QUESTIONS: alpha-helix "signals" in proteins

Ken Prehoda kenp at nmrfam.wisc.edu
Wed Jul 6 14:30:09 EST 1994

In article <2vekma$c3i at lyra.csx.cam.ac.uk>
Ben Davis, bjd12 at cus.cam.ac.uk writes:
>	OK. You can get an assignment of proteins under denaturing conditions -
>infact, its what I've spent the last year or so doing.

Great! My understanding is fairly limited. 

>	Two main ways of doing it:
[techniques deleted]
>	What people tend to see is that, for most (say > 80%) of the protein,
>the assignments are close to random coil values (remember 15N shift is
>sequence dependant that 1H, so you keep most of this dispersion - very
>useful), but some resonances deviate from random coil, usually by small
>amounts (say approx 0.2ppm max for non-labile protons, 0.4ppm for
>Tie this in with NOE data, you get evidence for non-random coil
>being adopted under "denaturing" conditions.

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.

>	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

>	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?

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

-Ken Prehoda
kenp at nmrfam.wisc.edu

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