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Capture images of the Covid-19 virus at atomic resolution.

Photographing the Covid-19 virus at atomic resolution, scientists discover its chemically infectious nature


The SARS-CoV-2 virus that causes the Covid-19 epidemic is just a spherical particle with a size of 100 nm. For ease of visualization, it is only 1/900th the diameter of a human hair. Using an electron microscope, a team of scientists at the Rocky Mountains Laboratory last month magnified this virus image 300,000 times, revealing the first detailed images of the structure of SARS-CoV -2.


These images confirm that SARS-CoV-2 is a corona virus strain with a structure of 4 parts: nuclear envelope (N), envelope (E), membrane (M) and spine (S). The artificial sheath forms the genetic core. It is again encased in proteins that make up the envelope and membrane of the virus.


Chụp được ảnh virus Covid-19 ở độ phân giải nguyên tử.

Chụp được ảnh virus Covid-19 ở độ phân giải nguyên tử.

The proteins mutate to the outside of the membrane, forming spikes that stick around the surface of SARS-CoV-2, giving it a crown-like appearance and a halo under the electron microscope.


It is this feature that has been used to name them, corona viruses with "corona" meaning "crown" or "halo". And again, these protein spikes play a very important role in the infection process of SARS-CoV-2 into host cells.



Research shows that when the viral spike finds the ACE2 (angiotensin-converting enzyme 2) receptors on the surface of human lung cells, they get inside and start taking over the cell to multiply. and cause disease.


Understanding the infection mechanism of SARS-CoV-2 through the ACE2 receptor is an important goal, because from that knowledge, scientists can develop a specific drug for Covid-19 or a specific type of drug. Vaccines work by blocking this cell infection mechanism.


Chụp được ảnh virus Covid-19 ở độ phân giải nguyên tử.

And recently, a team of Chinese scientists at the Key Laboratory of Biostructures in Zhejiang Province captured for the first time such images of the ACE2 receptor and protein spikes of SARS-CoV-2. resolution of 2.9 angstroms (0.29 nm), close to the atomic size (0.1-0.5 nm).


These 2D images were then folded and modeled using 3D software that explained for the first time the chemical infectious nature of SARS-CoV-2: Which molecular cluster of the spike protein was associated with which part? of the ACE2 receptor, by what type of chemical bond?


The ACE2 receptor image was rendered in 3D with atomic resolution.
The ACE2 receptor image was rendered in 3D with atomic resolution.

Based on this 3D real-time image, the scientists found that the protein spikes of SARS-CoV-2 actually consist of 2 subunits S1 and S2.


S1 contains the receptor binding domain (RBD), which is the weapon that the virus uses to bind to the peptisase (DP) domain on the ACE2 receptor of lung cells. Meanwhile, the S2 on the spine works to serve the virus itself, which is responsible for the fusion reaction on its protective membrane.


The images were taken under cryo-electron microscopy (cryo-EM), an imaging technique that can provide atomic resolution. In it, the Chinese scientists ordered recombinant and purified protein spikes, and then mixed it with ACE2 that they synthesized themselves.


That means this whole study did not use the complete SAR-CoV-2 virus. They're just taking pictures of the "scraped" viral spikes, like studying the fangs of a venomous snake.


The receptor binding domain (RBD), is the weapon that the virus uses to bind to the peptisase (DP) domain on the ACE2 receptor of lung cells.
The receptor binding domain (RBD), is the weapon that the virus uses to bind to the peptisase (DP) domain on the ACE2 receptor of lung cells.


Under cryo-EM microscopy, the scientists observed that during S1 binding to the ACE2 receptor, another cleavage site on S2 is exposed and cleaved by host proteases, a process process is very important for viral infection.


Each PD cluster on the ACE2 receptor allows only one viral RBD cluster to bind to. An extended loop region of RBD spans the α1 circular helix of ACE2-PD like a bridge.


The α2 helix and a loop connecting the nonparallel chains β3 and β4, of PD also make a limited contribution to RBD coordination. In the figure, these interactions are represented by the red dashed line:

Spikes of the SARS-CoV-2 virus (yellow), the ACE2 receptor on lung cells (green) and the chemical bonds between them.
Spikes of the SARS-CoV-2 virus (yellow), the ACE2 receptor on lung cells (green) and the chemical bonds between them.

The "cement" that binds the "bridgehead" of the RBD cluster north from the virus to α1 of PD interacts with the amino (N) and carboxyl (C) terminis. The N terminus binds to the RBD by hydrogen bonding. While some other segments of RBD bind to ACE2 through van der Waals forces.


Essentially, the chemical bonds that SAR-CoV-2 uses to enter human cells are similar to what the SARS virus did during the 2003 pandemic. However, it still has some of the most differences. determined, explaining the virus's higher affinity for cells, as well as the stronger spread of the current Covid-19 epidemic than the SARS epidemic 17 years ago:


Compare the binding snapshot of SARS-CoV-2 with ACE2 (orange and green) by superimposing it on the binding of the SARS virus to the same receptor (green and yellow)
Compare the binding snapshot of SARS-CoV-2 with ACE2 (orange and green) by superimposing it on the binding of the SARS virus to the same receptor (green and yellow)

The scientists said that both SARS and Codid-19 attack the ACE2 receptor found on the surface of lung cells. In addition, SARS had previously attacked both the intestines and kidneys of patients, where cells containing this receptor were also located. The heart also contains ACE2, but both SARS and Covid-19 let go of the hearts of patients, something scientists do not understand why.


Finally, with this new study, scientists hope to shed light on the infectious nature of the SARS-CoV-2 virus, providing an important document that will allow us to develop new strains of the virus. Treatment drugs and vaccines block the entry route of Covid-19.


The study was published in the journal Science.


















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