Special update on coronavirus puzzles

In this special update we take a look at some of the best-scoring antiviral proteins designed so far by Foldit players. We then step into the laboratory to see what testing these molecules is actually going to look like. See the blog for more details!

Check out the newest Coronavirus Binder Design: Round 3 puzzle!

This video features Lexi Walls, Ph.D., who recently published important research on SARS-CoV-2 (the virus that causes COVID-19).

(Thu, 03/12/2020 - 23:02  |  4 comments)
Joined: 09/24/2012
Groups: Go Science
Excellent

Your videos are excellent. Keep doing.

Just a question. If you know what is the binding site and possibly the human binding protein (entry point), why don't you give us the human protein for us to try to make a similar one ?

What is the role of the human protein? If we copy it, would it disturb some of the human protein function ?

bkoep's picture
User offline. Last seen 18 hours 56 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Good questions!

Yes, we do know how the human receptor binds to the CoV spike protein. In fact, that binding interaction is the starting structure for Beginner Puzzle (<150): Coronavirus!

You are also sharp to suggest that we mimic the human protein! That is the premise for the latest puzzle Coronavirus Binder Design: Round 3. In this puzzle, the starting structure includes a helix fragment from the human receptor ACE2 (the same as in the Beginner coronavirus puzzle). If we can design a new protein that includes this helix (and it folds up correctly), then our new designed protein should be able to make the same binding interactions with the CoV target.

The human receptor ACE2 is an enzyme that normally helps to regulate heart and kidney function (by breaking down a signaling peptide called angiotensin). The part of ACE2 that binds CoV is not directly involved in normal ACE2 enzyme function. We're pretty sure that we can copy the virus-binding part of ACE2 without interfering with normal ACE2 function—especially since we are only copying the surface residues of ACE2.

LociOiling's picture
User offline. Last seen 7 hours 29 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
for protein watchers

Here are the PDB entries for Dr. Walls' SARS-CoV-2 Spike Glycoprotein paper that bkoep cited:

Joined: 04/05/2020
Groups: None
CoV spike protein- binding interaction

just had to get this off my chest...looking at the spike receptors of this CoV-19 for a while is quite mesmerising , as such.
Is it at all possible through an early transmission( bat to human Etc)that that this spike protein is a cleverly mutated- new design of a fungal attack using its spiked receptors to bring on the array of clusters- thus magnifying and increasing the toxicity on migrating to the lungs..
So can we check and retrieve blood from suitable people who have recovered from the CoV-19 infection to retrieve any antibodies or similar and together with currently known anti fungal therapies( say for scabies-ringworm .. head lice... treatments... get them to bind in the petrie dish and see what happens and re introduce this resultant bind back into an infected Cov-19 patient on the premise this potential new antibody ( in the body of this spike protein will still interact in the cluster groups in the lung and through its receptor bind introduce this new antibody and en masse destroy this fake protein spike...I will now awaken from my dream state..my 5 cents worth that all started by just staring at this ugly spike protein- that looks like a parastic living arrangement.

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