Design a binder against coronavirus! This puzzle is similar to Rounds 1 and 2 of our Coronavirus Binder Design challenge. but with tighter limits on the allowed number of segments. The starting structure has 177 segments, and players may use no more than 182 total. See the Foldit blog for tips on making a successful protein binder!
In late 2019, a new highly-infections virus emerged out of Wuhan, China. This virus belongs to the coronavirus family, and is similar to the virus that caused the SARS epidemic in 2002. Coronaviruses display a "spike" protein on their surface, which binds tightly to a receptor protein found on the surface of human cells. Once the coronavirus spike binds to the human receptor, the virus can infect the human cell and replicate. In recent weeks, researchers have determined the structure of the 2019 coronavirus spike protein and how it binds to human receptors. If we can design a protein that binds to this coronavirus spike protein, it could be used to block the interaction with human cells and halt infection!
In this puzzle, players are presented with the binding site of the coronavirus spike protein. The backbone and most of the sidechains are completely frozen, except for flexible sidechains at the binding site, where the spike protein normally interacts with the human receptor protein. Players can design a new protein that binds to these sidechains, blocking interactions with the human receptor. In order to bind the coronavirus target, designs will need to make lots of hydrophobic contacts and H-bonds with the flexible sidechains at the binding site. But designs will also need to have lots of secondary structure (helices or sheets) and a large core, so that they fold up correctly! See the puzzle comments for Objective details.
Residue Count (max +275)
Penalizes extra residues inserted beyond the 177, at a cost of 55 points per residue. Players may use up to 182 residues in total.
Interaction Energy (max +500)
Monitors that all PHE, TYR, and TRP residues are scoring well.
Core Existence (max +2400)
Ensures that at least 25 percent of residues are buried in the core of the monomer unit.
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.
SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA in helices.
If we can't drag the segments we work on and only the "Arrow" tool is available, how can we expect to design a protein that is useful? We will spend more of our time fighting the User Interface rather than the design. I watched jeff101 design videos, and they are now useless.
Is this intentional that the tool-set has been reduced?
All of the regular design tools should be enabled in this puzzle. Some parts of the target protein are frozen, but you should still be able to pull on any part of the designable chain.
