QUESTIONS: alpha-helix "signals" in proteins

Kenneth Prehoda kenp at tuli
Thu Jul 7 20:31:13 EST 1994

[sorry about that mistaken post, my newsreader (read: me) made a
Simon Brocklehurst (Bioc) (smb18 at mole.bio.cam.ac.uk) wrote:
: kenp at banyo (Kenneth Prehoda) writes:

: >:     They're kinetically inaccessible.  That is, if you don't have 
: >: transition states of sufficiently low energy to allow the protein to
: >: pass through them, then you won't get to a particular energy minimum 
: >: (native state).

: >That's my point - they're kinetically inaccessible (in most cases) if
: >they are there at all.  So of what importance are they?

:   Sorry, we're agreed on this point!

:   But I think the pathway from the unfolded to the native state involves 
:   going over energy maxima, and I think this must be where our difference
:   opinion is (right or not?).

You deleted my question: again I ask you, do you believe it is valid
to use equilibrium constants when studying protein systems???  If so,
I don't see how you can argue kinetic control.

Nor did you answer my question concerning the importance of these
kinetically inaccessible states (if such a thing exists).

As to your second point, _by definition_ the folding pathway involves
going over energy maxima. 

:     1) Do you believe that when proteins fold they, do so along
:        particular pathways that are directed by the sequence?

:     2) Do you think that these pathways involve traversing energy
:        maxima (transition states)?

:     3) If yes to the transition state idea, do you think that these
:        states have some native like structure (e.g. partially native
:        secondary structure)?

:     4) Do you think that rather than going through transition states,
:        there is a roughly downhill path from the unfolded state to the
:        native state i.e. no significant maxima?

:      My answers are:

:        1) Yes

:        2) Yes
:        3) Yes

:        4) No

As I have said before, the overwhelming evidence is that protein folding
for most proteins is under thermodynamic control.  What this means
is that the final structure is COMPLETELY INDEPENDENT OF THE PATHWAY.

Of course there is some "transition state" involved in the folding
process.  However, this determines the _rate_ of folding, not the final
structure.  As such, the structure of the transition state only affects
the rate of folding.

There simply isn't a good argument for kinetic control.  What we are
concerned with is the pathway *between our observed folded state and
observed unfolded state*.  It is undeniable that equilibrium (for all
practical purposes), and therefore thermodynamic control is going
on here.  Otherwise, we wouldn't be using Keq's to describe the system.

:      It seems to me that the yes answer to question 3) is particulary
: important to arguments about kinetic control?

Maybe you could explain.  Even if kinetic control is indeed
true, the structure of the transition state still determines
the rate and not the end state.

: >I wish.  See Gellman et al. for extensive discussions.  My point
: >is that the role of hydrogen bonds in protein stability is
: >entirely _uncertain_ in contrast to your strong opinion otherwise.

:   I never meant to imply that hydrogen bonds were not important
:   contributors to the stability of the native state.

That doesn't fit with your previous quote shown below:

:     I agree that there is debate is some quarters about this. But
: a lot of the other suggestions (e.g. main-chain hydrogen bond formation
: directs folding) are just nonsense.

[back to current post]
:   I don't want to flog a dead horse, but I think the important question
:   about protein folding is:

:          How does the sequence of the protein limit the number of 
:    conformations that need to be explored to find the native state?

:         My feeling is that this search involves going uphill as well 
:    as downhill on the free energy surface, traversing highly populated 
:    intermediates and less highly populated transitions states.  
:    Characterising the structures of partly folded states (and even
:    completely "unfolded" [whatever that means] states) is obviously an
:    important step forward to understanding protein folding.

:     Do you really not think that understanding the mechanism(s) by
:     which proteins fold is interesting/important?

I believe it is an interesting academic question, but as far as
understanding the final protein structure, I believe it is irrelevant.
If you have a compelling argument otherwise, I will gladly change
that belief.

:   _________________________________________________________________________
:   |
:   |  ,_ o     Simon M. Brocklehurst,
:   | /  //\,   Oxford Centre for Molecular Sciences,
:   |   \>> |   Department of Biochemistry, University of Oxford,
:   |    \\,    Oxford, UK.
:   |           E-mail: smb at bioch.ox.ac.uk
:   |________________________________________________________________________

-Ken Prehoda
kenp at nmrfam.wisc.edu

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