User:Jeremiah C Hagler/SARS-CoV 2 Spike ACE2

Background Information

The SARS-CoV-2 spike protein is a key protein in the virus life cycle. The spike protein interacts with host cell receptors. In the case of the SARS-CoV-2 coronavirus, that receptor is ACE2, a membrane-bound protein commonly found on the surface of many types of epithelial cells all around the body, particularly in the respiratory tract. The viral spike protein binds to the host ACE2 protein when the virus encounters a receptive host cell. This binding triggers a complex series of protein interactions and rearrangements of spike protein tertiary and quaternary structure which results in the fusion of the viral lipid-bilayer envelope to the cell membrane and entry of the viral RNA genome into the host cell. The virus at this point now has access to the cellular machinery and will begin the biochemistry requireed for viral protein synthesis and genome replication.

Structure

Take a look at the complex structure on the right (you can press the spin button to stop roation of the molecule. You can manipulate the orientation of the molecule by click-dragging in any dimension. You can control the zoom level by using the middle wheel of your mouse (if you have one), spreading apart or bring two fingers together on your touch pad or touch screen.

1. How many polypeptides are shown in this structure? (Hint: count the number of differently colored units)

2. The spike protein is a homotrimer, made up of three identical subunits as you learned from the introduction to this lab. What are the colors of the three subunits that make up the homotrimer?

3. What color is the ACE2 receptor protein?

If you look carefully, you'll notice that the receptor-binding domain (RBD) of one of the three subunits (green) of the spike protein has projected out to interact with ACE2 molecule. This is a conformational change that the spike protein actually makes as it makes contact with the ACE2 receptor, and requires the action of a host-cell protease (an enzyme that cuts peptide bonds in proteins), known as furin, which cuts one of the spike protein subunits. Once cut, the RBD can rearrange into the projected-form, which allows a tight interaction between the spike protein and the ACE2 receptor. This conformational change can be seen in animated form [from [1]]to the right:

Let's focus in on the projected RBD domain. Click on the green link for a close up view of that RBD in isolation.

4. In this representation, what color is used for the alpha helices?

5. How many alpha helices are there in this structure?

6. What color is used for beta sheets?

Now, let's add the ACE2 receptor to the scene. Click on the link to see the RBD interaction with the ACE2 protein.

7. What kind of secondary structure(s) of the spike RBD appear to be most important for interaction with the ACE2 protein?

8. Which secondary structures on the ACE2 protein appear to be interacting with the RBD?

Now, let's take a closer look. Click on the popout button for the zoomed in RBD-ACE2 structure (bottom right of the structure box). A new window with the RBD-ACE2 structure will open. Then, right click on the 3D image (or ctrl-click for mac users), then:
a. "Select"-->"all"
b. Right click again, then "Style"-->"structures"-->"backbone"
c. Right click, then "Select"-->"proteins"-->"side chains"
Right click again, then "Style"-->"schemes"-->"sticks"

Now you are able to see all of the amino acid side chains in the two proteins.

• 7. If you were to alter amino acids in the RBD molecule to affect binding to the ACE2 protein, which would you alter? Keep in mind that amino acids within the alpha helices and beta sheets that have side chains that project towards the bound ACE2 protein play a crucial role in peptide binding. List 2 amino acids. (To answer this, move your cursor over an amino acid side chain (light blue) on the image in the area where you would alter something and let the program identify the amino acid for you (three letter code followed by a number at the beginning of the ID string that pops-up).

8. What two amino acids would you change on ACE2 to block binding of the coronavirus spike protein to the ACE2 receptor?