Counterpoint: MIT scientists translate coronavirus protein structure into music

MIT’s Markus Buehler specializes in developing AI models to design new proteins and is perhaps best known for using sonification to illuminate structural details that might otherwise prove elusive. Now his lab has applied that approach to model the vibrational properties of the spike protein responsible for the high contagion rate of the novel coronavirus (SARS-CoV-2). What they learn could one day help scientists figure out how best to stop the virus in its tracks, leading to potential therapies and hopefully preventing future deadly outbreaks.

The hierarchical elements of music composition (pitch, range, dynamics, tempo) are analogous to the hierarchical elements of protein structure, according to Buehler. Much like how music has a limited number of notes and chords and uses different combinations to compose music, proteins have a limited number of building blocks (its 20 amino acids) that can combine in any number of ways to create novel protein structures with unique properties. Each amino acid has a particular sound signature, akin to a fingerprint.

Any genre of music has patterns,” Buehler told Ars last year. “You’ll see universality in terms of sound, the tones, but you also see repetitive patterns, like motifs and movements in classical music. These kinds of patterns are also found in proteins.”  

Several years ago, Buehler led the team of MIT scientists that mapped the molecular structure of proteins in spider silk threads onto musical theory to produce the “sound” of silk in hopes of establishing a radical new way to create designer proteins. And as we reported last year, they subsequently developed an even more advanced system of making music out of a protein structure—and then converting it back to create novel proteins never before seen in nature. The team also developed a free app for the Android smartphone, called the Amino Acid Synthesizer, so users could create their own protein “compositions” from the sounds of amino acids.

“Our brains are great at processing sound,” Buehler recently explained to MIT News. “In one sweep, our ears pick up all of its hierarchical features: pitch, timbre, volume, melody, rhythm, and chords. We would need a high-powered microscope to see the equivalent detail in an image, and we could never see it all at once. Sound is such an elegant way to access the information stored in a protein.”

The novel coronavirus is no exception. As Buehler recently told MIT News:

Its protein spike contains three protein chains folded into an intriguing pattern. These structures are too small for the eye to see, but they can be heard. We represented the physical protein structure, with its entangled chains, as interwoven melodies that form a multi-layered composition. The spike protein’s amino acid sequence, its secondary structure patterns, and its intricate three-dimensional folds are all featured. The resulting piece is a form of counterpoint music, in which notes are played against notes. Like a symphony, the musical patterns reflect the protein’s intersecting geometry realized by materializing its DNA code.

The virus has an uncanny ability to deceive and exploit the host for its own multiplication. Its genome hijacks the host cell’s protein manufacturing machinery and forces it to replicate the viral genome and produce viral proteins to make new viruses. As you listen, you may be surprised by the pleasant, even relaxing, tone of the music. But it tricks our ear in the same way the virus tricks our cells. It’s an invader disguised as a friendly visitor. Through music, we can see the SARS-CoV-2 spike from a new angle, and appreciate the urgent need to learn the language of proteins.

According to Buehler, gaining a better understanding of these vibrational patterns will be crucial for designing effective drug therapies in the future, perhaps by searching for a protein with a similar melody and rhythm that would make it an effective antibody, thereby limiting the virus’s ability to infect hosts. On a more aesthetic level, “This musical art teaches us something about the fine line between [the] beauty of life and death as an opposite pole.”

https://arstechnica.com/?p=1667136