QUESTIONS: alpha-helix "signals" in proteins

Simon Brocklehurst Bioc smb18 at mole.bio.cam.ac.uk
Fri Jul 8 02:36:57 EST 1994


kenp at tuli (Kenneth Prehoda) writes:

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

(Stuff deleted!!!!!)

>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.

   I still think we might be talking at cross purposes! But here
goes.

   OK, start let's start with 100% of our protein unfolded and quickly
change the conditions so that the protein is allowed to start folding
straight away.

   At the point where we "start" the folding, the system is not at 
equilibrium, is it?   If you were studying the early stages of
folding in this way, why would equilibrium be relevant.

If the system proceeds to an equilibrium between unfolded and folded 
states, then by all means use an equilibrium constant in that context - 
but only when it's got there.

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

 See below

>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.

  See below          

>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.

  If you can only to proceed along the "folding coordinate" to the native
state, via the transition state, then the structure of the native state 
has been influenced by the structure of the transition state.  My point
is that if the system goes through a particular transition state, then
this determines what native state you see.

  So you could imagine that proteins could fold unproductively if
they go through the wrong transition state.

  This does seem to happen in real life.  Ever tried to overexpress a 
protein in a system that expresses really quickly?  Often the
protein doesn't fold to it's usual native state.  It's gone along
some "incorrect" folding pathway from which there's no return.  Express 
the protein more slowly and the protein folds properly.

>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.

  See above.

>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*.  

   Well I am concerned with it (the pathway)! I thought the your words in 
capital letters above ("COMPLETELY INDEPENDENT...") implied that you weren't!

> 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.

   What about this model for protein folding?

      Unfolded    --->  Intermediate -----> Native 
                 <---

    There's no equilibrium between the Unfolded and native states here.

>: >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.

     I'll say it again!  I don't think h-bond formation directs folding!


  _________________________________________________________________________
 |
 |  ,_ 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
 |________________________________________________________________________




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