Navigation Links
Meeting the ethanol challenge: Scientists use supercomputer to target cellulose bottleneck

Termites and fungi already know how to digest cellulose, but the human process of producing ethanol from cellulose remains slow and expensive. The central bottleneck is the sluggish rate at which the cellulose enzyme complex breaks down tightly bound cellulose into sugars, which are then fermented into ethanol.

To help unlock the cellulose bottleneck, a team of scientists has conducted molecular simulations at the San Diego Supercomputer Center (SDSC), based at UC San Diego. 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.

"By learning how the cellulase enzyme complex breaks down cellulose we can develop protein engineering strategies to speed up this key reaction," said Mike Cleary, who is coordinating SDSC's role in the project. "This is important in making ethanol from plant biomass a realistic 'carbon neutral' alternative to the fossil petroleum used today for transportation fuels."

The results were reported in the April 12 online edition of the Protein Engineering, Design and Selection journal, which also featured visualizations of the results on the cover.

A convergence of factors from looming global warming to unstable international oil supplies is driving a surge in renewable biofuels such as ethanol, with worldwide ethanol production more than doubling between 2000 and 2005. To date, corn has been the favorite ethanol source. While good news for farmers, corn prices have doubled in the past two years, and consumers worldwide are feeling the pinch as food prices climb.

A far better source is to produce ethanol from cellulose, easing pressure on foo d supplies and yielding greater greenhouse gas benefits. The fibrous part that makes up the bulk of plants, cellulose is the cheapest and most abundant plant material, from corn stalks left after harvest to wood chips from papermills and fast-growing weeds.

"Our simulations have given us a better understanding of the interactions between the enzyme complex and cellulose at the molecular level -- the computer model showed us how the binding portion of this enzyme changes shape, which hadn't been anticipated by the scientific community," said first author Mark Nimlos, a Senior Scientist at NREL. "These results are important because they can provide crucial guidance as scientists formulate selective experiments to modify the enzyme complex for improved efficiency."

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.

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.


'"/>

Source:University of California - San Diego


Related biology news :

1. Antarctic Treaty Meeting moves to protect frozen continent from non-native species
2. Latest advances in DNA sequencing highlighted at DOE Joint Genome Institute User Meeting
3. Corn waste potentially more than ethanol
4. Scientific issues associated with carbon-neutral energy sources such as cellulosic ethanol
5. Producing bio-ethanol from agricultural waste a step closer
6. Engineered yeast speeds ethanol production
7. With cellulosic ethanol, there is no food vs. fuel debate according to MSU scientist
8. Cellulosic ethanol: Fuel of the future?
9. Genome sequencing reveals key to viable ethanol production
10. Evolutionary scrap-heap challenge: Antifreeze fish make sense out of junk DNA
11. Scientists ID molecular switch in liver that triggers harmful effects of saturated and trans fats
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:6/20/2016)... 2016 Securus Technologies, a leading provider ... public safety, investigation, corrections and monitoring announced that ... has secured the final acceptance by all three ... Access Systems (MAS) installed. Furthermore, Securus will have ... installed by October, 2016. MAS distinguishes between legitimate ...
(Date:6/15/2016)... 15, 2016 Transparency Market ... Recognition Market by Application Market - Global Industry Analysis Size ... to the report, the  global gesture recognition market ... and is estimated to grow at a CAGR ... 2024.  Increasing application of gesture recognition ...
(Date:6/9/2016)... 9, 2016 Paris Police ... video security solution to ensure the safety of people and ... during the major tournament Teleste, an international technology ... services, announced today that its video security solution will be ... back up public safety across the country. The system roll-out ...
Breaking Biology News(10 mins):
(Date:6/23/2016)... , June 23, 2016  Blueprint Bio, a ... discoveries to the medical community, has closed its Series ... Matthew Nunez . "We have received a ... the capital we need to meet our current goals," ... provide us the runway to complete validation on the ...
(Date:6/23/2016)... ... June 23, 2016 , ... ClinCapture, the only free validated ... will showcase its product’s latest features from June 26 to June 30, 2016 ... on Disrupting Clinical Trials in The Cloud during the conference. DIA (Drug ...
(Date:6/23/2016)... -- Amgen (NASDAQ: AMGN ) today announced a ... sciences incubator to accelerate the development of new therapies ... QB3@953 was created to help high-potential life science and ... stage organizations - access to laboratory infrastructure. ... "Amgen Golden Ticket" awards, providing each winner with one ...
(Date:6/22/2016)... Research and Markets has announced the addition ... their offering. The global ... billion in 2013. The market is expected to grow at a ... 2020, increasing from $50.6 billion in 2015 to $96.6 billion in ... forecast period (2015 to 2020) are discussed. As well, new products ...
Breaking Biology Technology: