Regarding representation of chemicals

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SANKAR MAHESH R

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Aug 16, 2023, 9:36:21 PM8/16/23

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I'm Sankar Mahesh, a PhD student from India working on genome scale modeling.

I'm working on a metabolic pathway. When I add these reactions into the cell, should I ensure their right ionization state at pH 7 or it doesn't matter for the equilibrator calculations?

It will be helpful if someone can clarify this.

Elad Noor

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Aug 19, 2023, 8:05:32 AM8/19/23

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In general, you do not need to care about the protonations at all for the equilibrator calculations. By choosing a specific pH, the software finds the correct protonations for the Gibbs energy calculations (using the "Alberty method"). In fact, the stoichiometry of H+ in the model reactions is ignored even if you set it to a specific value.

The only place where protonations are important is in multi-compartment reactions. I assume that is not relevant in your case, but if it is I'll be happy to explain further.