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Beginner Puzzle: Snow Flea Antifreeze Protein

Closed since over 13 years ago

Beginner Overall

Summary

Created
June 10, 2012
Expires
Max points
100
Description

This puzzle is for veteran Foldit players to help new players, and practice using Rebuild after changing the structure (see puzzle comments for more info).

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Comments

beta_helix Staff Lv 1

As requested in the Forum post where we asked which Beginner Puzzles we should bring back (http://fold.it/portal/node/992729) we are reposting this more difficult Beginner Puzzle.
Because it's a tough one, it's worth 100 global points for everybody over 40 days.
_____________

If you are new to Foldit, here are detailed instructions to get you started:
http://fold.it/portal/node/988864

HINT TO EASILY MAKE A SHEET:

The rebuild tool takes structure assignment into account, so you can set the secondary structure to Sheet and then Rebuild. Foldit will then make a sheet out of that region.

ANOTHER HINT: If you are having trouble with this puzzle, try using the "Align Guide" tool:

By right clicking on a region of the protein (not the guide) it will pull up a menu with 6 tools. The bottom right one is "Align Guide". Clicking on it will align the native guide to the region of the protein you selected.
This will help you see what sections on your protein correspond to the guide!

Working with the guide is much more user friendly when you use the advanced viewing options.
In the game click on Menu->General Options and select "Show Advanced GUI" and click Done.
Click on View, turn on 'Show Outline,' set the background color to white, and view stubs on the sidechains, view the guide, and set color relative to guide. Turn all the other view options off."

For even more info: http://foldit.wikia.com/wiki/Tlaloc%27s_Strategy#Technique_for_Matching_a_Guide

brow42 Lv 1

Yay Snow Flea! :D

Last time infjamc gave some hints that were really useful for understanding why normal folding approaches didn't work well. To these I'll add that the loops are like twisted sheets that bond into triangles, and there are 2 disulfide bridges. From infjamc:

You might notice that the protein has an unusually high number of glycines. The lack of side chain in glycine is critical for the flexibility in the backbone configuration for this protein.
If a segment scores poorly relative to the guide despite that its backbone score is okay, check to see if it is a glycine. If so, consider rebuilding a short segment containing the glycine and its neighbors, with a zero-length band added to the glycine to keep it in place. (The idea is to see if flipping the backbone atom configuration would do the trick, e.g. via the formation of new hydrogen bonds.) 

The starting configuration for that puzzle was intentionally made incorrect. The correct structure has sheet-like extended segments, but the hydrogen bonding pattern is more complex. The pattern involves bonding to adjacent pieces in "3D" rather than "2D"-- more like "one to the left, one to the right, one below," etc.

When starting this puzzle, you might want to set the entire structure to sheet and then straighten out the protein entirely. This ensures that the incorrectly-formed hydrogen bonds in the starting configuration (a "giant helix") would not re-form easily and may make it easier to reshape the structure manually. 

If you use the Ctrl+Shift+V full-atom mode, the atoms on the same side should go "red, then two whites," or "white, then two reds" as opposed to the "one red, one white" pattern in a standard beta sheet.