Vibrations of coronavirus proteins may play a role in infection

When someone struggles to open a lock with a key that doesn’t quite seem to work, sometimes jiggling the key a bit will help. Now, new research from MIT suggests that coronaviruses, including the one that causes Covid-19, may use a similar method to trick cells into letting the viruses inside. The findings could be useful for determining how dangerous different strains or mutations of coronaviruses may be, and might point to a new approach for developing treatments.

Studies of how spike proteins, which give coronaviruses their distinct crown-like appearance, interact with human cells typically involve biochemical mechanisms, but for this study the researchers took a different approach. Using atomistic simulations, they looked at the mechanical aspects of how the spike proteins move, change shape, and vibrate. The results indicate that these vibrational motions could account for a strategy that coronaviruses use, which can trick a locking mechanism on the cell’s surface into letting the virus through the cell wall so it can hijack the cell’s reproductive mechanisms.

The team found a strong direct relationship between the rate and intensity of the spikes’ vibrations and how readily the virus could penetrate the cell. They also found an opposite relationship with the fatality rate of a given coronavirus. Because this method is based on understanding the detailed molecular structure of these proteins, the researchers say it could be used to screen emerging coronaviruses or new mutations of Covid-19, to quickly assess their potential risk.

The findings, by MIT professor of civil and environmental engineering Markus Buehler and graduate student Yiwen Hu, are being published today in the journal Matter.

All the images we see of the SARS-CoV-2 virus are a bit misleading, according to Buehler. “The virus doesn’t look like that,” he says, because in reality all matter down at the nanometer scale of atoms, molecules, and viruses “is continuously moving and vibrating. They don’t really look like those images in a chemistry book or a website.”

Buehler’s lab specializes in atom-by-atom simulation of biological molecules and their behavior. As soon as Covid-19 appeared and information about the virus’ protein composition became available, Buehler and Hu, a doctoral student in mechanical engineering, swung into action to see if the mechanical properties of the proteins played a role in their interaction with the human body.

The tiny nanoscale vibrations and shape changes of these protein molecules are extremely difficult to observe experimentally, so atomistic simulations are useful in understanding what is taking place. The researchers applied this technique to look at a crucial step in infection, when a virus particle with its protein spikes attaches


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