Dataset Information

Pritchard2002_glycolysis

ABSTRACT: from: Schemes of fluc control in a model of Saccharomyces cerevisiae glycolysis Pritchard, L and Kell, DB Eur. J. Biochem. 269(2002), 3894-3904. It represents a modified version of Teusink et al. Eur. J. Biochem. 267(2000), 5313-5329. The model is a translation from the GEPASI file encoded by Leighton Pritchard. This version uses the Vmaxes found by the best fit (R1) of Table 1 of the Pritchard and Kell paper and simulates a decrease of external glucose concentration from 100 to 2 mM. To reproduce the values in table 2 of the publication, set GLCo to 50 mM and compute the steady state. 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. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.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.

SUBMITTER: Nicolas Le Novère

PROVIDER: BIOMD0000000172 | BioModels | 2024-09-02

REPOSITORIES: BioModels

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Dataset's files

Source:

			Action	DRS
	BIOMD0000000172?filename=BIOMD0000000172-biopax2.owl	Owl
	BIOMD0000000172?filename=BIOMD0000000172-biopax3.owl	Owl
	BIOMD0000000172?filename=BIOMD0000000172-matlab.m	Other
	BIOMD0000000172?filename=BIOMD0000000172-octave.m	Other
	BIOMD0000000172?filename=BIOMD0000000172.m	Other

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Publications

Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis.

Pritchard Leighton L Kell Douglas B DB

European journal of biochemistry 20020801 16

We used parameter scanning to emulate changes to the limiting rate for steps in a fitted model of glucose-derepressed yeast glycolysis. Three flux-control regimes were observed, two of which were under the dominant control of hexose transport, in accordance with various experimental studies and other model predictions. A third control regime in which phosphofructokinase exerted dominant glycolytic flux control was also found, but it appeared to be physiologically unreachable by this model, and a ...[more]

PMID: 12180966

Similar Datasets

Project description:A systems biology study of two distinct growth phases of Saccharomyces cerevisiae cultures AM Martins, D Camacho, J Shuman, W Sha, P Mendes, V Shulaev, Current Genomics 2004 5:649-663 This is a model of yeast glycolysis and glycerol synthesis for high medium glucose concentration. It was constructed by joining the glycolysis model of Teusink et al. (2000) Eur J Biochem 267, 5313, modified by Pritchard and Kell (2002) Eur. J. Biochem. 269, 3894, with the glycerol synthesis model of Crownright et al. (2002) Appl. Env. Microbiol. 68, 4448. Glycerol transport was added as a first order reaction with parameters that comply with empirical data on internal/external glycerol ratios. Curation notes The model provided by the authors is available from http://www.mcisb.org/resources/models/martins04_original.xml . It contains one error: the kinetic law of glycerol 3-phosphate dehydrogenase has denominator of the form (1+NADH/Kdhap+NAD/Kg3p)*(1+DHAP/Knadh+G3P/Knad) rather than (1+DHAP/Kdhap+G3P/Kg3p)*(1+NADH/Knadh+NAD/Knad). This has now been corrected; steady states of the original model may be resolved by exchanging the order of substrates and products in COPASI . Some other cosmetic changes (e.g minutes to seconds) have also been carried out. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. 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. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. . 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.

Project description:Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Teusink,B et al.: Eur J Biochem 2000 Sep;267(17):5313-29. The model reproduces the steady-state fluxes and metabolite concentrations of the branched model as given in Table 4 of the paper. It is derived from the model on JWS online, but has the ATP consumption in the succinate branch with the same stoichiometrie as in the publication. The model was successfully tested on copasi v.4.4(build 26). For Vmax values, please note that there is a conversion factor of approx. 270 to convert from U/mg-protein as shown in Table 1 of the paper to mmol/(min*L_cytosol). The equilibrium constant for the ADH reaction in the paper is given for the reverse reaction (Keq = 1.45*10 4 ). The value used in this model is for the forward reaction: 1/Keq = 6.9*10 -5 . Vmax parameters values used (in [mM/min] except VmGLT): VmGLT 97.264 mmol/min VmGLK 226.45 VmPGI 339.667 VmPFK 182.903 VmALD 322.258 VmGAPDH_f 1184.52 VmGAPDH_r 6549.68 VmPGK 1306.45 VmPGM 2525.81 VmENO 365.806 VmPYK 1088.71 VmPDC 174.194 VmG3PDH 70.15 The result of the G6P steady state concentration (marked in red) differs slightly from the one given in table 4. of the publication Results for steady state: orig. article this model Fluxes[mM/min] Glucose 88 88 Ethanol 129 129 Glycogen 6 6 Trehalose 4.8 4.8 (G6P flux through trehalose branch) Glycerol 18.2 18.2 Succinate 3.6 3.6 Conc.[mM] G6P 1.07 1.03 F6P 0.11 0.11 F1,6P 0.6 0.6 DHAP 0.74 0.74 3PGA 0.36 0.36 2PGA 0.04 0.04 PEP 0.07 0.07 PYR 8.52 8.52 AcAld 0.17 0.17 ATP 2.51 2.51 ADP 1.29 1.29 AMP 0.3 0.3 NAD 1.55 1.55 NADH 0.04 0.04 Authors of the publication also mentioned a few misprints in the original article: in the kinetic law for ADH : the species a should denote NAD and b Ethanol the last term in the equation should read bpq /( K ib K iq K p ) in the kinetic law for PFK : R = 1 + λ 1 + λ 2 + g r λ 1 λ 2 equation L should read: L = L0*(..) 2 *(..) 2 *(..) 2 not L = L0*(..) 2 *(..) 2 *(..) To make the model easier to curate, the species ATP , ADP and AMP were added. These are calculated via assignment rules from the active phosphate species, P , and the sum of all AXP , SUM_P . 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. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.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.