Re: [Apbs-users] pH dependent binding energy and individual salt bridge calculations

[Gernot K. <ge...@ch...>]

Hi!

On Wed, 2008-08-06 at 14:04 -0400, Jayita Guhaniyogi wrote:
> I have two questions:
> 1) Is this a valid interpretation (realizing that this is only a
> prediction and I am assuming a static picture presented by the crystal
> structure at the different pHs, which is not going to be the case)? and,
> 
> 2) Is it possible to look at the binding energies of individual salt
> bridge interactions between a given pair of acidic and basic residues at
> the interface and make similar interpretations about their stability at a
> given pH? If so, how? The apbs output file lists individual atomic
> energies during the calculation of electrostatic energies. Can I use these
> to calculate binding energies of individual salt bridges? If so, how? I am
> guessing these aren't simply additive.

For pKA calculations with a focus on salt bridge stability you might
find the following web service interesting:

http://agknapp.chemie.fu-berlin.de/karlsberg

It is calculating pKA's based on electrostatic energies computed using
APBS (however, in addition, it is accounting for the statistic
interactions of titratable groups in the protein based on a Monte Carlo
procedure and the flexibility of hydrogens and salt bridges).

Greetings,
Gernot Kieseritzky