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415: Mini Protein Puzzle 1

Closed since over 11 years ago

Intermediate Overall Prediction

Summary


Created
April 30, 2011
Expires
Max points
100
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.

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Comments


beta_helix Staff Lv 1

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.

Rav3n_pl Lv 1

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 Staff Lv 1

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!

scottyler89 Lv 1

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?

Rav3n_pl Lv 1

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

Seagat2011 Lv 1

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

Seagat2011 Lv 1

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

beta_helix Staff Lv 1

This protein doesn't phosphorylate or oligamerize.

scottyler89,

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.