On the reproducibility of enzyme reactions and kinetic modelling

Work of the Gygli group...

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 ...

This study briefly shows how a Progress Curve (Time-Course) Analysis can look like.

This study briefly shows how a Selwyn test can be performed.

TBD

This study explores how to design an initial rate experiment. It starts with a "zero-round" experiment, which is used to design a "first-round" experiment, which then leads to the design of a "gold-round" experiment.

This Jupyter Notebook assists you in the design of initial rate experiments.

For help on installing the classical Jupyter Notebook, see here: https://jupyter.org/install

For documentation about Juypter Notebooks, see here: https://jupyter-notebook.readthedocs.io/en/stable/

There are multiple tutorials online that help you to learn how to use a Jupyter notebook.

The notebook is provided as an .ipynb and as a .pdf file.

The plots the script generates with the default values are also given as .png ...

This Jupyter Notebook assists you in the analysis of initial rate experiments.

For help on installing the classical Jupyter Notebook, see here: https://jupyter.org/install

For documentation about Juypter Notebooks, see here: https://jupyter-notebook.readthedocs.io/en/stable/

There are multiple tutorials online that help you to learn how to use a Jupyter notebook.

The notebook is provided as an .ipynb and as a .pdf file. The plots the script generates with the default input data are also given as ...

This Jupyter Notebook assists you in understanding how a Selwyn Test works.

For help on installing the classical Jupyter Notebook, see here: https://jupyter.org/install

For documentation about Juypter Notebooks, see here: https://jupyter-notebook.readthedocs.io/en/stable/

There are multiple tutorials online that help you to learn how to use a Jupyter notebook.

The notebook is provided as an .ipynb and as a .pdf file.

The plots the script generates with the default values are also given as .png ...

This Jupyter Notebook assists you in understanding how a progress curve experiment can look like.

For help on installing the classical Jupyter Notebook, see here: https://jupyter.org/install

For documentation about Juypter Notebooks, see here: https://jupyter-notebook.readthedocs.io/en/stable/

There are multiple tutorials online that help you to learn how to use a Jupyter notebook.

The notebook is provided as an .ipynb and as a .pdf file.

The plots the script generates with the default values are ...

Badly chosen substrate concentrations for an intital rate experiment give data that makes it difficult to fit with a kinetic model and judge the quality of the fit.

Well chosen substrate concentrations for an intital rate experiment give data that makes it easy to fit with a kinetic model and judge the quality of the fit and use it as a basis for the final gold-round experiment.

Very well chosen substrate concentrations for an intital rate experiment give data that makes it very easy to fit with a kinetic model and judge the quality of the fit.

An initial choice of 5 widely spaced substrates enables a first, rough estimate of Km to inform the design of first-round experiments.

This is the Jupyter Notebook to allow editing and working with the code. It is a simple example of how a Selwyn test can look like if it is passed (1.) or failed (2.).

This is the pdf of the Jupyter Notebook to allow looking at the notebook without installing anything. It is a simple example of how a Selwyn test can look like if it is passed (1.) or failed (2.).

This is the Jupyter Notebook to allow editing and working with the code. It is a simple example of how a progress curve experiment can look like.

This is the pdf of the Jupyter Notebook to allow looking at the notebook without installing anything. It is a simple example of how a progress curve experiment can look like.

This is the pdf of the Jupyter Notebook to allow looking at the notebook without installing anything.

NOTE THAT this pdf may be mangled when viewed on FAIRDOMHub, but should look fine when downloaded.

This is a zip file containing all the files and folders needed to analyse raw data, fit initial rates and create a "Michaelis-Menten plot". Instructions on usage are added in the notebook.

This is the Jupyter Notebook to allow editing and working with the code.

Design an initial rate experiment in four steps

This script aims to help you design high-quality initial rate experiments. It uses the Michaelis-Menten equation to simulate data for an enzyme with unknown enzyme reaction parameters. Four steps are needed:

1. Estimate the enzyme reaction parameters

Input: estimates of Km and vmax

and indicate the enzyme concentration concentration you are planning to use. If you have no ...

This is the pdf of the Jupyter Notebook to allow looking at the notebook without installing anything.

Design an initial rate experiment in four steps

This script aims to help you design high-quality initial rate experiments. It uses the Michaelis-Menten equation to simulate data for an enzyme with unknown enzyme reaction parameters. Four steps are needed: 1. Estimate the enzyme reaction parameters

Input: estimates of Km and vmax

and indicate the enzyme concentration concentration you are planning ...