QUESTIONS: alpha-helix "signals" in proteins

Ken Prehoda kenp at nmrfam.wisc.edu
Tue Jul 5 09:25:43 EST 1994

In article <2vbn6u$j4e at usenet.rpi.edu> Mark J. Dresser,  writes:
>QUESTIONS:  What role do/could tertiary interactions play in stabilizing
>the alpha-helix?

Probably a significant role, but this is only my opinion. There is a
great deal of work being done on small, helix forming peptides (cf.
Baldwin and coworkers).  But, the question one must ask is whether
secondary structure is present in the unfolded protein.  If it
is not (which seems to be the case - molten globules and other
curiosities not withstanding), then this seems good evidence that
tertiary structure is indeed necessary for secondary structure

>Does a protein first fold into its secondary structure elements and then
>its tertiary structure, afterwhich the original secondary structure
>remain as before the folding into the tertiary structure?  (If yes or
no, could
>you please provide references).

Since protein folding is believed to be thermodynamically controlled
(OK, see Agard, et al. for counterviews), this is really irrelevant
to what you seem to be getting at.  Remember that G is a state function
and is therefore independent of path.

>Rose proposes that "the folded structure of a protein is encrypted in
>aa secquence, written in a *code* that remians obscure". (Rose, G.D. et
>al. (1994) _Science_ 264, 1126).  What is the status of this obscure
>that he is referring to?  Is the existence of this *code* a widely held

The status of this "code" is abysmal.  We know very little about the
relationship of primary and higher order structures of proteins.  The
existence of such a code is certainly widely held (cf. Anfinsen and 
coworkers).  If we believe that all of the information is contained
in the sequence itself, then it follows that there should be some
type of code that determines protein structure.  But maybe the code
is different for every protein?

Looking forward to further discussion,
Ken Prehoda
kenp at nmrfam.wisc.edu

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