“The ribbon-diagram representation was invaluable,” said Anastassis Perrakis, a structural biologist at the Netherlands Cancer Institute and Utrecht University. It helped scientists communicate, teach and classify protein structure, and it captured the imaginations of scientists and nonscientists alike. It was able to “convince people how elegant [proteins] are and to see the complexity, without it being overwhelming,” Richardson said.

Today, ribbon diagrams are the ubiquitous face of proteins in scientific articles, textbooks and magazines, known for their particular combination of clarity and beauty. “It’s hard to imagine a scientific representation of data that is more meaningful,” said Philip Bourne, dean of the University of Virginia School of Data Science.

The diagrams have been so successful that it can be hard to remember that our cells are not, in fact, filled with colorful ribbons and broad arrows.

The Face of Proteins

Day in and day out, our cells are hard at work constructing different kinds of proteins. Proteins are made of strings of molecules called amino acids, and each amino acid has one or more side chains made up of several atoms “coming off it like a lollipop,” said Janet Thornton, a computational biologist who retired from the European Molecular Biology Laboratory last year. The amino acid backbone innately folds into a three-dimensional shape, known as a protein structure, which determines which other molecules the protein can bind to and, therefore, its function in a cell.

Once a structural biologist completed what used to be a years-long process of reconstructing a protein’s 3D structure, they faced a new problem: how to communicate that structure to other scientists. In truth, it’s impossibly difficult to represent a protein’s realistic structure. Proteins are minuscule, on the order of nanometers, and can contain hundreds of thousands of atoms. “If those atoms are all drawn and then joined together, it becomes very difficult to see,” Thornton said.

Richardson’s innovation was a reproducible method of representing the folds of a protein’s amino acid backbone without getting bogged down in the details of specific atomic arrangements. She relied on proteins’ tendency to fold into two energetically favorable shapes: coils called alpha helices and flat shapes called beta strands, which can line up into so-called beta sheets. Then there are loops, which connect alpha helices to beta strands like corner pieces in a puzzle.

There are other folding structures, and “people have come up with lots of names” for them, Perrakis said. “But at the end of the day, the ones that matter are the helices and the sheets.”