QUESTIONS: alpha-helix "signals" in proteins

Ken Prehoda kenp at nmrfam.wisc.edu
Thu Jul 7 19:23:51 EST 1994

In article <2vgk5j$2hv at lyra.csx.cam.ac.uk>
Ben Davis, bjd12 at cus.cam.ac.uk writes:
>	.2ppm deviation from random coil for a non-labile proton is significant;
>any structure present is going to be in fast exchange with other
>conformations, so you can't expect massive deviations. The same idea
>for NOE's - to see a long range NOE, the two protons would have to be in
>close proximity for a reasonable length of time, which is unlikely in a
>structure which is (at best) marginal. However, this doesn't mean the
>protein is unfolded - its not in a random walk conformation - but you do
>have to look hard for evidence of structure. These structures also tend
>be loose associations of hydrophobic sidechains, which (if there's no
>aromatic residue around) tend to produce only small changes in chemical
>shift anyway.

Isn't it true that any unfolded structures that have stabilizing
interactions will be favored over those that don't?  If so, then
one would expect that the protein would spend much more _time_ in
the stabilized conformation meaning deviations greater than
.2ppm.  The some goes for NOE's.

>Ben Davis,
>MRC Protein Function and Design,
>Cambridge, UK

-Ken Prehoda
kenp at nmrfam.wisc.edu

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