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Ribbon Diagrams

January 13, 2008

Ribbon Diagrams

They Turned Messy Data Into Beautiful Pictures

By Monte Basgall

Proteins are huge, complex molecules that run the cellular machinery of life and knowing their shapes can often provide important clues about how proteins interact with other parts of the cell. But determining those shapes as a way to understand nature and combat disease is dauntingly complex.

Because proteins are smaller than a wavelength of visible light, "taking their picture" has typically required a technique called X-ray crystallography to produce a pattern pinpointing individual atoms' locations. Unfortunately, the resulting jumble of complex data defies easy interpretation.

The Richardsons turned the jumble into a picture, playing a pioneering role in providing protein structure with a sense of substance and design. They helped translate crystallography data into something intuitive, even beautiful.

"I don't see how you could possibly describe a protein structure in a thousand words," Jane Richardson says. "But you can come a lot closer with one picture."

A seminal 1981 survey in the review journal Advances in Protein Chemistry first showed the scientific world what became known as "ribbon drawings" or "Richardson diagrams." They were Jane Richardson's hand-drawn interpretations of the structures that she, her husband and others had derived by bouncing X-rays off the atoms of crystallized proteins.

Today, much like standardized highway signs, the visual language of protein structure that the Richardsons invented is the standard in their field, although hand-made drawings have largely been replaced by computer graphics. Hardly a week goes by that a ribbon drawing isn't featured on the cover of at least one scientific journal.

"As Louis Sullivan, the famous architect, said, 'form always follows function,'" says Peter Agre, Duke professor of cell biology who shared the 2003 Nobel Prize in chemistry for determining the shape of a protein complex that lets water in and out of a cell. "Jane and David's work allowed us to reveal the form of proteins, and from there it was easier to understand their function."

The diagrams Agre and others use still follow Jane Richardson's formula. Corkscrew structures called alpha helices are shown as coiled ribbons. Molecular loops are depicted as round ropes. Extended protein segments, called beta strands, become ribboned arrows that twist together and gather visually into beta sheets.

Jane Richardson slightly exaggerated perspective in her drawings to accentuate their three-dimensional quality.

"I'm not good at drawing things in general," she says. "That's why it took me two whole years to work out how to do these things!"

Sitting in the Nanaline H. Duke building offices that they share with examples of their protein models -- one incorporated into a stained glass window -- the two biochemistry professors recalled how their collaboration on protein structure began at MIT, before they arrived at Duke in 1970.

In the early 1960s David was working on a Ph.D. at MIT. Jane, an amateur astronomer and science award winner in high school, had finished a master’s degree in philosophy at Harvard and tried teaching high school, but grew fascinated by her husband's work on protein structures and signed on as a lab technician to read out the raw X-ray data. After seven years of work they produced a 3-D image of all the atoms in a protein structure.

"We would look at the protein's backbone trace and try to draw on the blackboard what we called its 'signature,'" David recalled. "Jane developed from that what was later regularized into ribbon drawings. She wasn't the first to do ribbons, but she was the first to develop the rhetoric to make them into a language. I was there more or less for technical support," he added modestly.

"You were the one who was the expert at making the equipment work," she replied. "And I looked at the data quality."

In 1985, her ribbon schematics won Jane Richardson a prestigious MacArthur Fellowship. By then, the Richardson laboratory was a fixture at Duke, and the couple had diversified beyond interpreting protein structures to designing novel new kinds of proteins.

In 2006, Jane Richardson was also elected to the National Academies' Institute of Medicine, a special feat for someone who never received an M.D. or Ph.D.

Produced by: Monte Basgall senior science writer, Duke News and Communications.

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Stay tuned, Anuj. The

Stay tuned, Anuj. The Richardsons are using our three-D virtual environment (the DiVE)to work out some new modeling problems.

That's neat -- I actually

That's neat -- I actually never knew who developed the ribbon diagram (it's now such a standard visual representation for protein structure). Could only have been Duke faculty (should have known). But what's the next advancement in ribbon diagramming?

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