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September 25, 2008
Protein Folding: Complexity to Make More Complexity?
Want a hard problem? Something to really keep you challenged? Try protein folding. That'll eat up all those spare computational cycles you have lounging around and come back to ask for more. And it'll do the same for your brain cells, too, for that matter.
The reason is that a protein of any reasonable size has a staggering number of shapes it can adopt. If you hold a ball-and-stick model of one, you realize pretty quickly that there are an awful lot of rotatable bonds in there (not least because they flop around while you're trying to hold the model in your hands). My daughter was playing around with a toy once that was made of snap-together parts that looked like elbow macaroni pieces, and I told her that this was just like a lot of molecules inside her body. We folded and twisted the thing around very quickly to a wide variety of shapes, even though it only had ten links or so, and I then pointed out to her that real proteins all had different things sticking off at right angles in the middle of each piece, making the whole situation even crazier.
There's a new (open access) paper in PNAS that illustrates some of the difficulties. The authors have been studying man-made proteins that have substantially similar sequences of amino acids, but still have different folding and overall shape. In this latest work, they've made it up to two proteins (56 amino acids each) that have 95% sequence identity, but still have very different folds. It's just a few key residues that make the difference and kick the overall protein into a different energetic and structural landscape. The other regions of the proteins can be mutated pretty substantially without affecting their overall folding, on the other hand. (In the picture, the red residues are the key ones and the blue areas are the identical/can-be-mutated domains).
This ties in with an overall theme of biology - it's nonlinear as can be. The systems in it are huge and hugely complicated, but the importance of the various parts varies enormously. There are small key chokepoints in many physiological systems that can't be messed with, just as there are some amino acids that can't be touched in a given protein. (Dramatic examples include the many single-amino-acid based genetic disorders).
But perhaps the way to look at it is that the complexity is actually an attempt to overcome this nonlinearity. Otherwise the system would be too brittle to work. All those overlapping, compensating, inter-regulating feedback loops that you find in biochemistry are, I think, a largely successful attempt to run a robust organism out of what are fundamentally not very robust components. Evolution is a tinkerer, most definitely, and there sure is an awful lot of tinkering that's been needed.
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