Pymol License11/2/2021
In the case of the B.1.1.7 variant, which is a variant that is thought to be 30-50 percent more infectious than other variants in circulation, the mutations are at a location that allow the spike protein to bind better to the ACE2 receptor. The variants of SARS-CoV-2 that we keep hearing about typically have different mutations on the spike protein. This spike protein binds to a receptor on the human cell called the ACE2 receptor, and this allows the virus to infiltrate the cell. This virus gets inside the human cells by using something called a spike protein. Uses are covered by the Universitys license for that specific content.But first, here’s some background on SARS-CoV-2: COVID-19 is a disease caused by a strain of coronavirus called SARS-CoV-2. If you have been issued a license file, instead choose: 'Browse' for the license file you wish to install and then click 'Install License' to install the license file.The University of Alberta Libraries licenses a broad range of content for use by.
![]() Pymol Download The SpikeThese are structures of proteins that have been solved through various laboratory techniques. To do this, you want to go to a website called the Protein Data Bank, which contains published protein structures. Click yes, and you’re all set!Next, you need to actually download the spike protein structure.Each variant of the coronavirus has multiple mutations. Type “ fetch 6vxx” to get the structure of the spike.Left: type “ show surface” to get an image of just the protein’s surface.Right: type “ color white” to make the protein white.Now, let’s try and visualize some mutations. To make this into a more “interpretable” image, just type in “ show surface”, and you should see a bumpy blob — this is essentially what the surface of the protein looks like! (For those who are curious: the red parts are oxygen atoms and the blue parts are nitrogen atoms.) To make the structure the same color, let’s say white, type in the following command: “ color white”. If you’re successful, you should see a stringy, cartoon appearance of the protein. Or you can just type in “ fetch 6vxx” where you see “PyMOL >” (see picture below). You can download what is called the “PDB file” here.![]() Pymol License For That(For more information on how changes in your DNA lead to changes in proteins, see this Khan Academy page.)There are many differences between the “original” and the B.1.1.7 variant, but for this post, I wanted to just focus on one mutation. Changes in the amino acid cause the protein to change — in the case of B.1.1.7 variant, the changes let it bind to the ACE2 receptor better. The DNA codes for amino acids, and amino acids make up the protein. Macbook air firmware passwordYou should see three separate red spots (or three different highlighted amino acids) since the spike is actually made of three identical subunits — these three subunits are what scientists collectively call “the spike protein” (see the three subunits in the video below). Now, you should have an image of the spike with this amino acid highlighted in red. Then, you can color this amino acid by typing “ color red, sele”.
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