You can get the equilibrium constant directly from the standard free energy
of binding using basic thermodynamics. The potential of mean force will
give you the energy difference between two states along a reaction
coordinate averaged over the other degrees of freedom of the system. This
is a large part of the free energy, but don't forget that standard free
energies and equilibrium constants are dependent on a pre-defined "standard
state," typically 1 M or 1 atm/100bar in classical texts. The entropic
component, which you can consider to be the work necessary to bring a ligand
molecule in a given concentration into contact with the receptor molecule of
another concentration, is not captured by the PMF. Obviously this work is
dependent on that concentration, and is quite difficult to explicitly
calculate as I understand.
As reference, see the article
Zhou, H. & Gilson, M.K. Theory of Free Energy and Entropy in Noncovalent
Binding. Chemical Reviews 109, 4092-4107 (2009).
Hope this helps,
Jason
On Mon, Aug 30, 2010 at 10:44 AM, Catein Catherine
<askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
>
>
>
> How to calculate the equilibrium constant of a protein-drug binding
> reaction? Can I extract information from a potential of mean force plot?
>
>
>
> Best regards,
>
>
>
> Catherine
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Aug 30 2010 - 09:30:03 PDT
