAMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, FADHMAT sflcadC8*Vlcad*(C8AcylCoAMAT*(FADtMAT-FADHMAT)/(KmlcadC8AcylCoAMAT*KmlcadFAD)-C8EnoylCoAMAT*FADHMAT/(KmlcadC8AcylCoAMAT*KmlcadFAD*Keqlcad))/((1+C8AcylCoAMAT/KmlcadC8AcylCoAMAT+C8EnoylCoAMAT/KmlcadC8EnoylCoAMAT+C16AcylCoAMAT/KmlcadC16AcylCoAMAT+C16EnoylCoAMAT/KmlcadC16EnoylCoAMAT+C14AcylCoAMAT/KmlcadC14AcylCoAMAT+C14EnoylCoAMAT/KmlcadC14EnoylCoAMAT+C12AcylCoAMAT/KmlcadC12AcylCoAMAT+C12EnoylCoAMAT/KmlcadC12EnoylCoAMAT+C10AcylCoAMAT/KmlcadC10AcylCoAMAT+C10EnoylCoAMAT/KmlcadC10EnoylCoAMAT)*(1+(FADtMAT-FADHMAT)/KmlcadFAD+FADHMAT/KmlcadFADH)) KmlcadC8AcylCoAMAT = 123.0 uM; Vlcad = 0.01 uM per min per mgProtein; KmlcadC14EnoylCoAMAT = 1.08 uM; KmlcadFAD = 0.12 uM; KmlcadFADH = 24.2 uM; KmlcadC12EnoylCoAMAT = 1.08 uM; KmlcadC8EnoylCoAMAT = 1.08 uM; sflcadC8=0.4 dimensionless; Keqlcad = 6.0 dimensionless; KmlcadC16AcylCoAMAT = 2.5 uM; KmlcadC12AcylCoAMAT = 9.0 uM; KmlcadC10AcylCoAMAT = 24.3 uM; KmlcadC10EnoylCoAMAT = 1.08 uM; KmlcadC14AcylCoAMAT = 7.4 uM; KmlcadC16EnoylCoAMAT = 1.08 uM
C8AcylCoAMAT => C8EnoylCoAMAT + FADHMAT; C12AcylCoAMAT, C10AcylCoAMAT, C6AcylCoAMAT, C4AcylCoAMAT, FADtMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C6EnoylCoAMAT, C4EnoylCoAMAT, C8AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C6AcylCoAMAT, C4AcylCoAMAT, FADtMAT, C8EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C6EnoylCoAMAT, C4EnoylCoAMAT, FADHMAT, C8AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C6AcylCoAMAT, C4AcylCoAMAT, FADtMAT, C8EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C6EnoylCoAMAT, C4EnoylCoAMAT, FADHMAT sfmcadC8*Vmcad*(C8AcylCoAMAT*(FADtMAT-FADHMAT)/(KmmcadC8AcylCoAMAT*KmmcadFAD)-C8EnoylCoAMAT*FADHMAT/(KmmcadC8AcylCoAMAT*KmmcadFAD*Keqmcad))/((1+C8AcylCoAMAT/KmmcadC8AcylCoAMAT+C8EnoylCoAMAT/KmmcadC8EnoylCoAMAT+C12AcylCoAMAT/KmmcadC12AcylCoAMAT+C12EnoylCoAMAT/KmmcadC12EnoylCoAMAT+C10AcylCoAMAT/KmmcadC10AcylCoAMAT+C10EnoylCoAMAT/KmmcadC10EnoylCoAMAT+C6AcylCoAMAT/KmmcadC6AcylCoAMAT+C6EnoylCoAMAT/KmmcadC6EnoylCoAMAT+C4AcylCoAMAT/KmmcadC4AcylCoAMAT+C4EnoylCoAMAT/KmmcadC4EnoylCoAMAT)*(1+(FADtMAT-FADHMAT)/KmmcadFAD+FADHMAT/KmmcadFADH)) KmmcadC8AcylCoAMAT = 4.0 uM; KmmcadC12AcylCoAMAT = 5.7 uM; KmmcadC4AcylCoAMAT = 135.0 uM; KmmcadC10AcylCoAMAT = 5.4 uM; KmmcadFAD = 0.12 uM; KmmcadC10EnoylCoAMAT = 1.08 uM; KmmcadC4EnoylCoAMAT = 1.08 uM; Vmcad = 0.081 uM per min per mgProtein; KmmcadC6AcylCoAMAT = 9.4 uM; KmmcadC6EnoylCoAMAT = 1.08 uM; KmmcadFADH = 24.2 uM; sfmcadC8=0.87 dimensionless; KmmcadC8EnoylCoAMAT = 1.08 uM; KmmcadC12EnoylCoAMAT = 1.08 uM; Keqmcad = 6.0 dimensionless
