AMBER Archive (2006)

Subject: Re: AMBER: modeling of ligand concentrations

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Mon Oct 23 2006 - 18:44:46 CDT

Carlos Simmerling wrote:
> the way I learned Pchem, the overall free energy is the
> sum of the standard state contribution and the reaction
> quotient contribution. Your description sounds like the
> latter. Remember that deltaG^zero is the value with the
> concentrations in the standard state and actual deltaG
> depends on this as well as a concentration (activity) correction.
> The fact that free energies are concentration dependent
> doesn't require changing the standard state.
>

But then again, who knows who taught P Chem ! ;-)

For the rest of amberites:

As carlos, tom and dave mentioned, the standard concentration has
NOTHING to do with the concentrations of enzyme, ligand, etc. Those
relate to delta G^0.

Now, the standard concentration comes alive when one recognizes that
truly, equilibrium constants (including binding constants) should have
NO UNITS !

Hint:

What is ln(K) when K has units ?

So, when we say Ki is 10 nM, we are missusing basics P Chem terminology.
Not a problem provided we agree on nomenclature.

Now, the proper way to write equilibrium constant for E+A --> EA is NOT:

K = (EA)/(E)(A) but rather:

K = ((EA)/1M)/((E)/1M)((A)/1M)

for a starndard state of 1 M.

One 'could' change the standard state to something else, but unless you
tell everyone else in the world, the meaning of K is different than usual.

Also: The calculation of standard concentrations is FEP, etc, takes into
account the loss of translational degrees of freedom when you move from
two objects (E + A) into one (EA). This is related in a sense to
something called cratic entropy, and has been discussed in the late 90's
  in some beautiful papers by Mike Gilson and Jan Hermans separately.

With the hope of not having confused the issue more ! ;-)

Adrian

what is missing from this discussion, I believe is that 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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