QUESTIONS: alpha-helix "signals" in proteins

Ben Davis bjd12 at cus.cam.ac.uk
Thu Jul 7 05:07:47 EST 1994

Ken Prehoda (kenp at nmrfam.wisc.edu) wrote:

	<stuff deleted>

: I have read about this.  But to me, this just shows that there is very
: little structure in the unfolded state.  I mean .2ppm max deviation seems
: as strong support for fully unfolded.  As far as NOE's I can't remember
: any papers describing long range NOE's in an unfolded state.  I would
: appreciate any references.

	.2ppm deviation from random coil for a non-labile proton is significant;
any structure present is going to be in fast exchange with other (unfolded)
conformations, so you can't expect massive deviations. The same idea applies
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 to
be loose associations of hydrophobic sidechains, which (if there's no
aromatic residue around) tend to produce only small changes in chemical
shift anyway.

: >	Very good question - can you ever get a totally random coil protein ? I
: >suspect under say 6M GuHCl you'd be looking at "totally" denatured, since
: >all the aa would be interacting with solvent rather than other aa
: >(hopefully). As it is, proteins denatured by acid, by urea, by heat, by
: >truncation seem to show residual or marginal elements of structure.

: It depends greatly on the protein.  Many proteins will not unfold in 6M
: GuHCl.

	True. Just goes to show how hard it is to get a totally random coil ;).
I think getting an enviroment where there are no longer *any* interresidue
interactions is very hard - that most proteins under denaturing conditions
will show some structure (hydrophobic clustering or residual native-like).
(I think I just stuck my neck out ...) 

: >	My earlier point was that it'd be good to get an example of a protein
: >that *was* totally denatured - just as we need more folded structures,
: so we
: >need more examples of how proteins behace under denaturing conditions.

: Like I said before, I can't imagine a paper where the authors simply
: describe a denatured state that has no dispersion.  Sounds pretty 
: boring but maybe that's just me?

	Can you imagine going through the hassle of assigning a state with no
dispersion at all, then saying "well, its boring, lets not publish it after
all" ?. Even a negative result is interesting - it's all data. It'd tell
you that there was a sequence or conditions where there was *no* residual
structure, and since a lot of the folding expts assume they start with a
fully denatured state, this is important. 

: -Ken Prehoda
: kenp at nmrfam.wisc.edu


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

"They can make me do it, but they can't make me do it with dignity."

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