AMBER Archive (2009)

Subject: Re: [AMBER] Ki and G

From: Marek Maly (marek.maly_at_ujep.cz)
Date: Mon Sep 14 2009 - 13:41:33 CDT

Dear prof. Case,

regarding to terminology I have never saw label dA for
free energy of binding, I saw always dG and the letter G is here connected
probably with the specification GIBBS free energy - please see:

http://en.wikipedia.org/wiki/Thermodynamic_free_energy

Label A is rather used for Helmholtz free energy.

Also in Amber MM-PBSA tutorial

http://ambermd.org/tutorials/advanced/tutorial3/

is used dG for free energy of binding.

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).

I don't know how much is water compressibility important regarding to TdS
part of
free energy of binding between two molecules. If I am not wrong TdS is
connected
with change in degrees of freedom (usually reduction) caused by
complexation.
So I assume that important role here have for example flexibility of
molecular structure, strength of the interaction etc.
but OK I am not an expert on this field ...

But anyway my last, logic and principal question now is:

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
the only one possible check is through direct experimentally measured
values of the
free energy of binding (for example using calorimetry approach), which is
unfortunately
not so common/available like for example binding constant ?

Thanks in advance for this final answer !

      Best regards,

            Marek

Dne Mon, 14 Sep 2009 19:23:49 +0200 case <case_at_biomaps.rutgers.edu>
napsal/-a:

> On Mon, Sep 14, 2009, Marek Maly wrote:
>
>> Thomas is explicitly speaking about free ENTHALPY of binding, although
>> Bill is asking about relationship of the total free ENERGY of binding
>
> Strictly speaking (which is what Thomas was doing), G is "free enthalpy"
> and A is "free energy".
>
> However, widely in the literature, the term "free energy" is used to
> mean either G or A (where the context is used to make the distinction),
> and
> the term "free enthalpy" is much less commonly used. Note that in nearly
> incompressible liquids like water, G and A are almost the same, which is
> why
> "free energy" can often be used to refer to either one of these.
>
> Don't confuse, however free enthalphy (G) with enthalpy (H).
>
> ...hope this helps...dac
>
>
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