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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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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Heterologous Expression of Cryptomaldamide in a Cyanobacterial Host

Filamentous marine cyanobacteria make a variety of bioactive molecules that are produced by polyketide synthases, nonribosomal peptide synthetases, and hybrid pathways that are encoded by large biosynthetic gene clusters. These cyanobacterial natural products represent potential drug leads; however, thorough pharmacological investigations have been impeded by the limited quantity of compound that is typically available from the native organisms. Additionally, investigations of the biosynthetic gene clusters and enzymatic pathways have been difficult due to the inability to conduct genetic manipulations in the native producers. Here we report a set of genetic tools for the heterologous expression of biosynthetic gene clusters in the cyanobacteria Synechococcus elongatus PCC 7942 and Anabaena (Nostoc) PCC 7120. To facilitate the transfer of gene clusters in both strains, we engineered a strain of Anabaena that contains S. elongatus homologous sequences for chromosomal recombination at a neutral site and devised a CRISPR-based strategy to efficiently obtain segregated double recombinant clones of Anabaena. These genetic tools were used to express the large 28.7 kb cryptomaldamide biosynthetic gene cluster from the marine cyanobacterium Moorena (Moorea) producens JHB in both model strains. S. elongatus did not produce cryptomaldamide; however, high-titer production of cryptomaldamide was obtained in Anabaena. Furthermore, the methods developed in this study will facilitate the heterologous expression of biosynthetic gene clusters isolated from marine cyanobacteria and complex metagenomic samples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Silicon Nitride Surface Enabled Propane Dehydrogenation Catalyzed by Supported Organozirconium

Mesoporous silicon nitride (Si 3 N 4 ) is a nontraditional support for the chemisorption of organometallic complexes with the potential for enhancing catalytic activity through features such as the increased Lewis basicity of nitrogen for heterolytic bond activation, increased ligand donor strength, and metal–ligand orbital overlap. In this report tetrabenzyl zirconium (ZrBn 4 ) was chemisorbed on Si 3 N 4 , and the resulting supported organometallic species was characterized by Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS), Dynamic Nuclear Polarization-enhanced Solid State Nuclear Magnetic Resonance (DNP-SSNMR), and X-ray Absorption Spectroscopy (XAS). Based on the hypothesis that the nitride might enable facile heterolytic C–H bond activation along the Zr–N bond, this material was found to be a highly active (1.53 mol propene mol Zr –1 h –1 at 450 °C) and selective (99% to propylene) catalyst for propane dehydrogenation. In contrast, the homologous silica supported complex exhibited negligible activity under these conditions.

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

Pb:Sn Ratio-Driven Polytypism and Band Modulation in Photoresponsive Hexagonal Perovskitoids

Three-dimensional (3D) perovskites of the formula AMX 3 are known for their excellent optoelectronic properties, but their design is limited by the narrow range of A-site cations that can template the 3D corner-sharing structure, and many of the viable options have already been explored. These materials also face structural instability under environmental conditions. In contrast, 3D hexagonal perovskitoids, with the same chemical formula, may offer enhanced stability and richer structural diversity through a range of corner- and face-sharing octahedral configuration options, providing greater opportunities for structural design; however, challenges such as synthesis complexity and wide band gaps have hindered optoelectronic performance achieved to date. Herein, we synthesized a structural homologous series of mixed-metal hexagonal perovskitoids with the formula APb 1-x Sn x I 3 (x = 0, 0.25, 0.50, 0.75, 1; A = ethylammonium, guanidinium) and identified three polytypes (9R, 12R, 6H) using single-crystal X-ray diffraction (SCXRD). These structures exhibited increasing corner-sharing connectivity with higher Sn content, revealing a previously unobserved relationship between metal composition and structural evolution in perovskitoid materials. The incorporation of Sn reduced the band gap (tunable from 2.51 eV to 1.87 eV) and drove structural transformations, a trend seen also in density functional theory (DFT) calculations, which suggest a thermodynamic preference for Pb at face-sharing sites and Sn at corner-sharing sites. DFT band structure calculations and optical spectroscopy also reveal an anomalous behavior in these materials, which we term polytypic band modulation. This phenomenon combines conventional band bowing with the structural transformations that occur as Sn content increases, as observed in the band gap and in photoluminescence spectra. Photodiodes fabricated from thin films of these materials exhibited stable and pronounced photoresponses across various light intensities over time. Furthermore, the combination of templating 3D perovskitoids with multiple cations and alloying Pb and Sn, suggests a vastly underexplored phase space that offers new parameters to tune perovskitoids.

