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Hail to the Ribbon

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. 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 the beta-sheet motifs are represented by long flat arrows. Less organized loops between these regions are rendered as what look 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 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. (Offer void where prohibited).

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. See Ed Tufte’s The Visual Display of Quantitative Information for the classic presentation of this topic. 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. 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. The ribbon diagram is at just that point.

21 comments on “Hail to the Ribbon”

  1. Asdf says:

    Can anyone recommend a good book about presenting med chem data or is the book mentioned above the best ou there?

  2. loupgarous says:

    Thanks for a great capsule description for how to read ribbon diagrams! I’ve been seeing these things on the web seems like forever, and the formal description of what they mean has always been somewhat hard to understand. This essay gives the casual reader of protein chemistry articles incentive to buckle down and learn what information ribbon diagrams present.

  3. secret sauce says:

    I knew Jane was a great scientist – didn’t know she was such a good artist too! Thanks for the articles.

  4. Anonymous says:

    Had to pull out my copy of Dickerson and Geis (Structure and Action of Proteins, 1969) to see that they (and others?) were using ribbons, albeit without the planaria-like arrow-headed ribbons to indicate direction, in the 60s. D&G also used sausage-tubes to illustrate structure. I have seen Richardson’s name in D&G and many other works (e.g., Brandon & Tooze) but I didn’t realize how much she contributed to the ribbon enhancements and popularization.

    On a related note: “Who invented the arrow?” The organickers here will know that I am referring to the “curly arrow” that indicates electron movement, such as when we draw reaction mechanisms. I think I know the answer, based on reading many, many old papers. There were many ways used in the literature to indicate electron flow but it was the curly arrow that caught on. Your guesses?

    1. Derek Lowe says:

      Pretty sure I know this one, so I’ll sit out!

    2. Jeff says:

      Wasn’t that from Feynman Diagrams?

    3. MTK says:

      Ha!

      I can’t believe I don’t know the answer to this question.

    4. secret sauce says:

      Christopher Ingold?

    5. b says:

      I think it was Robert Robinson

      1. Lawrence E. Wolfe says:

        Close, Richard…

      2. Jon says:

        I was taught that Robinson was the first to use the curly arrow…

    6. Ru baby says:

      Definately MacMillan or baran

    7. MTK says:

      I googled it and got this article which is pretty interesting.

      https://www.chemistryworld.com/features/the-iconic-curly-arrow/3004840.article

  5. An Old Chemist says:

    Ingold introdued thr curly arrows to represent electron movement direction! I recall reading it in an article on the use of arrows in chemistry.

  6. Wavefunction says:

    Jane Richardson is a phenomenal scientist. Fun fact about her: she won the Westinghouse Science Contest in 1958 for calculating the trajectory of Sputnik.

  7. Some idiot says:

    A long time ago (in a galaxy far far away…) when I was a postdoc, I was part of a voluntary group that read textbooks onto tape for blind students. During this period of time I was helping read a real brick of an organic chemistry textbook onto tape. On numerous occasions I came to a complex diagram (sometimes structures, sometimes others). On so many occasions I stopped the tape and thought “how on earth am I going to explain this diagram to someone who is blind???” It really brought home to me how visual chemistry is (and therefore how important white/black boards are when discussing something complex). Since then I have always sought after simple (but accurate) ways of describing things, and really appreciate and admire those who can do so. And I think that Jane’s ribbon diagrams are up there with the best…! 🙂

  8. azetidine says:

    The problem with these diagrams (and with crystal structures for that matter), is that they are so aesthetically pleasing to the eye that it is impossible to judge their accuracy. In these cases, beauty = truth. They could be completely wrong (and probably are) but nobody can tell.

    1. anon the II says:

      I think it’s a bit out of line to ever say crystal structures are completely wrong unless fraud is involved. The crystallography experiment comes with some experimental errors that need to be understood. But they’re loaded with good information if you understand what you’re looking at.

      I’m sorry but I have to label your comment as “Fake News”.

  9. Dominic Ryan says:

    Ho boy, protein crystal structure quality, what a juicy topic!

    Honestly, I think outright fraud is pretty dramatically rare. That does not mean that you cannot have a mostly wrong structure. It just depends on what you care about.

    I have seen plenty of structures where the ligand, at least a very important part, was put in the wrong place even when there was lots of structure that was still correct. Another problem, I think of decreasing frequency, is assigning too many waters for the data available.

    There are lots of other protein structure quality metrics and this has been hashed out a great deal. My measure of right / wrong is pretty simple: do I trust the structure enough that I make actionable decisions based on the structure?

    1. structural biologist says:

      Interesting that the line of discussion goes from this glib indictment of ribbon diagrams and structure accuracy…

      Especially since the Richardsons are leaders in: structure validation!

      They’re a couple decades ahead of you here and published a few dozen things on this and work on it even to this day. 🙂

  10. hn says:

    Before investing serious effort on a structure-related project, consult a crystallographer to make sure your starting structures are reliable!

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