A new study published in the journal Nature Chemistry, reports the finding of glycan “gates” that helps SARS-CoV-2 to enter.
The findings show how glycans — molecules that make up a sugary residue around the edges of the spike protein — act as infection gateways.
The study’s lead author believes that the research team’s gate discovery could lead to novel therapies for SARS-CoV-2 infection. The virus is effectively stopped from opening to ingress and infection if glycan gates can be pharmacologically locked in the closed position.
The spike’s glycan coating deceives the human immune system by appearing to be nothing more than a sugary residue. Previous technologies that photographed these structures showed glycans in static open or closed positions, which didn’t pique scientists’ curiosity at first.
The researchers used supercomputing models to create dynamic pictures that showed glycan gates activating from one location to another, providing an unprecedented piece of the infection puzzle.
“We were actually able to watch the opening and closing. That’s one of the really cool things these simulations give you — the ability to see really detailed movies. When you watch them you realize you’re seeing something that we otherwise would have ignored. You look at just the closed structure, and then you look at the open structure, and it doesn’t look like anything special. It’s only because we captured the movie of the whole process that you actually see it doing its thing,” said the study author.
“Standard techniques would have required years to simulate this opening process, but with my lab’s ‘weighted ensemble’ advanced simulation tools, we were able to capture the process in only 45 days,” said Chong.
The computationally intensive simulations were first done on Comet at UC San Diego’s San Diego Supercomputer Center, then on Longhorn at UT Austin’s Texas Advanced Computing Center. The researchers were able to get atomic-level pictures of the spike protein receptor binding domain, or RBD, from over 300 different angles because of this processing capacity. Glycan “N343” was discovered to be the linchpin that pries the RBD from the “down” to the “up” position, allowing access to the ACE2 receptor on the host cell. N343 glycan activation is compared to a “molecular crowbar” process by the researchers.
The team created variants of the spike protein and tested to see how a lack of the glycan gate affected the RBD’s ability to open.
“We showed that without this gate, the RBD of the spike protein can’t take the conformation it needs to infect cells,” said the study author.
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