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Re: WSN: free energies calculstions (fwd)

Sender: stoutepf@chemsci1.es.dupont.com (Pieter Stouten)
Subject: Re: WSN: free energies calculstions

Hi Rafael,

>        I would like some references which calculate or measure the free
>energy change (DG) in transfering an alanine or glycine from water to a
>nonpolar solvent and the free energy change for the transfer of a valine
>from the same nonpolar solvent to water, all this to have an idea (quite
>approximated) about the ratio between the DG of a hydrogen bond and the
>DG of a hidrophobic interaction.
>        I know that the data I'm asking for is not enough to adress my
>problem but it may be seen as a first aproximation.
>
If you could be more specific about your ultimate goal, I could address the
issue more precisely. Hans Boehm has derived a scoring function (= free
energy function) for estimating the hydrophobic and hydrogen bond
contributions of protein/ligand interactions on the basis of experimental
binding constants of protein/ligand complexes.

TI   THE DEVELOPMENT OF A SIMPLE EMPIRICAL SCORING FUNCTION TO
     ESTIMATE THE BINDING CONSTANT FOR A PROTEIN LIGAND COMPLEX
     OF KNOWN 3-DIMENSIONAL STRUCTURE
AU   BOHM H J [his name may be spelled more correctly as BOEHM]
SO   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, (JUN 1994)
     Vol. 8, No. 3, pp. 243-256. ISSN: 0920-654X.

As to your question about transferring amino acids from water to an apolar
solvent, I would not be surprised if the equilibrium is vastly on the
aqueous side. I know that unblocked amino acids cannot be detected in the
vapour above an aqueous solution, the reason being that the stabilisation
of the zwitterionic form in water is very large. If you are interested in
the relative contributions of hydrogen bonding and the hydrophobic effect
(I would not use the misnomer hydrophobic interaction), I would use data on
blocked amino acids (or peptides) or on sidechain analogues. We have used
the latter to develop an effective solvation term.

TI   AN EFFECTIVE SOLVATION TERM BASED ON ATOMIC OCCUPANCIES FOR USE IN
     PROTEIN SIMULATIONS
AU   STOUTEN P F W; FROMMEL C; NAKAMURA H; SANDER C
SO   MOLECULAR SIMULATION, (1993) Vol. 10, No. 2-6, pp. 97. ISSN: 0892-7022.

I can give you references to other papers with experimental and/or
calculated data in them. Please let me know if you want those.

Hope this helps. Cheers, Pieter.


Pieter Stouten, Senior Research Scientist    ||
Computer Aided Drug Design Group             ||
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