Assays
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Kinetic characterisation and mathematical modelling of KDXD.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Initial rate kinetics
Using Taverna for mining and MATLAB for conversion into specific formats (cytoscape, SBTOOLBOX2)
Submitter: Sebastian Curth
Biological problem addressed: Model Analysis Type
Investigation: Modular Model Building
Study: Reactome Analysis
Kinetic characterisation and mathematical modelling of KGSADH.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Initial rate kinetics
In this experiment we glucose-pulsed an E. faecalis cultures re-suspended in 100 mM MES buffer at pH 6.5. Samples were taken in time to study intra- and extracellular metabolites. These data are used to construct a kinetic model of the catqabolism of E. faecalis
Submitter: Martijn Bekker
Assay type: Metabolomics
Technology type: Progressive Curve Experiment
Investigation: The Attic
In this experiment we glucose-pulsed an L. lactiss cultures re-suspended in 100 mM MES buffer at pH 6.5. Samples were taken in time to study intra- and extracellular metabolites. These data are used to construct a kinetic model of the catabolism of E. L. lactis
Submitter: Martijn Bekker
Assay type: Metabolomics
Technology type: Enzymatic Activity Measurements
Investigation: The Attic
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Srimani et al (2017) Molecular Systems Biology
Submitter: Sebastian Henkel
Biological problem addressed: Model Analysis Type
Investigation: Steady state studies for different oxygen avail...
Submitter: Sebastian Henkel
Biological problem addressed: Model Analysis Type
Investigation: Steady state studies for different oxygen avail...
Kinetic parameters (Km, kcat) of Gre2p measured by following the change in absorbance of NADPH at 340 nm for the conversion of nitrononane-2,8-dione (NDK) or hexane-2,5-dione. Initial rates at different substrate concentrations are measured.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Minireviews about each enzyme in the mitochindrial beta-oxidation model on which the final parameter choices (fixed-parameter model) and parameter sampling distributions (ensemble) were based.
Submitter: Christoff Odendaal
Biological problem addressed: Model Analysis Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model construction
Measurements on Km, Vmax and allosteric activation or inhibition of the main L-lactate dehydrogenase
Submitter: Martijn Bekker
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Investigation of glycolysis and pyruvate branch...
Measurements on Km, Vmax and allosteric activation or inhibition of the heterologously expressed (E. coli) and purifiied main L-lactate dehydrogenase
Submitter: Martijn Bekker
Assay type: Enzymatic Assay
Technology type: Enzymatic Activity Measurements
Investigation: Investigation of glycolysis and pyruvate branch...
Artificial transcription elongation compexes are assembled in vitro using synthetic deoxy-oligonucleotides (representing template and non template DNA strands), radiolabelled RNA (representing nascent transcript) and purified RNA polymerase. After high salt wash the incorrect NTP is added and reaction is allowed to proceed for the various amounts of time. Reaction is stopped by addition of formamide-containing loading solution and the products are resolved on high-percentage denaturing polyacryamide ...
Submitter: Nikolay Zenkin
Assay type: Reactomics
Technology type: Enzymatic Activity Measurements
Investigation: Wetlab approach to transcription fidelity
ITC multiple injection (MIM) experiments to determine the kinetic parameters of NDK (nitrononane-2,8-dione) and NADPH with Gre2p in 100 mM HEPES buffer pH 7.5 Data from ITC recurrent single injection (rSIM) experiments were used to achieve proper fitting of kcat values.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
ITC multiple injection (MIM) experiments to determine the kinetic parameters of NDK (nitrononane-2,8-dione) and NADPH with Gre2p in 100 mM KPi buffer pH 7.5 Data from ITC recurrent single injection (rSIM) experiments were used to achieve proper fitting of kcat values.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
ITC multiple injection (MIM) experiments to determine the kinetic parameters of NDK (nitrononane-2,8-dione) and NADPH with Gre2p in 1x PBS buffer pH 7.5 Data from ITC recurrent single injection (rSIM) experiments were used to achieve proper fitting of kcat values.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
ITC multiple injection (MIM) experiments to determine the kinetic parameters of NDK (nitrononane-2,8-dione) and NADPH with Gre2p in 0.1%Tween-20-100 mM KPi buffer pH 7.5 Data from ITC recurrent single injection (rSIM) experiments were used to achieve proper fitting of kcat values.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
ITC recurrent single injection (rSIM) to determine the kinetic parameters of NDK (nitrononane-2,8-dione) and NADPH with Gre2p in 100 mM KPi buffer, 1x PBS buffer and 100 mM HEPES buffer, all with pH 7.5
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...