One aspect of the new coronavirus that makes it so contagious and difficult to control is its ability to defeat the body’s innate immune defenses.
The new study examines NendoU, a viral protein responsible for the virus’s immune evasion tactics. The structure of this critical protein is studied in detail using a technique known as serial femtosecond X-ray crystallography.
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For the first time, the NendoU protein has been imaged at a resolution as high as 2.5 angstroms at room temperature. The resulting structure reveals key details of protein flexibility, dynamics and other properties with unprecedented precision. Such structural information is critical in the development of new drugs and could aid in the development of therapeutics to combat SARS CoV-2.
“Our study focuses on how COVID-19 is hidden from the immune system by the NendoU protein,” says Rebecca Jernigan, first author of the study and a research associate at Arizona State University’s Center for Applied Structural Biodesign Research. “As we understand the structure and mechanics of NendoU better, we have a better idea of how to develop antivirals against it.”
The discovery makes it possible to manufacture drugs that target external changes in proteins, such as those described in the new study. Such therapeutics would be particularly attractive as they are less prone to drug tolerance.
The Biodesign Center for Applied Structural Research has made significant strides in this type of structural research by unraveling many complex biological structures. The center is led by the study’s principal investigator, Petra Fromme.
“This study is so innovative that it shows for the first time that differences in protein flexibility play an important role in the functional mechanism of the immune system, which can then respond to and prevent serious infections,” says Fromm.
viral intrigue
Viruses have developed quite complex strategies to easily get rid of the body’s defense mechanisms. Research points to a set of tactics used by most infectious coronaviruses, a group of pathogens that include those that cause COVID-19 (SARS CoV-2), severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS).
A new study sheds light on how the NendoU protein helps SARS CoV-2 ostensibly hide from the immune system. When a virus binds to a receptor on a cell’s surface, it inserts its genetic material into the cell, causing the cell to make multiple copies of the viral genome, which is DNA or, in the case of coronaviruses, RNA.
When viruses such as SARS CoV-2 replicate inside cells, the growing RNA strands form a tail at the end known as a poly-U tail. This tail is unique to RNA viruses.
Human cells are equipped with sensors tuned to detect invading RNA viruses because the poly-U tail identifies them as foreign invaders and allows the immune system to target them. Research has shown that SARS CoV-2 uses the NendoU protein to attach and then cut off the poly-U tail. When NendoU chews on its poly-U tail, it makes the virus less visible to the immune system.
master of disguise
To prevent NendoU from hiding the virus, researchers need high-resolution images of the protein’s 3D structure. So far, bulk structures of the NendoU protein have only been obtained using a technique known as cryo-EM, in which, under cryogenic conditions, a sample of interest is flash-frozen and visualized using electron microscopy or X-ray crystallography of large frozen crystals. . This provided important clues about the nature of NendoU. Unfortunately, more information is needed before we can proceed with the development of a drug to suppress NendoU and attack the SARS CoV-2 virus with the immune system.
To achieve this, researchers need to describe the structure in detail enough to know where each atom in the protein is. And ideally, the structure should be determined in conditions close to natural conditions at room temperature.
But most current methods severely damage the protein itself, so in most cases data collection is performed in cryogenic conditions where any microscopic movement is frozen. To achieve this atomic-scale resolution at room temperature, a special X-ray machine known as the XFEL (X-ray Free Electron Laser) was required.
In the current study, the scientists obtained the first images on the road to an atomic-scale structure. Known as femtosecond burst crystallography, this technique involves crystallizing a protein sample into billions of tiny microcrystals and then transmitting them in an extremely short jet of high-power X-rays at room temperature, producing tens of thousands of diffraction arrays. patterns, each from a small microcrystal.
Ultra-short X-ray pulses, lasting just a few tens of femtoseconds, leave behind X-ray damage to the crystals, allowing data to be collected at room temperature under nearly physiological conditions. To give you an idea of the highly compressed timescale of these X-ray bursts, a femtosecond is equal to one quadrillionth of a second. Computers are used to assemble large batches of these x-rays, allowing researchers to create detailed 3D protein structures and study their dynamic behavior.
The researchers used femtosecond X-ray crystallography to reveal the substrate-bound structure of the NendoU protein. In living cells this would be the poly-U tail of the RNA strand, but for the study, a smaller molecule known as citrate was found at the RNA-binding site.
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An advantage of X-ray free electron laser structural investigations is that biological events can be studied in close proximity to their natural physiological states. The present results show that the room temperature structure of the NendoU protein is more flexible than the cryogenic structure.
“As in previous trials, we also found that NendoU forms a hexamer (six identical NendoU proteins linked together),” says Debra Hansen, co-author of the paper and associate professor at the center. Additionally, the researchers found that one half of the protein was more flexible than the other half, meaning it was more rigid.
The structural details revealed by the XFEL light show that the NendoU operates in a two-step process. First, the harder half of the protein binds to the active site of the substrate (in this case, the citrate molecule). The flexible half of the hexamer also binds citrate (or RNA), but less strongly. The stiff half releases this strand as soon as it completes its task of separating the RNA strand. Then this rigid part becomes flexible and the flexible part becomes rigid and the cycle repeats. This scissor-like action of the two main components of NendoU helps to delete the signal indicating the presence of a virus in the cell, halting the immune response.
XFEL images of these movements provide a detailed map for possible drug design. Future builds using room temperature conditions will show these various movements, and each map will allow the most accurate calculation of computational tools to combat COVID.
Previously Focus He talked about a new type of coronovirus. According to experts, a new subtype of the disease could cause a wave of the disease in the world.
Source: Focus
Ashley Fitzgerald is an accomplished journalist in the field of technology. She currently works as a writer at 24 news breaker. With a deep understanding of the latest technology developments, Ashley’s writing provides readers with insightful analysis and unique perspectives on the industry.