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September 2013

Emulating Biology on the Nanoscale to Meet the Fourth Grand Challenge

Mastering matter on the atomic and molecular levels provides the key to innovation in solar energy conversion, biofuels, and beyond

Kara Manke

Using a technique that combines bioinformatics with molecular dynamics simulations, researchers at the Center for Lignocellulose Structure and Formation have created a 3D model of the intracellular region of plant cellulose synthase. Here, the growing cellulose molecule (in green) is shown emerging from the active site of the cellulose synthase. Illustration courtesy of Dr. Yaroslava Yingling, NC State University.

Have the capabilities of human-made technologies surpassed those of Mother Nature?

On the surface, it may appear that the answer is yes. Human inventions can fly to the moon, transmit information around the globe in less than a second, and compute even faster than the human mind.

Take a closer look, however, and you will find that nature still has a lot to teach us. Living systems can generate fuels directly from sunlight, water, and carbon dioxide; they have complex metabolic pathways that can create new materials and energy sources; and they have developed robust molecular signaling and recognition processes.

Many of these capabilities arise from complex behavior at the level of atoms and molecules. As scientific methods to characterize and fabricate nanostructures mature, many of the processes that were previously in the domain of living systems are now within our grasp. The U.S. Department of Energy's Fourth Grand Challenge calls for scientists to use these abilities to create new technologies that rival or exceed those of living things.

Biohybrid light-harvesting antennas absorb a broader spectrum of sunlight. The light-harvesting antennas in plant cells supply the energy that is used to create fuel via photosynthesis. Photosynthetic systems turn carbon dioxide and water into oxygen and simple sugar molecules that fuel the organism. In this process, light-harvesting antennas play the key role of capturing sunlight and transferring the resulting energy to photosynthetic reaction centers, where the array of steps in this overall conversion reaction ensue.

For scientists attempting to mimic photosynthesis, the design of synthetic light-harvesting antennas presents an obstacle. Nature-made antennas of photosynthetic organisms are composed of light-absorbing pigments supported within a peptide "scaffold," which holds the pigments in the optimal positions to maximize energy transfer. While pigment analogs that absorb specific regions of the solar spectrum can be synthesized, scientists have not found a good way to stitch pigment molecules into a support structure.

Jonathan Lindsey and his collaborators at the Photosynthetic Antenna Research Center have solved this problem by taking advantage of a technique called semisynthesis, in which synthetic chemistry is played out with natural and synthetic materials. The light-harvesting complexes of photosynthetic organisms are formed by a process called self-assembly, in which the peptide and pigment molecules are spontaneously organized into a ring-shaped structure by attractive molecular forces. Lindsey altered synthetic pigment molecules so that they could be incorporated into this self-assembled structure, without changing their absorption properties.

"The challenge in energy sciences is not only to rival photosynthetic systems but to far exceed photosynthesis," says Lindsey. Indeed, using his synthetic pigments, it is possible to create artificial light-harvesting systems that can absorb a broader spectrum of sunlight than that utilized by plants.

Modeling the 3D structure of cellulose synthase. In plant anatomy, cellulose forms the backbone. This polymer, a linear chain of linked glucose molecules, forms the primary structural component of plant cell walls, and is useful both as a biomaterial and a precursor to biofuels.

As important as cellulose is, scientists still don't understand exactly how plants make cellulose. The 3D structure of cellulose synthase, the large protein responsible for linking together thousands of glucose molecules, has eluded scientists for more than 40 years. However, using a technique that combines known protein structures with molecular dynamics simulations, Yaroslava Yingling's group at the Center for Lignocellulose Structure and Formation has finally provided a 3D model of the intracellular region of this molecule.

These results, published in a recent issue of the Proceedings of the National Academy of Science, may one day allow scientists to tailor the properties of cellulose to fit specific applications. For example, amorphous cellulose is easier to break down and forms a better biofuel precursor, while crystalline cellulose is stiff and strong, more suitable for incorporation into new materials. Once the structure and function of plant cellulose synthase is well understood, it can be genetically modified to produce one type of cellulose over another.

Yingling foresees a day when cellulose with desired properties could be grown artificially. "If we really understand the nano-machinery of cellulose synthase, we could ask it to grow other polymeric systems -- there would be all kinds of interesting materials that we could synthesize," she said. "Once you understand it, the sky's the limit."

Materials with triangular pores to purify high-quality gasoline. You cannot fit a square peg in a round hole. Scientists at the Center for Gas Separations Relevant to Clean Energy Technologies Energy Frontier Energy Center used this old wisdom when designing a new nanostructured material for the purification of high-quality gasoline.

