Scientists identify key steps in process by which enzyme breaks down cellulose
Cellulosic biomass - one of the most abundant materials on the planet - can be converted into liquid fuels via thermochemical and biochemical processes. Thermochemical transformation consists of such processes as gasification and pyrolysis, whereas the biochemical route relies on enzymes that break down cellulose into sugars. If these conversion techniques become efficient, a wide range of biofuel feedstocks can be used, such as grasses and wood.
However, utilising enzymes remains slow and expensive because of a central bottleneck: the sluggish rate at which the cellulose enzyme complex breaks down tightly bound cellulose into sugars, which are then fermented into ethanol.
A team of UC San Diego scientists has now conducted molecular simulations at the San Diego Supercomputer Center (SDSC). 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.
The researchers reported their results in the April 12 online edition of the Protein Engineering, Design and Selection journal, which also featured visualizations of the results on the cover.
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 (picture, click to enlarge). This gives the enzyme a crucial foothold to begin the process of digesting or “unzipping” the cellulose into sugar molecules:
bioenergy :: biofuels :: energy :: sustainability :: cellulose :: biomass :: sugar :: simulation :: cellulase ::
To the scientists, the simulation is like a stop-motion film of a baseball pitcher throwing a curveball. In real-life the process occurs far too quickly to evaluate visually, but by using the supercomputer simulations to break the throw down into a step-by-step process, the scientists can see the precise details of the role of velocity, trajectory, movement, and arm angle. To undertake the large-scale simulations, the researchers used the CHARMM (Chemistry at HARvard Molecular Mechanics) suite of modeling software.
According to the researchers, an accurate understanding of the key molecular events required the simulations to run for some six million time steps over 12 nanoseconds (a nanosecond is one billionth of a second) in order to capture enough of the motion and shape changes of the enzyme as it interacted with the cellulose surface.
This is an extremely long time in molecular terms, and the computation-hungry simulations ran for some 80,000 processor-hours running on SDSC’s DataStar supercomputer.
Also participating in the study were Michael Crowley, William Adney, and Michael Himmel of the Department of Energy’s National Renewable Energy Laboratory (NREL); James Matthews and John Brady of Cornell University; Linghao Zhong of Penn State University; as well as Ross Walker, and Giridhar Chukkapalli of SDSC.
The research was partially funded by the Department of Energy’s Biomass Program and the National Science Foundation.
Movie: Molecular machines converting cellulose to bio fuel. Couresty: UC San Diego.
More information:
Mark R. Nimlos, et al. “Molecular modeling suggests induced fit of Family I carbohydrate-binding modules with a broken-chain cellulose surface” [*abstract], Protein Engineering Design and Selection, PEDS Advance Access published online on April 12, 2007, doi:10.1093/protein/gzm010
University of California San Diego: Meeting the Ethanol Challenge: Scientists Use Supercomputer to Target Cellulose Bottleneck - April 24, 207.
However, utilising enzymes remains slow and expensive because of a central bottleneck: the sluggish rate at which the cellulose enzyme complex breaks down tightly bound cellulose into sugars, which are then fermented into ethanol.
A team of UC San Diego scientists has now conducted molecular simulations at the San Diego Supercomputer Center (SDSC). 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.
The researchers reported their results in the April 12 online edition of the Protein Engineering, Design and Selection journal, which also featured visualizations of the results on the cover.
“By learning how the cellulase enzyme complex breaks down cellulose we can develop protein engineering strategies to speed up this key reaction. This is important in making ethanol from plant biomass a realistic ‘carbon neutral’ alternative to the fossil petroleum used today for transportation fuels.” - Mike Cleary, SDSC coordinatorThe simulations have given the researchers a better understanding of the interactions between the enzyme complex and cellulose at the molecular level - the computer model showed how the binding portion of this enzyme changes shape, which hadn’t been anticipated by the scientific community. "These results are important because they can provide crucial guidance as scientists formulate selective experiments to modify the enzyme complex for improved efficiency", says Mark Nimlos, lead author and Senior Scientist at NREL.
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 (picture, click to enlarge). This gives the enzyme a crucial foothold to begin the process of digesting or “unzipping” the cellulose into sugar molecules:
bioenergy :: biofuels :: energy :: sustainability :: cellulose :: biomass :: sugar :: simulation :: cellulase ::
To the scientists, the simulation is like a stop-motion film of a baseball pitcher throwing a curveball. In real-life the process occurs far too quickly to evaluate visually, but by using the supercomputer simulations to break the throw down into a step-by-step process, the scientists can see the precise details of the role of velocity, trajectory, movement, and arm angle. To undertake the large-scale simulations, the researchers used the CHARMM (Chemistry at HARvard Molecular Mechanics) suite of modeling software.
According to the researchers, an accurate understanding of the key molecular events required the simulations to run for some six million time steps over 12 nanoseconds (a nanosecond is one billionth of a second) in order to capture enough of the motion and shape changes of the enzyme as it interacted with the cellulose surface.
This is an extremely long time in molecular terms, and the computation-hungry simulations ran for some 80,000 processor-hours running on SDSC’s DataStar supercomputer.
Also participating in the study were Michael Crowley, William Adney, and Michael Himmel of the Department of Energy’s National Renewable Energy Laboratory (NREL); James Matthews and John Brady of Cornell University; Linghao Zhong of Penn State University; as well as Ross Walker, and Giridhar Chukkapalli of SDSC.
The research was partially funded by the Department of Energy’s Biomass Program and the National Science Foundation.
Movie: Molecular machines converting cellulose to bio fuel. Couresty: UC San Diego.
More information:
Mark R. Nimlos, et al. “Molecular modeling suggests induced fit of Family I carbohydrate-binding modules with a broken-chain cellulose surface” [*abstract], Protein Engineering Design and Selection, PEDS Advance Access published online on April 12, 2007, doi:10.1093/protein/gzm010
University of California San Diego: Meeting the Ethanol Challenge: Scientists Use Supercomputer to Target Cellulose Bottleneck - April 24, 207.
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