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.
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.