On 10/07/2012 12:02 AM, Boaz Shaanan wrote:
> Hi
>
> If you want to calculate the electrostatic properties of your protein/mutants you can use Delphi or APBS. Calculation of the dielectric constants is most challenging. I think that these two programs use some approximations to estimate the variation of dielectric constants between the outside (water with epsilon = 80 and inside with epsilon = 4 or whatever values you use as input) but I'm not sure they output those values.
For, APBS, the epsilon values used can be found in the
.in file generated by pdb2pqr if you use it to generate
the file driving APBS.
However, the variation is taken into account when reporting the
electrostatic potential which you can display using PyMol or
UCSF-chimera. As for the hydrophobicity - there are hydrophobicity
scales around (whether you believe them or not is a different matter)
which you can use to display on the surface, again by Pymol or Chimera
(and probably many other programs).
>
> My 2p/2c thoughts.
>
> Boaz
>
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
>
> E-mail: [log in to unmask]
> Phone: 972-8-647-2220 Skype: boaz.shaanan
> Fax: 972-8-647-2992 or 972-8-646-1710
>
>
>
>
>
> ________________________________________
> From: CCP4 bulletin board [[log in to unmask]] on behalf of Yarrow Madrona [[log in to unmask]]
> Sent: Saturday, October 06, 2012 4:48 PM
> To: [log in to unmask]
> Subject: [ccp4bb] calculating dialectric properties of enzyme active site
>
> Hello CCP4 list readers,
>
> Does anyone know how to calculate the dielectric properties of an enzyme
> active site? I would like to compare the polarity/hydrophobicity of
> similar proteins and different mutants.
>
> Thank you.
>
>
> --
> Yarrow Madrona
>
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697
>
|