The novel coronavirus enters the human cell with the help of a spike protein that is present on its envelope. Usually, our body replies to them by producing antibodies during its course of searching the appropriate receptor that is ACE2. But unfortunately, our body cannot recognize the virus particle during its entry into the cell. The answer to why is due to the presence of the sugar (glycans) that coats the spike protein. As a result, the virus camouflages itself as harmless from the defending antibody and easily enters the host cell.
Researchers have uncovered the atomic makeup of the sugary shield on the coronavirus by using Frontera supercomputer at Texas Advanced Computing Center (TACC). Simulation and modeling explain that the shield, called glycans, prime the virus for infection by changing the shape of its spike protein. Rommie Amaro, a professor of chemistry and biochemistry at UCSD, and colleagues have used computational methods to build data-centric models of the virus, followed by computer simulation to find out the answer to various questions.
They started with experimental datasets that showed the structure of the virus, including cryo-EM structures from the Jason McLellan Lab of the University of Texas at Austin, and from the lab of David at the University of Washington. These help the researchers to look at the structure more clearly. Also, the computer simulation has provided a cohesive picture of the spike protein along with the glycans and it also shows how exactly it looks like.
Roles of glycan in the spike protein
After analyzing the structure, scientists found the functions of the glycan in the spike protein. Initially, we have seen how this glycan helps in protecting the virus from the host antibody. Glycan, a sugar-like molecule coat each of 65-odd spike protein that adorns the coronavirus. It covers the surface of the viral spike protein, which is the most exposed part responsible for the initial infection of the host cell.
The study clearly shows that the spike protein has to undergo a large structural change to infect the human cell. For that to happen, the receptor-binding domain has to lift some pieces of the spike protein over the glycan shield. This holds well for open conformation. In the case of closed conformation, the shield completely covers the spike protein and blocks them from entering the cell. Amaro also said that in the open conformation, two glycans prop up the protein which makes them understand the role of glycans is not just restricted to shielding, but also in activating some chemical groups to provoke the spike proteins. When these processes are done, it is efficiently locked with te receptor and loaded into the human cell.
Even small research can make a big difference in succeeding war against COVID-19. This research team has used about 2.3 million Frontera node hours for molecular dynamics simulation and modeling to conclude the results. Thanks to Frontera for giving such information about the mechanism of how proteins move even in microseconds or milliseconds at a relative dynamic motion.
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