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1998: Symmetric D2 Tetramer Design: Limited Interface

Closed since almost 5 years ago

Intermediate Overall Design Symmetry

Summary

Created
May 26, 2021
Expires
Max points
100
Description

Design a D2 symmetric protein tetramer, with 4 identical chains of 80 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. 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. See the puzzle comments for more Objective details.

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Comments

bkoep Staff Lv 1

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

Core Existence: Monomer (max +2200)
Ensures that at least 22 residues are buried in the core of the monomer unit.

Core Limit: Complex (max +500)
Checks that no more than 116 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.

Bautho Lv 1

I can compensate the (probably too many) orange residues at the interfaces by having more green residues inside the monomer's core (instead of orange ones), which gives me full bonus.
Is this intended?

BootsMcGraw Lv 1

If there is no bonus for making H-bonds, then how do we know we have the monomers correctly making a complex? Is there some other metric that indicates we have what the scientists want?

I ask this, because all arrangements of the monomers that are close to each other that I have tried result in drastic score reductions, even when BUNS and clashes are removed. What's the point of bringing monomers together, if doing so doesn't result in improvement?