[Protein-analysis] Re: What experiment will let me detect merging of protein folding pathways?

jps via proteins%40net.bio.net (by sumida from bbri.org)
Mon Nov 24 10:26:04 EST 2008

On Nov 23, 12:47 pm, "Yutong Zhao" <rak... from gmail.com> wrote:
> Hi guys,
> I realized that the relax-tighten optimization approach found in most
> computational chemistry experiments may be ill-suited for the protein
> folding problem. So I'm developing a new merging-tree iterative deepening
> search algorithm that will navigate through the protein folding well.
> However, this algorithm hinges on one key assumption: there are many initial
> pathways in the protein folding landscape with a SIGNIFICANT amount of
> pathway convergence as the protein folds. A corollary of this assumption
> would be intermediates that result from the merges (nodes), which have the
> unique property of resulting from multiple merges and thus would be found in
> high frequency no matter how many times you refold a protein.
> I was looking through experimental techniques in circular dichroism and NMR,
> ideally something that would permit observation of a rapid decrease in
> fluctuations of a few, key, residues. Any ideas how I can find these things?
> Cheers,
> Yutong Zhao

NMR deuterium exchange, or proteolytic cleavage.  See Walter Englender
or Susan Marqusee's work.

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