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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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377 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structural Characterization and Dynamics of AdhE Ultrastructures from Clostridium thermocellum Show a Containment Strategy for Toxic Intermediates

Clostridium thermocellum, a cellulolytic thermophilic anaerobe, is considered by many to be a prime candidate for the realization of consolidated bioprocessing (CBP) and is known as an industry standard for biofuel production. C. thermocellum is among the best biomass degraders identified to date in nature and produces ethanol as one of its main products. Many studies have helped increase ethanol titers in this microbe; however, ethanol production using C. thermocellum is still not economically viable. Therefore, a better understanding of its ethanol synthesis pathway is required. The main pathway for ethanol production in C. thermocellum involves the bifunctional aldehyde-alcohol dehydrogenase (AdhE). To better understand the function of the C. thermocellum AdhE, we used cryo-electron microscopy (cryo-EM) to obtain a 3.28 A structure of the AdhE complex. This high-resolution structure, in combination with molecular dynamics simulations, provides insight into the substrate channeling of the toxic intermediate acetaldehyde, indicates the potential role of C. thermocellum AdhE to regulate activity and cofactor pools, and establishes a basis for future engineering studies. The containment strategy found in this enzyme offers a template that could be replicated in other systems where toxic intermediates need to be sequestered to increase the production of valuable biochemicals.

09 BIOMASS FUELS↗
DOE OSTI2020

Chromatin activity precipitation method and system

Methods and systems for identifying binding sites in macromolecules using small molecule mimics of naturally occurring molecules is disclosed. A reactive probe is provided that mimics small molecule cofactors. A target macromolecule is irreversibly bound to the probe in vivo to selectively pull down or precipitate probe-bound macromolecules. The macromolecules may be, but are not limited to, DNA, RNA, and proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

BETO 2021 Peer Review - Cell Free and Immobilization Technologies (CFIT)

Today, several key factors negatively impact the production of fuels and chemicals from renewable sources. Common hindrances in the biological production of biochemicals are: (1) end-product or intermediate toxicity to the microbial biocatalyst, (2) the diversion of carbon to biomass formation, and (3) co-production of undesired byproducts. A particularly attractive alternative is to eliminate the biocatalyst entirely and instead operate the desired metabolic pathways in isolation, thus circumventing the roadblocks of biological toxicity, lower yields, and lack of specificity. However, cell-free enzyme systems still suffer from low productivities owing in part to the effects of free diffusion of intermediates, lack of long term enzyme stability, cofactor cost or inefficient recycling rates, and finally, the cost of enzyme production/purification. This project represents a new effort to propose innovative and cost competitive routes to producing biochemicals from a variety of feedstocks using cell free approaches. These routes will help reduce the current risk and cost associated with classical cell free production. Cell free technologies show promise for application to the production of toxic/inhibitory products or products difficult to separate from microbial growth media and can help reduce the production barriers in multiple areas of biological conversion of feedstocks to biochemicals.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2021

Electrochemical flow-cell for hydrogen production and nicotinamide dependent target reduction, and related methods and systems

Methods and systems for hydrogen production or production of a reduced target molecule are described, wherein a nicotinamide co-factor dependent membrane hydrogenase or a nicotinamide co-factor dependent membrane enzyme presented on a nanolipoprotein adsorbed onto an electrically conductive supporting structure, which can preferably be chemically inert, is contacted with protons or a target molecule to be reduced and nicotinamide cofactors in presence of an electric current and one or more electrically driven redox mediators. Methods and systems for production of hydrogen or a reduced target molecule are also described wherein a membrane-bound hydrogenase enzyme or enzyme capable or reducing a target molecule is contacted with protons or the target molecule, a nicotinamide co-factor and a nicotinamide co-factor dependent membrane hydrogenase presented on a nanolipoprotein particle for a time and under condition to allow hydrogen production or production of a reduced target molecule in presence of an electrical current and of an electrically driven redox mediator.

Hoeprich, Jr., Paul D.↗
DOE OSTI2021

Coupled Microbial-Conversion and Computational-Fluid-Dynamics (CFD) Models for Butanediol Production in Micro-Aerated Reactors

