Towards Reproducible Enzyme Modeling

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 these properties are dynamic light scattering (DLS), UV-Vis spectrophotometry and isothermal titration calorimetry (ITC) respectively. The workflow is standardized by the use of SOPs and python-scripted data analysis. We have used the NADPH-dependent alcohol dehydrogenase Gre2p as a challenging enzyme to demonstrate the power of this workflow. Our work highlights the utility for combined binding and kinetic studies for such complex multi-substrate reactions and the importance of sample quality control during experiments.

Investigation 2: A practical guide to designing initial rate experiments for the determination of enzyme reaction parameters and an example of reproducible raw data with the associated modelling process is given. A Jupyter Notebook is provided to assist in the choice of substrate concntrations in initial rate experiments to obtain "gold-standard" kinetic fits. This Notebook also shows how noise in the raw data affects the linear fit, and how measuring more datapoints can circumvent problems arising from very noisy raw data. A Jupyter Notebook is provided with example data from investigation 1 to reproducibly model enzyme reaction parameters.

Programme: Gygli Group


Funding codes:
  • Funded by the Federal Ministry of Education and Research (BMBF) and the Baden-Württemberg Ministry of Science as part of the Excellence Strategy of the German Federal and State Governments. The work was also supported through the Helmholtz program “Materials Systems Engineering“ under the topic “Adaptive and Bioinstructive Materials Systems”.

Public web page: Not specified

Organisms: No Organisms specified

FAIRDOM PALs: No PALs for this Project

Project start date: 1st Nov 2019

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