Python Workflow for Analysis of Specific Activities and DLS data
Gre2p activity monitored by NADPH absorbance using different enzyme concentrations. Activity is measured after different storage conditions (treatments) and in presence of different amounts of tween. Also analysis of DLS data of homogeneity of Gre2p samples measured before and after these treatments.
A python workflow is used to analyse the data and create a plot of the data. It requires the following directory structure:
./Script_for_S13andS18.py ./Script_for_S22.py ./Script_for_S15.py
and as input:
./SpAc_diff_conditions.CSV ./SpAc_diff_Tween.CSV ./DLS_Z-average_Tween.CSV ./DLS_Z-average_PBSandHEPES.CSV ./DLS_PDI.CSV ./DLS_PDI_BSA_stirr.CSV ./DLS_PDI_BSA_shake.CSV ./DLS_Z-average_BSA_stirr.CSV ./DLS_Z-average_BSA_shake.CSV
SEEK ID: https://fairdomhub.org/sops/484?version=2
Filename:
python_DLSandSpAc_1.1.zip
Format: Zip file
Size: 1.03 MB
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Created: 27th Apr 2021 at 12:06
Last updated: 6th Jul 2021 at 09:01
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Version History
Version 2 (latest) Created 6th Jul 2021 at 07:50 by Gudrun Gygli
Added the csv-files and the scripts for figure S15 and changed the figure names in the existing scripts (Script_forS13andS16, Script_for_S20) to match the numbering of the revised document (Script_forS13andS18, Script_for_S22).
Version 1 (earliest) Created 27th Apr 2021 at 12:06 by Gudrun Gygli
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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 Gre2p activity by following the change in NADPH absorbance at 340 nm for the conversion of different substrates.
Submitter: Gudrun Gygli
Investigation: Workflow for characterization of enzymes under ...
Assays: Kinetic parameters of Gre2p, Selwyn test of Gre2p, Specific activity of Gre2p
Measure homogeneity of an enzyme sample (Gre2p) with DLS (dynamic light scattering).
Homogeneity of the Gre2p samples in KPi Buffer before and after different treatments, including different amounts of tween-20 in the buffer (0.01, 0.1, 1.0%).
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Specific activity of Gre2p measured by following the change in absorbance of NADPH at 340 nm for the conversion of nitrononane-2,8-dione (NDK).
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Homogeneity of the Gre2p samples in HEPES and PBS Buffer before and after different treatments.
Submitter: Gudrun Gygli
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
Homogeneity of the Gre2p samples in KPi Buffer before and after different treatments, including different amounts of BSA in the buffer (7.5 µM and 75 µM).
Submitter: Felix Ott
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Workflow for characterization of enzymes under ...