Cations↗
DOE OSTI2025

Electronic Structure Progression across the ACu 2 Q 2 (MQ 2 ) n Semiconductor Series

Moving beyond the engineering of known materials and elemental substitution within common structure types is critical for designing unique properties. Here, we present a new homologous series, ACu 2 Q 2 (MQ 2 ) n (A = Sr, Ba, 2Na; MQ 2 = ZrS2, HfSe 2 ), establishing 11 new members. In β-BaCu 2 Q 2 and Na 2 Cu 2 Se 2 (n = 0), the [Cu 2 Q 2 ] 2– motifs extend in two dimensions, whereas those in α-BaCu 2 Q 2 extend in three dimensions. Hence, there are two structural evolutions within the ACu 2 Q 2 (MQ 2 )n family driven by the polymorphism of the host structures. MQ 2 (n → ∞) displays 2D layers of edge-sharing [MQ 6 ] 8– octahedra that are 1-octahedron-thick and connected via van der Waals bonding. Each insertion of MQ 2 into ACu 2 Q 2 incorporates [MQ 6 ] 8– octahedra extending infinitely in one direction, confined to being 1-octahedron-thick in the second direction, with n controlling the number of [MQ 6 ] 8– octahedra in the third direction. Therefore, increasing n predictively expands the [Cu 2 MnQ 2n+2 ] 2– network in the direction controlled by n and relative to the A + /A 2+ ions. We demonstrate that for a given set of elements, one can enforce a “Host(Insertion)n” formula to systematically evolve both crystal and electronic structures from the host (n = 0) to the insertion (n → ∞) materials through intermediate values of n. Specifically, the energetic misalignment of the electronic band extrema of the parents predictively determines the band extrema and the resulting band gaps of all intermediate n members.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Assessing the Impacts of Conformational Fluxionality on Copper(II/I) Electron Transfer Self-Exchange

Typical Cu(II/I) complexes exhibit hallmark structural changes during their electron transfer (ET) reactions that result from the (pseudo) Jahn-Teller distortions and changes in polarizability inherent to their d 10 / d 9 configurations. Given that such structural changes incur large reorganization energy penalties, slow the rates of ET are characteristic of these compounds. Notwithstanding, we recently reported a set of Cu(II/I) complexes that undergo significant and well-defined structural changes during their redox reactions yet exhibit rapid (> 10 5 M ‒1 s ‒1 ) ET self-exchange rate constants ( k 11 ). To explain these results we proposed a pre-equilibrium model in which inherent conformational fluxionality in one of the two oxidation states provides access to pathways involving lower reorganization energies during the ET event. Herein we report our results testing this hypothesis through the preparation and study of a homologous series of compounds exhibiting varying extents of con-formational fluxionality in the Cu(I) state. We characterize these compounds electrochemically, structurally, and by varia-ble temperature NMR spectroscopy to provide experimental evidence for increase fluxionality across the series. We then correlate the trend with increasing k 11 through NMR linewidth broadening experiments, further taking care to define the impacts of solvent impurities therein. Finally, the nature of the conformational rearrangements, and their relation to increased k 11 are explored computationally to reveal differential Boltzmann populations of conformers across the series. The cumulative results of these studies support a previously underappreciated strategy for overcoming barriers to slow ET kinetics: via the incorporation of conformational fluxionality.

