puzzle picture
971: Ebola glycoprotein peptide inhibitor design (REPOSTED as 971c)
Status: Closed

Summary

Name: 971: Ebola glycoprotein peptide inhibitor design (REPOSTED as 971c)
Status: Closed
Created: 08/18/2014
Points: 0
Expired: 08/27/2014 - 23:00
Difficulty: Intermediate
Description: We would like you to design a small (25-residue) peptide that can bind to and block the Ebola glycoprotein. The glycoprotein is a viral surface protein that allows the Ebola virus to enter human cells. A small peptide inhibitor of this protein would therefore represent a candidate therapeutic for treating this deadly disease. We are starting you with a hotspot "stub" that was the top-scoring result from the earlier stub-finding puzzle, number 846. (Congratulations to AnthropicDreams!) We have extended this stub with twenty-two additional residues that you can design. A small peptide in this size range probably won't fold the way a protein would. Some considerations -- good hydrophobic packing, lack of holes in the core, good hydrogen bonding, presence of secondary structure, etc. -- will be the same, but in addition, heavy disulfide cross-linking is often necessary for stability in this size range. You will get a considerable bonus for forming up to three disulfide bonds (for a total of five, counting the two disulfide bonds already present in the Ebola target protein). Many natural plant and animal toxins are small peptides, and it is common to see three disulfide bonds in a "leapfrog" pattern (i.e. cys1-cys4, cys2-cys5, cys3-cys6) for maximal stability. The starting point for this puzzle has three disulfides in this "leapfrog" pattern, but this might not be the optimal disulfide placement or backbone topology. Feel free to change the secondary structure, move the disulfides around, or otherwise improve on this!
Categories:

Top Groups

RankGroupScorePoints
16 An Art That's Smart11,2160
17Piratenpartei Deutschland10,2020

Top Evolvers

Top Soloists

RankPlayerGroupScorePoints
16gloverd 82 1780 Go Science11,7380
17reefyrob 82 1780 Beta Folders11,6660
18caglar 82 1780  11,6610
19Bletchley Park 22 19 Contenders11,6580
20joremen 82 47  11,6110


Need this puzzle? Log in to download.  

Comments

wisky's picture
User offline. Last seen 13 weeks 1 day ago. Offline
Joined: 07/13/2011
Error!

When trying to idealize SS on this puzzle, I get a pop saying "Setup not TYPE_CARTESIAN." This has probably already been noted.

v_mulligan's picture
User offline. Last seen 1 year 3 weeks ago. Offline
Joined: 03/04/2009
Groups: None
Definitely odd

That is definitely odd -- that particular error shouldn't be coming up in that situation. I have been able to reproduce it, though, and will talk to the devs about it at our weekly meeting.

wisky's picture
User offline. Last seen 13 weeks 1 day ago. Offline
Joined: 07/13/2011
Two more problems!

http://fold.it/portal/node/998352

^^^^^^

Neither of these issues are normal behavior. I pulled the design piece away from the ebola protein and after Mutate All (Y) over 75% of the residues ended up being arginines or lysines. This has happened before: https://fold.it/portal/node/996185
Seems like Puzzle 971 might need some adjustments :)

Get Started: Download
  Windows    OSX    Linux  
Windows
(7/8/10)
OSX
(10.7 or later)
Linux
(64-bit)

Are you new to Foldit? Click here.

Are you a student? Click here.

Are you an educator? Click here.
Search
Only search fold.it
Recommend Foldit
User login
Soloists
Evolvers
Groups
Topics
Top New Users
Sitemap

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