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1163: 80 Residue Monomer Design
Status: Closed


Name: 1163: 80 Residue Monomer Design
Status: Closed
Created: 11/26/2015
Points: 100
Expired: 12/04/2015 - 23:00
Difficulty: Intermediate
Description: This is a basic 80 residue design puzzle without any Fragment Filter. See the puzzle comments for filter details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!
Categories: Design, Overall

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gitwut's picture
User offline. Last seen 20 weeks 5 days ago. Offline
Joined: 05/18/2012
Groups: Contenders
See the puzzle comments for filter details?

Where are the filter details? I see no comments.

bkoep's picture
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Joined: 11/15/2012
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Sorry! Here are the details for the filters on this puzzle:

Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence: Ensures that at least 30% of the residues are buried in the core of your design.

Secondary Structure: Checks that no more than 50% of residues are in helices; penalties are incurred if more than 50% of residues form helices.

Secondary Structure Design: Penalizes all CYS residues. Penalizes GLY, ALA, and PRO residues in helices and sheets.

viosca's picture
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Joined: 10/16/2013
Why the penalty on alanine?

I've noticed that many of the design puzzles penalize Alanine. But I've noticed that many of the non-design puzzles, those sequences found in nature, have alanines in helices. Why the penalty?

bkoep's picture
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Joined: 11/15/2012
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Great question!

The short answer is that alanines don't make a very stable core.

Alanine is indeed very common in natural proteins, and does favor α-helical structure. And, by default, an alanine-rich α-helix scores really well in Foldit.

However, since alanine has such a small sidechain, an alanine-rich helix has a "featureless" shape. You can imagine the sides of the helix would be relatively smooth (whereas a helix with larger sidechains would present an irregular, studded surface). If you were to design several of these helices into a bundle with an alanine-rich core, you would get a protein that forms helices in solution—and would probably even form a bundle to bury the alanines. But, the smooth sides of those alanine-rich helices would allow them to pack against each other in many different ways, effectively forming many different bundles. So instead of all the protein copies in a sample forming the same structure, you would get a wide mix of helical bundles with slightly different packing, constantly changing shape as the helices slide against one another. We say this protein exhibits molten globule behavior.

Instead, we prefer designs with bulky, interdigitated sidechains in the core. With only one way to efficiently pack those sidechains together, all the protein copies are expected to adopt a single, well-defined structure.

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