2015: Symmetric D2 Tetramer Design: H-bond Networks

Closed since over 4 years ago

Summary

• Created: July 07, 2021
• Expires: July 14, 2021 at 23:00 UTC
• Max points: 100

Description

Design a D2 symmetric protein tetramer, with 4 identical chains of 70 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.

Top groups

• 11. SETI.Germany 1 pt. 15,125

Top evolvers

• 1. Bletchley Park 100 pts. 28,493
• 2. toshiue 74 pts. 27,607
• 3. mirp 54 pts. 27,508
• 4. Bruno Kestemont 38 pts. 27,487
• 5. NinjaGreg 27 pts. 27,487
• 6. silent gene 18 pts. 27,486
• 7. kyoota 12 pts. 27,484
• 8. Maerlyn138 8 pts. 27,482
• 9. Galaxie 5 pts. 27,130
• 10. phi16 3 pts. 26,891

Comments

[bkoep]

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

Core Existence: Monomer (max +2000)
Ensures that at least 20 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.