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.
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.
Media contacts: Warren Froelich 858-822-3622 or Paul Tooby 858-822-3654
Paul Tooby | EurekAlert!
Organic-inorganic heterostructures with programmable electronic properties
30.03.2017 | Technische Universität Dresden
Researchers use light to remotely control curvature of plastics
23.03.2017 | North Carolina State University
The Institute of Semiconductor Technology and the Institute of Physical and Theoretical Chemistry, both members of the Laboratory for Emerging Nanometrology (LENA), at Technische Universität Braunschweig are partners in a new European research project entitled ChipScope, which aims to develop a completely new and extremely small optical microscope capable of observing the interior of living cells in real time. A consortium of 7 partners from 5 countries will tackle this issue with very ambitious objectives during a four-year research program.
To demonstrate the usefulness of this new scientific tool, at the end of the project the developed chip-sized microscope will be used to observe in real-time...
Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.
The results will be published on March 22 in the journal „Astronomy & Astrophysics“.
Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...
Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.
Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...
In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...
Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.
Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...
20.03.2017 | Event News
14.03.2017 | Event News
07.03.2017 | Event News
30.03.2017 | Health and Medicine
30.03.2017 | Health and Medicine
30.03.2017 | Medical Engineering