Dataset Information

Teusink2000_Glycolysis

ABSTRACT: 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.

SUBMITTER: Nicolas Le Novère

PROVIDER: BIOMD0000000064 | BioModels | 2008-09-16

REPOSITORIES: BioModels

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Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.

Teusink B B Passarge J J Reijenga C A CA Esgalhado E E van der Weijden C C CC Schepper M M Walsh M C MC Bakker B M BM van Dam K K Westerhoff H V HV Snoep J L JL

European journal of biochemistry 20000901 17

This paper examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes. In nongrowing, anaerobic, compressed Saccharomyces cerevisiae the values of the kinetic parameters of most glycolytic enzymes were determined. For the other enzymes appropriate literature values were collected. By inserting these values into a kinetic model for glycolysis, fluxes and metabolites were calculated. Under the same conditions f ...[more]

PMID: 10951190

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Project description:2×10^7 HL60 cells were treated with 10 uM ATRA for 2 and 5 days, and conducted Hi-C to study the chromosomal architecture. Cells were fixed by 1% formaldehyde (v/v) for 15 min at room temperature (RT) with slowly rotation. Cells were lysed by 550 μl lysis buffer (500 μl 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630 and 50 μl protease inhibitors) using a homogenizer, and harvested the chromatin at 5,000 rpm and washed twice. The pellet was added 1% SDS and incubated at 65 oC for 10 min, then quenched by Triton X-100. The chromatin was digested by 600 U MboI (NEB, Ipswich, USA) at 37 oC overnight. The next day, enzymes were inactivated by 10% SDS at 65 oC for 30 min, and the restriction fragment overhangs were filled in using biotin-14-dCTP and Klenow at 37 oC for 45 min, and the ligation was conducted in 7.61 ml ligation mix (745 μl 10% Triton X-100, 745 μl 10x ligation buffer (500 mM Tris-HCl pH 7.5, 100 mM MgCl2, 100 mM DTT), 80 μl 10 mg/ml BSA, 80 μl 100 mM ATP and 5.96 ml water) for 4 h at 16°C. The blunt-end Hi-C ligation was sonicated and pull down by streptavidin beads, then purified by ethanol. Hi-C library was prepared for paired ending sequencing using NEBNext® UltraTM DNA Library Prep Kit for Illuina® (NEB). For regular 3C ligation, after enzymes inactivation, 10 μl 1 U/μl T4 DNA ligase was added to incubate at 16°C overnight. The interaction was detected by qPCR using the specific 3C primers (Table 1) followed by DNA purification. Hi-C was conducted in PE-150. An iterative method for Hi-C mapping with initial length 30bp, if it fails to map uniquely, the next round of mapping for additional 20 bp continued, this procedure lasts until the full read length reaches 150bp. The Hi-C reads were mapped to the human reference genome (assembly GRCh38) using bowtie2 (v2.2.9). The reads mapped to the same restriction fragment, the reads less than 500bp and PCR duplicates were all removed. Hi-C contact maps were normalized using ICE.

Dataset Information

Teusink2000_Glycolysis

Publications

Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.

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