http://www.youtube.com/watch?v=PjdPTY1wHdQ

http://www.rcsb.org/pdb/explore/explore.do?structureId=1JNV

Looking through the numerous topological children nodes of Sandwich (at the T level), I notice three representative sandwich topologies that seem especially ripe for being turned into toys by applying a little bit of evolutionarily-inspired tinkering.  These are the Neurophysin II Chain A topology (CATH code 2.60.9) , the ATP synthase epsilon chain domain 1 topology(phew, that’s a mouthful! easier to say CATH code 2.60.15), and the Gamma-B crystalline domain 1 topology (CATH code 2.60.20).

What’s fun about these three domain topologies?  Let’s tinker…

In 1977, Francois Jacob, fresh from his pioneering studies of gene transcription with Jacques Monod, delivered a stimulating lecture on the topic of Molecular and Evolutionary Tinkering at UC Berkeley (later published in Science magazine). Jacob pointed out how important it is in any type of design effort to begin with a picture of how a thing works since if you want to understand or improve the thing the most common route to success is to tinker with the existing picture.

We should listen to Jacob.  As we build our protein projects, let’s unleash our instincts to tinker

More quotes from Jacob’s 1977 lecture

• “To produce a valuable observation, one has first to have an idea of what to observe, a preconception of what is possible.  Scientific advances often come from uncovering a hithertounseen aspect of things as a result, not so much of using some new instrument, but rather of looking at objects from a different angle.”  (p. 1161, my italics)
• “[Tinkering] has several aspects in common with the process of evolution. Often, without any well-defined long-term project, the tinkerer gives his materials unexpected functions to produce a new object. From an old bicycle wheel, he makes a roulette; from a broken chair the cabinet of a radio. Similarly evolution makes a wing from a leg or a part of an ear from a piece of jaw. Naturally, this takes a long time. Evolution behaves like a tinkerer who, during eons upon eons, would slowly modify his work, unceasingly retouching it, cutting here, lengthening there, seizing the opportunities to adapt it progressively to its new use.” (p. 1164)
• “It is at the molecular level that the tinkering aspect of natural selection is perhaps most apparent. What characterizes the living world is both its diversity and its underlying unity. The living world contains bacteria and whales, viruses and elephants, organisms living at -20C in polar areas and others at 70C in hot springs. All these objects, however, exhibit a remarkable unity of chemical structures and functions. Similar polymers, nucleic acids or proteins, always made of the same basic elements, the four bases and the 20 amino acids, play similar roles. … New functions developed as new proteins appeared. But these were merely variations on previous themes. … The probability that a functional protein would appear de novo by random association of amino acids is practically zero. In organisms as complex and integrated as those that were already living a long time ago, creation of entirely new nucleotide sequences could not be of any importance in the production of new information. The appearance of new molecular structures during much of biological evolution must, therefore, have rested on alteration of preexisting ones.” (p. 1164)

http://www.rcsb.org/pdb/explore/explore.do?structureId=3S4G

http://www.rcsb.org/pdb/explore/explore.do?structureId=4AED

This origami structure is made up of flowers glued together. The virus looks like it has flowers embedded too!

I am going to make a series of 5 or so T-shirts with chemistry-cat style puns on them using common proteins that people who don’t know a ton about science will (hopefully) still get. I’ll include a simple line drawing of the structure on the shirt as well.

Similar to this, but with a protien theme