puzzle picture
1721: IL-7R Binder Redesign: Round 9
Status: Closed

Summary

Name: 1721: IL-7R Binder Redesign: Round 9
Status: Closed
Created: 08/28/2019
Points: 100
Expired: 09/01/2019 - 23:00
Difficulty: Intermediate
Description: Design a protein that binds IL-7R!

Interleukin 7 receptor (IL-7R) is a protein that helps regulate the human immune system, and is an important target in cancer therapy research. In this puzzle, players start with two frozen helices bound to the IL-7R target (also frozen). Players can fold and design about 20 residues flanking the binding helices, with the goal of creating a well-folded protein that can bind the IL-7R target! Players may also redesign residues on the backside of the binding helices, but residues at the IL-7R interface are frozen in place. The most promising designs will have lots of helical and/or sheet structure with only short loops, and will have a well-packed, buried core. There are several Objectives in place; see the puzzle comments for details.

This is the seventh ninth puzzle in the IL-7R binder series, meant to generate a large diversity of designs that can be tested in a high-throughput binding experiment! Due to time constraints, puzzles in this series will be online for only 4 days at a time. See the blog for more information. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!
Categories: Design, Overall

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1Go Science11,689100
2Anthropic Dreams11,64663
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4Beta Folders11,56421
5Contenders11,53311

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Comments

bkoep's picture
User offline. Last seen 10 hours 49 min ago. Offline
Joined: 11/15/2012
Groups: None
Objectives

Residue IE Score (max +500)
Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence (max +1000)
Ensures that at least 25% of residues are buried in the protein core.

SS Design (max +200)
Penalizes all CYS residues. Penalizes GLY, ALA, SER, THR in helices. Penalizes GLY, ALA in sheets.

Residue Count (max +100)
Penalizes extra residues inserted beyond 110, at a cost of 20 points per residue. Players may use up to 115 residues in total.

vakobo's picture
User offline. Last seen 1 hour 36 min ago. Offline
Joined: 06/05/2008
Groups: Russian team
SS Design bonus

i'v got +250 instead of +200

bkoep's picture
User offline. Last seen 10 hours 49 min ago. Offline
Joined: 11/15/2012
Groups: None
Strange

Hmm, that shouldn't be possible... Can you share your solution with scientists? Could be a bug.

robgee's picture
User offline. Last seen 19 hours 28 min ago. Offline
Joined: 07/26/2013
Seventh puzzle ?

Quote
"This is the seventh puzzle in the IL-7R binder series"

Really !! Are you sure ??

bkoep's picture
User offline. Last seen 10 hours 49 min ago. Offline
Joined: 11/15/2012
Groups: None
Good catch!

Glad to see some close reading of the puzzle descriptions ;)

vakobo's picture
User offline. Last seen 1 hour 36 min ago. Offline
Joined: 06/05/2008
Groups: Russian team
Upload

I've shared this solution. It is very unstable - any wiggle drops +250 bonus down to normal value

LociOiling's picture
User offline. Last seen 4 hours 58 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
moveable section of IL-7R

As noted by JSmith48 in global chat, segments 46-51 can move.

If you draw 3 bands from these segments to a point in space, and change the strength of each band to 10, wiggle will move the section a long way. The other snippets of IL-7R can't be moved this way.

When you disable or delete the bands, there is some tendency for 46-51 to migrate back closer to where it started. It never shows any red constraint lines, however, even with "show constraints" checked in view options.

bkoep's picture
User offline. Last seen 10 hours 49 min ago. Offline
Joined: 11/15/2012
Groups: None
Oops!

That was an oversight on our part; segments 46-51 are supposed to be fixed in place! I don't expect this to have a huge effect on the puzzle results, but we'll have to take a close look at the solutions after the puzzle closes.

LociOiling's picture
User offline. Last seen 4 hours 58 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
previous rounds have immovable IL-7R

I checked the previous four rounds of this series. Segments 46-51 don't move in these puzzles.

Joined: 06/06/2013
Groups: Gargleblasters
server crash -- would more time help

lots of us found ourselves locked out due to server shut down. If you need a revisit let us know, though Fiendish has a stunning fold for this

vakobo's picture
User offline. Last seen 1 hour 36 min ago. Offline
Joined: 06/05/2008
Groups: Russian team
stable SS Design +250

Shared it with scientists. Segment 65 became valid

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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