* 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/ > >> > >> > >> > > >
