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New Delhi: Scientists at the Indian Institute of Science Education and Research (IISER) Kolkata have decoded various dynamic compositions of the SARS-Kovi-2 spike protein – a nuclear machine that allows the coronavirus to enter our cells. Scientists say the research could serve as a ‘recipe’ for Kovid-19 vaccine developers.
Most vaccines developed worldwide work on a simple basic principle: delivering the body to spike proteins – which form protrusions appearing on the outer surface of the novel coronavirus – confusing the body into believing it has been attacked. Stimulates a pathogen and therefore the immune response.
For this reason, the 3D structure of the spike protein was one of the first to be thoroughly studied and characterized, and even now, researchers are trying to learn as much as possible about the spike protein of SARS-Covy-2.
Also read: Scientists claim coronavirus progression – ‘spike’ protein map could pave way for vaccination
Progress of IISER
The stability of each biomolecular structure is governed by a parameter called ‘free energy’ which is fundamental in understanding how it will react with the surroundings of the molecule.
What scientists at IISIR Kolkata have done is describe this energy-free energy release profile for various compositions of the SARS-Kovi-2 spike protein.
Spike proteins are made up of three interconnected chains of amino acids, the building blocks of proteins, said Sushmita Roy, an assistant professor at IISER Kolkata.
The interactions between these chains cause a very unique set of dynamics in the spike protein, which Roy describes as the “dance of the spike protein”. These interactions can cause the top of each chain of amino acids to rotate upwards or downwards. The continuous shift from top to bottom position creates a ‘dance’.
In a study published in Journal of Physical Chemistry Letters, The team identified states in which the spike protein, SARS-CoV-2, helps host human cells.
“When the chains are upwards, they become more exposed, which helps them find and build host cell receptors.”
According to the researchers, these states stimulate the human body’s immune response, and therefore understanding it helps in the formulation of vaccines that induce better immunity.
The team used existing data on the structure of the spike protein to discover the ‘free energy’ associated with the various compositions and determined which structures lead to affinity for the ACE2 receptor, the enzyme with which the spike protein enters. Human cells.
“In our study, we found possible structural structures in spike proteins. We found that when one or two chains are terminated, ACE2 receptors can bind very well, ”Roy said.
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How study can help
The researchers said in the study that the interaction-level information of spike proteins could provide a deeper insight into the development of effective therapeutic targets as well as design vaccines.
Most vaccine formulations mimic the coronavirus spike protein, making the body believe it has been attacked by the virus. As a result the body launches an immune response, and also learns to recognize spike proteins. This allows the body to prepare with a stronger immune response to deal with the real, live virus next time.
“We can say that our study is like a recipe for manipulating spike protein. Now that we know the molecular level mechanism of spike protein, vaccine manufacturers can tweak the amino acid chain to get the best configuration of spike protein.
This is not the first time a team has attempted to decode the formation of a molecular layer of spike protein. However, this previous study used cryogenic electron microscopy (cryo-EM) which failed to capture the changing dynamics of the structures.
The IISIR Kolkata team’s computational study, however, was able to create a detailed map of structural changes in response to spike protein interactions.
The study also highlighted some of the differences between the SARS-COV-2 spike structures and the spike proteins of the SARS virus that caused the epidemic in 2003.
“Although the structures are very similar, the dynamics of the spike protein are different,” Rae said.
The up-and-down movement in SARS-Cavi-2 viruses is more frequent than the dynamics of spike proteins in SARS and MERS viruses, which may be one reason why the novel coronavirus spreads so fast, he added. .
Also read: The world’s most powerful supercomputers have joined the race to stop coronaviruses
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