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Sunday, January 16, 2011

Watching proteins fold

We now have the human genome completely sequenced. However, that information isn’t particularly useful unless we also know something about the proteins that our genomes encode. Unfortunately, predicting the final structure of a protein (which is critical for that protein’s function) from its DNA sequence has been challenging, not least of which because the folding process takes place in under a millisecond. Enter Michael Gross, Jiawei Chen and Don Rempel of Washington University, who have invented a way to observe proteins folding.

Example of a protein going from linear strand to three dimensional folded enzyme.

The researchers used a protein called ‘barstar’ as a model. This small (110 amino acids long) has a known primary structure (linear sequence of amino acids) and a known tertiary structure (the final, fully folded polypeptide). What was not known was the exact folding process required to go from one to the other. Here’s what the researchers did:

Samples of cold (unwound) barstar were placed in extremely thin hollow fibers, along with hydrogen peroxide (H2O2). The mixture was hit with two rapid laser pulses. The first pulse warmed up the solution enough for the protein strands to begin to fold. The second pulse broke up the H2O2, creating the highly reactive hydroxyl (-OH) radical. This radical added oxygen atoms to the exposed portions of the barstar protein. As Gross explains,

Imagine that you suspended a styrofoam model of a partially folded protein and spray-painted it blue. The outside parts would be painted blue; those buried within would remain white.

A microsecond after the second laser pulse, the excess –OH was removed. The protein was then ‘weighed’ in a mass spectrometer to see how much oxygen had been added.

This process was repeated 500 times in rapid succession, giving the scientists snap shot views of the protein in the processing of folding. The technique was successful with barstar, and may lead to helpful insights about other proteins as well.