Protein dynamics

Artworks representing spinning ATP synthase

Let’s examine a really successful use of molecular graphics for understanding protein structure and function. Chapter 2 of The Machinery of Life by David Goodsell gets the ball rolling (gets the turbine turning?) with a splendid graphic illustration of ATP synthase, the enzyme that manufactures ATPThe 3D structure of the enzyme molecule is represented as a static multimeric protein embedded in a membrane (not shown in the book but shown below in Goodsell’s illustration in The Molecule of the Month for Dec. 2005):


Other graphic artists have added animation to illustrate how protons streaming from one side of the membrane to another provide kinetic energy that forces the inner axle of the ATP synthase to turn relative to the stationary stator.  Here are some examples:



The dance of protein synthesis

Chapter 2 of The Machinery of Life then picks up on the theme of complementarity of nucleic acids as the basis for storing and transmitting genetic information.  This topic is especially relevant in our course, Protein Portraits, because nucleic acids serve as the blueprints and the catalytic machinery for building protein molecules.

Take a close look at Figure 2.6 and relish the finely crafted artistic view of the small subunit of a ribosome sitting in wait for the several other factors and ingredients required to build a new protein chain.  One of those items is the large ribosomal subunit (which you can view in its full glory as the October 2000 Molecule of the Month), while the others include the messenger RNA, a full palette of transfer RNA’s each charged with one of the twenty amino acids, a collection of initiation factors, and last but not least, empowering molecules of ATP and GTP.  While you can find dozens of staid but true representations of the process of protein synthesis in various biochemistry and cell biology textbooks, you might want to also spend 10 minutes to take a look at the animated dance version of protein synthesis found here as a youtube video (the dance is introduced by Paul Berg, the discoverer of DNA ligase).


The dancers and musicians are Stanford hippies from 1971.  But is this art?  Here’s a comment on the video made by the National Performing Arts Convention:

What ends up being an entertaining 70’s hippy dance fest (it really heats up around minute 9 when the groovy drums and flute come in) is also an interesting case study of using dance and movement as a way to visualize very complex and impossible to see biological processes.  Keep in mind that this is before the advent of complex computer modeling.

A similar though bleaker view of the dance video is presented here by the Turkish artis Elmas Deniz in the Istanbul-based forum called Open Systems:

Today my boyfriend showed me a video — which he found out about from an interview with Julian Assange and Google CEO Eric Schmidt [1] — directed in 1971 by Robert Alan Weiss for the Department of Chemistry of Stanford University. An epic about protein synthesis, where you can see a hundred hippie students making music, dancing in order to represent a biological event. Assange’s argument is that realizing the same type of performance as an education method would not be possible today …

No doubt there will always be a give-and-take between artistic creativity on one hand and science-technology on the other.  Working on our protein portraits gives us an opportunity to jump right in to the middle of that dance partnership.

Process artwork:  Depicting the dynamics of life

Ordinarily we would see the process depicted in a much less graphic manner, as in the following chart taken off of wikipedia:


Both manners of depicting a dynamic process are successful, but which sticks better in your mind after closing the page?

Are there other ways of depicting the dynamics of cholesterol metabolism in the human body?  Like cheeseburgers, of course!

Cholesterol art

Or look up Figure 3.2 in Goodsell’s book, The Machinery of Life.  He presents a highly original dynamic view of the process of cholesterol synthesis (well, he actually takes us only through to the lanosterol step, explaining that the completion of the cholesterol molecule requires additional steps).

Thanks to art, animation, and the creative artists that are steadily inventing new ways of illustrating the very fast and the very small, the dynamic processes of the molecules of life are becoming more and more familiar to we, the denizens of the macroscopic world.

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