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 Bridge structure and energetics in peptides. JCTC, 4,
2008 (2008) - Carlos Simmerling
Salt bridge can be defined as the interaction involving charged groups in
the protein. You¹ll find the cutoff distance to define the salt bridge in a
protein structure varies, but definitely > 3.5 A (used for H-bonds). Using a
cutoff distance of 4.0 A might be too strict and 6.0 A would be too
generous. Something in-between like 4.5 A sounds reasonable.
The energy of Salt-bridge varies depending on the medium (whether buried
or external). For buried salt bridge the energy can be as high as 30 kJ/mol
(compare to H-bonding of 2 6 kJ/mole).
It should be mentioned that Petsko in his ³Protein Structure and Function²
made a distinction between long-range electrostatic interaction between
charged groups and the salt-bridge. He considered the salt bridge as a
strong H-bond between two charged groups (cutoff < 3.5 A, typical distance
2.8 A).
But in most of the papers (computational chemistry papers) you will find
the salt bridge defined as mentioned above with variable cutoff distance.
HTH,
Ibrahim
On 10/16/08 10:39 AM, "Jayashankar" <[EMAIL PROTECTED]> 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]> 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]
>> http://personalpages.manchester.ac.uk/staff/leonard.chavas/
>>
>>
>>
>
>
