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1995: Symmetric Trimer Design: H-bond Networks

Closed since almost 5 years ago

Intermediate Overall Design Symmetry

Summary

Created
May 19, 2021
Expires
Max points
100
Description

Design a symmetric protein trimer, with 3 identical chains of 60 residues each! 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.

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Comments

bkoep Staff Lv 1

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -150 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.

H-bond Network (max +1800)
Rewards networks that comprise at least 2 H-bonds involving core residues.
Between 1 and 9 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.

milkshake Lv 1

Hi frood, thanks for the report, it would help us if you could open up a solution where the crashing happens and use the "upload to scientists" feature. In the description box you could type some info about how to make it crash (for example, just click mutate and wait, or what-have-you.)

Thanks!

Bautho Lv 1

I don't really understand the H-bond network filter.

In one example, I have 4 blue H-bonds in a row.
Serine-OH to Aspartate-O to Glutamine-NH to Aspartate-O to Arginine-NH
It says Interface HBonds: 3 (0 credited)
However, I only see two Glutamine-NHs from a neighboring protein have 2 bonds to two different Aspartate-Os.
All other residues are in one individual protein.

Polars Satisfied: 58.8235 %
I don't really understand how this odd number is calculated?
It would be more helpful if you could write something like "4 out of 13 possible atoms satisfied" into the filter

bkoep Staff Lv 1

Yes, the H-Bond Network Objective is rather complicated, but that's because there are a lot of different aspects that make up a good H-bond network! You have probably already seen it, but there is a brief write-up about the Objective on the blog.

It's difficult to tell without seeing your solution, but it sounds like your network is below 75% satisfied so it will not receive any bonus. It does seem strange that it reports 3 interface bonds if you only see 2 bonds that span the interface. That could be a bug – can you share your solution with scientists?

That is helpful feedback about reporting the raw numbers for the satisfaction calculation! I think we should be able to address that.

Bautho Lv 1

Thanks for the reply, Brian.
Unfortunately I did not have time anymore for the puzzle and will share my solutions with the next puzzles :)