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arXiv · 2110.10419

On the reproducibility of enzyme reactions and kinetic modelling

Gudrun Gygli
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Abstract

Enzyme reactions are highly dependent on reaction conditions. To ensure reproducibility of enzyme reaction parameters, experiments need to be carefully designed and kinetic modelling meticulously executed. Furthermore, to enable the judgement of the quality of enzyme reaction parameters, the experimental conditions, the modelling process as well as the raw data need to be reported comprehensively. By taking these steps, enzyme reaction parameters can be open and FAIR (findable, accessible, interoperable, re-usable) as well as repeatable, replicable and reproducible. This review discusses these issues and provides a practical guide to designing initial rate experiments for the determination of enzyme reaction parameters and gives an open, FAIR and re-editable example of the kinetic modelling of an enzyme reaction. Both the guide and example are scripted with Python in Jupyter Notebooks and are publicly available (https://fairdomhub.org/investigations/483). Finally, the prerequisites of automated data analysis and machine learning algorithms are briefly discussed to provide further motivation for the comprehensive, open and FAIR reporting of enzyme reaction parameters.

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Gudrun Gygli. 2021-10-20. On the reproducibility of enzyme reactions and kinetic modelling. https://arxiv.org/abs/2110.10419

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