Singh, Aditi↗
DOE OSTI2025

Electrochemical Observation and pH Dependence of All Three Expected Redox Couples in an Extremophilic Bifurcating Electron Transfer Flavoprotein with Fused Subunits

Bifurcating enzymes employ energy from a favorable electron transfer to drive unfavorable transfer of a second electron, thereby generating a more reactive product. They are therefore highly desirable in catalytic systems, for example, to drive challenging reactions such as nitrogen fixation. While most bifurcating enzymes contain air-sensitive metal centers, bifurcating electron transfer flavoproteins (bETFs) employ flavins. However, they have not been successfully deployed on electrodes. Herein, we demonstrate immobilization and expected thermodynamic reactivity of a bETF from a hyperthermophilic archaeon, Sulfolobus acidocaldarius (SaETF). SaETF differs from previously biochemically characterized bETFs in being a single protein, representing a concatenation of the two subunits of known ETFs. However, SaETF retains the chemical properties of heterodimeric bETFs, including possession of two FADs: one that undergoes sequential 1-electron (1e) reductions at high E° and forms an anionic semiquinone, and another that is amenable to lower-E° 2e reduction, including by NADH. We found homologous monomeric ETF genes in archaeal and bacterial genomes, accompanied by genes that also commonly flank heterodimeric ETFs, and SaETF’s sequence conservation is 50% higher with bETFs than with canonical ETFs. Thus, SaETF is best described as a bETF. Our direct electrochemical trials capture reversible redox couples for all three thermodynamically expected redox events. We document electrochemical activity over a range of pH values and reveal a conformational change coupled to proton acquisition that affects the electrochemical activity of the higher-E° FAD. Thus, this well-behaved monomeric bETF opens the door to bioinspired bifurcating devices or bifurcation on a chip.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

The Effect of Intracrystalline Water on the Mechanical Properties of Olivine at Room Temperature

Abstract The effect of small concentrations of intracrystalline water on the strength of olivine is significant at asthenospheric temperatures but is poorly constrained at lower temperatures applicable to the shallow lithosphere. We examined the effect of water on the yield stress of olivine during low‐temperature plasticity using room‐temperature Berkovich nanoindentation. The presence of water in olivine (1,600 ppm H/Si) does not affect hardness or yield stress relative to dry olivine (≤40 ppm H/Si) outside of uncertainty but may slightly reduce Young’s modulus. Differences between water‐bearing and dry crystals in similar orientations were minor compared to differences between dry crystals in different orientations. These observations suggest water content does not affect the strength of olivine at low homologous temperatures. Thus, intracrystalline water does not play a role in olivine deformation at these temperatures, implying that water does not lead to weakening in the coldest portions of the mantle.

58 GEOSCIENCES↗
DOE OSTI2020

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin that accumulates in terrestrial and marine food webs, with potential impacts on human health. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet, British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicts that Marinimicrobia HgcAB proteins contain the highly conserved amino acid sites and folding structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognized.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Photoferrotrophy and phototrophic extracellular electron uptake is common in the marine anoxygenic phototroph Rhodovulum sulfidophilum

Photoferrotrophy allows anoxygenic phototrophs to use reduced iron as an electron donor for primary productivity. Recent work shows that freshwater photoferrotrophs can use electrons from solid-phase conductive substances via phototrophic extracellular electron uptake (pEEU), and the two processes share the underlying electron uptake mechanism. However, the ability of marine phototrophs to perform photoferrotrophy and pEEU, and the contribution of these processes to primary productivity is largely unknown. To fill this knowledge gap, we isolated 15 new strains of the marine anoxygenic phototroph Rhodovulum sulfidophilum on electron donors such as acetate and thiosulfate. We observed that all of the R. sulfidophilum strains isolated can perform photoferrotrophy. Furthermore, we chose strain AB26 as a representative strain to study further, and find that it can also perform pEEU from poised electrodes. We show that during pEEU, AB26 transfers electrons to the photosynthetic electron transport chain. Furthermore, systems biology-guided mutant analysis shows that R. sulfidophilum AB26 uses a previously unknown diheme cytochrome c protein, which we call EeuP, for pEEU but not photoferrotrophy. Homologs of EeuP occur in a range of widely distributed marine microbes. Overall, these results suggest that photoferrotrophy and pEEU contribute to the biogeochemical cycling of iron and carbon in marine ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure and properties of densified silica glass: characterizing the order within disorder

