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415: Mini Protein Puzzle 1
Status: Closed


Name: 415: Mini Protein Puzzle 1
Status: Closed
Created: 04/30/2011
Points: 100
Expired: 05/07/2011 - 13:00
Difficulty: Intermediate
Description: This tiny domain is an independently-folding piece of a larger protein involved in Brain function. We haven't had much luck arriving at low-energy native-like structures of these small domains using Rosetta, so we are hoping you can help us! More details in the puzzle comments.
Categories: Overall, Prediction

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1Mark- 77 125 Contenders8,885100
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3lazystar 84 1577 foldeRNA8,87094
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beta_helix's picture
User offline. Last seen 12 hours 19 min ago. Offline
Joined: 05/09/2008
Groups: None
More info:

Another purpose of this puzzle is to introduce miniproteins and structured peptides, which have implications for biomaterials design and will certainly appear again in future puzzles.

Folding up miniproteins may require a slightly different approach: less large-scale structure manipulation, but more detailed tweaking and careful arrangement of sidechains and small loops.

Joined: 06/17/2010
Any suggestions

what we need or should do to that locked loop?
Also would be cool to not lock possibility of change secondary structure on it. I not see it is flat like sheet or not...

beta_helix's picture
User offline. Last seen 12 hours 19 min ago. Offline
Joined: 05/09/2008
Groups: None
You need to accommodate it somehow

We have kept the ligand frozen and it's up to you to make it interact with the rest of the miniprotein in a favorable way.

We can post it as a contest later if you would like to play around with it, but that is actually why it is frozen: we don't want you playing around with and changing the topology of the ligand!

Joined: 06/17/2010
I only want

to change secondary structure (not shape) of locked loop to se how it is bended :)

Joined: 08/09/2010
Groups: foldeRNA
ligand modification

If the poly-proline ligand is truely where the this domain of the protein binds, might it be better to freeze the two ends in 3D space, and allow the center to be flexable?

Joined: 08/24/2010

After accepting the ligand does the protein undergo oligomerization, or are we to treat the protein as a traditional monomer.

Joined: 08/24/2010

And also if you can speak to whether it undergoes phosphorylation, resulting in a conformational change, if it is relevant.

beta_helix's picture
User offline. Last seen 12 hours 19 min ago. Offline
Joined: 05/09/2008
Groups: None

This protein doesn't phosphorylate or oligamerize.


It probably wouldn't have hurt to let the middle of the ligand wiggle a bit, but not too much since poly-prolines are not as flexible as a typical 10 amino acid peptide chain.

We wanted to start off conservatively, maybe next time we'll unlock the sidechains (not that Prolines can move much) and allow more flexibility.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons