Kinetic data from different acetoacetyl-CoA reductases

These folders contain experimental records, calculation datasheets and scripts to simulate or find best-fitted kinetic parameters from certain enzymatically catalyzed reactions. These reactions were catalyzed by four engineered enzymes derived from the acetoacetyl-CoA reductase encoded by the phaB1 gene from Cupriavidus necator. The DNA and amino acid sequences of these enzymes are provided. It is also provided the DNA sequence map of the vector where the amino acid encoding sequences for these engineered enzymes were inserted. Inside the folder named "kinetic data" it is also possible to find a TXT file with a detailed description of the content. The experimental conditions of the enzymatic assays is carefully explained. Briefly, this folder contains (1) the raw experimental data recorded with the software Gen 5 (Biotek). (2) It is also possible to find Microsoft Excel datasheets with the records of raw absorbance in time together with initial substrates, initial enzyme and product concentrations in time (reaction progress curves). Most of these progress curves were analyzed with the software DYNAFIT (Biokin) to obtain the kinetic parameters. The progress curves highlighted in red in the Microsoft Excel files were not considered for the statistical analysis due to experimental errors. The progress curves highlighted in yellow in the Microsoft Excel files were considered after the elimination of some outlier points. (3) Scripts enabling two kind of statistical analyses with DYNAFIT were included: scripts to make model discrimination analyses of the different reaction progress curves obtained in every single experiment, and scripts to calculate the confidence intervals for the kinetic parameters using a Monte Carlo approach. We included the scripting manual of DYNAFIT to understand the synthaxis of these scripts .(4) It is included two MATLAB scripts to make a comparison between the kinetic parameters obtained using the Michaelis-Menten model and the true kinetic parameters of a BiBi reversible reaction. (5) Finally, we included DYNAFIT, MATLAB and Microsoft Excel files enabling the calculation of the relative use of NADH over NADPH by one of the engineered enzymes, and also to calculate the metabolic flux capacity of this enzyme.