If you thought you were familiar with the SARS-CoV-2 spike protein, think again. According to a new study, the spike protein has a secret feature—a starting gate. It consists of glycans. When the gate is closed, the spike protein’s receptor binding domain (RBD) stays hidden, safe from the prying eyes of the immune system. When the gate is open, out leaps the RBD.

At this point, the starting gate analogy breaks down. The RBD is no thoroughbred. It doesn’t have to be. The race to the host receptor is too short.

That last observation suggests that it might be hard to rein in RBD, once it is in the running. So, it might be best to keep the starting gate closed. In fact, this possibility was raised in the new study, which was led by Rommie Amaro, PhD, professor of chemistry and biochemistry at the University of California, San Diego (UCSD), and Lillian Chong, PhD, associate professor of biophysics at the University of Pittsburgh.

Amaro, Chong, and colleagues used supercomputer simulations to show how RBD transitions from a “down” state and an “up” state. In the down state, RBD is shielded by glycans—molecules that make up a sugary residue around the edges of the spike protein. In the up state, RBD is exposed and capable of binding to the human angiotensin-converting enzyme 2 receptor.

The up and down states had been seen before, in snapshots obtained by cryo-electron microscopy and cryo-electron tomography. But now, thanks to Amaro and colleagues, what happens in between these states has been captured.

“We were actually able to watch the opening and closing,” Amaro said. “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.”

“Standard techniques would have required years to simulate this opening process,” Chong added. “But with my lab’s ‘weighted ensemble’ advanced simulation tools, we were able to capture the process in only 45 days.”

Detailed findings appeared in Nature Chemistry, in an article titled, “A glycan gate controls opening of the SARS-CoV-2 spike protein.” The article described how Amaro, Chong, and colleagues ran over 130 µs of weighted ensemble simulations of the fully glycosylated spike ectodomain. The simulations, they reported, allowed them to “characterize more than 300 continuous, kinetically unbiased RBD-opening pathways.”

“Together with ManifoldEM analysis of cryo-electron microscopy data and biolayer interferometry experiments, we reveal a gating role for the N-glycan at position N343, which facilitates RBD opening,” the article’s authors wrote. “Residues D405, R408, and D427 also participate.”

These details could help scientists develop new therapeutics to counter SARS-CoV-2 infection. If glycan gates could be pharmacologically locked in the closed position, then the virus is effectively prevented from opening to entry and infection. “Without this gate,” Amaro emphasized, “the virus basically is rendered incapable of infection.”

The computationally intensive simulations were first run on Comet at the San Diego Supercomputer Center at UCSD and later on Longhorn at the Texas Advanced Computing Center at Univeristy of Texas (UT) Austin. Such computing power provided the researchers with atomic-level views of the RBD from more than 300 perspectives.

The investigations revealed glycan N343 as the linchpin that pries the RBD from the “down” to “up” position to allow access to the host cell’s ACE2 receptor. The researchers describe N343 glycan activation as similar to a “molecular crowbar” mechanism.

Jason McLellan, PhD, an associate professor of molecular biosciences at UT Austin, and his 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. “Without this gate,” McLellan said, “the RBD of the spike protein can’t take the conformation it needs to infect cells.”

 

Supercomputer-driven simulations have been used to visualize how the spike protein of the SARS-CoV-2 virus uses a glycan gate. When the gate is in the “down” position, the spike’s receptor binding domain (RBD) is shielded from the immune system. When the gate is in the “up” position, the RBD is exposed and capable of engaging host cell receptors. In this image, the glycan N343 (magenta) is acting as a molecular crowbar to open the gate and reveal the RBD (cyan). [Amaro Lab, UC San Diego]