BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=curation_notes.txthttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=BIOMD0000000042.pdfhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=BIOMD0000000042-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=BIOMD0000000042-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=BIOMD0000000042_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=manifest.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=curation_image.pnghttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=BIOMD0000000042.scihttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=BIOMD0000000042-matlab.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=BIOMD0000000042.sedmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=BIOMD0000000042-octave.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=BIOMD0000000042.cpshttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=BIOMD0000000042.pnghttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=BIOMD0000000042.vcmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=BIOMD0000000042.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=metadata.rdfhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000042?filename=BIOMD0000000042.odeprimary200OKNicolas Le NovèreManually curatedordinary differential equation modelL2V4https://www.ebi.ac.uk/biomodels/BIOMD000000004217029704falseBioModelsSBMLModelsNielsen1998 Glycolysis1998MODEL6622455387K Nielsen, P G Sørensen, F Hynne, H G BusseK Nielsen17029704, We report sustained oscillations in glycolysis conducted in an open system (a continuous-flow, stirred tank reactor; CSTR) with inflow of yeast extract as well as glucose. Depending on the operating conditions, we observe simple or complex periodic oscillations or chaos. We report the response of the system to instantaneous additions of small amounts of several substrates as functions of the amount added and the phase of the addition. We simulate oscillations and perturbations by a kinetic model based on the mechanism of glycolysis in a CSTR. We find that the response to particular perturbations forms an efficient tool for elucidating the mechanism of biochemical oscillations.. 1-2, 72. Department of Chemistry and CATS, H.C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.lenov@ebi.ac.ukEBML-EBIBIOMD0000000042We report sustained oscillations in glycolysis conducted in an open system (a continuous-flow, stirred tank reactor; CSTR) with inflow of yeast extract as well as glucose. Depending on the operating conditions, we observe simple or complex periodic oscillations or chaos. We report the response of the system to instantaneous additions of small amounts of several substrates as functions of the amount added and the phase of the addition. We simulate oscillations and perturbations by a kinetic model based on the mechanism of glycolysis in a CSTR. We find that the response to particular perturbations forms an efficient tool for elucidating the mechanism of biochemical oscillations.A new type of flow reactor (UCSTR) has been developed that uses anisotropic ultrafiltration membranes in a continuous flow stirred tank reactor (CSTR) to facilitate the study of nonlinear enzyme catalyzed reactions. The design allows the study of enzymes with subunit molecular weights > or = 9000 dalton and protein concentrations up to at least 2 mg/ml under flow conditions with a residence time of 3 min or more, in a reactor of volume 1.67 ml. The UCSTR allows continuous potentiometric or spectrophotometric measurement without design change. Calibration of reactor performance was carried out by reproducing pH oscillations in the ferrocyanide-hydrogen peroxide reaction. Experimental verification of oscillatory glycolysis in the UCSTR was carried out with extract of rat skeletal muscle. Input feeds were fructose-6-phosphate and ATP with low concentrations of phosphate as buffer. Oscillations in pH, sustained for over eight hours, were observed. A six-step mechanism, including product activation and substrate inhibition, seven concentration variables, and four enzymes sufficed simulate the pH oscillations observed in the UCSTR.We present an analysis of glycolysis based on experimental findings and an interpretation based on concepts of efficiency, resonance response, and control features available in highly nonlinear reaction kinetics. We begin with a model for the glycolytic mechanism that is comprehensive, includes a large number of known activations and inhibitions of enzymes by metabolites, and couples the phosphofructokinase (PFKase) and the pyruvate kinase (PKase) reactions. The PFKase and PKase reactions and the coupling between them are modeled according to experimental information, but we do not attempt to model the glyceraldehyde-3-phosphate dehydrogenase-3-phosphoglycerate kinase reaction. We use experimental data to obtain the best estimates for the kinetic parameters and test the model by calculating the concentration variations of the intermediate metabolites. We confirm oscillatory behavior and calculate the ATP/ADP ratio and the free-energy dissipation for an extended range of the kinetic parameters as a function of the driving force for the glycolytic pathway, a measure of which is the total adenine nucleotide concentration. We find agreement of the calculated results with experimental findings except for the insufficiently represented reactions. Our model shows that the average ATP/ADP ratio is increased and the average free-energy dissipation is decreased in an oscillatory compared with a steady state mode of operation. The average values of the ATP/ADP ratio and of the free energy dissipation change abruptly past the onset of sustained oscillations.Glycolytic pH oscillations in a flow reactor.Sustained oscillations in glycolysis: an experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations.Oscillations and control features in glycolysis: numerical analysis of a comprehensive model.Nielsen K K, Sørensen P G PG, Hynne F F, Busse H G HGTermonia Y Y, Ross J JHocker C G CG, Epstein I R IR, Kustin K K, Tornheim K KfalseNielsen1998_Glycolysis This model was automatically converted from model BIOMD0000000042 by using libSBML . According to the BioModels Database terms of use , this generated model is not related with model BIOMD0000000042 any more. 2024-08-212024-09-022005-09-13BIOMD0000000042R00771R00299R00756R01070R01015R01061R00658R01518R01512R00200R00224R00754R001272.7.1.25.3.1.92.7.1.114.1.2.135.3.1.11.2.1.122.7.2.35.4.2.14.2.1.112.7.1.404.1.1.11.1.1.712.7.4.3sce00010REACT_1383REACT_1164REACT_1840REACT_1693REACT_587REACT_1400REACT_1771REACT_1911REACT_799REACT_15711702970464548928061224CHEBI:15422CHEBI:16761CHEBI:16027CHEBI:17234CHEBI:20935CHEBI:16905CHEBI:29052CHEBI:15846CHEBI:16908CHEBI:16001CHEBI:18021CHEBI:15361CHEBI:15343CHEBI:16236MODEL6622455387BIOMD0000000042GO:0006096GO:0005737GO:0006754GO:0006172GO:0006735GO:0009435GO:0046323GO:0006002GO:0030388GO:0019683GO:0042867GO:0046187GO:0006068GO:0006196GO:0006001C00002C00008C00020C00293C05345C05378C00118C00003C00004C00236C00074C00022C00084C004694932