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Supercomputers, stomachs, and biofuels

Klaus Schulten. Image courtesy the University of Illinois at Urbana-Champaign, US.

The Romantic poet William Blake claimed he could see all the world in a grain of sand, but with the aid of XSEDE, Klaus Schulten can see the future of biofuels inside a cow's stomach.

Using molecular dynamics and single molecule force spectroscopy, Schulten, computational biologist at the University of Illinois at Urbana-Champaign, US modeled the bond between two cellulosomal proteins bacteria use to digest plants in cow stomachs.

Schulten and colleagues published their landmark modeling in the December 2014 issue of Nature Communications.

The strength of this protein bond is formidable when constructed by bacteria into the finger-like cellulosomes. This complex construction facilitates digestion by enzymes, and requires tremendous force to disassemble. Schulten's study measured the amount of force required to deconstruct the cellulosomes.

Funding for the study came from the NSF and the US National Institutes of Health, as well as the European Research Council and the Excellence Cluster Center for Integrated Protein Science Munich.

Schematic of selected components of the R. flavefaciens cellulosome. The complex responsible for maintaining bacterial adhesion to cellulose is highlighted in orange. Courtesy Klaus Schulten.

"In order to engineer things, we need to harness the system and we need to view the results of modifications that the engineers are applying," Schulten says. "For that, we need a microscope that sees the chemical details and the physical characteristics - that is only available through computing."

Biofuels from grass, straw, corn stalks, and other roughage found in cow stomachs prove too costly to mass produce. However, modeling this protein bond can lead to bioengineered bacteria that can bring cheaper enzymes needed to bust the protein bond. With any luck, we'll soon be able to fill our fuel tanks with cow gut enzymes and drive to Texas.

The bimolecular bond was simulated on the Stampede supercomputer at the Texas Advanced Computing Center (TACC), US and on the Blue Waters supercomputer of the National Center for Supercomputing Applications (NCSA), US.

"The simulations are a kind of computational microscope that tells engineers what is happening," Schulten says.

See more of Dr. Schulten's computational microscope work here.

Read more about how supercomputers help solve puzzle-like bond for biofuels here.

--Lance Farrell

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