QUESTIONS: alpha-helix "signals" in proteins

Simon Brocklehurst Bioc smb18 at mole.bio.cam.ac.uk
Wed Jul 6 13:10:49 EST 1994

sre at al.cam.ac.uk (Sean Eddy) writes:

>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?

  But the protein chain becomes more constrained when it forms
  intramolecular hydrogen bonds, compared to when it is making
  h-bonds with solvent.

  -- Simon

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

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