Biocurious is a weblog about biology, quantified.

Fanciful structures, part II

by PhilipJ on 25 October 2007

A few days ago I posted an image containing the “structures” of three different molecules: a nanotube synthase, a rotary motor, and a DNA scaffold:

Of these three, only one molecule has atomic-level structural data, another has been synthesized and characterised, but no structural data exists yet, and the third is speculation. I asked which was which.

We didn’t get a lot of feedback, but that which we did was interesting. Both Eva and Narin guessed that the nanotube synthase was the solved crystal structure, but then disagreed on which was made up and which was at least synthesized and characterised.

Funny enough, it is the nanotube synthase (the first structure above) which doesn’t exist! In his book Bionanotechnology, David Goodsell outlines what would be required to engineer an enzyme capable of synthesizing carbon nanotubes, but it is just foresight on David’s part, and the structure is fictitious.

It may not come as a surprise to regular Biocurious readers that the DNA scaffold is then the molecule which has been synthesized and characterised, but lacks a crystal structure. We’ve talked a lot about DNA nanostructures recently, and this is one which is believed to be synthesized.

That leaves the rotary motor as the actually solved crystal structure, and it’s a famous one to boot. It’s a section of the F1F0 ATPase, and you can access the NMR-derived structure from the PDB with entry 1c17.

These structures come from Making the step from chemistry to biology and back by David Goodsell in the November issue of Nature Chemical Biology (subscription required). Goodsell talks at length about the recent advances in techniques which get us closer to visualizing the molecules of life at the mesoscale*, the confusing “middle ground” between chemistry and life. The end of the article is used to discuss the value in pictures themselves, where he (not surprisingly, and rightly so) gives images their due as a powerful way to think about molecules, with the example given of Jane Richardson’s ribbon diagrams, which have come to dominate the way we think about and visualize protein structures. But he stresses that pictures are dangerous, and the example of the three structures above is a perfect example. It is now possible to create entirely realistic images of entirely fictitious molecules, so extra care must be taken to quote citations where actual crystal structures have been used, else “even the most preposterous hypothesis” can be made to look familiar and plausible.

He also stresses, though, that speculative pictures can be useful in their own right. He ends his commentary with a challenge to the reader:

I invite you to look at whatever you’re studying right now—a drug molecule, a ribosome, a polysaccharide, a certain sequence of DNA—and take a moment to think about it in its cellular context. Could you sketch a picture of your molecule as it exists inside (or outside) a living cell? Do you know where it is and what it looks like and when it does its job? Are there any major pieces of information missing that leave enticingly blank holes in this mental picture? Speculative pictures that show the larger context of a given subject are an efficient way to uncover these gaps; they often lead to new mysteries to be explored and solved.

I just wish I could sketch those pictures as well as David does.

* I’m adding this paper to my “List of Papers To Read When I’m Down on Science”, along with Laughlin et al’s The middle way and The theory of everything.



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