QUESTIONS: alpha-helix "signals" in proteins

Joshua Cherry cherry at watneys.med.utah.edu
Sat Jul 9 11:58:16 EST 1994


In article <2vkll4$r19 at news.doit.wisc.edu> Ken Prehoda <kenp at nmrfam.wisc.edu> writes:
   
   In article <CHERRY.94Jul8152635 at watneys.med.utah.edu>
   Joshua Cherry, cherry at watneys.med.utah.edu writes:
   >   That's my point - they're kinetically inaccessible (in most cases) if
   >   they are there at all.  So of what importance are they?  
   >
   >That's exactly what kinetic control means--that the distribution of
   >products of a reaction (in this case folding) is not in accord with
   >the equilibrium distribution due to kinetic considerations.  Part of 
   >the importance of such states, if they do exist, is that 
   >they would imply that thermodynamic stability is no guaranty that a 
   [etc...]

   You missed my point.  What I am saying is that if there is some
   state that has a free energy lower than our observed state, it is
   irrelevant, if it cannot be reached.  In other words, although
   having a lower free energy state implies that the system is not
   at equilibrium, for all practical purposes, the system is at
   equilibrium if it takes the age of the universe to reach that 
   global minimum.

I don't think I missed your point.  _My_ point is that you seem to
oppose even the meaningfulness of the suggestion that there is 
kinetic control of protein folding, but your argument is essentially
a statement of kinetic control.  You say "it's not kinetic control,
it's just that bla bla bla."  The problem is that bla bla bla is 
exactly kinetic control.  As for the implications of there being
inaccesible states, I touched on this, but it was mostly lost in
your [etc...] above.  If such states do exist, they imply that
the native state is not the most thermodynamically stable one. 
They raise the question of why the native state _is_ kinetically
accesible, and whether this accesibility is a special characteristic
(along with stability over unfolded) with which we should be 
concerned.  

   >I remember something about ts mutants which don't fold at the
   >restrictive temperature, but, if folded at the permissive temperature,
   >remain stable at the restrictive temperature.  If such mutations 
   >are not rare aberrations, but common ways of breaking a refined
   >function, then the kinetics of folding are quite important.

   You are talking about mutations that change the stability of the
   protein.  What does this have to do with the folding pathway?

No, not on one (my intended) interpretation of these results.  If the
native state were unstable at the restrictive temperature, then 
moving the folded protein from the permissive to the restrictive
temperature would result in denaturation.  It doesn't.  It's hard
to see how to explain these results without a kinetic argument.  I
suppose it's a formal possibility that _unfolding_ of the destabilized
protein is slow at the restrictive temperature, but it seems more
likely to me that folding is slow.  If this interpretation is correct,
this has _everything_ to do with the folding pathway.  

   >>   To put it
   >>   another way, do you believe it is valid to use equilibrium constants
   >>   when studying protein systems?
   >>Certainly in some contexts.  It must be true that the native state
   >is (under native conditions) favored over the unfolded state
   >(otherwise we'd never call it the folded state, it would just be
   >one of the substates of unfolded protein).  However, if Simon
   >is right, then application of equilibrium constants to determine
   >which state is thenative state would sometimes lead you to false
   conclusions.
   >You would conclude that the (hypothetical) more stable, kinetically
   >inaccessible state was the native one.

   First, the equilibrium constant is not used to determine which state
   is the native state.  This must be know before hand (spectroscopically,
   for example).

   Second, how would you conclude that an inaccessible state is the native
   state, if by definition the inaccessible state can't be reached?
   Sounds pretty strange...

Well, you wouldn't if you paid attention to kinetics.  That's the whole
point.  If you merely considered equilibrium constants (forget about how
you obtain them), you might conclude that some kinetically 
inaccesible state was native.  Not my mistake, but that 
of those who insist that equilibrium constants are everything
in protein folding.  I'm not saying that you're insisting on this,
but you did rephrase your view in terms of the question of whether
it was valid to use equilibrium constants when studying proteins.
If the answer is "yes, as long as you consider rate constants as
well", that's hardly a point in your favor.

Josh Cherry
cherry at watneys.med.utah.edu



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