Microbial conversion of substrates to macromolecules has been widely used in the synthesis of value-added products in pharmaceutical and biotechnology industries. These bioreactions are also being investigated in the production of low-value commodities such as biofuels [1]. Gas-liquid mass-transfer and transport-reaction coupling are important challenges when designing and scaling up these reactor systems. Experiments in wellmixed small-scale reactors have enabled characterization of microbial reactivity, while their coupling with macroscale transport remains relatively unexplored. In this work, we use a coupled metabolic-CFD model to study the action of a genetically engineered microbe Zymomonas mobilis [2] on sugars to produce 2,3-Butanediol (BDO). BDO is an important hydrocarbon intermediate that can be catalytically upgraded to several fuels and chemicals [3]. An important aspect to this particular microbial conversion is the need for micro-aerated environments as opposed to traditional aerobic fermentation. Slight variations in oxygen concentration can result in competing reaction pathways that disable BDO production. Hence, gas-liquid mass transfer and transport need to be optimized in large-scale reactors to maximize BDO production, for which CFD is a valuable tool. The aerobic-fermentation CFD model previously developed by the authors [5] for simulating bubble-column and airlift reactors at scale was used in this study. The Reynolds-averaged mass, momentum and energy transport equations for interpenetrating gas and liquid phase are solved in this model along with the transport and interphase mass transfer of oxygen. Our previous work used a phenomenological model for microbial oxygen uptake that neglected microbial growth and other reaction pathways. In this work, a detailed metabolic model enabled prediction of product formation and inhibition pathways. In order to manage computational cost, we used a subcycling technique [6] that takes advantage of the clear separation in transport (~ 200 sec) and reaction (~ 2-3 hours) timescales. The CFD model is first solved to steady state, after which the metabolic model is advanced at every cell in the computational domain using the local oxygen concentration. The CFD model is then run to achieve a new steady state that provides a new oxygen distribution for the metabolic model. This process, where reaction and fluid updates are interleaved together, is iterated until reactants are completely exhausted. This work will examine the performance of different reactor designs such as bubble column and airlift reactors at scale (250-500 m3). Oxygen mass-transfer coefficient and distribution are critically analyzed among reactors, and optimization studies pertaining to aeration is presented. Furthermore, it has been observed in experiments that high BDO production may be achieved by manipulating the aerobic environment over the course of reaction, such that oxygen concentration is high during the growth phase, and very low as sugar is depleted. This characteristic will be addressed by our simulations for which a timedependent scheduling strategy for aeration is presented that maximizes BDO production. [1] Humbird, D., Davis, R., and McMillan, J., Aeration costs in stirred-tank and bubble column bioreactors, Biochemical Engineering Journal, 127, 161—166, 2017 [2] Yang, S., Mohagheghi, A., Franden, M. A., Chou, Y.-C., Chen, X., Dowe, N., Himmel, M. E., and Zhang, M., Metabolic engineering of zymomonas mobilis for 2, 3-butanediol production from lignocellulosic biomass sugars. Biotechnology for biofuels, 9(1):189, 2016 [3] Kim, S. J., Sim, H. J., Kim, J. W., Lee, Y. G., Park, Y. C., and Seo, J. H., Enhanced production of 2,3-butanediol from xylose by combinatorial engineering of xylose metabolic pathway and cofactor regeneration in pyruvate decarboxylase-deficient Saccharomyces cerevisiae. Bioresource Technology, 245:1551–1557, 2017 [4] Weller, H., Tabor, G., Jasak, H. and Fureby, C., A tensorial approach to computational continuum mechanics using object-oriented techniques, Computers in physics, 12, 6, 620--631, 1998

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2023

A quantitative assessment of (bacterio)chlorophyll assignments in the cryo-EM structure of the Chloracidobacterium thermophilum reaction center

Chlorophylls and bacteriochlorophylls are the primary pigments used by photosynthetic organisms for light-harvesting, energy transfer, and electron transfer. Many molecular structures of (bacterio)chlorophyll-containing protein complexes are available, some of which contain mixtures of different (bacterio)chlorophyll types. Differentiating these, which sometimes are structurally similar, is challenging but is required for leveraging structural data to gain functional insight. The reaction center complex from Chloroacidobacterium thermophilum has a hybrid (bacterio)chlorophyll antenna system containing both chlorophyll a and bacteriochlorophyll a molecules. The recent availability of its cryogenic electron microscopy (cryo-EM) structure provides an opportunity for a quantitative analysis of their identities, and chemical environments. Here, we describe a theoretical basis for differentiating chlorophyll a and bacteriochlorophyll a in a cryo-EM map, and apply the approach to the experimental cryo-EM maps of the (bacterio)chlorophyll sites of the chloroacidobacterial reaction center. The comparison reveals that at ~2.2-Å resolution, chlorophyll a and bacteriochlorophyll a are easily distinguishable, but the orientation of the bacteriochlorophyll a acetyl moiety is not; however, the latter can confidently be assigned by identifying a hydrogen bond donor from the protein environment. Furthermore, this study reveals the opportunities and challenges in assigning (bacterio)chlorophyll types in structural biology, the accuracy of which is vital for downstream investigations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structure of a dimeric photosystem II complex from a cyanobacterium acclimated to far-red light

