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 that
stabilize certain conformation. If you consult any computational chemistry
paper you won't find any quoted salt-bridges at 8 A distance.
Ibrahim
On 10/16/08 1:58 PM, "Nadir T. Mrabet" <[log in to unmask]>
wrote:
> 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: [log in to unmask]
>
>
>
>
> 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" <[log in to unmask]>
>> 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: [log in to unmask]
>>>
>>>
>>> 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 <[log in to unmask]
>>>> <mailto:[log in to unmask]>> 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: [log in to unmask]
>>>> <mailto:[log in to unmask]>
>>>> http://personalpages.manchester.ac.uk/staff/leonard.chavas/
>>>>
>>>>
>>>>
>>>>
>>
>>
>>
>
>
