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Revision as of 05:12, 16 October 2018
CenozoicModeling Saturation Kinetics
Enzyme kinetics is the study of how fast reaction proceeds when influenced by a catalyst. Our project involves a single substrate mechanism where the chemical of concern (substrate) causes the stress pathways within the mammalian system to be activated. The activation of the stress pathways results in the production of eGFP as the product. eGFP production is measured in terms of fluorescence intensity. Therefore, in order to further interpret our results, we used a Michaelis- Menten model to fit our data. The values of the constants obtained from the equation are used to validate the effectiveness of our biosensor.
What do the numbers mean?
The Michaelis Menten equation shown above allows for the calculation of Km ( the Michaelis-Menten constant) and Vm( maximum reaction velocity). Vm tell us the rate of product formation and Km gives us the ratio of the dissociation rate to the association rate. Km is also the corresponding substrate concentration at which the reaction velocity is one-half the maximum reaction velocity. Therefore, a smaller Km implies a greater reaction velocity and vice versa. This Km value also informs us about the binding affinity of the substrate to the enzyme. In the case of our project, the Km value helps us determine the sensitivity range of our promoters.
MATLAB code
To fit the Michaelis-Menten model to our data we used MATLAB. We took advantage of the NLINFIT function in order to extrapolate the values of the parameters Vm and Km as well as their 95% confidence intervals. The MATLAB code takes in the substrate concentration and fluorescence intensity data points and returns the Vm and Km values for the given input.