C12EnoylCoAMAT => C10AcylCoAMAT + AcetylCoAMAT + NADHMAT; C16EnoylCoAMAT, C14EnoylCoAMAT, C10EnoylCoAMAT, C8EnoylCoAMAT, NADtMAT, CoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, C4AcetoacylCoAMAT, C12EnoylCoAMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C10EnoylCoAMAT, C8EnoylCoAMAT, NADtMAT, CoAMAT, C10AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, NADHMAT, AcetylCoAMAT, C4AcetoacylCoAMAT, C12EnoylCoAMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C10EnoylCoAMAT, C8EnoylCoAMAT, NADtMAT, CoAMAT, C10AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, NADHMAT, AcetylCoAMAT, C4AcetoacylCoAMAT sfmtpC12*Vmtp*(C12EnoylCoAMAT*(NADtMAT-NADHMAT)*CoAMAT/(KmmtpC12EnoylCoAMAT*KmmtpNADMAT*KmmtpCoAMAT)-C10AcylCoAMAT*NADHMAT*AcetylCoAMAT/(KmmtpC12EnoylCoAMAT*KmmtpNADMAT*KmmtpCoAMAT*Keqmtp))/((1+C12EnoylCoAMAT/KmmtpC12EnoylCoAMAT+C10AcylCoAMAT/KmmtpC10AcylCoAMAT+C16EnoylCoAMAT/KmmtpC16EnoylCoAMAT+C16AcylCoAMAT/KmmtpC16AcylCoAMAT+C14EnoylCoAMAT/KmmtpC14EnoylCoAMAT+C14AcylCoAMAT/KmmtpC14AcylCoAMAT+C10EnoylCoAMAT/KmmtpC10EnoylCoAMAT+C12AcylCoAMAT/KmmtpC12AcylCoAMAT+C8EnoylCoAMAT/KmmtpC8EnoylCoAMAT+C8AcylCoAMAT/KmmtpC8AcylCoAMAT+C6AcylCoAMAT/KmmtpC6AcylCoAMAT+C4AcetoacylCoAMAT/KicrotC4AcetoacylCoA)*(1+(NADtMAT-NADHMAT)/KmmtpNADMAT+NADHMAT/KmmtpNADHMAT)*(1+CoAMAT/KmmtpCoAMAT+AcetylCoAMAT/KmmtpAcetylCoAMAT)) KmmtpC14EnoylCoAMAT = 25.0 uM; KmmtpC8EnoylCoAMAT = 25.0 uM; KmmtpC16AcylCoAMAT = 13.83 uM; KmmtpCoAMAT = 30.0 uM; KmmtpC16EnoylCoAMAT = 25.0 uM; KmmtpC12EnoylCoAMAT = 25.0 uM; KmmtpAcetylCoAMAT = 30.0 uM; Vmtp = 2.84 uM per min per mgProtein; KmmtpC12AcylCoAMAT = 13.83 uM; KmmtpC8AcylCoAMAT = 13.83 uM; KmmtpC14AcylCoAMAT = 13.83 uM; KmmtpC6AcylCoAMAT = 13.83 uM; sfmtpC12=0.81 dimensionless; KmmtpC10EnoylCoAMAT = 25.0 uM; Keqmtp = 0.71 dimensionless; KicrotC4AcetoacylCoA = 1.6 uM; KmmtpNADMAT = 60.0 uM; KmmtpNADHMAT = 50.0 uM; KmmtpC10AcylCoAMAT = 13.83 uM
C10EnoylCoAMAT => C8AcylCoAMAT + AcetylCoAMAT + NADHMAT; C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C8EnoylCoAMAT, NADtMAT, CoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C6AcylCoAMAT, C4AcetoacylCoAMAT, C10EnoylCoAMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C8EnoylCoAMAT, NADtMAT, CoAMAT, C8AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C6AcylCoAMAT, NADHMAT, AcetylCoAMAT, C4AcetoacylCoAMAT, C10EnoylCoAMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C8EnoylCoAMAT, NADtMAT, CoAMAT, C8AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C6AcylCoAMAT, NADHMAT, AcetylCoAMAT, C4AcetoacylCoAMAT