The biochemistry of cell: how to picture it (Introduction)

by David Turell , Friday, August 23, 2024, 18:40 (91 days ago) @ David Turell

Invented by Jane Richardson:

https://www.quantamagazine.org/how-colorful-ribbon-diagrams-became-the-face-of-proteins...

"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.”

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"In her year of sketching, Richardson came up with simple ways to illustrate these basic shapes. Alpha helices are coils that look like the tails of decorative ribbons, curled with the edge of a pair of scissors. Beta strands are arrows that point in the direction in which the amino acid chain was built. And thin wires represent the loops and turns that connect the structures. “That allowed us to follow the chain round and to see these folds and visualize them in three dimensions,” Thornton said.

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"Richardson’s ribbon diagram has become so ubiquitous, it can be difficult to imagine proteins looking any other way. Bourne often reminds his students that proteins don’t actually look like that.

“'A protein is nothing like a ribbon,” he said. It’s much more dynamic, he added. Sure, proteins’ backbones fold up into structures like the coils and sheets that the ribbon diagrams represent. But researchers can’t actually see those structures when they image proteins.

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"As simplifications, ribbon diagrams have their limitations, of course. They can’t convey some structural elements, such as tunnels or pockets where other molecules might bind — information critical for understanding how proteins work and designing drugs to target them. They also don’t communicate structure well for larger proteins or complexes of multiple proteins.

“'It gives you a three-dimensional view of the shape, but it also hides a lot of the features that we know to be true about proteins,” Bourne said. “So that then can narrow one’s thinking.” He called this “the curse of the protein ribbon diagram” in a 2022 essay.

"Another popular representation is the space-filling model, which shows how much room atoms take up and looks more like an actual protein. It can show proteins’ pockets and tunnels — but it can’t represent the protein architecture, such as helices and sheets. “It depends what you want to show,” Perrakis said. Many researchers look at different types together to glean all the important structural information. What a protein looks like, Richardson said, is how you choose to represent it."

Comment: protein structures are extremely complex which implies the 3-D shapes help form the functions. Please see the illustrations. They each represent the structures of thousands of protein parts. This shows that design is required.