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1921: Designable Linker: Coronavirus Spike Binder

Closed since almost 2 years ago

Intermediate Overall Design


November 25, 2020
Max points

This is the fourth puzzle in the designable linker series! We are providing parts of two of the best-known designed binders to the SARS-CoV-2 spike, and are challenging players to link them together with a rigid linker! The two helical bundles are the parts of the two binders. They are currently connected with a flexible alanine linker that needs to be redesigned. We have also included the parts of the actual spike that are within 15 angstroms of the termini of the binders, so you know what regions your binder has to avoid to prevent clashing. The big thing for puzzles like these is to have buried hydrophobics at the interface between the linker and the binder helices. Packing the linker against the helices can help it maintain its shape.

Currently everything is frozen except for the linker and the sidechains of several residues that can pack nicely with any designed linker. The linker residues are completely designable. The two binder domains are held in place with strong constraints.

We have included a few objectives to help players generate well-folded designs. They are the same as in the previous puzzle.

It is a difficult problem to design a linker that can hold the binders in place. This type of puzzle is new for Foldit, and we are excited to see what players come up with! Good Luck and Happy American Thanksgiving!

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neilpg628 Staff Lv 1

Residue Count (max +550)
Penalizes extra residues inserted beyond the starting 240, at a cost of 55 points per residue. Players may use up to 250 residues in total.

Core Existence (max +2400)
Ensures that at least 35 percent of residues are buried in the core of the monomer unit.

Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.

SS Design (max +500)
Prohibits 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.

BootsMcGraw Lv 1

Anyone else experiencing constant crashing of the game while playing this puzzle? There is no one action I do that causes the crash.