puzzle picture
828: Abeta Loop Closure A
Status: Closed

Summary

Name: 828: Abeta Loop Closure A
Status: Closed
Created: 12/23/2013
Points: 100
Expired: 01/06/2014 - 23:00
Difficulty: Intermediate
Description: This puzzle builds on a piecewise design solution from Puzzle 808. Build loops to close the cutpoints between secondary structure elements to create an Abeta-binding protein! The two starting structures were derived from a single solution by Grom and Rita_Gat, but have different loop arrangements. Reset the puzzle to cycle through both starting structures. See the puzzle comments for more details. This puzzle will be open for two weeks.
Categories: Design, Overall

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Comments

bkoep's picture
User offline. Last seen 8 hours 58 min ago. Offline
Joined: 11/15/2012
Groups: None
More information:

We've tried to estimate the number of residues required to close each loop, but you may prefer to distribute these residues differently. You can delete residues from one loop and reinsert them into another, although you cannot add additional residues to this puzzle.

There is no RMSD filter for this puzzle, but there are some constraints to help keep the secondary structure pieces in place. Note also that you can wiggle the backbone of the Abeta peptide, although there are constraints to keep the two Abeta strands in a sheet.

Joined: 05/19/2009
Groups: Contenders
Needs NEW CLIENT

You forgot to mention that this puzzle REQUIRES the latest client. Older clients will give an error message and refuse to load this puzzle.

Joined: 05/19/2009
Groups: Contenders
Needs NEW CLIENT

You forgot to mention that this puzzle REQUIRES the latest client. Older clients will give an error message and refuse to load this puzzle.

v_mulligan's picture
User offline. Last seen 47 weeks 1 day ago. Offline
Joined: 03/04/2009
Groups: None
Latest version required

Ah, true -- the puzzle does require the latest version of the game. We found a few bugs that appeared with puzzles that had cutpoints in the starting configuration, so the programmers had to fix those before we released this puzzle.

wisky's picture
User offline. Last seen 4 weeks 4 days ago. Offline
Joined: 07/13/2011
Abeta backbone free? Why is

Abeta backbone free?

Why is the abeta backbone free? All the other puzzles in this series have had the backbone of abeta locked.

bkoep's picture
User offline. Last seen 8 hours 58 min ago. Offline
Joined: 11/15/2012
Groups: None
Flexible backbone

We know that the Abeta peptide is pretty flexible in solution, and is very likely to change shape upon binding—especially if the new shape makes better interactions with the binding protein. We do expect that these changes would be small, and that the peptide will generally favor a two-stranded beta sheet.

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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