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Re: [ccp4bb] Definition of salt bridge |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Definition of salt bridge From: Ibrahim Moustafa I {- dot -} moustafa {- at -} PSU {- dot -} EDU Date: 2008-10-16 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" 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: Nadir.Mrabet@medecine.uhp-nancy.fr > > > 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 >> >> >> 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: Leonard.Chavas@manchester.ac.uk >> >> http://personalpages.manchester.ac.uk/staff/leonard.chavas/ >> >> >> > CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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