AMBER Archive (2009)

Subject: Re: [AMBER] Ki and G

From: steinbrt_at_rci.rutgers.edu
Date: Mon Sep 14 2009 - 15:09:55 CDT

Hi,

slightly off-topic, regarding the free energy/enthalpy thing, this seems
to me a naming difference in German and American science education.

I learned in Physical Chem. 101 that there is a *free* enthalpy G = H - TS
into which entropy and enthalpy go and a free energy A (or F) = U - TS
comprising internal energy and entropy, while the enthalpy is just the
internal energy corrected for constant pressure H = U + pV and therefore G
= A + pV

in an american textbook I guess you find G denoted as the Gibbs free
*energy* and A as the Helholtz (?) free energy, so sorry if the name
enthalpy was confusing.

This need not concern ourselves much, because the only meaningful quantity
in ligand binding is G (be it called free enthalpy or energy) because
cells (usually) live at constant pressure and more important, experiments
are done at constant pressure. Dave is right of course that in nearly
incompressible solid/liquid states one can normally assume G=F, unless we
change the volume of the system a lot.

> But OK this is not so important, I think that much more important and
> little surprising is the fact, that binding constant,
> (which is the experimental measure of the strength of the inter-molecular
> interaction) is related only to enthalpic part (dH)
> of the free energy of binding and do not reflect whole free energy of
> binding (dH-TdS).

no, sorry if I gave that impression, the binding constant is absolutely
connected to the entropic (and enthalpic) parts.

> Is there any experimental (common if possible) quantity which could be
> connected
> (by some mathematical formula) with whole FREE ENERGY OF BINDING (dH-TdS)
> and so
> could be used to check the accuracy of the whole binding energy
> calculation ? or

If someone publishes a binding constant Kb that is directly connected to
the free energy you calculate dG = - RT ln (Kb). But as stated before, be
sure that that is really what the experimentalists measured, as many
things are called binding constants without strictly being that.

Regards,

Thomas

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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