Photosystem II (PSII) is the water-splitting enzyme central to oxygenic photosynthesis. To drive water oxidation, light is harvested by accessory pigments, mostly chlorophyll (Chl) a molecules, which absorb visible light (400–700 nm). Some cyanobacteria facultatively acclimate to shaded environments by altering their photosynthetic machinery to additionally absorb far-red light (FRL, 700–800 nm), a process termed far-red light photoacclimation or FaRLiP. During far-red light photoacclimation, FRL-PSII is assembled with FRL-specific isoforms of the subunits PsbA, PsbB, PsbC, PsbD, and PsbH, and some Chl-binding sites contain Chls d or f instead of the usual Chl a. The structure of an apo-FRL-PSII monomer lacking the FRL-specific PsbH subunit has previously been determined, but visualization of the dimeric complex has remained elusive. Here, we report the cryo-EM structure of a dimeric FRL–PSII complex. The site assignments for Chls d and f are consistent with those assigned in the previous apo-FRL-PSII monomeric structure. All sites that bind Chl d or Chl f at high occupancy exhibit a FRL-specific interaction of the formyl moiety of the Chl d or Chl f with the protein environment, which in some cases involves a phenylalanine sidechain. The structure retains the FRL-specific PsbH2 subunit, which appears to alter the energetic landscape of FRL-PSII, redirecting energy transfer from the phycobiliprotein complex to a Chl f molecule bound by PsbB2 that acts as a bridge for energy transfer to the electron transfer chain. Collectively, these observations extend our previous understanding of the structure-function relationship that allows PSII to function using lower energy FRL.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Effects of soluble electron shuttles on microbial iron reduction and methanogenesis

In many aquatic and terrestrial ecosystems, iron (Fe) reduction by microorganisms is a key part of biogeochemical cycling and energy flux. The presence of redox-active electron shuttles in the environment potentially enables a phylogenetically diverse group of microbes to use insoluble iron as a terminal electron acceptor. We investigated the impact that different electron shuttles had on respiration, microbial physiology, and microbial ecology. We tested eight different electron shuttles, seven quinones and riboflavin, with redox potentials between 0.217 and −0.340 V. Fe(III) reduction coupled with acetate oxidation was observed with all shuttles. Once Fe(III) reduction began to plateau, a rapid increase in acetate consumption was observed and coincided with the onset of methane production, except in the incubations with the shuttle 9,10-anthraquinone-2-carboxylic acid (AQC). The rates of iron reduction, acetate consumption, methanogenesis, and the microbial communities varied significantly across the different shuttles independent of redox potential. In general, shuttles appeared to reduce the overall diversity of the community compared to no shuttle controls, but certain shuttles were exceptions to this trend. Geobacteraceae were the predominant taxonomic family in all enrichments except in the presence of AQC or 1,2-dihydroxyanthraquinone (AQZ), but each shuttle enriched a unique community significantly different from the no shuttle control conditions. This suggests that the presence of different redox-active electron shuttles can have a large influence on the microbial ecology and total carbon flux in the environment.

Anaerobic Redox Reactions↗
DOE OSTI2021

Editorial: Cell Free Biocatalysis for the Production of Bioproducts

Biological approaches show promise for the sustainable and cost competitive production of commodity fuels and chemicals. A lot of efforts have been devoted to engineering microbial chassis to produce select fuels and chemicals. These approaches have had some level of success exemplified, of course, by the production of ethanol at high yield and titer but also recent successes with commodity chemicals such as 1,4-butanediol, 1,3-propanediol, and even to some extent with sustainable aviation fuel intermediates such as farnesene. However, many of these processes still suffer from low yields, usually below the standard needed to drive a sustainable and atom efficient bioeconomy. Additionally, for many other chemicals and fuel precursors, titers and yields are only a fraction of what they are for ethanol. Indeed, there exist many limiting factors associated with the use of microbial biocatalysts. Some of these factors include the diversion of carbon from products to sustain growth and biomass formation, the production of byproducts or regulatory mechanisms, the toxicity of end products or intermediates, and the difficulty of separating products from growth media.

09 BIOMASS FUELS↗
DOE OSTI2023

Advancing Our Understanding of Pyranopterin-Dithiolene Contributions to Moco Enzyme Catalysis

The pyranopterin dithiolene ligand is remarkable in terms of its geometric and electronic structure and is uniquely found in mononuclear molybdenum and tungsten enzymes. The pyranopterin dithiolene is found coordinated to the metal ion, deeply buried within the protein, and non-covalently attached to the protein via an extensive hydrogen bonding network that is enzyme-specific. However, the function of pyranopterin dithiolene in enzymatic catalysis has been difficult to determine. This focused account aims to provide an overview of what has been learned from the study of pyranopterin dithiolene model complexes of molybdenum and how these results relate to the enzyme systems. This work begins with a summary of what is known about the pyranopterin dithiolene ligand in the enzymes. We then introduce the development of inorganic small molecule complexes that model aspects of a coordinated pyranopterin dithiolene and discuss the results of detailed physical studies of the models by electronic absorption, resonance Raman, X-ray absorption and NMR spectroscopies, cyclic voltammetry, X-ray crystallography, and chemical reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