Can we have a metal to bind to? (693)

Case number:845799-994864
Topic:Biochem
Opened by:Susume
Status:Closed
Type:Suggestion
Opened on:Sunday, March 31, 2013 - 06:50
Last modified:Tuesday, April 9, 2013 - 05:47

When you release the open phase of 693 denovo #22, would it be possible to give us an iron-sulfur cluster to bind the cystines to? They seem to be extremely well conserved in homologs but are too close together for a disulfide between them to make much sense - I'm thinking they are likely part of the active site. We could more likely get that part of the backbone right if we had the right sort of thing to bind to. People who don't want to mess with the metal could drag it away from the protein and forget it.

(Sun, 03/31/2013 - 06:50  |  3 comments)


tamirh's picture
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assigning

beta_helix's picture
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I'm looking into this.
We usually just add a bunch of distance constraints to Rosetta when we think there is a metal-binding site (but I know that nobody enjoys those in Foldit!)

I know that in the early ligand puzzles (when we didn't confine the ligand to a specific area) it was possible to get a better score by moving the ligand to the other side of the protein (as well as doing other naughty things to the ligand!).

If it would be possible to avoid that, while still letting players move the metal away if they don't want it, then we could try it!

beta_helix's picture
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I'm sorry Susume, but we weren't able to provide you with an iron-sulfur cluster for Puzzle 699.

It might have been possible if some of the homologs were metal-binding, but it's just those cysteines that are conserved.

I agree that this protein is an Iron-Sulfur Cluster Scaffold Homolog, maybe we'll be able to repost this puzzle with templates so that you can thread your sequence onto those homologs (and hopefully then the cysteines will be in the correct vicinity).

I'm sorry we weren't able to get this working for you.

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