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 these calculations. certainly no theoretical paper
alone "shows" anythign unless tested experimentally -charges are -most
of the time- not located in non-polar environments inside proteins,
they are solvated by protein groups (see eg papers by warshel et al),
such as main chain carbonyls and amides. go through any protein and
see where the "buried" charges are. arc repressor is one of the very
few examples that seem to indicate that charges in proteins are
destabilizing. most of the time you probably cannot replace them with
hydrophobic residues. ...you simply cant put a hydrophobic residue
there because the local environment will be designed for hydrogen
bonding partner where the side chain head group would be (these also
tend to be some sorts of domain interfaces in larger proteins where
you can find more of them). proteins are heterogenous environments, in
this sense. surface salt bridges/ionic networks are quite well known
to be one way of stabilization for thermostable proteins.
tommi
Quoting Jayashankar <[EMAIL PROTECTED]>:
*
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 residues.
previous study had shown that most of the salt bridges are destabilizing
towards proteins
(Z. Hendsch and B. Tidor, 1994, Protein Science, 3, 211-226).
3.Arc repressor gained in stability upon mutation of the buried charged
residues, that form a salt bridge triad, in its core with the hydrophobic
residues.
(Waldburger et al., 1995, Nature Struct. Biol. 2, 122-128).
4.Some had found the salt bridges to be stabilizing
(e.g. S. Marqusee and R. Sauer, 1994, Protein Science 3, 2217-2225; D. Xu,
C. J. Tsai, R. Nussinov, 1997, JMB 265, 68 - 84).*
*5.Majority of salt bridges are formed between the charged residues that are
close in amino acid sequence also.
S. Kumar and R. Nussinov, 1999, J. Mol. Biol. 293, 1241-1255.
*
*6.The fluctuations are due to the variations in location of the ion pairing
residues as well as geometrical orientation of the side chain charged groups
in the ion pair.
S. Kumar and R. Nussinov, 2000, Proteins, 41, 485-497.
*
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Thu, Oct 16, 2008 at 7:39 PM, Ibrahim Moustafa <[EMAIL PROTECTED]>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 --
>> ------------------------------------------------------------
>> Chavas Leonard, Ph.D. @ home
>> Research Associate
>> Marie Curie Actions Fellow
>> ------------------------------------------------------------
>> Faculty of Life Sciences
>> The University of Manchester
>> The Michael Smith Building
>> Oxford Road
>> Manchester Lancashire
>> M13 9PT
>> ------------------------------------------------------------
>> Tel: +44(0)161-275-1586
>> e-mail: [EMAIL PROTECTED]
>> <mailto:[EMAIL PROTECTED]>
>> http://personalpages.manchester.ac.uk/staff/leonard.chavas/
>>
>>
>>
>
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street address: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
Tel. +358-9-191 58903
Fax +358-9-191 59940
