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1932: Symmetric Tetramer Design: H-bond Networks
Status: Closed


Name: 1932: Symmetric Tetramer Design: H-bond Networks
Status: Closed
Created: 12/18/2020
Points: 100
Expired: 12/25/2020 - 23:00
Difficulty: Intermediate
Description: Design a symmetric protein tetramer, with 4 identical chains that assemble together! 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.
Categories: Design, Overall, Symmetry

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bkoep's picture
User offline. Last seen 2 days 17 hours ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff

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 +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.

grogar7's picture
User offline. Last seen 1 hour 4 min ago. Offline
Joined: 10/03/2011
H-bond network bonus

For a symmetric trimer, this bonus accepts a maximum of 9 h-bonds. Shouldn't it be set for 12 h-bonds for a tetramer??

grogar7's picture
User offline. Last seen 1 hour 4 min ago. Offline
Joined: 10/03/2011
addendum to the above: it

addendum to the above: it seems that one would have to make 12 inter-unit bonds to get credit for 9 !!

bkoep's picture
User offline. Last seen 2 days 17 hours ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
You're right!

That's an oversight in the puzzle set up; we'll be sure to fix it in future tetramer puzzles!

Joined: 12/06/2008
Groups: Contenders
Why planar symmetry?

Dimers and trimers align with planar symmetry. In these puzzles, the tetramers also align in a plane. Why wouldn't they align in a tetrahedron, since that conformation is the most efficient way to cram four of something into a given sphere?

bkoep's picture
User offline. Last seen 2 days 17 hours ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
No particular reason

We could certainly design tetramers with tetrahedral (T) or dihedral (D2) symmetry instead of cyclic (C4) symmetry! The symmetry operators are different, of course, so those would require a different puzzle setup. But we have run D2 design puzzles in the past, and we will surely run more in the future.

A tetrahedral assembly does require a more extensive interface, since each subunit must make contact with all 3 of its partners. For this reason, I suspect it may be a more difficult design target than a C4 assembly (we've seen that large designed interfaces can jeopardize protein solubility).

Edit: Actually, I don't think we could design a true tetrahedron with only 4 protein subunits. A tetrahedron has 4x C3 symmetry axes. Each of your "subunits" would need to have perfect C3 symmetry, which is practically impossible for a single protein chain. Natural tetrahedral assemblies include at least 12 protein chains.

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