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Drooling on the Pillow

Sunday, May 22, 2005

Look At Me, I'm A Microbiotechnologist! 

I've always been fascinated by proteins. No kidding.

They're strings or necklaces of amino acids and there are millions of them. They average a hundred or so amino acids but they can be as few as a dozen or there can be thousands. They're the fundamental biological invention of life. They're not exactly organisms, but without them organisms could never have developed. And every one has a job.

Here's the cool part. As soon as a protein chain is assembled in a cell and before it can perform its tasks it folds. In an almost metaphysical act of origami it transforms from a chain to a machine, folding and assembling itself in a precise order into a unique shape. This folding process involves hundreds or thousands of parts, takes as little as a millionth of a second and must be done exactly right. Misfolding results in flawed structures, inert enzymes and diseases such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, and Parkinson's disease.

And no one knows how or why it does it. No idea. There's not even any real theories.

For instance, hemoglobin is a protein most people have heard of. It travels in the red blood cells and carries oxygen from the lungs to where it's needed. The whole purpose of hemoglobin is to form a ring in the very center of which a single atom of iron bonds equally with the acids on all four sides of it. That atom oxidizes in the lungs and de-oxidizes in the capillaries where the oxygen is needed.

Okay, the reason I bring it up is that I signed up some time ago for a distributed computing project at Stanford University called Folding-at-Home. (I can't figure out how to prevent it from being a email link if I use the @.)

That's one of those deals where a research project uses down time on private computers (more than 1 million of them in this case) to work on vast projects. It was used for the human genome project and in a number of astrophysical projects. It was the original idea behind the internet.

Right now my computer is working on the folding sequence of p2003-ab1-42-4mer-opls GROMACS core.

Can't wait to see how it comes out.
Posted by: Sluggo / 12:05 PM
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