A correspondent sent along this item, celebrating the inventor of something that’s so ubiquitous in molecular biology and protein chemistry that you have to think for a moment to realize that it had an inventor: the ribbon diagram. That’s Jane Richardson of Duke, who started there in 1969, back when there were only about 20 entries in what was not yet the PDB because that hadn’t been invented yet, either.

The ribbon diagram came along in about 1980. For those outside the field, it’s a way to represent protein structure. It takes the primary sequence (one amino acid after another) and simplifies the general direction of that twisting, folding chain as if it were a piece of ribbon.

Beta-Sheet Motifs

That reveals quite a bit of structure that otherwise tends to get lost in the tangle of bonds and side chains. The alpha-helices turn into coils that look exactly as if some ribbon had unspooled off a roll of it in your hand and long flat arrows represent the beta-sheet motifs.

Less organized loops between these regions are rendered as what looks like pieces of thick wire or rope. Looking at proteins this way lets you see common and related structures much more easily: the beta barrel (that’s one at right, and you can see a red alpha-helix in back), the “Greek key,” beta-hairpins, coiled-coils, beta-propellers, helix-loop-helix motifs and many more.

Protein Structures

Protein structures vary infinitely, but they do not vary in infinite ways, and if that reminds you of Cantor‘s theory of sets, as far as I’m concerned you’ve done everything you can accomplish for a Monday and can take the rest of the day off.

Visual representations of this kind are extremely important because many people’s information bandwidth is highest through that channel. Our pattern-matching brains are geared toward that sort of thing sometimes a little too much so, and a look at a well-constructed diagram can impart far more information in a meaningful way, and more quickly, than almost any other method.

Some find him a little doctrinaire for their graphical tastes, but you ignore his thinking on these issues at your peril. The ribbon diagram is an illustration of one of the most powerful (and potentially dangerous) principles of graphic presentation: leaving things out.

Amino Acids

As you can see from the illustration above, you lose the side chain residues of the amino acids (even though they’re crucial parts of protein function) in the service of showing you the shape of the protein backbone (also crucial, of course).

So there are purposes for which a ribbon diagram alone is useless, but for its primary purpose, it’s excellent. Like the line attributed to Einstein (it’s a paraphrase of one that’s less lapidary), a scientific theory should be as simple as it can be, but no simpler.