The broken symmetry in the atomic-scale ordering of glassy versus crystalline solids leads to a daunting challenge to provide suitable metrics for describing the order within disorder, especially on length scales beyond the nearest neighbor that are characterized by rich structural complexity. Here, we address this challenge for silica, a canonical network-forming glass, by using hot versus cold compression to (i) systematically increase the structural ordering after densification and (ii) prepare two glasses with the same high-density but contrasting structures. The structure was measured by high-energy X-ray and neutron diffraction, and atomistic models were generated that reproduce the experimental results. The vibrational and thermodynamic properties of the glasses were probed by using inelastic neutron scattering and calorimetry, respectively. Traditional measures of amorphous structures show relatively subtle changes upon compacting the glass. The method of persistent homology identifies, however, distinct features in the network topology that change as the initially open structure of the glass is collapsed. The results for the same high-density glasses show that the nature of structural disorder does impact the heat capacity and boson peak in the low-frequency dynamical spectra. Densification is discussed in terms of the loss of locally favored tetrahedral structures comprising oxygen-decorated SiSi 4<:sub> tetrahedra.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Discovery of a chemical probe for PRDM9

PRDM9 is a PR domain containing protein which trimethylates histone 3 on lysine 4 and 36. Its normal expression is restricted to germ cells and attenuation of its activity results in altered meiotic gene transcription, impairment of double-stranded breaks and pairing between homologous chromosomes. There is growing evidence for a role of aberrant expression of PRDM9 in oncogenesis and genome instability. Here we report the discovery of MRK-740, a potent (IC 50 : 80 ± 16 nM), selective and cell-active PRDM9 inhibitor (Chemical Probe). MRK-740 binds in the substrate-binding pocket, with unusually extensive interactions with the cofactor S-adenosylmethionine (SAM), conferring SAM-dependent substrate-competitive inhibition. In cells, MRK-740 specifically and directly inhibits H3K4 methylation at endogenous PRDM9 target loci, whereas the closely related inactive control compound, MRK-740-NC, does not. The discovery of MRK-740 as a chemical probe for the PRDM subfamily of methyltransferases highlights the potential for exploiting SAM in targeting SAM-dependent methyltransferases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Observation of dissipative chlorophyll-to-carotenoid energy transfer in light-harvesting complex II in membrane nanodiscs

Abstract Plants prevent photodamage under high light by dissipating excess energy as heat. Conformational changes of the photosynthetic antenna complexes activate dissipation by leveraging the sensitivity of the photophysics to the protein structure. The mechanisms of dissipation remain debated, largely due to two challenges. First, because of the ultrafast timescales and large energy gaps involved, measurements lacked the temporal or spectral requirements. Second, experiments have been performed in detergent, which can induce non-native conformations, or in vivo, where contributions from homologous antenna complexes cannot be disentangled. Here, we overcome both challenges by applying ultrabroadband two-dimensional electronic spectroscopy to the principal antenna complex, LHCII, in a near-native membrane. Our data provide evidence that the membrane enhances two dissipative pathways, one of which is a previously uncharacterized chlorophyll-to-carotenoid energy transfer. Our results highlight the sensitivity of the photophysics to local environment, which may control the balance between light harvesting and dissipation in vivo.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural snapshots of human DNA polymerase μ engaged on a DNA double-strand break

Genomic integrity is threatened by cytotoxic DNA double-strand breaks (DSBs), which must be resolved efficiently to prevent sequence loss, chromosomal rearrangements/translocations, or cell death. Polymerase μ (Polμ) participates in DSB repair via the nonhomologous end-joining (NHEJ) pathway, by filling small sequence gaps in broken ends to create substrates ultimately ligatable by DNA Ligase IV. Here we present structures of human Polμ engaging a DSB substrate. Synapsis is mediated solely by Polμ, facilitated by single-nucleotide homology at the break site, wherein both ends of the discontinuous template strand are stabilized by a hydrogen bonding network. The active site in the quaternary Pol μ complex is poised for catalysis and nucleotide incoporation proceeds in crystallo. These structures demonstrate that Polμ may address complementary DSB substrates during NHEJ in a manner indistinguishable from single-strand breaks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Biased localization of actin binding proteins by actin filament conformation

