Thursday, April 17, 2008


So somewhere in between enzymology studying and preparing for Germany and everything else, for some reason, I got this image of the enzyme of study in the class and how the function of it might look if you were to look at it in 3D-space. I came to realize that although manufacturers of textbooks like to define proteins as

a) circles
b) ovals
c) ellipsoids
or d) oblong

and better textbooks show them as ribbon diagrams (one of which you can see at the top of this page), all of these pictures paint a really static picture of enzymes and proteins, and we really don't do them justice.

I came up with a better analogy than circles for proteins.* Transformers. Thousands of moving parts, all coordinated to align together for perfect function. In the case of allosteric enzymes, you have a complete transformation form one form to another. One form can perform reactions, but nowhere near as well as the others. Just like Optimus Prime can fight the Decepticons as a truck, but he's much badder ass in battle mode, complete with sword and all. My adrenaline is rising just writing this. You laugh, but just you wait.

Do you see what I'm doing? Combining science (boring) with a summer blockbuster movie (exciting!). I should teach this stuff. Or maybe I could turn it into a business. You pay me, I give you a sweet-ass analogy. We need more of me running the show when it comes to this stuff.

Patting myself on the back is the funnest thing ever.

Seriously, though, the reductionism that biochemists use to study proteins in many ways loses sight of the dynamics of the system. It becomes all to easy to forget that you're talking about a system that is extremely complex in its entirety when you're looking at what Asp36 binds to and how His253 is protonated and .......zzzzzzz.....

It may be time for a better, more holistic (though I hate that word) approach to biochemistry. And why stop there? molecular biologists get really hung up on the concept of genes and particular, specific functions of them, evolutionary biologists spend ages reflecting on relative rates of evolution and other mundane details, ignoring the big picture. We need a little more Hollywood in science.

Let's get Michael Bay in on this, he could make it happen.

*rather, it came to me in a bout of inexplicable inspiration

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