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
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