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 Mrabet
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]
Ibrahim Moustafa wrote:
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.
Ibrahim
On 10/16/08 12:10 PM, "Nadir T. Mrabet" <[EMAIL PROTECTED]>
wrote:
--
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,
Salt bridges (or ion pairs) can be long-range (up to 7-8 Ang). They obey
Coulomb's law.
In contrast, H-bonds are short-range and are further anisotropic.
For those with general interest in electrostatics, I suggest to go back
to the
1978 paper of Max Perutz:
Electrostatic Effects in Proteins
Science (1978) 201 (4362), 1187-1191.
Nadir Mrabet
Jayashankar wrote:
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]
<mailto:[EMAIL PROTECTED]>> wrote:
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, at far as I understand (based on "Structure and Mechanism in
Protein Science - Alan Fersht), you have a salt bridge when two
groups are making an hydrogen bond that is favored by
electrostatic interaction, electrostatic energies being weak in
water. To quote the author of the book, let say you have the
following equilibrium:
E-NH3+ ------- OH2 + OH2 ------- -O2C-S <==> E-NH3+
------- -O2C-S + H2O ------- H2O
The right-hand side equation would be more "favorable", as the
electrostatic interaction will be more stable than in the
left-hand side where both ions would be in contact with water
molecules.
HTH
Kind regards.
-- Leo --
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The University of Manchester
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