Tutorial-l Mailing List

From: Olivier Beyens (Olivier.Beyens_at_uantwerpen.be)
Date: Tue Jul 20 2021 - 09:25:51 CDT

Hi everyone,

I have a question regarding the section 1.1 'Theoretical underpinnings' of the tutorial on protein:ligand standard binding free energies:

[cid:39b99bd6-033b-49c4-853a-13f330224731]

[cid:84d2315d-f554-433c-a04e-9d032a3c63f5]

When transforming equation (4) into equation (5), they use [ligand] = N/V_bulk . However I was wondering why one can say that the concentration of the ligand at equilibrium is N/V_bulk, since at equilibrium sometimes one of the ligands is bound to the protein. Thus I would expect the equilibrium concentration of the ligand to be [ligand] = (N - p_bound)/V_bulk. Now when N is large this doesn't really matter, but we apply these equations on a system with only one ligand... So my question is, why are we allowed to say that [ligand] = N/V_bulk at equilibrium?

I have seen this equation being used in many of prof. Roux's papers, however I have always broke my head about this... I hope you can clear a few things up for me!

Kind regards,

Olivier


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