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1014: 75 Residue Monomer Design: Core Existence

Closed since almost 8 years ago

Intermediate Overall Design


November 14, 2014
Max points

In this puzzle, we've updated the way the Core Existence filter identifies core residues. The new method is more similar to what is used in the Baker Lab, and should also be a little faster. Click the "Show" checkbox beneath the Core Existence filter to see which residues have been identified as Core (orange), Boundary (green), or Surface (blue). There are several other filters in effect; see the puzzle comments for 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!

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bkoep Staff Lv 1

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

Core Existence: Ensures that at least 25% of the residues are buried in the core of your design.

Fragment Score: Scans for parts of your design that are unlikely to fold up naturally. Use Rebuild and Remix tools to fix these regions of your design!

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

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

BootsMcGraw Lv 1

Agreed. Alanine is a classic component of helices. Why is it being penalized, when it is found in helices more often than any other AA, except for glutamate and methionine?

bkoep Staff Lv 1

You bring up a good point that alanine has a high propensity to form helices. The short answer is that characteristics of natural proteins are not always good for designed, ideal proteins.

The problem is that a hydrophobic core made up of alanine is somewhat "slippery." That is, a helix with a lot of alanine on one face will be somewhat smooth and featureless, due to the small size of the alanine side chain. Because of this smoothness, that helix may be able to slide and pack against the core in multiple ways, with very little change in energy.

When designing small, ideal proteins like this, it's desirable to have helices and sheets that fit together in the core and lock into place like puzzle pieces. This ensures that there is only one favorable conformation for the protein, increasing its stability.

To compound this matter, our score function tends to favor alanine in the core because it allows the helix and sheet backbones to come into close proximity and pack against one another. Again, this non-specific type of packing is not desirable.

gitwut Lv 1

I've noticed that it is much more difficult to keep sheets from deforming in the early handfolding stages. I'm guessing that this is due to the new core filter? It's taken me a couple of hours to form four workable sheets (still not to my liking), whereas previously it would only have taken about 15 minutes. I also resorted to disabling the filters but it didn't make things much easier.

These monomer puzzles are already annoying enough to make me consider skipping them altogether. I feel like I've been blindfolded, hogtied and thrown into a tar pit. :