DataEntryID 51
    General information
      Manuscript title: Dynamic simulation of an in vitro multi-enzyme system.
      PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/17239859
      Journal: FEBS Letters
      Year: 2007
      Authors: Nobuyoshi Ishii, Yoshihiro Suga, Akiko Hagiya, Hisami Watanabe, Hirotada Mori, Masataka Yoshino, Masaru Tomita
      Affiliations: Institute for Advanced Biosciences, Keio University, Japan
      Keywords: dynamic simulation, enzyme kinetics, metabolism, glycolysis, in vitro
      Full text article: https://kimosys.org/rails/active_storage/blobs/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbThFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--b8e3128d37c561482ee23924cd4a52c3647a6ff8/Ishii_2007.pdf
      Project name: not specified

    Experiment description
      Organism: Escherichia coli
      Strain: K-12 AG1
      Data type: time-series data of metabolites
      Data units: mM
      Execution date: not specified

    Experimental details
      Temperature (°C): 37.0
      pH: not specified
      Carbon source: glucose
      Culture mode: batch
      Process condition: aerobic
      Dilution rate (h⁻¹): —
      Working volume: 0.2 L
      Biomass concentration (g/L): not specified
      Medium composition: LB medium supplemented with 50 µg/ml chloramphenicol to OD600=0.5
      General protocol information: Sampling Method: Samples were obtained 2 h after addition of 0.1 mM isopropyl-b-D-thiogalactopyranoside (IPTG); Quenching: cells were collected by centrifugation (6000 r.p.m., 5 min at 4 ºC) and resuspended in 10 ml of cold buffer I [50 mM sodium phosphate (pH 7.0), 200 mM NaCl, Protease inhibitor (Complete Mini EDTA-Free, Roche Diagnostics, Basel, Switzerland)].; Extraction list: sonication; Analysis list: enzymatic;
      Methods description: Measurement of metabolite concentrations - A sample was added to 100 mM MOPS buffer (pH 7.2) containing 0.1 mM NADH, 20 mM MgCl2, 5 mM ATP, and 2 mM DTT (I), and maintained at 37 ºC. Then, 1.8 U/ml ALD, 31 U/ml G3PDH, and 90 U/ml TIM (II), 3 U/ml PfkA (III), 18 U/ml Pgi (IV), and 10 U/ml Glk (V) were added sequentially, and A340 was recorded at each step. Concentrations of fructose-1,6-diphosphate (FDP), F6P, G6P, and glucose were calculated from the difference in A340 between I and II, II and III, III and IV, and IV and V, respectively. The FDP concentration of each sample was calibrated by the measured value of a known concentration standard solution of FDP treated using the same procedure employed for sample preparation.
      Data file: http://kimosys.org/repository/51/download?parameter=1134; 
      Alternative formats: http://kimosys.org/repository/51/attached_files/27/download; 

    Submission and curation
      Entered by: Administrator KiMoSys
      Created: 2013-05-13 14:45:37 UTC
      Updated: 2020-04-24 16:10:31 UTC
      Version: 0
      Status: (reviewed) 2013-12-06 17:17:38 UTC
      Views: 264
      Downloads: 60