sfmtpC10*Vmtp*(C10EnoylCoAMAT*(NADtMAT-NADHMAT)*CoAMAT/(KmmtpC10EnoylCoAMAT*KmmtpNADMAT*KmmtpCoAMAT)-C8AcylCoAMAT*NADHMAT*AcetylCoAMAT/(KmmtpC10EnoylCoAMAT*KmmtpNADMAT*KmmtpCoAMAT*Keqmtp))/((1+C10EnoylCoAMAT/KmmtpC10EnoylCoAMAT+C8AcylCoAMAT/KmmtpC8AcylCoAMAT+C16EnoylCoAMAT/KmmtpC16EnoylCoAMAT+C16AcylCoAMAT/KmmtpC16AcylCoAMAT+C14EnoylCoAMAT/KmmtpC14EnoylCoAMAT+C14AcylCoAMAT/KmmtpC14AcylCoAMAT+C12EnoylCoAMAT/KmmtpC12EnoylCoAMAT+C12AcylCoAMAT/KmmtpC12AcylCoAMAT+C8EnoylCoAMAT/KmmtpC8EnoylCoAMAT+C10AcylCoAMAT/KmmtpC10AcylCoAMAT+C6AcylCoAMAT/KmmtpC6AcylCoAMAT+C4AcetoacylCoAMAT/KicrotC4AcetoacylCoA)*(1+(NADtMAT-NADHMAT)/KmmtpNADMAT+NADHMAT/KmmtpNADHMAT)*(1+CoAMAT/KmmtpCoAMAT+AcetylCoAMAT/KmmtpAcetylCoAMAT)) KmmtpC14EnoylCoAMAT = 25.0 uM; KmmtpC8EnoylCoAMAT = 25.0 uM; KmmtpC16AcylCoAMAT = 13.83 uM; KmmtpCoAMAT = 30.0 uM; KmmtpC16EnoylCoAMAT = 25.0 uM; KmmtpC12EnoylCoAMAT = 25.0 uM; KmmtpAcetylCoAMAT = 30.0 uM; Vmtp = 2.84 uM per min per mgProtein; KmmtpC8AcylCoAMAT = 13.83 uM; KmmtpC12AcylCoAMAT = 13.83 uM; KmmtpC14AcylCoAMAT = 13.83 uM; KmmtpC6AcylCoAMAT = 13.83 uM; KmmtpC10EnoylCoAMAT = 25.0 uM; Keqmtp = 0.71 dimensionless; KicrotC4AcetoacylCoA = 1.6 uM; KmmtpNADMAT = 60.0 uM; KmmtpNADHMAT = 50.0 uM; KmmtpC10AcylCoAMAT = 13.83 uM; sfmtpC10=0.73 dimensionless
C8EnoylCoAMAT => C8HydroxyacylCoAMAT; C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C6EnoylCoAMAT, C4EnoylCoAMAT, C16HydroxyacylCoAMAT, C14HydroxyacylCoAMAT, C12HydroxyacylCoAMAT, C10HydroxyacylCoAMAT, C6HydroxyacylCoAMAT, C4HydroxyacylCoAMAT, C4AcetoacylCoAMAT, C8EnoylCoAMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C6EnoylCoAMAT, C4EnoylCoAMAT, C8HydroxyacylCoAMAT, C16HydroxyacylCoAMAT, C14HydroxyacylCoAMAT, C12HydroxyacylCoAMAT, C10HydroxyacylCoAMAT, C6HydroxyacylCoAMAT, C4HydroxyacylCoAMAT, C4AcetoacylCoAMAT, C8EnoylCoAMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C6EnoylCoAMAT, C4EnoylCoAMAT, C8HydroxyacylCoAMAT, C16HydroxyacylCoAMAT, C14HydroxyacylCoAMAT, C12HydroxyacylCoAMAT, C10HydroxyacylCoAMAT, C6HydroxyacylCoAMAT, C4HydroxyacylCoAMAT, C4AcetoacylCoAMAT