New RIT visual modeling of coronavirus leads to discovery of behavior of second cellular ‘touchpoint’

Science

HENRIETTA, N.Y. (WROC) — Rochester Institute of Technology announced in a press release Monday the publishing of a new paper from faculty member Gregory Babbitt and graduate student Patrick Rynkiewicz ’20 (bioinformatics and computational biology), ’21 MS (bioinformatics) that showed the ways the novel coronavirus might attach to cells.

They used a new system that combines genetic sequencing technology to gather data on proteins and video game level graphics processors, which outputs into a readout that allows Babbitt to see a simulation of the cell itself.

While Babbitt admits that the result may look something like a blob, this visual readout his team to see how protein cells move, with a reasonable degree of accuracy… As in they can measure movement down to nanoseconds, whereas cellular movement is most accurate measured in femtoseconds (Babbitt casually explains as a quadrillionth of a second).

This movement gives them the information that just looking at a genetic sequence can tell.

Using this new system, they were able to find that the SARS-CoV-2 virus has two touchpoints, and unlike other beta coronaviruses that are less harmful and are circulating currently among humans, it has a second protein “touchpoint” that is more “transient,” and drifts between the other available touchpoints on ACE 2 receptor in human lungs.

“Right at the beginning of the ACE 2, there’s these helical structures that the virus likes to likes to interact with,” said Babbitt. “And (lower on the cell) there’s two sites that had been mentioned in previous papers in Nature and Science… But we found a third.”

“It may be that this slipperiness allows it to crossover, so it’s not being highly specific, so it can really take an ACE 2 from a lot of species,” he said.

They hypothesize that this “molecular dynamic” movement might be why the SARS-CoV-2 virus made the jump from bats in China to humans, as well as what makes the virus and its variants so virulent.

They also hypothesize that newer variants are becoming better at latching onto one of the specific touchpoints.

Babbitt says that understanding this movement will allow virologists to possibly better understand how this virus can mutate, and while he says that his team’s analysis was just confined to the touchpoints, this could lead to better treatments and prevention methods.

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