Design an initial rate experiment (pdf)

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 to use. If you have no estimates to give, try the experiment with the suggested initial values. 2. "Zero-round" experiment

Input: estimates from 1. and 5 broadly spaced substrate concentrations. Output: fake Michaelis-Menten plot for these parameters to obtain an intial first guess of Km

"First-round" experiment

Input: estimates from 1. and 10 better spaced substrate concentrations to obtain an intial first guess of Km. Output: fake Michaelis-Menten plot for these parameters to obtain a better guess of Km

"Gold-round" experiment

Input: estimates from 1. and 10 perfectly spaced substrate concentrations to obtain an intial first guess of Km. Output: fake Michaelis-Menten plot for these parameters to obtain Km and vmax values.

This notebook only requires your input for the variables (e.g. Km, vmax, S0 and others). You can run the notebook with your parameters and see how they influence the plots, and then keep modifying until oyu get an experimental design that gives you high-quality data.