QUESTIONS: alpha-helix "signals" in proteins

Simon Brocklehurst Bioc smb18 at mole.bio.cam.ac.uk
Thu Jul 7 17:39:29 EST 1994

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?).

   Maybe now's the time to clarify a few points?

    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

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

(stuff deleted)

(talking about side-chain conformations in helices...)
>Well, the researchers in the field that I have talked to believe
>that these restrictions do cause energetic differences which is
>one contribution the the "propensity."

   I don't disagree that this is important. It's just that you seemed 
   to imply that alanine residues are helix forming 'cos they don't make 
   any unfavourable steric nteractions.

   I was just pointing out that some people think otherwise i.e. they
   think that alanines intrinsically (i.e. on their own!) like to 
   be in a helical conformation.  (Personally, I don't have strong opinions 
   on this matter).

 (stuff deleted)

>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.

  I do believe that the hydrophobic side-chains of residues get
  together at least on the same time-scale as H-bonds form, and 
  quite likely before.  Thus I don't see how H-bond formation directs

>For one thing, how do you measure the strength of a hydrogen bond?
  Tricky do this well:

  You can do protein engineering experiments to _try_ to estimate
  the strength of hydrogen bonds involving side-chains (see some of
  Fersht's work).

  You can monitor rates of hydron exhange of amide protons by solution homo
  and heteronuclear magnetic resonance spectroscopy.  But the 
  interpretation is complicated by motions other than transient
  breaking of hydrogen bonds.  This does give a handle on main-chain
  H-bonds though.

  I'm sure there are loads of ways of doing this, but it's late and
  I can't think of any off hand!

  Anyway, depending on the conditions the protein is under, the relative
  strengths of all kinds of non-covalent interactions will change.

  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?

  |  ,_ 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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