AMBER Archive (2006)

Subject: Re: AMBER: modeling of ligand concentrations

From: David A. Case (
Date: Tue Oct 24 2006 - 20:56:14 CDT

On Tue, Oct 24, 2006, Thomas Steinbrecher wrote:
> >Just to clarify, say we model the reaction E + A --> EA as single molecular
> >species in the standard state (everything is at 1M concentration).
> >
> >2. We obtain a dG^0 of -7kcal/mol from 1M standard state terms.
> >
> >So, as David says in the above exerpt, if we wanted to compute the free
> >energy change for any other concentrations, how would we do this? Would
> >sombody be willing to provide a simple (hypothetical) example? Say our
> >ligand is 0.1M and our receptor is 0.01M ...
The "..." here is important ---------------- ^. As Thomas has shown, if you
start with these concentrations and assume that the system comes to
equilibrium, you can find all the concentrations. But at equilibrium, dG is
zero, so that doesn't help you much (I presume?)

If you want dG at some other concentration, you have to specify what *all* of
the other concentrations are. Then you can use:

> The free energy change is given by
> dG = dG^0 + RT ln K
> with K = ( [EI] / [E]*[I] )

So, I still suspect that the question needs to be formulated better: if you
are not at equilibrium in terms of concentrations, where are you? (At some
steady state concentration? That would be pretty common in enzyme kinetics.)
Why do you want to know what dG is there (i.e. what are you going to do with
the number once you get it)?


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