QUESTIONS: alpha-helix "signals" in proteins

Sean Eddy sre at al.cam.ac.uk
Wed Jul 6 18:35:23 EST 1994

In article <2veoju$dur at lyra.csx.cam.ac.uk> smb18 at mole.bio.cam.ac.uk (Simon Brocklehurst (Bioc)) writes:
  >1) There is no thermodynamic (!!) advantage for main-chain polar groups
  >   to make intramolecular hydrogen bonds rather than to make hydrogen
  >   bonds with solvent -- is there?

I've always thought that there was a favorable entropic term. If you
make intramolecular H-bonds, you free up a lot of individual water
molecules that would otherwise be constrained.  Even though the newly
freed waters go and H-bond to other waters in solution (so there's no
significant enthalpic contribution) it seems like the number of
degrees of freedom in the system increase, so the entropy increases.
Is this wrong?

- Sean Eddy
- MRC Laboratory of Molecular Biology, Cambridge, England
- sre at mrc-lmb.cam.ac.uk

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