What experiment will let me detect merging of protein folding pathways?

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What experiment will let me detect merging of protein folding pathways?

Yutong Zhao
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
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Re: What experiment will let me detect merging of protein folding pathways?

jps-3
On Nov 23, 12:47 pm, "Yutong Zhao" <[hidden email]> 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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