Hexanes, molecules with six carbon atoms and 14 hydrogen atoms, are one component of gasoline. They can come in a variety of different shapes: some are linear, some contain one branch, and others contain two branches. Those hexanes with two branches have the highest fuel octane rating, and form the highest quality gasoline.

In a Science paper, Zoey Herm and her colleagues in Jeffrey Long's group reported using a metal-organic framework with triangular channels to separate linear hexanes from branched hexanes. As hexanes travel through this nanoporous material, linear hexanes become trapped within the grooves and are held in place by intermolecular forces. The bulky nature of the branched hexanes orients them into the central empty pore space, so that they pass more quickly through the material. This method is more energy efficient than other techniques used to produce high-quality gasoline and could reduce the use of toxic additives to boost fuel octane ratings.

Herm's work is just one example of how nanoporous materials are being used to separate and trap mixtures of small molecules. These technologies are proving key to the development of cleaner burning fuels and the capture of carbon dioxide before it enters the atmosphere.

Outlook. These examples show that a true understanding of the nanotechnology of both living and artificial systems can lead to unexpected innovations. Often, technological progress is made by co-opting the molecular machinery that biology has already created, but only once that machinery has been fully understood and mastered. The process of evolution has had approximately 3.8 billion years to engineer the complex molecular dance that makes life possible, but human technology is rapidly catching up.

More Information

Reddy KR, J Jiang, M Krayer, MA Harris, JW Springer, E Yang, J Jiao, DM Niedzwiedzki, D Pandithavidana, PS Parkes-Loach, C Kirmaier, PA Loach, DF Bocian, D Holten, and JS Lindsey. 2013. "Palette of Lipophilic Bioconjugatable Bacteriochlorins for Construction of Biohybrid Light-Harvesting Architectures." Chemical Science 4:2036-2053. DOI: 10.1039/C3sc22317e

Sethaphong L, CH Haigler, JD Kubicki, J Zimmer, D Bonetta, S DeBolt, and YG Yingling. 2013. "Tertiary Model of a Plant Cellulose Synthase." Proceedings of the National Academy of Science 110:7512-7517. DOI: 10.1073/pnas.1301027110

Herm Z, BM Wiers, JA Mason, JM van Baten, MR Hudson, P Zajdel, CM Brown, N Masciocchi, R Krishna, and JR Long. 2013. "Separation of Hexane Isomers in a Metal-Organic Framework with Triangular Channels." Science 340:960-964. DOI: 10.1126/science.1234071

Acknowledgments

Reddy et al.: This work was supported by the Photosynthetic Antenna Research Center, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences.

Sethaphong et al.: Work by Latsavongsakda Sethaphong, Candace H. Haigler, James D. Kubicki, and Yaroslava G. Yingling was supported as part of the Center for Lignocellulose Structure and Formation, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Work by Seth DeBolt was supported by the National Science Foundation. Work by Jochen Zimmer was supported by the National Institutes of Health. Work by Dario Bonetta was supported by the National Science and Engineering Research Council of Canada.

Herm et al.: This work was supported through the Center for Gas Separations Relevant to Clean Energy Technologies, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Matthew R. Hudson acknowledges support from the National Institute of Standards and Technology National Research Council Postdoctoral Associateship Program. Norberto Masciocchi acknowledges partial funding from the Cariplo Foundation.

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More Information

Reddy KR, J Jiang, M Krayer, MA Harris, JW Springer, E Yang, J Jiao, DM Niedzwiedzki, D Pandithavidana, PS Parkes-Loach, C Kirmaier, PA Loach, DF Bocian, D Holten, and JS Lindsey. 2013. "Palette of Lipophilic Bioconjugatable Bacteriochlorins for Construction of Biohybrid Light-Harvesting Architectures." Chemical Science 4:2036-2053. DOI: 10.1039/C3sc22317e

Sethaphong L, CH Haigler, JD Kubicki, J Zimmer, D Bonetta, S DeBolt, and YG Yingling. 2013. "Tertiary Model of a Plant Cellulose Synthase." Proceedings of the National Academy of Science 110:7512-7517. DOI: 10.1073/pnas.1301027110

Herm Z, BM Wiers, JA Mason, JM van Baten, MR Hudson, P Zajdel, CM Brown, N Masciocchi, R Krishna, and JR Long. 2013. "Separation of Hexane Isomers in a Metal-Organic Framework with Triangular Channels." Science 340:960-964. DOI: 10.1126/science.1234071

Disclaimer: The opinions in this newsletter are those of the individual authors and do not represent the views or position of the Department of Energy.