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1864: Symmetric Trimer Design: Limited Interface

Closed since over 2 years ago

Intermediate Overall Design Symmetry


July 15, 2020
Max points

Design a symmetric protein trimer, with 3 identical chains that assemble together! This puzzle has no H-Bond Network objective, but there is "Core Limit: Complex" objective meant to limit the size of the interface between symmetric chains. An interface that is too large, with too many orange hydrophobics, can prevent the individual subunits from folding properly. The "Core Limit: Complex" objective will incur penalties if there are too many buried residues in the total assembly. 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 +2000)
Ensures that at least 20 residues are buried in the core of the monomer unit.

Core Limit: Complex (max +500)
Checks that no more than 72 residues are buried in the symmetric complex, including the interface between monomer units.

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

HuubR Lv 1

The last sentence of the Description ("no limits on the Complex Core", "H-bond Networks") confuses me. It seems to contradict the first part of the description: "no H-Bond Network objective, but there is "Core Limit: Complex" objective".

Was the last sentence unintentionally copied from the previous Symmetry puzzles, or am I missing the point here?

bkoep Staff Lv 1

The last sentence was a mistake that was shamelessly copied from previous puzzles. I've updated the puzzle description.