Coronavirus protein ‘shakes off’ some antibodies by changing shape

A new study suggests that part of the SARS-CoV-2 virus shifts its shape based on its surroundings, throwing off potentially protective antibodies that might prevent it from causing COVID-19. 

The shapeshifting rids the coronavirus of certain antibodies that attach to it, say the study’s authors, who are based at the Vaccine Research Center of the National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health; Frederick National Laboratory for Cancer Research; Johns Hopkins University; and Columbia University. The findings were published in Cell Host and Microbe

The target, called “spike,” is a protein on the surface of the membrane that encapsulates the coronavirus. It’s the anchor that the virus uses to dock with and enter a host’s cells. Once inside, the virus hijacks the cells and uses them to make more virus. 

Finding a way to elicit antibodies that attach to spike is therefore crucial for halting an infection and giving humans some degree of immunity. However, the shapeshifting described in the study could present a challenge. 

A diagram showing three 3D models of the COVID-19 spike protein with 2D representations of antibodies showing how the antibodies will slowly detach
Some antibodies can only attach to spike’s receptor-binding domain (shown here as “RBD”) at bloodstream pH when the domain is in the open or ‘up’ position, but as the virus enters the cell through the endosomal pathway, the pH decreases, the domain closes, and the antibodies are forced to detach. 

Antibodies and acidity 

The scientists observed that one crucial section of the protein, called the “receptor-binding domain,” changes its position based on the pH—the acidity or alkalinity—of its environment. The domain is the hook on the anchor, the part of spike that’s responsible for actually attaching the virus to the cell. 

Spike has three identical copies of the domain. At the neutral pH level found in the human bloodstream, one of them is in the open or ‘up’ position, says study co-lead author Yaroslav Tsybovsky, Ph.D., a microscopist in the Electron Microscopy Laboratory at Frederick National Laboratory. Certain antibodies recognize and attach to the open, exposed domain, lowering the coronavirus’ chances of docking with and entering a cell. 

But the study results indicate that the effect doesn’t always last. If the virus succeeds in entering a cell via a mechanism called the “endosomal pathway”—where the pH is much more acidic than in the bloodstream—the receptor-binding domain on spike closes itself off, shaking off the antibodies that attached to it. Freed, the virus can take over the cell and spread the infection. 

“The antibodies that develop are partially—not all of them, but a big pool of antibodies—developed to those regions which … are only available when the receptor-binding domain is in the ‘up’ position,” Tsybovsky said. 

Consequently, these antibodies may be less effective at blocking the virus. By extension, vaccines that use the version of spike with an open domain to prime an antibody response could give humans some immunity but may not be fully optimized, even if they work well. 

“With this information, the chances of getting good vaccines are higher,” Tsybovsky said. 

However, he adds that the findings’ full implications for immunity to COVID-19 aren’t clear yet. The study looked at individual spike that was produced in a cell culture and not the entire virus itself, which may behave differently. It also isn’t clear whether the domain’s movement is part of SARS-CoV-2’s built-in machinery to avoid the immune system or merely an unfortunate coincidence. 

Studies to answer these questions are underway. A team at the Vaccine Research Center has also begun engineering a version of spike with a domain that stays closed, which might offer a more effective means for vaccination. 

An unexpected discovery 

Tsybovsky and Tyler Stephens, another microscopist at Frederick National Laboratory, conducted many of the study’s intensive electron microscopy scans. They were the first on the team to identify a shapeshifting phenomenon in spike, although they didn’t expect to encounter it: Tsybovsky and Stephens were simply testing the Vaccine Research Center’s versions of spike for their suitability for research and vaccine development.  

“Originally, this was supposed to be like a quality control little study,” Tsybovsky said. 

The proteins had been formulated at the bloodstream pH (the standard for many vaccine products). Tsybovsky and Stephens knew that many types of proteins change their shapes depending on pH, so they began looking at spike’s structure at different pH levels. As they watched the structure change, they became determined to get high-resolution scans.

The pair worked with Frederick National Laboratory’s National Cryo-Electron Microscopy Facility, a resource for high-resolution imaging, to collect much of the data for the study. The facility typically handles cancer-related projects but started taking on COVID-19 work during the shutdowns of spring 2020.

Two 3D structures
3D structures of the spike protein constructed from cryo-EM images. One receptor-binding domain (green) is in the ‘up’ position at pH 5.5 (left) but closes off at the more acidic pH 4.0 (right).

“It is very satisfying to be able to do something useful about this pandemic and be involved in something that might help to come up with treatments and better vaccines,” said Ulrich Baxa, Ph.D., director of the facility.

At the same time, Tsybovsky and Stephens began working with the Vaccine Research Center, Johns Hopkins, and Columbia to uncover more of the protein’s behavior and structure. 

“From then on, it became completely crazy. … It didn’t matter if it was Monday or Sunday, day or night,” the work was getting done, Tsybovsky said. 

Further examinations pinpointed the receptor-binding domain’s movements. 

Thanks to the collaboration and substantial around-the-clock work, the team completed the initial study in just two months, a breakneck pace for this type of research. That dash gave them additional time to then investigate more deeply and fine-tune their models to produce more concrete results and images. 

In fact, one of their structures of spike holds the record for highest available resolution achieved to date, and the study’s findings may help scientists understand other high-risk viruses. 

“The discovery of immune evasion through pH-dependent locking of the receptor-binding domains in the down position is not only relevant to developing vaccines against SARS-CoV-2,” Tsybovsky said. “Structure and sequence comparisons suggest this strategy may also be employed by related coronaviruses, such as those causing SARS and MERS, extending the implications of this work.” 

 

By Samuel Lopez, staff writer; image contributed by Yaroslav Tsybovsky