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Protein Preludes

By Sean Henahan, Access Excellence

3d proteinWashington, DC (3/20/98)- A Texas researcher has tuned in to music to describe the structure of proteins and genes. She hopes the new approach may ease the task of teaching the complexities of cellular biology.

"Over a decade ago, I heard a colleague on the music faculty talk about composing. As he discussed how he went about selecting, modifying, and organizing musical themes, I was struck by the parallels between musical structure and the structure of proteins and the genes that encode them," said biologist Mary Anne Clark at Texas Wesleyan University in Fort Worth, TX.

View: 3-D representation of Bovine gamma crystallin protein
Listen: a musical representation of  same midi file

She eventually linked up with computer music pioneer John Dunn at  Algorithmic Arts who had created a computer program that transformed protein sequences into music. The two worked together to refine the "sonification of proteins" into more sophisticated music than earlier efforts had produced. Clark took into account higher-level structural features of proteins, such as regions of helix formation and other folding patterns. This added additional depth to the music.

The two were united in the goals of conveying something not only about the primary amino acid sequence and the folding patterns of proteins but also making audible the esthetic patterning of nature's deep structure. The result is a sonic playback of protein structures disguised as a CD of "art music."

This novel approach can help demonstrate the relationship between similar structures in different organisms. For example, the music of the human protein hemoglobin and that of the globin in a tuatara, an exotic three-eyed lizard, are recognizably variations on a theme, she notes. Although the similarities between the two sequences can be seen in their written records, they are more impressive when heard. Clark uses amino acid solubilities to assign pitches to specific amino acids in the sequences, so that even when the absolute sequences vary, strings of adjacent amino acids that have the same solubility relationships will produce similar musical phrases.

"The tuatara would seem to have little in common with humans," Clark says, "but the similarities indicate that both proteins are variations on a theme that was in existence before the divergence of the mammalian and reptile lineages 200 million years ago. Other variations of beta-globin can be found in Australian ghost bats, Brazilian tapirs, Kenyan clawed frogs, Antarctic dragon fish, and Emperor penguins. Although the beta-globin sequences aren't identical, they all would be recognizable as variations on a theme if converted to music."

Clark hopes the audio CD she and Dunn are producing will be a valuable teaching tool for students studying genetics or protein chemistry.

"I love to walk into the music building, which on my campus is next door to the science building. Through the doors of the practice rooms, I can hear fragments of 1000 years of written music, played or sung by the current generation of music students, some with finesse, some with hesitation, some with wild improvisation. I think that if somehow I could walk into a living cell, I would hear something similar - the ribosomes ticking away at the synthesis of proteins, playing out their amino acid sequences, note by note, according to a genetic score that is reproduced sometimes with utter fidelity, sometimes with a few unscheduled substitutions, and sometimes with stunningly inventive flourishes. Every generation of cells in every living organism plays the genetic score of its species. However, while the history of music as we know it goes back some 1000 years, the history of genetic music is at least 3.8 billion years in the making," she notes.

UC Santa Cruz biologist David Deamer is a pioneer in the creative use of DNA patterns to synthesize music. His system uses raw data derived from the light absorption spectra of the four bases (adenine, cytosine, thymine,  guanine) that make up the DNA molecule is converted into sonic frequencies. These are programmed and sent to a synthesizer, and then arranged into four pitch collections (or four 'scales' based on the individual base molecules).

Related information on the Internet
Gene Music Samples
Algorithmic Arts
MIT Article: Music of Proteins 
Dr. Deamer's DNA Music

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