Jungle rot on the supercomputer

In search of a better way to make biofuels, scientists simulate the hunger of a famous fungus with their "virtual microscope."


Andrew Leonard
April 25, 2007 11:27PM (UTC)

I just watched a supercomputer-generated molecular simulation of a fungi-derived enzyme attempting to grab hold of a loose strand of cellulose. I wouldn't call it riveting cinema, but it was still compelling, in a mildly creepy way. At first, the enzyme appeared to float aimlessly over the impassive cellulose, randomly flicking molecular tendrils this way and that. But ever so gradually, it began to "fit" itself around a mishapen blob of cellulose protruding from the larger mass.

There was no satisfying denouement in the snippet I saw. In the endgame, the enzyme is supposed to latch on tight and then "unzip" the cellulose into fragments that it transforms into sugar. This is the key step necessary for converting fibrous plant matter into ethanol -- the so-called cellulosic technology that anyone interested in biofuels has been hearing so much about lately. If only we could figure out how to cheaply convert cellulose into ethanol, we could usher in an era in which biofuels didn't have to be made from sugar cane or corn kernels, but instead, could be generated from practically anything that grows.

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According to Paul Tooby, a science writer who works for the San Diego Supercomputing Center, "the central bottleneck" preventing this magical era from arriving "is the sluggish rate at which the cellulose enzyme complex breaks down tightly bound cellulose into sugars, which are then fermented into ethanol." (Thanks to Biopact for the link.)

Enter the supercomputer. Using advanced molecular modeling techniques, a team of scientists have programmed the San Diego supercomputer to simulate what they think is happening when one particular enzyme attempts to chew on some tough plant cell walls. Thus the animated horror flick, in which the zombie microbe searches relentlessly for a chance to begin its relentless degradation.

Tooby, in a masterful example of clear science writing, describes how the simulation can help biofuel researchers move forward:

By using "virtual molecules," they have discovered key steps in the intricate dance in which the enzyme acts as a molecular machine -- attaching to bundles of cellulose, pulling up a single strand of sugar, and putting it onto a molecular conveyor belt where it is chopped into smaller sugar pieces...

What the scientists found in their simulations -- a "virtual microscope" that let them zoom in on previously invisible details -- is that initially the binding part of the enzyme moves freely and randomly across the cellulose surface, searching for a broken cellulose chain. When it encounters an available chain, the cellulose itself seems to prompt a change in the shape of the enzyme complex so that it can straddle the broken end of the cellulose chain. This gives the enzyme a crucial foothold to begin the process of digesting or "unzipping" the cellulose into sugar molecules.

Incidentally, history buffs will be pleased to know that the particular enzyme being simulated is derived from a strain of fungi called Trichoderma reesei. Also known as "jungle rot," T. reesei was originally isolated from a canvas tent used by American soldiers on Bougainville Island during World War II by researchers mobilized by the military in a desperate attempt to find out why everything made out of cotton in the South Pacific was disintegrating before their eyes. T. reesei has since become one of the great workhorses of the industrial enzyme world -- used for everything from the production of stone-washed jeans to making chicken feed more easily digestible. Iogen, one of the more advanced commercial enterprises attempting to perfect cellulosic ethanol technology, employs a family of souped-up, genetically enhanced enzymes derived from T. reesei.

Jungle rot never smelled so sweet.


Andrew Leonard

Andrew Leonard is a staff writer at Salon. On Twitter, @koxinga21.

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