What do we know: COVID-19 and Protein Folding

On April 9, Simon finished his World Science Scholars course “From Chemistry to Living materials” and had his final live session with MIT’s Professor Markus Buehler who works on COVID-19. Professor Buehler, who leads the Laboratory for Atomistic and Molecular Mechanics (LAMM), shared some cutting edge stuff, some of it not even published yet. Here’re the important takes:

COVID-19 can travel much further than 6 feet/ 1.8 meters, namely at least 20 feet/ 6 meters. Human coughing produces gas clouds that initially rise up (due to their warm temperature) and then hang/ float in the air/ follow the air currents for a prolonged period of time.

screenshot from Professor Buehler’s live session

We still know very little about the COVID-19 virus. Its RNA contains 30,000 letters, but we only recongnize 29 proteins. We’re studying the structure of those proteins as we speak.

Looks like its mortality rate is quite high.

We don’t have the luxury of spending two years in the lab, growing the virus and applying the trial and error method. So our main hope is computation (computational material science), trying to understand the virus mechanistically.

Proteins are like folded spaghetti, unfolding them will destroy their structure and neutralize the virus. You can help look for ways to unfold the proteins via this app: https://fold.it/ (The most promising solutions will be tested at the University of Washington Institute for Protein Design in Seattle.)

What is mainly being studied are the ways to destroy the protein structure of the virus’s spikes. That can be done in several ways:

1. What is the virus’s thermostability? This is what is primarily being looked at, as it is still unclear how each protein reacts to temperature fluctuations.
2. What makes COVID-19 so infectious is the flexibility of its spike protein. Is there a way to make the spike protein more rigid (less flexible)? Maybe another protein or maybe a totally different engineering solution.
3. Destroying the protein with sound, with acoustic waves. Analyzing the protein’s vibrations and trying to find a frequency that can “shatter” the protein when excited (similar to how high pitched sound can shatter a glass).

Targeting the entire structure of the virus can damage human cells, so scientists want to target specific proteins/ frequencies.

This Science Magazine story with a video clip featuring Professor Buehler’s lab and COVID-19 proteins encoded as sound, “Corona music”.

screenshot from Professor Buehler’s live session (on the left you can see the protein’s spaghetti-like structure)
Simon and Neva observing diffusion, something professor Buehler also covered in the course.

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