The assembly of actin filaments into distinct cytoskeletal structures plays a critical role in cell physiology, but how proteins localize differentially to these structures within a shared cytoplasm remains unclear. Here, we show that the actin-binding domains of accessory proteins can be sensitive to filament conformational changes. Using a combination of live cell imaging and in vitro single molecule binding measurements, we show that tandem calponin homology domains (CH1–CH2) can be mutated to preferentially bind actin networks at the front or rear of motile cells. We demonstrate that the binding kinetics of CH1–CH2 domain mutants varies as actin filament conformation is altered by perturbations that include stabilizing drugs and other binding proteins. These findings suggest that conformational changes of actin filaments in cells could help to direct accessory binding proteins to different actin cytoskeletal structures through a biophysical feedback loop.

42 ENGINEERING↗
DOE OSTI2021

Structural basis for proficient oxidized ribonucleotide insertion in double strand break repair

Reactive oxygen species (ROS) oxidize cellular nucleotide pools and cause double strand breaks (DSBs). Non-homologous end-joining (NHEJ) attaches broken chromosomal ends together in mammalian cells. Ribonucleotide insertion by DNA polymerase (pol) μ prepares breaks for end-joining and this is required for successful NHEJ in vivo. We previously showed that pol μ lacks discrimination against oxidized dGTP (8-oxo-dGTP), that can lead to mutagenesis, cancer, aging and human disease. Here we reveal the structural basis for proficient oxidized ribonucleotide (8-oxo-rGTP) incorporation during DSB repair by pol μ. Time-lapse crystallography snapshots of structural intermediates during nucleotide insertion along with computational simulations reveal substrate, metal and side chain dynamics, that allow oxidized ribonucleotides to escape polymerase discrimination checkpoints. Abundant nucleotide pools, combined with inefficient sanitization and repair, implicate pol μ mediated oxidized ribonucleotide insertion as an emerging source of widespread persistent mutagenesis and genomic instability.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

ECNet is an evolutionary context-integrated deep learning framework for protein engineering

Abstract Machine learning has been increasingly used for protein engineering. However, because the general sequence contexts they capture are not specific to the protein being engineered, the accuracy of existing machine learning algorithms is rather limited. Here, we report ECNet (evolutionary context-integrated neural network), a deep-learning algorithm that exploits evolutionary contexts to predict functional fitness for protein engineering. This algorithm integrates local evolutionary context from homologous sequences that explicitly model residue-residue epistasis for the protein of interest with the global evolutionary context that encodes rich semantic and structural features from the enormous protein sequence universe. As such, it enables accurate mapping from sequence to function and provides generalization from low-order mutants to higher-order mutants. We show that ECNet predicts the sequence-function relationship more accurately as compared to existing machine learning algorithms by using ~50 deep mutational scanning and random mutagenesis datasets. Moreover, we used ECNet to guide the engineering of TEM-1 β-lactamase and identified variants with improved ampicillin resistance with high success rates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites

Abstract Microbes produce a broad spectrum of antibiotic natural products, including many DNA-damaging genotoxins. Among the most potent of these are DNA alkylating agents in the spirocyclopropylcyclohexadienone (SCPCHD) family, which includes the duocarmycins, CC-1065, gilvusmycin, and yatakemycin. The yatakemycin biosynthesis cluster in Streptomyces sp. TP-A0356 contains an AlkD-related DNA glycosylase, YtkR2, that serves as a self-resistance mechanism against yatakemycin toxicity. We previously reported that AlkD, which is not present in an SCPCHD producer, provides only limited resistance against yatakemycin. We now show that YtkR2 and C10R5, a previously uncharacterized homolog found in the CC-1065 biosynthetic gene cluster of Streptomyces zelensis , confer far greater resistance against their respective SCPCHD natural products. We identify a structural basis for substrate specificity across gene clusters and show a correlation between in vivo resistance and in vitro enzymatic activity indicating that reduced product affinity—not enhanced substrate recognition—is the evolutionary outcome of selective pressure to provide self-resistance against yatakemycin and CC-1065.

59 BASIC BIOLOGICAL SCIENCES↗