The question of where we're going with the design puzzles was also raised in chat the other day.
The science team never tells us everything, but there might be some clues to what they're looking for in the recent puzzles.
The current design puzzles don't have don't have secondary structure limits. For a long time, there was a penalty if you had more than half the segments in helixes.
They've also removed the ideal loops and core exists filters (conditions or objectives). There still some restrictions on which amino acids you can use where, and the big rings get some special attention, but it's much more of a protein sandbox than it was for a while.
The surfin' hot dogs that became so familiar will still score well, but the current design rules favor helical bundles.
We've also seen the return of hydrogen bond network puzzles, and these puzzles just happen to involve helical bundles.
In the PDB, there are some examples of designed helical bundles from the Baker Lab, such as 4UOS and 4TQL. They're not exact matches for anything we've seen, but do seem to be somewhat related.
The article High thermodynamic stability of parametrically designed helical bundles from the Baker Lab gives some background on where these proteins came from.
There's also De Novo Design of Helical Bundles as Models for Understanding Protein Folding and Function (not from the Baker Lab), with another take on designing with helixes.
Both these papers are a few years old, but the hydrogen bond network puzzles seem to be pointing toward some new activity. Maybe the recent changes to design puzzle objectives are suggesting a parallel track.
One thing that jumps out is that scientists have been successful at getting these lab designs to fold up on their own. Maybe some helical bundles designed by Foldit players will also make the cut. Someday the Design Puzzle Results page on the wiki may get a few more entries.