sfcrotC8*Vcrot*(C8EnoylCoAMAT/KmcrotC8EnoylCoAMAT-C8HydroxyacylCoAMAT/(KmcrotC8EnoylCoAMAT*Keqcrot))/(1+C8EnoylCoAMAT/KmcrotC8EnoylCoAMAT+C8HydroxyacylCoAMAT/KmcrotC8HydroxyacylCoAMAT+C16EnoylCoAMAT/KmcrotC16EnoylCoAMAT+C16HydroxyacylCoAMAT/KmcrotC16HydroxyacylCoAMAT+C14EnoylCoAMAT/KmcrotC14EnoylCoAMAT+C14HydroxyacylCoAMAT/KmcrotC14HydroxyacylCoAMAT+C12EnoylCoAMAT/KmcrotC12EnoylCoAMAT+C12HydroxyacylCoAMAT/KmcrotC12HydroxyacylCoAMAT+C10EnoylCoAMAT/KmcrotC10EnoylCoAMAT+C10HydroxyacylCoAMAT/KmcrotC10HydroxyacylCoAMAT+C6EnoylCoAMAT/KmcrotC6EnoylCoAMAT+C6HydroxyacylCoAMAT/KmcrotC6HydroxyacylCoAMAT+C4EnoylCoAMAT/KmcrotC4EnoylCoAMAT+C4HydroxyacylCoAMAT/KmcrotC4HydroxyacylCoAMAT+C4AcetoacylCoAMAT/KicrotC4AcetoacylCoA) KmcrotC16EnoylCoAMAT = 150.0 uM; KmcrotC12EnoylCoAMAT = 25.0 uM; KicrotC4AcetoacylCoA = 1.6 uM; KmcrotC4EnoylCoAMAT = 40.0 uM; Vcrot = 3.6 uM per min per mgProtein; Keqcrot = 3.13 dimensionless; KmcrotC8EnoylCoAMAT = 25.0 uM; KmcrotC14EnoylCoAMAT = 100.0 uM; KmcrotC10HydroxyacylCoAMAT = 45.0 uM; KmcrotC8HydroxyacylCoAMAT = 45.0 uM; KmcrotC6EnoylCoAMAT = 25.0 uM; KmcrotC10EnoylCoAMAT = 25.0 uM; KmcrotC14HydroxyacylCoAMAT = 45.0 uM; KmcrotC4HydroxyacylCoAMAT = 45.0 uM; KmcrotC16HydroxyacylCoAMAT = 45.0 uM; KmcrotC12HydroxyacylCoAMAT = 45.0 uM; sfcrotC8=0.58 dimensionless; KmcrotC6HydroxyacylCoAMAT = 45.0 uM
C6AcylCarCYT => C6AcylCarMAT; CarMAT, CarCYT, C6AcylCarCYT, CarMAT, C6AcylCarMAT, CarCYT, C6AcylCarCYT, CarMAT, C6AcylCarMAT, CarCYT Vfcact*(C6AcylCarCYT*CarMAT-C6AcylCarMAT*CarCYT/Keqcact)/(C6AcylCarCYT*CarMAT+KmcactCarMAT*C6AcylCarCYT+KmcactC6AcylCarCYT*CarMAT*(1+CarCYT/KicactCarCYT)+Vfcact/(Vrcact*Keqcact)*(KmcactCarCYT*C6AcylCarMAT*(1+C6AcylCarCYT/KicactC6AcylCarCYT)+CarCYT*(KmcactC6AcylCarMAT+C6AcylCarMAT))) KmcactC6AcylCarMAT=15.0 uM; Vfcact = 0.42 uM per min per mgProtein; KmcactCarCYT = 130.0 uM; KmcactC6AcylCarCYT=15.0 uM; KmcactCarMAT = 130.0 uM; Keqcact = 1.0 dimensionless; KicactCarCYT = 200.0 uM; KicactC6AcylCarCYT=56.0 uM; Vrcact = 0.42 uM per min per mgProtein
C6KetoacylCoAMAT => C4AcylCoAMAT + AcetylCoAMAT; C16KetoacylCoAMAT, C14KetoacylCoAMAT, C12KetoacylCoAMAT, C10KetoacylCoAMAT, C8KetoacylCoAMAT, C4AcetoacylCoAMAT, CoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, C6KetoacylCoAMAT, C16KetoacylCoAMAT, C14KetoacylCoAMAT, C12KetoacylCoAMAT, C10KetoacylCoAMAT, C8KetoacylCoAMAT, C4AcetoacylCoAMAT, CoAMAT, C4AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, AcetylCoAMAT, C6KetoacylCoAMAT, C16KetoacylCoAMAT, C14KetoacylCoAMAT, C12KetoacylCoAMAT, C10KetoacylCoAMAT, C8KetoacylCoAMAT, C4AcetoacylCoAMAT, CoAMAT, C4AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, AcetylCoAMAT