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Installing Jmol and general usage
 
Jmol is a molecular modeling program many of you will use in Biochemistry.
 
Install Java if you have not already
Download Jmol 
Uncompress the zip file
Double-click on Jmol.jar in the uncompressed directory.
You may need to give your operating system permission to run Jmol.
            MacBook: System Preferences --> Security and Privacy --> General
            Windows: http://wiki.jmol.org/index.php/Support/Windows
 
Download and uncompress the COVID_Spike directory

File --> Console to get the command line console in Jmol.

Commands to be typed in the console window will be listed in Courier.

You may copy and paste the commands (in Courier) from this document into the console window.

 

Open files by going to File menu, finding the COVID_spike file directory, then Open (File --> Open)

                         

Right-Click (PC) or Control-click (Mac) to get pop-up menu.

Go to Style in the pop-up.

Menu commands will be listed in Helvetica. For example, to display the selected atoms in ball-and-stick style:

            Style --> Scheme --> Ball and Stick

 

In the image window, figure out how to zoom in and out, and how to rotate the molecule. On my computer (MacBook Pro), pressing down on the mouse pad with one finger and moving it rotates the molecule. Sliding up and down with two fingers without pressing down zooms the molecule in and out.

 

You should zoom and rotate ALL the molecules you examine after each display change.

 

Spike and ACE2 receptor complex

 

File --> Open spike_ACE2.pdb

     ribbons only

     select :S; color [0 0.5 1]

     select :R; color [1 0.5 0]

 

Select sidechains on the spike (S) within 6.0 Å of ACE2 (R) and vice versa, and then re-center on the interface:

     select within (6.0, :R) and :S and sidechain or within (6.0, :S) and not :S and sidechain

            View --> Define Center

 

Select atoms on ACE2 (R) within 6.0 Å of spike (S), and display as spacefill: 

     select within (6.0, :S) and :R

            Style --> Scheme --> CPK Spacefill

Select sidechain on spike (S) within 6.0 Å of ACE2 (R) and display as ball and stick: 

     select within (6.0, :R) and :S and sidechain

            Style --> Scheme --> Ball and Stick

 

List the spike atoms within 6Å of ACE2:

     show selected

 

What spike protein amino acid sidechains (NOT atoms) are at the interface with ACE2?

 

Spike and neutralizing antibody complex

 

File --> Open spike_neutralizing_Ab.pdb

     ribbons only

     select :S; color [0 0.5 1]

     select :A; color [1 0.5 0]

 

Select sidechains on the spike (S) within 6.0 Å of the antibody (A) and vice versa, and then re-center on the interface:

     select within (6.0, :A) and :S and sidechain or within (6.0, :S) and not :S and sidechain

            View --> Define Center

 

Select atoms on the antibody (A) within 6.0 Å of spike (S), and display as spacefill: 

            select within (6.0, :S) and :A

            Style --> Scheme --> CPK Spacefill

 

Select sidechain on spike (S) within 6.0 Å of antibody (A) and display as ball and stick: 

     select within (6.0, :A)  and :S and sidechain

            Style --> Scheme --> Ball and Stick

 

List the spike atoms within 6Å of the antibody:

     show selected

 

What spike protein amino acid sidechains (NOT atoms) are at the interface with the antibody?

 

Based on the two interfaces you have examined, what spike protein positions might the virus mutate to retain binding to the ACE2 receptor, yet reduce binding to neutralizing antibodies elicited by an earlier infection or vaccination with the original virus?

 

Questions on Canvas

 

Describe the SARS-CoV-2 genetic material.

 

How do SARS-CoV-2 viruses enter host cells?

 

Why are antibodies useful for defending animals from pathogens?

 

How are virus-producing infected cells dealt with?

 

Why is the immune response to a 2nd encounter with pathogen so much faster than the initial encounter?

 

What are traditional vaccines composed of?

 

What is novel about the Pfizer/BioNTech, Moderna, Johnson & Johnson, and Oxford/AstraZeneca vaccines compared to traditional vaccines?

 

Why might antibodies elicited against one version of a pathogen be less effective against other variants?

 

What spike protein amino acid sidechains are at the interface with ACE2?

 

What spike protein amino acid sidechains are at the interface with the antibody?

 

Based on the two interfaces you have examined, what spike protein positions might the virus mutate to retain binding to the ACE2 receptor, yet reduce binding to neutralizing antibodies elicited by an earlier infection or vaccination with the original virus?

 

Why does the wild-type spike protein adopt multiple conformations?

 

Why might mutations that lock spike protein to the pre-fusion conformation be more likely to elicit antibodies that block infection?

 

Can the engineered viruses in the Johnson & Johnson and AstraZeneca vaccines cause infections?


If you are unable to install Jmol, you may view this video to answer the questions. 
Navin Pokala, PhD
navin.pokala at nyit dot edu

Department of Biological and Chemical Sciences
New York Institute of Technology
Theobald Science Center, Room 423
​Old Westbury, NY 11568-8000
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