Molecule Porn Flicks

In the last post, Vleeptron had suspected that its Folding@Home software that's been invisibly, silently Doing Something in the bowels of the Vleeptron Computer for years might have been up to Some Kind of Digital Monkey Business, like strip poker or surfing for molecule porn.

Our suspicions have been confirmed. Maybe. You'll have to

watch the movie

and decide for yourselves.

Is it a significant step along the road to finding the Cure for HIV/AIDS?

Or is it Molecule Porn?

The Official Story is that the 200,000 volunteer PCs around the world (including a handful in Iran) are using their unused Thinking About Nothing time to compute the secrets of Protein Folding -- how a simple 1-dimension string of chemical beads (called amino acids, there are 20 different kinds) can fold itself into an extremely complex and irregular 3-dimensional solid molecule called a Protein.

As I grok the Theory, the Folding@Home project started investigating protein folding with Baby Steps, trying to make a digital computer mathematically reproduce the precise way, centisecond by centisecond, that very small sequences of amino acids Fold themselves into their final "tertiary" 3-dimensional solid protein molecules.

It's just possible that even I could grasp this process for a sequence with 10 or 12 beads (if you gave me eight years, and if Amy, Vleeptron's Official Real Biochemist, was willing to talk me through it for hours on the phone every night).

But Life doesn't get Real with such tiny and fictitious sequences and pretend proteins. The Real Stuff consists of sequences with scores or hundreds of RNA nucleotide beads, and produces big proteins measured in kiloDaltons -- molecules with the equivalent mass of thousands of hydrogen atoms. Molecules like insulin, hæmoglobin, the chain of proteins that make blood clot, the chain of proteins (ATP, ADP) that convert sugars into usable bio-energy.

And the way the chains of beads fold into those big proteins are the nightmare of massive computation for which Professor Vijay Pande of Stanford University (Palo Alto, California USA) created the worldwide Folding@Home network.

Well. Here's a Folding Baby Step that Folding@Home has successfully computed and understands.

"Understanding" in this case is a Movie, which will (or might or should) open in your QuickTime Video. If it works, what you will be watching is how two very small, similar molecules interact -- i.e., Fold -- in 3D space centisecond by centisecond until they finally assume their final 3D solid form.

Technically they're called dimers. Because Vleeptron is Dumb As Rocks, we shall ask Wikipedia to explain that:

... a dimer refers to a molecule composed of two similar subunits or monomers linked together. It is a special case of a polymer ... Its more common usage refers to dimers as certain types of sugar: sucrose, for example, is a dimer of a glucose molecule and a fructose molecule.

A physical dimer is a term that designates the case where intermolecular interaction brings two identical molecules closer together than other molecules. There are no covalent bonds between the physical dimer molecules. Acetic acid is such a case where hydrogen bonds provide the interaction.

Alles ist klar perfekt, ja?

Oh ... use your mouse on the QuickTime slider control to pause and forward and reverse the Movie, don't just watch it at the movie's own speed (which I suspect is the speed at which this reaction takes place in Nature). The more you pause and replay and forward and back this Movie, the more you "understand" what this Folding Stuff is all about.

I'm convinced it's two small molecules dancing the Lambada ("the Forbidden Dance") or the Nuevo Tango. I think the movie would go well with some Astor Piazzolla bandoneon music for a soundtrack.

It's a Baby Step on the way to finding cures for HIV/AIDS, a variety of cancers, Alzheimer's Disease, Huntington's Disease -- any bio-trouble whose cause involves Proteins.

Folding@Home has posted about a dozen of these strange and starkly beautiful Dancing Molecule Movies, all produced and directed by Nature and a few billion years of Natural Selection, as painstakingly revealed by 200,000 linked Central Processing Units all over the world (including Bob's). I just chose this one to start.

Click on all of them. Spend an hour watching the Proteins Fold. Spend an hour watching human beings get smarter with the help of their Silicon Friends, from Baby Steps to Functional Chemical Understanding.

Did you like the Movie?

Here's another.

In this one, an artificial protein -- one designed not by Nature, but by Human Beings -- folds. F@H describes it thus:

UNFOLDING OF DESIGNED PROTEIN

This protein was designed by the Mayo Lab to fold into a "zinc finger" fold (a protein fold which typically binds to DNA).