puzzle picture
1986: Biotin Ligand Binder Design
Status: Closed

Summary

Name: 1986: Biotin Ligand Binder Design
Status: Closed
Created: 04/28/2021
Points: 100
Expired: 05/05/2021 - 23:00
Difficulty: Intermediate
Description: Design a binding pocket for the biotin ligand! Biotin is an important vitamin, and is necessary for the regular function of many metabolic proteins. One bacterial protein called streptavidin binds to the biotin ligand extremely tightly. The biotin-streptavidin pair is well known for being one of the tightest ligand-binding interactions in all of biology. We'd like to design proteins that can bind ligands just as tightly, but this is a difficult protein design challenge. The streptavidin protein has a binding pocket that fits closely around biotin ligand and satisfies all of its buried polar atoms, and this is essential for the tight binding between the two molecules.

In this puzzle, players are challenged to design a binding pocket for biotin. We've provided the streptavidin backbone as the starting structure, but players can completely redesign the protein or reposition the ligand within the binding pocket. Try to design a binding pocket with high Contact Surface and zero BUNS! See the puzzle comments for Objective details.
Categories: Design, Overall

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Comments

bkoep's picture
User offline. Last seen 1 day 16 hours ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

Contact Surface Metric (max +2000)
Measures how much of your binder surface is in close contact with the target protein. The goal Contact Surface is 200 or more.

Buried Unsats (max +500)
Penalizes 100 points for each polar atom that cannot make any hydrogen bonds.

OWM3's picture
User offline. Last seen 19 hours 45 min ago. Offline
Joined: 03/08/2020
Groups: Gargleblasters
The puzzle looks broken.

The puzzle looks broken.

OWM3's picture
User offline. Last seen 19 hours 45 min ago. Offline
Joined: 03/08/2020
Groups: Gargleblasters
Whatever

You may ignore this comment, I had to restart my foldit instance to fix a damn glitch :)

spdenne's picture
User offline. Last seen 14 hours 6 min ago. Offline
Joined: 10/01/2011
Groups: Void Crushers
This puzzle crashes (on windows)

****** Encountered Crash at ..\..\..\source\src\core\chemical\ResidueType.cc:4071
unknown atom_name: ' CA ' in residue BTN

milkshake's picture
User offline. Last seen 1 day 23 hours ago. Offline
Joined: 07/17/2019
Groups: None
Thanks

Thank you spdenne, we have a lead on how to fix this.

milkshake's picture
User offline. Last seen 1 day 23 hours ago. Offline
Joined: 07/17/2019
Groups: None
In the meantime, disabling

In the meantime, disabling the view option "Show backbone issues" should prevent the crash.

spdenne's picture
User offline. Last seen 14 hours 6 min ago. Offline
Joined: 10/01/2011
Groups: Void Crushers
Thank you

for the work-around

Joined: 12/07/2007
Groups: Contenders
Its hard to do much redesign

Its hard to do much redesign when you can't add or delete segments.

bkoep's picture
User offline. Last seen 1 day 16 hours ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
That's good to know!

We probably don't want to allow extra residues in these puzzles. But in future puzzles we should be able to allow deletions and re-insertions.

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