In Simbiology, how to graphically represent an enzyme production and its activity simultaneously?

my serine recombinase s expressed on a plasmid. its substrate (dna sequence flanked by it two recombinase attachment site) is on the same plasmid.

So, enzyme is being produced gradually with fixed amount of substrate.

aas bxb1 activity is embedded in the flipping reaction pointing a link between bxb1 species and flipping reaction is with no effect.

How could I account for increasing amount of bxb1 concentration in the cell? i .e How do I link bxb1 production to its Michaelis–Menten kinetics represented by flipping reaction?

Answer 1

[Jeremy Huard]

Hi Hassan,

let me try and summarize to make sure I understood your question correctly: you defined the 'flipping' reaction with the built-in Michaelis-Menten kinetics and defined bxb1 as both reactant and product of this reaction. While the resulting graph shows a link between bxb1 and the reaction, its reaction rate is not influenced by bxb1. Is this correct?

If this is the case, there are several ways to achieve what you are asking for:

1. Vm (or Vmax) is defined as the total enzyme concentration multiplied by the catalytic rate constant (kcat) of the enzyme-substrate complex dissociating to give free enzyme and product. So, you could define a repeated assignment such as Vm = kcat*bxb1.
2. You could also edit the reaction rate of the 'flipping' reaction directly by multiplying by bxb1, making sure that all units are consistent. Your reaction rate could look like this: kcat*bxb1*unflipped/(Km+unflipped)
3. You could split the Michaelis-Menten into its set of elementary reactions. But this would add parameters to your model and is probably not what you want.

I would recommend to try 1 or 2. You can also keep bxb1 defined as both reactant and product. This will help you visualize the reaction dependency on bxb1.

Best regards,

Jérémy

[Hassan Hijazi]

yes, your summary is 100 % correct. I am very grateful for your sharp insights.