ORNL's supercomputer shows how microbial enzymes turn plant cellulose into sugar.
Harnessing the capabilities of one of the world's most powerful supercomputers, the largest biological simulation ever conducted at Oak Ridge National Laboratory is providing insights on converting cellulose from green plants into sugar. The supercomputer's ability to create a visualization of a million atoms promises to help researchers design more efficient methods for producing biofuels.
Like humans, microbes depend on sugar for energy. Fungi and bacteria obtain sugar from cellulose, the glucose polymer that composes cell walls in trees and other plants on land and in the ocean. These microorganisms produce cellulases, enzymes that work together to extract glucose from cellulose and turn the sugar into energy.
Computational biologists from ORNL and the National Renewable Energy Laboratory in Colorado, along with a researcher from Cornell University, are modeling bacterial and fungal cellulases in action at ORNL. Researchers "watch" these simulated enzymes attack digital cellulose strands, transfer a strand's sugar molecules to the enzyme's catalytic zone and chemically digest the sugar to provide the microbe with energy. The key to increasing the efficiency and lowering the cost of ethanol production using sugar from cellulose in trees and other biomass is to understand how cellulases degrade cellulose. Such understanding may lead to genetic engineering of the degradation mechanisms, speeding the biofuel production process.
John Brady of Cornell developed the original model of a cellulase molecule processing cellulose fibers under an optical microscope. Led by NREL's Mike Himmel, other collaborators include Ed Uberbacher and Phil LoCascio, researchers in ORNL's Genome Analysis and Systems Modeling Group, and Pavan K. Ghattyvenkatakrishna, a University of Akron graduate student who works in the GASM Group.
"We are studying the dynamics of cellulase at work on cellulose," says Uberbacher. "The model's cellulose resembles wood under a microscope. The individual strands are sugars strung together as a long polymer chain. The cellulase enzyme comes down and pulls a strand from the bundle forming the glucose polymer. The cellulase feeds the sugar fiber up to another domain of the enzyme that catalyzes the removal of the six-carbon sugar from the fiber. The process is a crucial step in making ethanol fuel from biomass."
The goals of the project include understanding how the cellulase enzyme functions, how it recognizes cellulose strands and how the chemistry is accomplished inside the enzyme. The group also hopes to determine what the rate-limiting steps are that might be genetically engineered to make cellulase more efficient at degrading cellulose into glucose.
The ORNL team performs the modeling using molecular dynamic simulations on 1,000 to 2,000 processors of "Jaguar," the Laboratory's Cray XT3 supercomputer. Jaguar, part of the Department of Energy's National Center for Computational Sciences, will perform more than 100 trillion calculations per second this year. Visualization in the nearby EVEREST lab has sparked new hypotheses and insights into how the enzyme flexes its shape and interacts with the solid substrate. Each simulation to test ideas about how the enzyme works runs for a number of days.
"Cellulase works one 1,000 times slower than most enzymes in our bodies," LoCascio says. "It takes perhaps 100 nanoseconds for this cellulase to move down one cellulose fiber and clip off a sugar molecule."
Jeremy Smith, molecular biophysicist and the first joint Governor's Chair appointee at UT and ORNL, uses both computing and neutron scattering to examine the positions and motions of atoms in cellulose-digesting enzymes (see "A Closer View: Jeremy Smith" article).
"Humans want to make alcohol out of plants, but plants do not want to be made into alcohol," he says. "We hope to learn why the enzymes we introduce do not degrade cellulose very fast and why plant cell walls will not cooperate and break down quickly."
Smith conducts neutron studies and simulations of cellulosomes, spider-like molecular machines that microbes create outside their cells to degrade cellulose effectively. "While working at the University of Heidelberg in Germany my colleagues and I published work on how cellulosome components talk to each other," he says, adding that he plans to continue his cellulosome research using the backscattering spectrometer at ORNL's Spallation Neutron Source.
Computational biologists hope to explore the diversity among cellulases and figure out why some cellulases work better at extremely high temperatures while others prefer lower temperatures. LoCascio points out that ocean bacteria, which live in extremely hot thermal vents and have no access to sunlight, make cellulases that degrade ocean biomass. One question researchers hope to address is how fungal cellulases that extract sugars from tree cellulose differ from bacterial cellulases produced on the forest and ocean floors under different conditions.—Carolyn Krause
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