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June 25, 2013

Kraken Chews on Gribble Data for Industrial Enzyme Research

Alex Woodie

Several years ago, a diminutive marine crustacean called the Gribble landed on the biofuel industry’s radar for its unique ability to digest wood in salty conditions. Now, researchers in the US and the UK are putting the University of Tennessee’s Kraken supercomputer to work modeling an enzyme in the Gribble’s gut, which could unlock the key to developing better industrial enzymes in the future.

Marine biologists in the UK made an important discovery about the Gribble in 2010. Apparently, the wood-boring critters had so-called “family-7” enzymes living in their gut. Family-7 enzymes are usually only found in fungi, which have traditionally been the main sources of the enzymes that biofuel researchers are interested in.

Armed with this information, a group of researchers from the University of Portsmouth in the UK, the U.S. Department of Energy’s National Renewable Energy Laboratory (NREL), and the University of Kentucky set out to better understand the Gribble and its enzymes.

The U.K. researchers isolated one of the family-7 enzymes in the Gribble, called Cel7B, and solved its structure with X-ray diffraction, providing a good static view of the entity. Meanwhile, the NREL enlisted the UT’s Kraken supercomputer to perform molecular dynamics (MD) simulations on Cel7B, which provided a detailed view of Cel7B’s activity.

Kraken is a Cray XT5 supercomputer housed at the Oak Ridge National Laboratory and operated by the UT’s National Institute for Computational Sciences (NICS). In 2009, Kraken became the world’s first academic supercomputer to enter the petascale range, which means it performed more than one thousand trillion operations per second.

At the time, Kraken was only the fourth supercomputer of any kind to break the petascale barrier. The 112,800-core Opteron-based system debuted on the Top 500 list of the world’s biggest supercomputers in June 2011 at number 11. It has not run the LINPACK test again, and slipped to number 30 on the June 2013 edition of the list. The 9,400-node cluster continues to help scientists in the fields of astronomy, chemistry, and meteorology. 

The MD simulations on Kraken have already led to several potentially valuable discoveries about the Gribble’s enzyme, according to NREL’s Gregg Beckham. For example, the researchers found “that the charge on the enzyme’s surface was immense,” Beckham tells the NICS.

High negative surface charge is typically correlated with salt tolerance. Indeed, the researchers found that Cel7B remained active in water up to six times saltier than ocean water. This is potentially valuable because it means Cel7B may be hardy in high-solids, industrial environments. Enzymes with high-solids tolerance have the potential to save industrial biofuel operations money because they require a smaller reactor and less water, Beckham says.

The work with Kraken, which is being funded by the National Science Foundation’s eXtreme Science and Engineering and Discovery Environment (XSEDE), is still on-going. Up next: comparing Cel7B with other family-7 enzymes, with the goal of better understanding this class of enzymes and potentially modifying them for industrial use.

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