Subject: Dielectric Constant of 4

From: James Robinson <[email-masked]>
Date: Tue, 26 Nov 2002 10:36:11 -0000

When building homology models of proteins, is there a particular reason why force-field dielectric constants are set to 4. Does this apply just modelling GPCR models or to a wide range of enzymes and proteins?

Thanks in advance.

James

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From: Mikael Johansson <[email-masked]>
Date: Tue, 26 Nov 2002 17:35:55 +0200 (EET)

Hello James and All!

On Tue, 26 Nov 2002, James Robinson wrote:

> When building homology models of proteins, is there a particular reason
> why force-field dielectric constants are set to 4. Does this apply just
> modelling GPCR models or to a wide range of enzymes and proteins?

I guess the epsilon=4 convention has arisen as a reasonable guess for the
dielectric constant in a protein environment. It is probably very hard to
make reliable measurements of epsilon in a protein, but epsilon=4 should
not be ridiculously wrong. Lacking a good reason for not using epsilon=4
makes it a good "standard".

The topic is discussed for example in
T. Simonson, D. Perahia, Proc. Natl. Acad. Sci. USA 92 (1995) 1082-1086

Have a nice day,
    Mikael J.
    http://www.helsinki.fi/~mpjohans/

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From: Eric Bennett <[email-masked]>
Date: Tue, 26 Nov 2002 12:25:04 -0500

> T. Simonson, D. Perahia, Proc. Natl. Acad. Sci. USA 92 (1995) 1082-1086

The history of this may in part extend back to older "empirical" modeling
studies like the following, in which epsilon=4 (distance-dependent) and
epsilon=2 (constant) were found to give better agreement with a high
resolution crystal structure:

M. Whitlow and M. M. Teeter, J. Am. Chem. Soc. 108 (1986) 7163-7172

-- 
Eric Bennett ( [email-masked] ; http://www.pobox.com/~ericb )

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From: Rick Venable <[email-masked]>
Date: Tue, 26 Nov 2002 12:28:43 -0500

> > T. Simonson, D. Perahia, Proc. Natl. Acad. Sci. USA 92 (1995) 1082-1086

A note on the distance-dependent dielectric: it's not epsilon=4 (just
another fixed value), but epsilon=r, i.e. the dielectric is the distance
between a pair of atoms when computing the electrostatic energy from the
standard Coulomb expression.  A computational advantage for this was
that one could use r**2 to compute the energy for an atom pair, and
avoid taking a square root.

> M. Whitlow and M. M. Teeter, J. Am. Chem. Soc. 108 (1986) 7163-7172

=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   [email-masked]
ALT email:  [email-masked]
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=

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From: Eric Bennett <[email-masked]>
Date: Tue, 26 Nov 2002 13:40:29 -0500

> avoid taking a square root.

You can still use a scale factor with a distance-dependent dielectric.  So
my original email had a typo, but the correction is that E=4r (rather than
E=r or E=4).  Of course you could do E=r or E=2r etc. but the paper I was
citing favored E=4r (distance dependent with scale factor) or E=2
(constant).

In any event, the take home message about the historical origins of how E
is chosen are the same.