529: CO2 and You!

Closed since almost 14 years ago

Summary

• Created: March 14, 2012
• Expires: March 21, 2012 at 23:59 UTC
• Max points: 100

Description

Help fix this novel carbon-fixing enzyme. Try varying loop length and structures to make better scoring interactions with the ligand. In this puzzle, the first of a series, up to 7 residues can be added, and up to 10 can be removed. If you are new to Foldit, make sure you have completed Intro Puzzle 5-2, 7-1 through 7-4, 8-1 & 8-2 before trying this Advanced Science Puzzle. More info in the puzzle comments.

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Comments

[beta_helix]

depts.washington.edu

CO2ProjectWebsite.pdf

With many other questions answered in the Scientist Chat with CEiben: http://fold.it/portal/node/992115

As mentioned in the chat, please post any questions for CEiben about this Puzzle here!

[brow42]

Just a heads up, I think segments 33, 60, 61, 119, 169, 248, 380, and 410 are what rav3n calls 'wiggle locked'. Bands to these are ignored.

[CEiben]

@thom001
Designing new loops and interactions for ligand 420 (C1) is preferred over 419 (B1). It's not clear a priori what kinds of interactions will help so I recommend being creative.

@brow42
I'm having trouble reproducing the 'wiggle lock'. When I wiggle after banding between 33 and 60, the residues move together on my computer. More information on how to reproduce this lock would be very helpful since it's not intentional in this puzzle.

[brow42]

I test these by making a strength 10 band between the segment and a locked segment, such as 1. I then do wiggle for 1 iteration, and check the change in score. Then I quickload for the next segment. The listed segments all show a change in score identical the unbanded case.

In the latest flu design puzzle, all the wiggle locked segments had constraints, but not all of the segments with constraints were locked. That was the first time I used this method.

I modified http://fold.it/portal/recipe/39029 for the new puzzle, but didn't upload it because my main client is doing other stuff. I can probably upload a new version in the morning.

[mottiger]

is a consecutive numbering of the editable segments possible?
as it is right now, it is impossible to run a rebuilding script or at least it is not possible to run my top fav: DRW.

[mbinfield]

Question based on my total ignorance of dynamics at this scale: is there any reason to worry about how the ligands move into place? They seem to be in the center of the protein, so I don't see an obvious path in or out. Is it possible for us to change the backbone in such a way that the ligands are nicely bonded into place, but there's no way for them to actually reach that position or leave it?

[beta_helix]

so hopefully it'll be fixed in the new Flu Puzzle that will be posted next week.

Thanks for your patience with this one.

[beta_helix]

but sadly there is no way for us to do this, Rosetta needs the entire chain to be numbered consecutively.
You'll need to work on rebuilding the loops individually when using that script instead of all of them at the same time.

[mbinfield]

It's possible to make a rebuilding script that works on specified non-consecutive portions of the protein. You just need to talk Rav into making the necessary modifications to DRW (assuming it's not already in the options somewhere; I haven't looked.)

[mbinfield]

(Above comment intended to reply to mott, below.)