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828: Abeta Loop Closure A

Closed since about 12 years ago

Intermediate Overall Design

Summary

Created
December 24, 2013
Expires
Max points
100
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.

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Comments

bkoep Staff Lv 1

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.

Bletchley Park Lv 1

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

Bletchley Park Lv 1

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 Lv 1

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 Lv 1

Abeta backbone free?

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

bkoep Staff Lv 1

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.