Analysis of data from ITC experiments (binding)
Python workflow for the analysis of ITC-BIND, ITC-MIM and ITC-(r)SIM experiments. Organized in a *.zip folder. Requires the following directory structure:
./ITC_analysis.py ./input/BINDING/.apj ./input/BINDING/.csv ./input/KINETICS/.apj ./input/KINETICS/.csv ./scripts/binding_neu.py ./scripts/kinetics_neu.py
And can be executed by running python ITC_analysis.py in the directory. Filenames for the input *.apj and *.csv files are defined in ITC_analysis.py. The output directory is written by the workflow, and output pngs and csvs are organized in a ./output/BINDING or ./output/KINETICS directory
Note: the same workflow is used for the analysis of all data from ITC experiments, but different functions in the workflows are used for analysis of binding or kinetics data.
SEEK ID: https://fairdomhub.org/assays/1457
Experimental assay
Projects: Towards Reproducible Enzyme Modeling
Investigation: Workflow for characterization of enzymes under different reaction conditions
Study: ITC binding experiments
Assay position:
Assay type: Experimental Assay Type
Technology type: Technology Type
Organisms: No organisms
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Created: 27th Apr 2021 at 06:45
Last updated: 5th May 2021 at 12:02
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https://orcid.org/0000-0001-9119-1778Polyglot European Scientist. I thrive working in interdisciplinary environments combining the study of enzyme reactions and mechanisms with bioinformatics, molecular modelling, automated data analysis and data stewardship.
Work of the Gygli group...
Projects: Test Project (dummy), Towards Reproducible Enzyme Modeling
Web page: Not specified
Investigation 1: An experimental workflow to provide detailed information of the molecular mechanisms of enzymes is described. This workflow will help in the application of enzymes in technical processes by providing crucial parameters needed to plan, model and implement biocatalytic processes more efficiently. These parameters are homogeneity of the enzyme sample (HES), kinetic and thermodynamic parameters of enzyme kinetics and binding of reactants to enzymes. The techniques used to measure ...
An experimental workflow to provide detailed information of the molecular mechanisms of enzymes is described. This workflow will help in the application of enzymes in technical processes by providing crucial parameters needed to plan, model and implement biocatalytic processes more efficiently. These parameters are homogeneity of the enzyme sample (HES), kinetic and thermodynamic parameters of enzyme kinetics and binding of reactants to enzymes. The techniques used to measure these properties are ...
Submitter: Gudrun Gygli
Studies: DLS measurements (homogeneity of an enzyme sample), ITC binding experiments, ITC kinetic experiments (enzyme activity), Spectrophotometric Activity Measurements
Assays: Analysis of data from ITC experiments (binding), Analysis of data from ITC experiments (kinetics), Binding of HK to Gre2p (ITC-BIND), Binding of NADP+ to Gre2p in HEPES Buffer (ITC-BIND), Binding of NADP+ to Gre2p in KPi Buffer (ITC-BIND), Binding of NADP+ to Gre2p in PBS Buffer (ITC-BIND), Binding of NADPH to Gre2p in HEPES Buffer (ITC-BIND), Binding of NADPH to Gre2p in KPi Buffer (ITC-BIND), Binding of NADPH to Gre2p in PBS Buffer (ITC-BIND), Binding of NADPH to Gre2p in Tween-KPi Buffer (ITC-BIND), Binding of NDK to Gre2p (ITC-BIND), DLS measurements in 2 buffers, DLS measurements in KPi Buffer and in KPi buffer with Tween added, DLS measurements in KPi buffer with BSA added, Kinetic parameters of Gre2p, Kinetics of the reaction of NDK and NADPH with Gre2p (ITC-MIM) in HEPES ..., Kinetics of the reaction of NDK and NADPH with Gre2p (ITC-MIM) in KPi bu..., Kinetics of the reaction of NDK and NADPH with Gre2p (ITC-MIM) in PBS bu..., Kinetics of the reaction of NDK and NADPH with Gre2p (ITC-MIM) in Tween-..., Kinetics of the reaction of NDK and NADPH with Gre2p (ITC-rSIM) in 3 buf..., Selwyn test of Gre2p, Specific activity of Gre2p
Measure binding of reactants to Gre2p by ITC (isothermal titration calorimetry).
Submitter: Gudrun Gygli
Investigation: Workflow for characterization of enzymes under ...
