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