1980: Symmetric Tetramer Design: H-bond Networks

Closed since almost 5 years ago

Summary

• Created: April 14, 2021
• Expires: April 21, 2021 at 23:00 UTC
• Max points: 100

Description

Design a symmetric protein tetramer, with 4 identical chains that assemble together! This puzzle includes a Secondary Structure Objective, so no more than 50% of your design can form helices. 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

• 1. Go Science 100 pts. 21,151
• 2. Contenders 70 pts. 20,791
• 3. Beta Folders 47 pts. 20,655
• 4. Anthropic Dreams 30 pts. 20,124
• 5. Gargleblasters 19 pts. 19,671
• 6. Marvin's bunch 11 pts. 19,371
• 7. Void Crushers 7 pts. 18,641
• 8. L'Alliance Francophone 4 pts. 18,315
• 9. BOINC@Poland 2 pts. 15,896
• 10. Australia 1 pt. 14,941

Top soloists

• 11. HuubR 58 pts. 19,559
• 12. mirp 55 pts. 19,556
• 13. dcrwheeler 52 pts. 19,516
• 14. martinzblavy 49 pts. 19,345
• 15. frood66 46 pts. 19,343
• 16. Vinara 43 pts. 19,174
• 17. Galaxie 41 pts. 19,074
• 18. robgee 38 pts. 19,065
• 19. hpaege 36 pts. 19,016
• 20. spdenne 34 pts. 18,641

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.

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).

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

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.

Secondary Structure (max +500)
No more than 50% of residues may form helices. Extra helices are penalized at 10 points per residue.

[jeff101]

<pre>It would be helpful if web pages like this for future Symmetric Design Puzzles would say how many residues are in each monomer.

Next, it would be nice if some tetramer puzzles would
flip adjacent monomers with respect to each other. I
think most of the tetramer puzzles so far have had all
4 monomers pointing the same direction (you might call
this a uuuu (all-up) configuration), but some tetramer
designs I'd like to try would work better with a udud
(up-down-up-down) configuration, in which adjacent
monomers point in opposite directions. It might also
be interesting to try designing tetramers with a uudd
(up-up-down-down) configuration.

Finally, I still have some trimer design ideas, so I
ask that you post at least one more trimer design
puzzle.

Thanks!</pre></code>