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?).
: 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
: folding.
: >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: |________________________________________________________________________
