Placeholder image of a protein
Icon representing a puzzle

1945: Designable Linker: Coronavirus Spike Binder

Closed since about 5 years ago

Intermediate Overall Design

Summary

Created
January 20, 2021
Expires
Max points
100
Description

This is the twelfth 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 to encourage structural rigidity. Packing the linker against the helices can help it maintain its shape. We are allowing for select residues on the binders to be fully designable to encourage hydrophobic packing.




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. The major new one is the ContactMolecularSurfaceScore objective that was just released into Foldit. This is a combination of two different Rosetta metrics that are supposed to reward complexes where the linker has good shape complementary and low binding energy with respect to the binders. This should help keep the linker rigid. As we get more data on the proper threshold values, we hope that this will help binder design across a range of interfaces. We have capped the objective at your CMS + 700. We have also removed the Secondary Structure Objective to encourage a diverse pool of solutions.

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!

Top groups

  1. Avatar for Rechenkraft.net 11. Rechenkraft.net 1 pt. 6,449
  2. Avatar for Trinity Biology 12. Trinity Biology 1 pt. 6,295
  3. Avatar for Biochem-AD17 13. Biochem-AD17 1 pt. 5,915
  4. Avatar for Team China 14. Team China 1 pt. 5,852
  5. Avatar for Dr. Moore BIO 181 15. Dr. Moore BIO 181 1 pt. 2,016
  1. Avatar for Enzyme
    1. Enzyme Lv 1
    100 pts. 13,941
  2. Avatar for grogar7 2. grogar7 Lv 1 97 pts. 13,748
  3. Avatar for phi16 3. phi16 Lv 1 93 pts. 13,744
  4. Avatar for spvincent 4. spvincent Lv 1 89 pts. 13,596
  5. Avatar for ichwilldiesennamen 5. ichwilldiesennamen Lv 1 86 pts. 13,488
  6. Avatar for ucad 6. ucad Lv 1 83 pts. 13,485
  7. Avatar for ZeroLeak7 7. ZeroLeak7 Lv 1 79 pts. 13,238
  8. Avatar for NinjaGreg 8. NinjaGreg Lv 1 76 pts. 13,226
  9. Avatar for LociOiling 9. LociOiling Lv 1 73 pts. 13,121
  10. Avatar for nspc 10. nspc Lv 1 70 pts. 13,099

Comments

Deleted user

Residue Count (max +250)
Penalizes extra residues inserted beyond the starting 240, at a cost of 25 points per residue beyond 250. Players may use up to 260 residues in total.

Core Existence: LCB1 (max +2400)
Ensures that at least 34 percent of residues are buried in the core of the LCB1-linker unit.

Core Existence: LCB3 (max +2400)
Ensures that at least 34 percent of residues are buried in the core of the LCB3-linker unit.

Core Existence: Linker (max +2400)
Ensures that at least 35 percent of residues are buried in the core of the LCB3-linker 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.

ContactMolecularSurface (max +700)
Checks that the designed linker has an energetically favorable interface with the binders.
</br>

grogar7 Lv 1

It is stated in the puzzle description and Objectives list above that CMS bonus is capped at 700. I just started designing a linker and have 892 points under CMS bonus. 'nuff said!

Deleted user

Hi Grogar
The puzzle description says the CMS is capped at your CMS + 700. The CMS score should be visible in the objectives panel and you will never get more than 700 beyond that.