Subject: Implicit Solvation

From: [email-masked] (Laurent Chiche)
Date: Thu, 6 Oct 94 07:32:56 +0200

Hi,
A summary was recently posted on the list about
"What people are doing to approximate solvation effects in energy calculations"

Beside references by the Eisenberg and the Honig groups (deliberately ommitted),
few additional references might be cited (although most are included in more
recent reviews):

1	W.C. Still et al. (J. Amer. Chem. Soc 112, 6127-6129, 1990)
2	Yu, Pettitt and Karplus (J. Amer. Chem. Soc. 113, 2425-2434, 1991)
3	Cramer and Truhlar (Science 256, 213-217, 1992)
4	Holm and Sander (J. Mol. Biol. 225, 93-105, 1992)
5	Holm and Sander (Proteins, 14, 213-223, 1992)
6	Schiffer Caldwell Kollman and Stroud (Protein. Sci. 1, 396-400, 1992)
7	Schiffer Caldwell  Stroud and Kollman (Molec. Simul. 10, 121, 1993)

Conclusion of the summary was:

> Finally, when using the "Eisenberg" approach of surface area changes and
> atomic solvation parameters:
>
>        1) It is currently unclear as to what is the most appropriate
>           set of atomic solvation parameters to use for docking
>           or protein folding.
>
>        2) Given the potential benefits of such a calculation there
>           seem to be surprisingly few tests of this method.

Reference 7 above specifically addressed these questions. I would also like to
add that we applied with some success the "Eisenberg approach" of implicit
solvation to NMR based structural studies:
 -Chiche, Gaboriaud, Heitz, Mornon, Castro and Kollman (Proteins, 6, 405-417, 1989)
	"Use of restrained molecular dynamics in water to determine 3D protein structure:
	Prediction of the 3D structure of Trypsin inhibitor EETI II"
 -LeNguyen, Heitz, Chiche, ElHajji and Castro (Protein. Sci. 2, 165-174, 1993)
	"Characterization and 2D NMR study of the stable [9-15, 21-27] 2 disulfide
	intermediate in the folding of the 3 disulfide trypsin inhibitor EETI II"

and that we have a paper in press in which we test the usefulness of this
approach for homology modeling (using atomic solvation params from ref 7 above):
 -Cregut, Liautard and Chiche (to appear in Prot. Engineering, vol 7 no 11, 1994)
	"Homology modeling of annexin I: implicit solvation improves side chain 
	prediction, and combination of evaluation criteria allows recognition of
	different types of conformational errors"

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