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??
addendum to the above: it seems that one would have to make 12 inter-unit bonds to get credit for 9 !!
That's an oversight in the puzzle set up; we'll be sure to fix it in future tetramer puzzles!
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?
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.
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.