sfmckatC6*Vmckat*(C6KetoacylCoAMAT*CoAMAT/(KmmckatC6KetoacylCoAMAT*KmmckatCoAMAT)-C4AcylCoAMAT*AcetylCoAMAT/(KmmckatC6KetoacylCoAMAT*KmmckatCoAMAT*Keqmckat))/((1+C6KetoacylCoAMAT/KmmckatC6KetoacylCoAMAT+C4AcylCoAMAT/KmmckatC4AcylCoAMAT+C16KetoacylCoAMAT/KmmckatC16KetoacylCoAMAT+C16AcylCoAMAT/KmmckatC16AcylCoAMAT+C14KetoacylCoAMAT/KmmckatC14KetoacylCoAMAT+C14AcylCoAMAT/KmmckatC14AcylCoAMAT+C12KetoacylCoAMAT/KmmckatC12KetoacylCoAMAT+C12AcylCoAMAT/KmmckatC12AcylCoAMAT+C10KetoacylCoAMAT/KmmckatC10KetoacylCoAMAT+C10AcylCoAMAT/KmmckatC10AcylCoAMAT+C8KetoacylCoAMAT/KmmckatC8KetoacylCoAMAT+C8AcylCoAMAT/KmmckatC8AcylCoAMAT+C4AcetoacylCoAMAT/KmmckatC4AcetoacylCoAMAT+C6AcylCoAMAT/KmmckatC6AcylCoAMAT+AcetylCoAMAT/KmmckatAcetylCoAMAT)*(1+CoAMAT/KmmckatCoAMAT+AcetylCoAMAT/KmmckatAcetylCoAMAT)) KmmckatC14AcylCoAMAT = 13.83 uM; KmmckatC10KetoacylCoAMAT = 2.1 uM; sfmckatC6=1.0 dimensionless; KmmckatCoAMAT = 26.6 uM; KmmckatC6KetoacylCoAMAT = 6.7 uM; Keqmckat = 1051.0 dimensionless; KmmckatC12KetoacylCoAMAT = 1.3 uM; KmmckatC8KetoacylCoAMAT = 3.2 uM; KmmckatC4AcetoacylCoAMAT = 12.4 uM; KmmckatC16KetoacylCoAMAT = 1.1 uM; KmmckatC12AcylCoAMAT = 13.83 uM; KmmckatC8AcylCoAMAT = 13.83 uM; KmmckatC10AcylCoAMAT = 13.83 uM; KmmckatC6AcylCoAMAT = 13.83 uM; Vmckat = 0.377 uM per min per mgProtein; KmmckatC16AcylCoAMAT = 13.83 uM; KmmckatC14KetoacylCoAMAT = 1.2 uM; KmmckatC4AcylCoAMAT = 13.83 uM; KmmckatAcetylCoAMAT = 30.0 uM
C4AcetoacylCoAMAT => AcetylCoAMAT; C16KetoacylCoAMAT, C14KetoacylCoAMAT, C12KetoacylCoAMAT, C10KetoacylCoAMAT, C8KetoacylCoAMAT, C6KetoacylCoAMAT, CoAMAT, C4AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, C4AcetoacylCoAMAT, C16KetoacylCoAMAT, C14KetoacylCoAMAT, C12KetoacylCoAMAT, C10KetoacylCoAMAT, C8KetoacylCoAMAT, C6KetoacylCoAMAT, CoAMAT, C4AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, AcetylCoAMAT, C4AcetoacylCoAMAT, C16KetoacylCoAMAT, C14KetoacylCoAMAT, C12KetoacylCoAMAT, C10KetoacylCoAMAT, C8KetoacylCoAMAT, C6KetoacylCoAMAT, CoAMAT, C4AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, AcetylCoAMAT sfmckatC4*Vmckat*(C4AcetoacylCoAMAT*CoAMAT/(KmmckatC4AcetoacylCoAMAT*KmmckatCoAMAT)-AcetylCoAMAT*AcetylCoAMAT/(KmmckatC4AcetoacylCoAMAT*KmmckatCoAMAT*Keqmckat))/((1+C4AcetoacylCoAMAT/KmmckatC4AcetoacylCoAMAT+C4AcylCoAMAT/KmmckatC4AcylCoAMAT+C16KetoacylCoAMAT/KmmckatC16KetoacylCoAMAT+C16AcylCoAMAT/KmmckatC16AcylCoAMAT+C14KetoacylCoAMAT/KmmckatC14KetoacylCoAMAT+C14AcylCoAMAT/KmmckatC14AcylCoAMAT+C12KetoacylCoAMAT/KmmckatC12KetoacylCoAMAT+C12AcylCoAMAT/KmmckatC12AcylCoAMAT+C10KetoacylCoAMAT/KmmckatC10KetoacylCoAMAT+C10AcylCoAMAT/KmmckatC10AcylCoAMAT+C8KetoacylCoAMAT/KmmckatC8KetoacylCoAMAT+C8AcylCoAMAT/KmmckatC8AcylCoAMAT+C6KetoacylCoAMAT/KmmckatC6KetoacylCoAMAT+C6AcylCoAMAT/KmmckatC6AcylCoAMAT+AcetylCoAMAT/KmmckatAcetylCoAMAT)*(1+CoAMAT/KmmckatCoAMAT+AcetylCoAMAT/KmmckatAcetylCoAMAT)) KmmckatC14AcylCoAMAT = 13.83 uM; KmmckatC10KetoacylCoAMAT = 2.1 uM; KmmckatCoAMAT = 26.6 uM; KmmckatC6KetoacylCoAMAT = 6.7 uM; Keqmckat = 1051.0 dimensionless; KmmckatC12KetoacylCoAMAT = 1.3 uM; KmmckatC8KetoacylCoAMAT = 3.2 uM; KmmckatC4AcetoacylCoAMAT = 12.4 uM; KmmckatC16KetoacylCoAMAT = 1.1 uM; KmmckatC12AcylCoAMAT = 13.83 uM; KmmckatC8AcylCoAMAT = 13.83 uM; KmmckatC10AcylCoAMAT = 13.83 uM; KmmckatC6AcylCoAMAT = 13.83 uM; Vmckat = 0.377 uM per min per mgProtein; sfmckatC4=0.49 dimensionless; KmmckatC16AcylCoAMAT = 13.83 uM; KmmckatC14KetoacylCoAMAT = 1.2 uM; KmmckatC4AcylCoAMAT = 13.83 uM; KmmckatAcetylCoAMAT = 30.0 uM
C16EnoylCoAMAT => C14AcylCoAMAT + AcetylCoAMAT + NADHMAT; C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C8EnoylCoAMAT, NADtMAT, CoAMAT, C16AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, C4AcetoacylCoAMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C8EnoylCoAMAT, NADtMAT, CoAMAT, C14AcylCoAMAT, C16AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, NADHMAT, AcetylCoAMAT, C4AcetoacylCoAMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C8EnoylCoAMAT, NADtMAT, CoAMAT, C14AcylCoAMAT, C16AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, NADHMAT, AcetylCoAMAT, C4AcetoacylCoAMAT 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)) KmmtpC14EnoylCoAMAT = 25.0 uM; KmmtpC8EnoylCoAMAT = 25.0 uM; KmmtpC16AcylCoAMAT = 13.83 uM; KmmtpCoAMAT = 30.0 uM; KmmtpC16EnoylCoAMAT = 25.0 uM; KmmtpC12EnoylCoAMAT = 25.0 uM; KmmtpAcetylCoAMAT = 30.0 uM; Vmtp = 2.84 uM per min per mgProtein; KmmtpC12AcylCoAMAT = 13.83 uM; KmmtpC8AcylCoAMAT = 13.83 uM; KmmtpC14AcylCoAMAT = 13.83 uM; KmmtpC6AcylCoAMAT = 13.83 uM; KmmtpC10EnoylCoAMAT = 25.0 uM; Keqmtp = 0.71 dimensionless; KicrotC4AcetoacylCoA = 1.6 uM; KmmtpNADMAT = 60.0 uM; KmmtpNADHMAT = 50.0 uM; KmmtpC10AcylCoAMAT = 13.83 uM; sfmtpC16=1.0 dimensionless
C14EnoylCoAMAT => C12AcylCoAMAT + AcetylCoAMAT + NADHMAT; C16EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C8EnoylCoAMAT, NADtMAT, CoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, C4AcetoacylCoAMAT, C14EnoylCoAMAT, C16EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C8EnoylCoAMAT, NADtMAT, CoAMAT, C12AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, NADHMAT, AcetylCoAMAT, C4AcetoacylCoAMAT, C14EnoylCoAMAT, C16EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, C8EnoylCoAMAT, NADtMAT, CoAMAT, C12AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C6AcylCoAMAT, NADHMAT, AcetylCoAMAT, C4AcetoacylCoAMAT