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This thread will cover an analysis of the protein structure of the COVID-19 Spike Protein (S) using readily available protein structural evaluation tools. As well as countering claims that the virus was produced in a lab. The resources here are available to you and are Free.
Feel free to work along with me or work along with this thread in order to determine, for yourself, information regarding the structure of the Spike Protein. (Indicated in Red)
1. Visualizing the Spike Protein.
First, you will need to download Pymol: https://pymol.org/2/ This program will allow you to take information from the Protein Database (PDB) and visualize numerous proteins found in the wild, including SARS-COV-2 Spike Protein.
First, you will need to download Pymol: https://pymol.org/2/ This program will allow you to take information from the Protein Database (PDB) and visualize numerous proteins found in the wild, including SARS-COV-2 Spike Protein.
We will be using the SARS-COV-2 PDB Code (6VXX): https://www.rcsb.org/structure/6VXX Here is a link to the datasheet regarding the information obtained by structural biologists.
In your loaded Pymol, go to the command line and type in "Fetch 6VXX", then press "Enter"
In your loaded Pymol, go to the command line and type in "Fetch 6VXX", then press "Enter"
This is the first step in visualizing the Spike Protein. You can get a feel for the structure of the spike by twirling the spike protein around in 3D space. As you will notice, the Spike protein has 3 subsections, that's called a trimer, this is specifically a homotrimer.
Next, we will go to "Display --> Sequence" in order to see the sequence of this protein. We will be obtaining the FASTA file from the website, but these different letters correspond to the various types of amino acids.
Now, we will go to the corresponding FASTA file which is located here in order to find out some information regarding this spike protein. You can follow this link:
https://www.uniprot.org/uniprot/P0DTC2
Scroll down to "Sequence" and click on it. You'll now get the amino acid sequence.
https://www.uniprot.org/uniprot/P0DTC2
Scroll down to "Sequence" and click on it. You'll now get the amino acid sequence.
The FASTA file reads out every amino acid in the spike protein in order - this can be used in order to confirm a variety of concepts in protein biochemistry. We'll start by verifying the proof on http://uniprot.org regarding the Transmembrane Helix.
From this, we're going to do our first scientific confirmation of another scientist's work! Scroll down to Subcellular Location on the Uniprot website. Find "Transmembrane Helix". We're going to confirm the presence, first, of a transmembrane helix.
A Transmembrane helix is a secondary structure that is present through a membrane as seen in Pink here. We will be going to the TMHMM Server v. 2.0 to determine the presence of this transmembrane helix: http://www.cbs.dtu.dk/services/TMHMM/
Now, with your FASTA file - copy and paste it to this website as marked here (Img 1). Image 2 shows the file copy and pasted. Then click "Extensive with graphics" and "Submit".
Congratulations, we've verified the location of our transmembrane helix! We get a reading of 1214-1236 amino acid (Residue) positions for the TM helix. The Uniprot website says 1214-1234. Within range, which is excellent.
Now let's see if this coronavirus was 'built in a lab'. We will compare it to several other coronaviruses that we know: MERS-COV ( https://en.wikipedia.org/wiki/Middle_East_respiratory_syndrome) will be our first attempt. Again, go to the Uniprot website and fetch the FASTA file for the spike protein.
https://www.uniprot.org/uniprot/A0A140AYZ5 Uniprot website for the MERS-COV Spike Protein. Again, go down to Sequence and click "FASTA"
Okay, now that we have both MERS-COV and SARS-COV-2 Spike protein Fasta files, we need to compare them. For that, we'll use BLASTp. This program compares amino acid sequences and looks for 'identity matches'. https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=blasttab
After copy and pasting the MERS-COV Spike Protein sequence and the SARS-COV-2 Spike Protein Sequence, you can "BLAST" it and get your alignment and identity data.
From this result, we obtain an Identity of 34.82%! Okay, so what does this value mean?
1. A protein identity of 34.82% indicates that the spike proteins of MERS and SARS-COV-2 are different.
2. This protein identity is the result of evolutionary shifts in the protein structure, not lab-grade production, as you would see a much higher percentage identity.
2. This protein identity is the result of evolutionary shifts in the protein structure, not lab-grade production, as you would see a much higher percentage identity.
3. If the percentage identity was much higher (90%+) we might say that these spike proteins are very similar to one another, and then that would indicate scientists coded to produce this spike protein. However, that is NOT the case as we see a % rating of 34.82%. It is distinct.
Please list your questions and inquiries below, I'll be happy to respond to them.
This separate website further indicates that other scientists believe that "Two features of the virus, the mutations in the RBD portion of the spike protein and its distinct backbone, rules out laboratory manipulation as a potential origin for SARS-CoV-2." https://www.sciencealert.com/here-s-what-scientists-think-of-the-coronavirus-was-made-in-a-lab-rumour
