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2009: Symmetric D2 Tetramer Design: H-bond Networks
Status: Closed

Summary

Name: 2009: Symmetric D2 Tetramer Design: H-bond Networks
Status: Closed
Created: 06/23/2021
Points: 100
Expired: 06/30/2021 - 23:00
Difficulty: Intermediate
Description: Design a D2 symmetric protein tetramer, with 4 identical chains of 60 residues each! Unlike the cyclical C4 symmetry that we are used to, the proteins in this puzzle will come together as a "dimer of dimers" with D2 symmetry. The H-bond Network Objective encourages players to build buried, satisfied H-bond networks at the interface between symmetric chains. H-bond networks are a great way to introduce polar residues at the interface, but it's important that all of the bondable atoms make hydrogen bonds! We've also adjusted the H-bond Network Objective so that poor-scoring H-bonds may not contribute to networks; poor-scoring H-bonds will be displayed in red. This puzzle uses the Buried Unsats Objective, with a large penalty for buried polar atoms that can't make H-bonds. In this puzzle, there are no limits on the Complex Core, but we've included the Complex Core objective so players can see the core residues that can be incorporated into H-bond Networks.
Categories: Design, Overall, Symmetry

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Comments

bkoep's picture
User is online Online
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -200 points per atom (not including symmetric copies).

Core Existence: Monomer (max +1600)
Ensures that at least 16 residues are buried in the core of the monomer unit.

Core: Complex (max +0)
Awards no bonuses or penalties. Click Show to see which residues count as "Core" for the H-bond Network objective.

Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.

H-bond Network (max +2400)
Rewards networks that comprise at least 2 H-bonds involving core residues.
Between 1 and 12 H-bonds should cross the interface between symmetric units.
Networks must be at least 75% satisfied (i.e. 75% of all bondable atoms in a network must make a H-bond).

SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA in helices.

Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.

alcor29's picture
User offline. Last seen 4 hours 56 min ago. Offline
Joined: 11/16/2012
ALA loaded incorrectly

I could not load an alanine in a loop because it was greyed out. Don't think that's intended.

jeff101's picture
User offline. Last seen 14 hours 27 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Does auto secondary structure say the segment is helix or sheet?

I'm guessing that if you run auto secondary structure
on that "loop" segment, Foldit will say the segment is
a helix or sheet instead of a loop. Maybe if you distort 
that segment enough that its backbone hydrogen bonds 
break, it will be treated as a loop instead. You might 
also try using the Blueprint Tool to place a short ideal 
loop there. Another idea is to try mutating to proline
before mutating to alanine. Proline's backbone N won't
form hydrogen bonds like other amino acids do. Maybe
this will force the segment to become loop so you can
then mutate it to alanine. Yet another idea is to find
the segment in the Rama Map and move it out of the red
and blue regions (I think this can be done in the 
Selection Interface). Then mutate it to alanine. Then 
move it in the Rama Map back to where it started.

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