Re: [Apbs-users] dielectric constant value

[Nathan B. <nat...@wu...>]

Short answer:  the choice of dielectric constant is
application-dependent.  My opinion:  if you explicitly include
conformational flexibility (e.g., using several different protein
conformations), then a smaller dielectric coefficient (2-4) is
justified.  If you do not explicitly include flexibility, then a
larger dielectric coefficient (12-20) is more appropriate.

Some relevant literature includes:

Simonson T.  Dielectric relaxation in proteins: Microscopic and
macroscopic models.  International Journal of Quantum Chemistry.  75
(1), 45-57, 1999.=20
http://www3.interscience.wiley.com/cgi-bin/abstract/55001580/ABSTRACT

Roux B, Simonson T.  Implicit solvent models.  Biophysical Chemistry.=20
78 (1-2), 1-20, 1999.  http://dx.doi.org/10.1016/S0301-4622(98)00226-9

Krishtalik LI, Kuznetsov AM, Mertz EL.  Electrostatics of proteins:
Description in terms of two dielectric constants simultaneously.=20
Proteins-Structure Function and Genetics.  28 (2), 174-82, 1997.=20
http://www3.interscience.wiley.com/cgi-bin/abstract/52455/ABSTRACT

Warshel A, Papazyan A.  Electrostatic effects in macromolecules:
Fundamental concepts and practical modeling.  Current Opinion in
Structural Biology.  8 (2), 211-7, 1998.=20
http://dx.doi.org/10.1016/S0959-440X(98)80041-9

Dong F, Vijaykumar M, Zhou HX.  Comparison of calculation and
experiment implicates significant electrostatic contributions to the
binding stability of barnase and barstar.  Biophysical Journal.  85
(1), 49-60, 2003.=20
http://www.biophysj.org/cgi/content/abstract/85/1/49



On 3/27/06, ari...@ch... <ari...@ch...> w=
rote:
> dear apbs users,
>     In  http://apbs.sourceforge.net/doc/tutorial/x78.html,
> it has been written that,
>   "Biomolecular dielectric constants range from 2 (electronic polarizatio=
n
> only) to 20 (implicit side chain relaxation) with the specific value
> dependent on the application."
>      How one can be sure about what is the dielectric constant value.
> While i am generating the apbs input file from PDB2PQR it is giving the
> value of 2. I want to calculate the change in electrostatic solvation
> energy of a big protein due to conformational change of some residue. Can
> someone suggest me some literature also ?
>         Thank you,
>                                arijit
>
>
>
>
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--
Assistant Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/