I am not sure where this was getting at, but i would just point out to
you that continuum electrostatics (that you refer to) tend to
overestimate the "desolvation" penalties (that is if you assume the
whole protein interior has a dielectric of 2-4. while there may be
other benefits for the
Hi Nader,
By significant, I mean those interactions that withstand the normal
structural fluctuations of the structure. In MD simulation, two ion-pairs at
a distance of 8 A won't stay for long and will disappear early during the
simulation. So, they cannot be considered as non-bonded interactions
*
Dear Francisco,
1.Transfer of a salt bridge from water to nonpolar environment costs ~10 -
16 kcal/mol (B. Honig and W. L. Hubell, 1984, PNAS 81, 5412-5416).
2.The energy penalty paid due to the desolvation of the charged residues may
not be recovered by favorable interaction among the charged
The problem lies with your definition of "significant".
If it is non null, then any interaction is significant (dual-pan balance
concept).
Coulomb's energy is a function of 1/r^2, therefore at 8 Angs, it is
still 15% of Emax.
Even H-bonds are sometimes considered relevant up to 5 Angs.
Nadir M
Yes, it is electrostatic interaction. But when searching for a salt-bridge
in a protein structure it won't be considered a significant non-bonded
interactions at 8 A distance. Also, the electrostatic interaction extends
beyond 8 A. For a significant interaction the distance need to be < 8A.
Ibra
--
Pr. Nadir T. Mrabet
Cellular & Molecular Biochemistry
INSERM U-724
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
Fax: +33 (0)3.83.68.32.79
E-mail: [EMAIL PROTECTED]
Hi,
You can find more information about salt-bridges in the following
references:
1) Ion-pairs in Proteins. JMB, 168, 867-885 (1983) - Thornton
2) Investigation of Salt Bridge Stability in a Generalized Born solvent
model. JCTC, 2, 115-127 (2006) - Carlos Simmerling
3) Evaluation of Salt Bri
Dear Fransico,
*Salt bridges are close range electrostatic interaction which depend on
conformer population.
*S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Thu, Oct 16, 2008 at 8:21 AM, Chavas Leo <[EMAIL PROTECTED]> wrote:
> Dear Franci
Dear Francisco --
On 15 Oct 2008, at 17:05, Francisco J. Enguita wrote:
how
can you define a salt-bridge within a protein structure ?
According to Wikipedia:
a salt bridge in proteins is "a relatively weak ionic bond between
positively and negatively charged side-chains of proteins."
Now,
Dear All
I've got some comments from a recent paper review about salt bridges.
I would like to ask a very basic question about protein structure : how
can you define a salt-bridge within a protein structure ?.
Thanks. All the best.
Francisco
--
-
Fran
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