Studying Protein Structure Can Be A Musical Experience

Many researchers use software such as RasMol to visualize three-dimensional structures of proteins. But what if a researcher is blind? What's the best way to navigate those same proteins?

Timothy Cordes, a blind medical scientist at the University of Wisconsin, Madison, faces this challenge every day in his X-ray crystallography research. In the past, he had to go through several steps to figure out the spatial relationships of atoms and amino acid residues in a protein. "For everything I wanted to look at, I'd have to go into one program and write a file and then read it in another," he says. "I realized I needed a tool to help me streamline the process."

So Cordes developed software that allows him to navigate a protein structure simply by listening through headphones for musical cues; different atoms are represented by different musical instruments. For example, if Cordes moves his cursor to a carbon atom, he might hear the sound of a piano. If he's at an oxygen atom, he might hear the sound of a flute. As he moves from one atom to another above it, the pitch increases. And if he shifts the cursor from left to right, he'll hear the sound move from his left ear to his right ear. "It's pretty intuitive," Cordes says.

He says the program can also help sighted researchers by adding another dimension to their understanding of protein structures. Cordes plans to publish a paper about his program later this year and will make the software available for free on the Internet. He says the open-source code will allow others to modify the program according to their own needs. "I'm using this tool for proteins, but three-dimensional data is all around us, and this approach could just as easily be applied to geology or architecture."

In related work published in May in Genome Biology, Rie Takahashi and Jeffrey H. Miller of the University of California, Los Angeles, converted amino acid sequences in proteins into musical notes with the goal of enabling visually impaired scientists to hear protein patterns (2007, 8, 405). Examples of their work can be found at www.mimg.ucla.edu/faculty/miller_jh/gene2music/home.html.

"By converting genomic sequences into music, we hope to achieve several goals, which include investigating sequences by the vision impaired," the authors write. "Another aim is to attract young people into molecular genetics by using the multidisciplinary approach of fusing music and science."