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1891: Symmetric Trimer Design: H-bond Networks

Closed since about 2 years ago

Intermediate Overall Design Symmetry


September 16, 2020
Max points

Design a symmetric protein trimer, with 3 identical chains that assemble together! Note the Interaction Energy Objective, which will penalize poorly-scoring large residues that can lead to unwanted protein aggregation. 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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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 +3000)
Ensures that at least 30 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.

Bruno Kestemont Lv 1

After optimizing a monomer, when I freeze it and I move it to the direction of the other chains, the buried unsat filter changes even if the monomers are still far away from each other:

Moving from about 100 A to about 80 A, the BUNS changes from 4 buried to 6.
Then from 80 A to 50 A: no change (6).

Then turning it around at about 50 A: 13 BUNS.

Moving very far away: 15 BUNS

Credit Best to 4 BUNS (far away). Turning it on itself in order to parallel de trimers: 10 BUNS

bkoep Staff Lv 1

Yes, this is a side effect of the algorithm we're using to calculate BUNS.

The calculation uses a voxel grid to approximate whether each atom is buried or if it is exposed to water. This approximation is fast, but unfortunately it means that the calculation is sensitive to small translations and rotations of your protein.