All other aspects of how the simulation runs is ready. I am now creating a class in python called "Enzyme", however the following problem is not yet solved:
In BRENDA I have found the Kcat and KM values for ATP and glucose for hexokinase. In this bisubstrate reaction, how can I compute the reaction rate if I know enzyme, ATP and glucose concentrations? The problem I have is that I need to get Vmax from somewhere but for bisubstrate reactions I cannot compute Vmax from Kcat (because there are two).
Is computing Vmax as the enzyme concentration multiplied by the lowest Kcat an option?
Am I making a mistake by using Michaelis-Menten kinetics?
All help is welcome and appreciated :)
kcat is determined from Vmax originally, so you can use the simple formula
Vmax= kcat[E]. Even though there are 2 substrates, there is only one Vmax.
To calculate the initial rate of the reaction at any particular pair of substrate concentrations, you need the rate equation. The proper rate equation to use for a bisubstrate enzyme depends on the kinetic mechanism. (In the case of hexokinase, there are also allosteric effectors to consider.)
I saw an old paper on rat skeletal muscle hexokinaseArticle Kinetic studies with skeletal-muscle hexokinase
which gave the kinetic mechanism as Ordered Bi Bi with ATP binding first. I don't know if this is the right mechanism for the enzyme you are concerned with. If so, the kinetic rate equation for the initial rate in the forward direction is
v = Vmax[A][B]/{KiaKmB+KmA[B]+KmB[A]+[A][B]}
where [A] is [ATP] and [B] is [glucose]. You also need to know the kinetic constants Kia, KmA and KmB to calculate the rate, unless [A]>>KmA and [B]>>KmB. You may have KmA and KmB already, but you still need Kia.
I saw another paper (https://www.jbc.org/article/S0021-9258(19)42887-1/pdf) that gave the kinetic mechanism as Random Bi Bi. The initial rate equations for the two mechanisms are mathematically indistinguishable, however.
If you are not restricted to initial rate conditions, then you need to use the complete rate equation incorporating the products ADP and G6P, and all the kinetic constants associated with them. The equations are shown in the two papers, but it's unlikely you will have all the necessary values to use them unless you or someone else has made a very thorough study of your enzyme.
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