sfmtpC14*Vmtp*(C14EnoylCoAMAT*(NADtMAT-NADHMAT)*CoAMAT/(KmmtpC14EnoylCoAMAT*KmmtpNADMAT*KmmtpCoAMAT)-C12AcylCoAMAT*NADHMAT*AcetylCoAMAT/(KmmtpC14EnoylCoAMAT*KmmtpNADMAT*KmmtpCoAMAT*Keqmtp))/((1+C14EnoylCoAMAT/KmmtpC14EnoylCoAMAT+C12AcylCoAMAT/KmmtpC12AcylCoAMAT+C16EnoylCoAMAT/KmmtpC16EnoylCoAMAT+C16AcylCoAMAT/KmmtpC16AcylCoAMAT+C12EnoylCoAMAT/KmmtpC12EnoylCoAMAT+C14AcylCoAMAT/KmmtpC14AcylCoAMAT+C10EnoylCoAMAT/KmmtpC10EnoylCoAMAT+C10AcylCoAMAT/KmmtpC10AcylCoAMAT+C8EnoylCoAMAT/KmmtpC8EnoylCoAMAT+C8AcylCoAMAT/KmmtpC8AcylCoAMAT+C6AcylCoAMAT/KmmtpC6AcylCoAMAT+C4AcetoacylCoAMAT/KicrotC4AcetoacylCoA)*(1+(NADtMAT-NADHMAT)/KmmtpNADMAT+NADHMAT/KmmtpNADHMAT)*(1+CoAMAT/KmmtpCoAMAT+AcetylCoAMAT/KmmtpAcetylCoAMAT)) KmmtpC14EnoylCoAMAT = 25.0 uM; KmmtpC8EnoylCoAMAT = 25.0 uM; KmmtpC16AcylCoAMAT = 13.83 uM; KmmtpCoAMAT = 30.0 uM; KmmtpC16EnoylCoAMAT = 25.0 uM; KmmtpC12EnoylCoAMAT = 25.0 uM; KmmtpAcetylCoAMAT = 30.0 uM; Vmtp = 2.84 uM per min per mgProtein; KmmtpC12AcylCoAMAT = 13.83 uM; KmmtpC8AcylCoAMAT = 13.83 uM; KmmtpC14AcylCoAMAT = 13.83 uM; KmmtpC6AcylCoAMAT = 13.83 uM; KmmtpC10EnoylCoAMAT = 25.0 uM; Keqmtp = 0.71 dimensionless; KicrotC4AcetoacylCoA = 1.6 uM; KmmtpNADMAT = 60.0 uM; KmmtpNADHMAT = 50.0 uM; KmmtpC10AcylCoAMAT = 13.83 uM; sfmtpC14=0.9 dimensionless
C8EnoylCoAMAT => C6AcylCoAMAT + AcetylCoAMAT + NADHMAT; C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, NADtMAT, CoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, C4AcetoacylCoAMAT, C8EnoylCoAMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, NADtMAT, CoAMAT, C6AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, NADHMAT, AcetylCoAMAT, C4AcetoacylCoAMAT, C8EnoylCoAMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C10EnoylCoAMAT, NADtMAT, CoAMAT, C6AcylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, C10AcylCoAMAT, C8AcylCoAMAT, NADHMAT, AcetylCoAMAT, C4AcetoacylCoAMAT sfmtpC8*Vmtp*(C8EnoylCoAMAT*(NADtMAT-NADHMAT)*CoAMAT/(KmmtpC8EnoylCoAMAT*KmmtpNADMAT*KmmtpCoAMAT)-C6AcylCoAMAT*NADHMAT*AcetylCoAMAT/(KmmtpC8EnoylCoAMAT*KmmtpNADMAT*KmmtpCoAMAT*Keqmtp))/((1+C8EnoylCoAMAT/KmmtpC8EnoylCoAMAT+C6AcylCoAMAT/KmmtpC6AcylCoAMAT+C16EnoylCoAMAT/KmmtpC16EnoylCoAMAT+C16AcylCoAMAT/KmmtpC16AcylCoAMAT+C14EnoylCoAMAT/KmmtpC14EnoylCoAMAT+C14AcylCoAMAT/KmmtpC14AcylCoAMAT+C12EnoylCoAMAT/KmmtpC12EnoylCoAMAT+C12AcylCoAMAT/KmmtpC12AcylCoAMAT+C10EnoylCoAMAT/KmmtpC10EnoylCoAMAT+C10AcylCoAMAT/KmmtpC10AcylCoAMAT+C8AcylCoAMAT/KmmtpC8AcylCoAMAT+C4AcetoacylCoAMAT/KicrotC4AcetoacylCoA)*(1+(NADtMAT-NADHMAT)/KmmtpNADMAT+NADHMAT/KmmtpNADHMAT)*(1+CoAMAT/KmmtpCoAMAT+AcetylCoAMAT/KmmtpAcetylCoAMAT)) sfmtpC8=0.34 