Projects: Simulation Foundries, CML for thermophysical properties of mixtures, Test Project (dummy), Towards Reproducible Enzyme Modeling
Institutions: University of Stuttgart, Karlsruhe Institute of Technology (KIT)
https://orcid.org/0000-0001-9119-1778Expertise: enzyme kinetics, enzymes, Enzymatic reactions, biochemical enzyme characterization, Biochemistry, molecular simulation, molecular modeling, Programming, Bioinformatics, Computational Biology
Tools: Gromacs, Python, Molecular Dynamics, bash, Biochemistry, Bioinformatics, Biochemistry and protein analysis, Enzyme assay, enzyme kinetics, isothermal titration calorimetry, dynamic light scattering, Spectrophotometry
Polyglot 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.
Projects: KOSMOBAC
Institutions: University of Aberdeen
I am postdoc in the group of Prof Ian Booth in Aberdeen working on the biochemical and biophysical characterisation of bacterial channels.
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 ...
Organisms: No organisms
SOPs: SOP for ITC-MIM experiments, SOP for usage of the ITC
Data files: ITC-MIM experiment for the reaction of NADPH an..., ITC-MIM experiment for the reaction of NADPH an...
Snapshots: No snapshots
ITC binding (BIND) experiment to determine the binding parameters of NADPH to Gre2p in 100 mM KPi Buffer with 0.1% Tween-20 added.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Study: ITC binding experiments
Organisms: No organisms
SOPs: SOP for ITC-BIND experiments, SOP for usage of the ITC
Data files: ITC-BIND experiment for NADPH binding to Gre2p ..., ITC-BIND experiment for NADPH binding to Gre2p ...
Snapshots: No snapshots
ITC multiple injection experiment for the reaction of NADPH and NDK with Gre2p in 0.1%Tween-20-KPI buffer (100 mM, pH 7.5) at 25 °C. *.csv file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC multiple injection experiment for the reaction of NADPH and NDK with Gre2p in 0.1%Tween-20-KPI buffer (100 mM, pH 7.5) at 25 °C. *.apj file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC recurrent single injection experiment for the reaction of NADPH and NDK with Gre2p in KPi, PBS and HEPES buffer (100, 1x, 100 mM, respectively, all at 25°C and pH 7.5). In this csv file, the data for the analysis of the both injection peaks is stored. *.csv file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC recurrent single injection experiment for the reaction of NADPH and NDK with Gre2p in KPi, PBS and HEPES buffer (100, 1x, 100 mM, respectively, all at 25°C and pH 7.5). In this apj file, the data for the analysis of the second injection peak is stored. *.apj file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC recurrent single injection experiment for the reaction of NADPH and NDK with Gre2p in KPi, PBS and HEPES buffer (100, 1x, 100 mM, respectively, all at 25°C and pH 7.5). In this apj file, the data for the analysis of the first injection peak is stored. *.apj file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC multiple injection experiment for the reaction of NADPH and NDK with Gre2p in PBS buffer (1x, pH 7.5) at 25 °C. *.csv file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC multiple injection experiment for the reaction of NADPH and NDK with Gre2p in PBS buffer (1x, pH 7.5) at 25 °C. *.apj file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC multiple injection experiment for the reaction of NADPH and NDK with Gre2p in KPI buffer (100 mM, pH 7.5) at 25 °C. *.csv file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC multiple injection experiment for the reaction of NADPH and NDK with Gre2p in KPI buffer (100 mM, pH 7.5) at 25 °C. *.apj file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC multiple injection experiment for the reaction of NADPH and NDK with Gre2p in HEPES buffer (100 mM, pH 7.5) at 25 °C. *.csv file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC multiple injection experiment for the reaction of NADPH and NDK with Gre2p in HEPES buffer (100 mM, pH 7.5) at 25 °C. *.apj file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC binding experiment for the binding of NADP+ to Gre2p in HEPES buffer (100 mM, pH 7.5) at 25 °C. *.csv file.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC binding experiment for the binding of NADP+ to Gre2p in KPi buffer (100 mM, pH 7.5) at 25 °C. *.csv file.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC binding experiment for the binding of NADPH to Gre2p in PBS buffer (1x, pH 7.5) at 25 °C. *.csv file.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC binding experiment for the binding of NADPH to Gre2p in HEPES buffer (100 mM, pH 7.5) at 25 °C. *.csv file.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC binding experiment for the binding of NADPH to Gre2p in KPi buffer (100 mM, pH 7.5) at 25 °C. *.csv file.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC binding experiment for the binding of NADPH to Gre2p in PBS buffer (1x, pH 7.5) at 25 °C. *.apj file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC binding experiment for the binding of NADP+ to Gre2p in KPi buffer (100 mM, pH 7.5) at 25 °C. *.apj file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC binding experiment for the binding of NADPH to Gre2p in KPi buffer (100 mM, pH 7.5) at 25 °C. *.apj file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC binding experiment for the binding of NADP+ to Gre2p in HEPES buffer (100 mM, pH 7.5) at 25 °C. *.apj file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
ITC binding experiment for the binding of NADPH to Gre2p in HEPES buffer (100 mM, pH 7.5) at 25 °C. *.apj file
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
SOP describing how to perform an ITC binding experiment with a MicroCal PEAQ ITC by Malvern. Note: the DOIs from the Chemotion database for the synthesis of HK and NDK are missing in this version beacuse the DOIs do not exist yet (as of 27.04.21)
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
Investigations: Workflow for characterization of enzymes under ...
Studies: ITC binding experiments
Assays: Binding of HK to Gre2p (ITC-BIND), Binding of NADP+ to Gre2p in HEPES Buffer (ITC-..., 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-..., 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 (..., Binding of NDK to Gre2p (ITC-BIND)
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
SOP describing how to perform an ITC (recurrent) single injections experiment with a MicroCal PEAQ ITC by Malvern.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
SOP describing how to perform an ITC multiple injections experiment with a MicroCal PEAQ ITC by Malvern.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
Investigations: Workflow for characterization of enzymes under ...
Studies: ITC kinetic experiments (enzyme activity)
Assays: Kinetics of the reaction of NDK and NADPH with ..., Kinetics of the reaction of NDK and NADPH with ..., Kinetics of the reaction of NDK and NADPH with ..., Kinetics of the reaction of NDK and NADPH with ...
SOP describing the steps for use of the ITC device (MicroCal PEAQ ITC by Malvern).
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Investigations: Workflow for characterization of enzymes under ...
Studies: ITC binding experiments, ITC kinetic experiments (enzyme activity)
Assays: Binding of HK to Gre2p (ITC-BIND), Binding of NADP+ to Gre2p in HEPES Buffer (ITC-..., 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-..., 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 (..., Binding of NDK to Gre2p (ITC-BIND), Kinetics of the reaction of NDK and NADPH with ..., Kinetics of the reaction of NDK and NADPH with ..., Kinetics of the reaction of NDK and NADPH with ..., Kinetics of the reaction of NDK and NADPH with ..., Kinetics of the reaction of NDK and NADPH with ...