puzzle picture
879: Ebola Binder Design with Disulfides
Status: Closed

Summary

Name: 879: Ebola Binder Design with Disulfides
Status: Closed
Created: 04/21/2014
Points: 150
Expired: 04/30/2014 - 23:59
Difficulty: Intermediate
Description: This is a design puzzle with 37 residues, near the interface of a target glycoprotein from the Ebola virus. At the binding site of the Ebola protein, there is already a helix designed by scientists in the Baker Lab, but the helix will not fold up by itself! Build a scaffold around the starting design that will fold up properly and stabilize the binding helix! There are strong constraints to keep the binding helix in place, and you may not mutate residues at the interface. You may not add additional residues to the design, but you may delete residues from one end of the design and reinsert them at the other end. You will receive an (extremely) large bonus for making up to 2 disulfide bonds. Remember to share your favorite designs using the Share with Scientist tool, even if those are not your best-scoring solutions!
Categories: Design, Overall

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Comments

bkoep's picture
User offline. Last seen 33 min 37 sec ago. Offline
Joined: 11/15/2012
Groups: None
Beware cutpoints!

In our pre-release testing, this puzzle was especially vulnerable to crashes when working with cutpoints. Beware in particular scripts that open and close a large number of cutpoints.

Due to some urgency on behalf of the Baker Lab scientists and some experimental constraints, we decided to go ahead and post the puzzle rather than wait for the next fix/test/release cycle. We are currently investigating the cause of the crashes, and if we find that the problem is straightforward to solve, we may release a hotfix to address this bug.

Thank you for your patience!

Joined: 12/27/2012
Groups: Beta Folders
This puzzle breaks some recipes...

There is a ligand attached to segment 134 in the frozen section of the puzzle. The ligand is only visible with the "Show All" sidechains option (Shift-A in the Windows selection interface).

Segment 134 has some interesting features that break existing recipes. It has an amino acid of "unk", which may cause problems with recipes that expect a valid one-letter amino acid code.

Segment 134 has a secondary structure code of "H". Previous puzzles have used a secondary structure code of "M" for ligands. This means recipes don't have a way of detecting the presence of the ligand in this puzzle.

Segment 134 has a nil energy score (from current.GetSegmentEnergyScore). The nil value crashes the venerable "print protein lua2 V0", recipe 31098, when it attempts to round the value. Other recipes that check scoring at the segment level may encounter similar problems.

There's also an unlikely long straight "soda straw" between segments 104 and 105. The impact and meaning of this unusual feature is not clear.

Joined: 12/27/2012
Groups: Beta Folders
revisited this issue...

My previous statement that "[s]egment 134 has a nil energy score" is incorrect. The nil value was the hydropathy index, which is determined via a table lookup in the recipe. There was no table entry for an amino acid code of 'unk'.

Look for a new recipe "print protein 2.0", coming soon to the recipe store.

Joined: 12/27/2012
Groups: Beta Folders
yet another revisit...

Just to clear the air (?) the strange segment 134 is a glycan, which is what makes the whole thing a glycoprotein.

The same glycan showed up again in puzzle 1378b. The July 2017 science chat mentions glycans, see this science chat comment for more details.

Joined: 06/24/2008
Groups: Void Crushers
The brown/pinkish bar

What is the brown/pinkish bar [by the helix with seg 126] in this protein??

bkoep's picture
User offline. Last seen 33 min 37 sec ago. Offline
Joined: 11/15/2012
Groups: None
Imaginary bond

The target Ebola glycoprotein is actually much bigger than what is shown in the puzzle. Some parts are not visible because we don't know the structure of that domain, or we removed the domain to reduce the size of the puzzle. Because Foldit doesn't know about the missing domain, it tries to connect the broken ends with an "imaginary" bond.

You can ignore the imaginary bonds when designing your protein, as they should not affect scoring.

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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