dimensionless; KmmtpC14EnoylCoAMAT = 25.0 uM; KmmtpC8EnoylCoAMAT = 25.0 uM; KmmtpC16AcylCoAMAT = 13.83 uM; KmmtpCoAMAT = 30.0 uM; KmmtpC16EnoylCoAMAT = 25.0 uM; KmmtpC12EnoylCoAMAT = 25.0 uM; KmmtpAcetylCoAMAT = 30.0 uM; Vmtp = 2.84 uM per min per mgProtein; KmmtpC12AcylCoAMAT = 13.83 uM; KmmtpC8AcylCoAMAT = 13.83 uM; KmmtpC6AcylCoAMAT = 13.83 uM; KmmtpC14AcylCoAMAT = 13.83 uM; KmmtpC10EnoylCoAMAT = 25.0 uM; Keqmtp = 0.71 dimensionless; KicrotC4AcetoacylCoA = 1.6 uM; KmmtpNADMAT = 60.0 uM; KmmtpNADHMAT = 50.0 uM; KmmtpC10AcylCoAMAT = 13.83 uM
AcetylCoAMAT => ; AcetylCoAMAT, AcetylCoAMAT Ksacesink*(AcetylCoAMAT-K1acesink) K1acesink=70.0 uM; Ksacesink=6000000.0 l per min per mgProtein
C16AcylCoAMAT => C16EnoylCoAMAT + FADHMAT; C14AcylCoAMAT, C12AcylCoAMAT, FADtMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, FADtMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, FADHMAT, C16AcylCoAMAT, C14AcylCoAMAT, C12AcylCoAMAT, FADtMAT, C16EnoylCoAMAT, C14EnoylCoAMAT, C12EnoylCoAMAT, FADHMAT sfvlcadC16*Vvlcad*(C16AcylCoAMAT*(FADtMAT-FADHMAT)/(KmvlcadC16AcylCoAMAT*KmvlcadFAD)-C16EnoylCoAMAT*FADHMAT/(KmvlcadC16AcylCoAMAT*KmvlcadFAD*Keqvlcad))/((1+C16AcylCoAMAT/KmvlcadC16AcylCoAMAT+C16EnoylCoAMAT/KmvlcadC16EnoylCoAMAT+C14AcylCoAMAT/KmvlcadC14AcylCoAMAT+C14EnoylCoAMAT/KmvlcadC14EnoylCoAMAT+C12AcylCoAMAT/KmvlcadC12AcylCoAMAT+C12EnoylCoAMAT/KmvlcadC12EnoylCoAMAT)*(1+(FADtMAT-FADHMAT)/KmvlcadFAD+FADHMAT/KmvlcadFADH)) KmvlcadC14AcylCoAMAT = 4.0 uM; KmvlcadC14EnoylCoAMAT = 1.08 uM; KmvlcadFAD = 0.12 uM; KmvlcadFADH = 24.2 uM; KmvlcadC12AcylCoAMAT = 2.7 uM; KmvlcadC12EnoylCoAMAT = 1.08 uM; Vvlcad = 0.008 uM per min per mgProtein; KmvlcadC16EnoylCoAMAT = 1.08 uM; KmvlcadC16AcylCoAMAT = 6.5 uM; sfvlcadC16=1.0 dimensionless; Keqvlcad = 6.0 dimensionless
Curator's comment:
(added: 15 Jan 2014, 10:52:41, updated: 15 Jan 2014, 10:52:41)
The plots in Figures 3a and 3b of the reference paper that corresponds to the standard model is reproduced here. The steady-state flux (vacesink) and concentration of certain entities (CoAMAT and FreeCoA) through variable substrate (Palmityl CoA (C16AcylCoACYT)) concentration from 0 to 200 microM is plotted here. FreeCoA is [CoAMATt]-[CoAMAT]. The model was simulated using Copasi v4.11 (Build 64). The plots were generated using Gnuplot.