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Slicing proteins with Occam's Razor
Date:9/30/2010

arrangements of its atoms than there are stars in the universe. And each of these arrangements slightly changes a protein's function.

"But what are the important motions that control its function?" asks Chu.

"Relating the structure of a protein to what it is doing is the holy grail," he says. For myoglobin at least, the two UVM scientists seem to have brought the prize a lot closer to hand.

Their method -- called temperature derivative spectroscopy or TDS -- involves cooling myoglobin to as low as -450 degrees Fahrenheit, about 18 degrees above absolute zero, and then measuring its oxygen-binding process. At these chilly temperatures, each protein basically gets stuck in just one arrangement. These individual atomic arrangements can't be observed directly, but, using infrared light, a pack of myoglobin molecules does yield a kind of group portrait -- a summing, called a TDS surface -- of the position of all the proteins as they bind to the oxygen in carbon monoxide.

The Vermont scientists' innovation comes largely from what they have been able to do with this group portrait.

"This scenario is called an inverse problem," DeWitt notes, "we have measured the effect but want to determine the cause." Unfortunately, a bit like asking what two numbers add up to ten, there are many solutions.

But, usually, nature does not build wasteful structures -- and though the universe is undoubtedly complex, it does not seem given to capricious complexity. In other words, the scientific principle of parsimony -- what philosophy students encounter as Occam's Razor -- suggests that the least complex explanation is the most likely.

Applying a mathematical version of this idea from Bayesian statistics, called the principle of maximum entropy, DeWitt and Chu went looking for the simplest solution to the TDS surface created by their group of myoglobin molecules. And the answer: the motion of the distal histidine most simply expl
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Contact: Joshua Brown
joshua.e.brown@uvm.edu
802-656-3039
University of Vermont
Source:Eurekalert  

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