Assays: Analysis of data from ITC experiments (binding), Binding of HK to Gre2p (ITC-BIND), Binding of NADP+ to Gre2p in HEPES Buffer (ITC-BIND), Binding of NADP+ to Gre2p in KPi Buffer (ITC-BIND), Binding of NADP+ to Gre2p in PBS Buffer (ITC-BIND), Binding of NADPH to Gre2p in HEPES Buffer (ITC-BIND), Binding of NADPH to Gre2p in KPi Buffer (ITC-BIND), Binding of NADPH to Gre2p in PBS Buffer (ITC-BIND), Binding of NADPH to Gre2p in Tween-KPi Buffer (ITC-BIND), Binding of NDK to Gre2p (ITC-BIND)
ITC binding experiment for the binding of (5S,8S)-anti hydroxyketone (HK) to Gre2p. Note that binding was unsuccessful. *.apj file, experiment titrating 1 mM HK.
ITC binding experiment for the binding of (5S,8S)-anti hydroxyketone (HK) to Gre2p. Note that binding was unsuccessful. *.apj file, experiment titrating 200 mM HK.
ITC binding experiment for the binding of (5S,8S)-anti hydroxyketone (HK) to Gre2p. Note that binding was unsuccessful. *.csvfile, experiment titrating 1 mM HK.
ITC binding experiment for the binding of (5S,8S)-anti hydroxyketone (HK) to Gre2p. Note that binding was unsuccessful. *.csv file, experiment titrating 200 mM HK.
ITC binding experiment for the binding of NADPH to Gre2p in 0.1% Tween-20 - KPi buffer (100 mM, pH 7.5) at 25 °C. *.apj file
ITC binding experiment for the binding of NADPH to Gre2p in 0.1% Tween-20 - KPi buffer (100 mM, pH 7.5) at 25 °C. *.csv file
ITC binding experiment for the binding of NADP+ to Gre2p in HEPES buffer (100 mM, pH 7.5) at 25 °C. *.apj file
ITC binding experiment for the binding of nitrononane-2,8-dione (NDK) to Gre2p. Note that binding was unsuccessful. *.apj file, experiment titrating 1 mM NDK.
ITC binding experiment for the binding of nitrononane-2,8-dione (NDK) to Gre2p. Note that binding was unsuccessful. *.apj file, experiment titrating 100 mM NDK.
ITC binding experiment for the binding of NADP+ to Gre2p in HEPES buffer (100 mM, pH 7.5) at 25 °C. *.csv file.
ITC binding experiment for the binding of nitrononane-2,8-dione (NDK) to Gre2p. Note that binding was unsuccessful. *.csv file, experiment titrating 1 mM NDK.
ITC binding experiment for the binding of nitrononane-2,8-dione (NDK) to Gre2p. Note that binding was unsuccessful. *.csv file, experiment titrating 100 mM NDK.
ITC binding experiment for the binding of NADPH to Gre2p in HEPES buffer (100 mM, pH 7.5) at 25 °C. *.apj file
ITC binding experiment for the binding of NADP+ to Gre2p in KPi buffer (100 mM, pH 7.5) at 25 °C. *.apj file
ITC binding experiment for the binding of NADP+ to Gre2p in PBS buffer (1x, pH 7.5) at 25 °C. Note that for successfull fitting, the stoichiometry of binding had to be fixed at 0.85, in agreement with data from the other binding experiments. *.apj file
ITC binding experiment for the binding of NADPH to Gre2p in HEPES buffer (100 mM, pH 7.5) at 25 °C. *.csv file.
ITC binding experiment for the binding of NADPH to Gre2p in PBS buffer (1x, pH 7.5) at 25 °C. *.csv file.
ITC binding experiment for the binding of NADP+ to Gre2p in KPi buffer (100 mM, pH 7.5) at 25 °C. *.csv file.
ITC binding experiment for the binding of NADP+ to Gre2p in PBS buffer (1x, pH 7.5) at 25 °C. Note that for successfull fitting, the stoichiometry of binding had to be fixed at 0.85, in agreement with data from the other binding experiments. *.csv file.
ITC binding experiment for the binding of NADPH to Gre2p in KPi buffer (100 mM, pH 7.5) at 25 °C. *.apj file
Python workflow for the analysis of ITC-BIND, ITC-MIM and ITC-(r)SIM experiments. Organized in a *.zip folder. Requires the following directory structure:
./ITC_analysis.py ./input/BINDING/.apj ./input/BINDING/.csv ./input/KINETICS/.apj ./input/KINETICS/.csv ./scripts/binding_neu.py ./scripts/kinetics_neu.py
And can be executed by running python ITC_analysis.py in the directory. Filenames for the input *.apj and *.csv files are defined in ITC_analysis.py. The output directory is written by ...
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
