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Thank you Gert - very clear explanation.. Eleanor On 16 July 2018 at 13:31, Gert Vriend <[log in to unmask]> wrote: > Dear Eleanor, > > Salt bridges are a compromise between entropy and enthalpy. If, say, an > Asp and an Arg side chain are a bit restricted in their freedom and the > charges are close, enthalpy wins, and if they are very exposed, and not > close at all, entropy wins. The enthalpic gain upon protein folding from > obtaining one salt bridge has been given many values in the literature, but > in practice boils down to about 1 kCal/Mole. The enthalpic contribution is > a bit higher than 1kcal/Mole when the positive and negative charges are > very close to each other (in which case you loose entropy upon folding). > Most salt bridges are at the surface where they continuously compromise > between entropy and enthalpy. So, they move around, but most of the time > the charges are close together, and that is why you can see them with Xray. > When the two charged groups come close to each other there are always > certain local conformations that are preferred over others. Those > (sometimes multiple) locally preferred conformations we see in Xray if we > have good crystals. It does not matter, however, how many local > conformations we observe. It is just one salt bridge, and its energetic > contribution to protein folding remains (very roughly, and this is > practical experience for which no good theory exists) about 1kCal/Mole. > > Gert > > On 11-7-2018 16:52, Eleanor Dodson wrote: > > How do people decide on what is a salt bridge within a molecule and how to > count them for those Tables? > > I have been looking at 2z2f - paper claims some score..- > > But there are several residues in alternate conformation > > with NZ A to OE1A and NZ A to OE1B and NZ B to OE1B etc > > Is that one salt bridge or 3 salt bridges???? > > PISA lists salt bridges between molecules but not within a molecule I dont > think? > > Suggestions gratefully received. > Eleanor > > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1