Research Frontiers in Bioinspired Energy Molecular-Level Learning from Natural Systems: Report of a Workshop (2012) / Chapter Skim
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2 Summary of Speaker Presentations
2 Summary of Speaker Presentations
Pages 7-32
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Dutton's work has revealed common machinery in enzymes driven by electron transfer (Moser et al., 1992)
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found in most physiological enzymatic reactions. Natural energy systems have evolved a general and simple engineering for electron transfer that can be used for understanding uncharacterized, naturally occurring oxidoreductases, and in constructing synthetic enzymes.
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For example, such a maquette could provide a photocatalytic function for solar energy applications.
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. Although her work is not spe cifically focused on bioinspired energy, Boston's work explores extreme environments, specifically subsurface earth.
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11 SUMMARY OF SPEAKER PRESENTATIONS FIGURE 2-3 Slimy strings of bacteria often called "snottites" are found in caves Boston has explored. This cluster was found in Cueva de Villa Luz, Tabasco, Mexico.
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:907-917. SYNTHETIC BIOLOGY If you understand electron transfer, you ought to be able to build your own electron transfer stuff.
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Although the following results have not been published, according to Benner, he and his collaborators have successfully created synthetic DNA that replicates in artificial cells and is capable of Darwinian evolution. He explained that such synthetic biological systems are ideal and desirable because they do not carry around the billion years of "baggage" like natural systems (i.e., components that are useful for the natural organism, but not necessarily for the function of the desired application)
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Benner's artificial orthogonal DNA base pairs K, X, ZP, V, J, iso-C, and iso-G, created by shuffling donors/acceptors. SOURCE: Stephen Benner, presentation slide.
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. As described by Lanyi, in a retinal-based ion pump, retinal isomerization after photon absorption initiates molecular rearrangements and results in ion uptake on one side of the membrane, translocation, and then release on the other side -- the extracellular side of halophilic archaea.
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. Thauer discussed anaerobic oxidation of methane with sulfate as an electron acceptor.
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However, there was early evidence from Reeburgh in the 1970s that contradicts this. Now, Thauer said, there is no doubt that methane can be used by anaerobes to fuel their energy metabolism using either sulfate, MnIV, FeIII, or nitrite as the terminal electron acceptor (Figure 2-7)
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18 FIGURE 2-7 Schematic of the global methane cycle, which highlights the different microorganisms involved in catalyzing the an Fig 2-7.eps aerobic oxidation of methane with nitrite (magenta) and sulfate (orange)
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This area is extensively studied in insects and has inspired the development of many nanometric photonic structures. –Marian Plotkin Marian Plotkin, from the University of Singapore, discussed the possible ability of the oriental hornet to harvest solar energy (Plotkin et al., 2010)
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The yellow cuticle contains a pigment believed to harvest solar energy for the oriental hornet. The brown cuticle is composed of the epicuticle, which is the outermost part of the cuticle, the exo-endocuticle, and the hypocuticle.
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-- The oriental hornet cuticle is a photonic structure capable of harvesting sunlight. • The pigment xanthopterin within the cuticle transforms sunlight into electrical energy, which may serve the metabolic activity performed within the pigment layer, hence aiding in the digging activity.
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Insects are able to construct durable, precise, and complex nanometric structures in their cuticle. Plotkin's main mes sage was that the oriental hornet cuticle structure and its self-assembly processes during metamorphosis could serve as a model for improving the design of photonic structures.
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Eukaryotic life in general uses organic carbon as electron donor and oxygen as electron acceptor, whereas the prokaryotes (methanogens, FE reducers, and deni trifers) use many other acceptors, taking advantage of abundant and ubiquitous energy sources and oxidants available.
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They are MtrA, MtrB, and MtrC (Mtr = metal reduction) , as shown in the conceptual model for extracellular electron transfer in Shewanella sp.
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. Initially, his group developed fuel cells to take advantage of the electron transfer properties of the bacteria in an anaerobic environment coupled to an abiotic electron acceptor on the other side of the cell.
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2007. Specific bonds between an iron oxide surface and outer membrane cytochromes MtrC and OmcA from Shewanella oneidensis MR-1.
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The other project Wolfe-Simon spoke about is the recently published research on a microbe, GFAJ-1 (found in high-arsenic soda lakes in Cali fornia and Nevada, Figure 2-12) , that appears to sustain its growth using arsenic instead of phosphorus, for example, in DNA (Wolfe-Simon et al., 2011)
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Seeman, from New York University, discussed his work on using DNA's chemical information for bottom-up nanoscale control of the structure of matter and taking natural material and making an unnatural object from it. More biomimetic than bioinspired, Seeman described how the chemical information contained in DNA can be used to direct methods of organizing matter and making nanoscale mechanical devices such as assembly lines.
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. Seeman said his lab focuses on DNA because "nucleic acid sequences can be programmed and synthesized, leading to informationbased structural, dynamic, and catalytic chemistry." As illustrated in Figure 2-14, the intellectual goal of structural DNA nanotechnology is to control the structure of matter in three dimensions (3D)
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SOURCE: Illustrations by David Goodsell, based on the RCSB Protein Data Bank entry 3gbi. Used by permission.
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2010. A proximity-based programmable DNA nanoscale assembly line.
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