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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 1,549 records · Page 86
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Crystal structure of Clostridium difficile toxin A

Clostridium difficile infection is the leading cause of hospital-acquired diarrhoea and pseudomembranous colitis. Disease is mediated by the actions of two toxins, TcdA and TcdB, which cause the diarrhoea, as well as inflammation and necrosis within the colon. The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host. The multidomain toxins enter cells by receptor-mediated endocytosis and, upon exposure to the low pH of the endosome, insert into and deliver two enzymatic domains across the membrane. Eukaryotic inositol-hexakisphosphate (InsP6) binds an autoprocessing domain to activate a proteolysis event that releases the N-terminal glucosyltransferase domain into the cytosol. Here, we report the crystal structure of a 1,832-amino-acid fragment of TcdA (TcdA 1832 ), which reveals a requirement for zinc in the mechanism of toxin autoprocessing and an extended delivery domain that serves as a scaffold for the hydrophobic α-helices involved in pH-dependent pore formation. A surface loop of the delivery domain whose sequence is strictly conserved among all large clostridial toxins is shown to be functionally important, and is highlighted for future efforts in the development of vaccines and novel therapeutics.

bacterial pathogenesis↗
DOE OSTI2015

Human DNA polymerase θ grasps the primer terminus to mediate DNA repair

DNA polymerase θ protects against genomic instability via an alternative end-joining repair pathway for DNA double-strand breaks. Polymerase θ is overexpressed in breast, lung and oral cancers, and reduction of its activity in mammalian cells increases sensitivity to double-strand break–inducing agents, including ionizing radiation. Reported in this paper are crystal structures of the C-terminal polymerase domain from human polymerase θ, illustrating two potential modes of dimerization. One structure depicts insertion of ddATP opposite an abasic-site analog during translesion DNA synthesis. The second structure describes a cognate ddGTP complex. Polymerase θ uses a specialized thumb subdomain to establish unique upstream contacts to the primer DNA strand, including an interaction with the 3'-terminal phosphate from one of five distinctive insertion loops. Finally, these observations demonstrate how polymerase θ grasps the primer to bypass DNA lesions or extend poorly annealed DNA termini to mediate end-joining.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Cooperative adsorption of carbon disulfide in diamine-appended metal–organic frameworks

Over one million tons of CS 2 are produced annually, and emissions of this volatile and toxic liquid, known to generate acid rain, remain poorly controlled. As such, materials capable of reversibly capturing this commodity chemical in an energy-efficient manner are of interest. Recently, we detailed diamine-appended metal–organic frameworks capable of selectively capturing CO 2 through a cooperative insertion mechanism that promotes efficient adsorption–desorption cycling. We therefore sought to explore the ability of these materials to capture CS 2 through a similar mechanism. Employing crystallography, spectroscopy, and gas adsorption analysis, we demonstrate that CS 2 is indeed cooperatively adsorbed in N,N-dimethylethylenediamine-appended M 2 (dobpdc) (M = Mg, Mn, Zn; dobpdc 4- = 4,4'-dioxidobiphenyl-3,3'-dicarboxylate), via the formation of electrostatically paired ammonium dithiocarbamate chains. In the weakly thiophilic Mg congener, chemisorption is cleanly reversible with mild thermal input. Finally, this work demonstrates that the cooperative insertion mechanism can be generalized to other high-impact target molecules.

36 MATERIALS SCIENCE↗
DOE OSTI2021

High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication

DNA ligase 1 (LIG1, Cdc9 in yeast) finalizes eukaryotic nuclear DNA replication by sealing Okazaki fragments using DNA end-joining reactions that strongly discriminate against incorrectly paired DNA substrates. Whether intrinsic ligation fidelity contributes to the accuracy of replication of the nuclear genome is unknown. Here, we show that an engineered low-fidelity LIG1 Cdc9 variant confers a novel mutator phenotype in yeast typified by the accumulation of single base insertion mutations in homonucleotide runs. The rate at which these additions are generated increases upon concomitant inactivation of DNA mismatch repair, or by inactivation of the Fen1 Rad27 Okazaki fragment maturation (OFM) nuclease. Biochemical and structural data establish that LIG1 Cdc9 normally avoids erroneous ligation of DNA polymerase slippage products, and this protection is compromised by mutation of a LIG1 Cdc9 high-fidelity metal binding site. Collectively, our data indicate that high-fidelity DNA ligation is required to prevent insertion mutations, and that this may be particularly critical following strand displacement synthesis during the completion of OFM.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Tuning local chemistry of P2 layered-oxide cathode for high energy and long cycles of sodium-ion battery

Layered transition-metal oxides have attracted intensive interest for cathode materials of sodium-ion batteries. However, they are hindered by the limited capacity and inferior phase transition due to the gliding of transition-metal layers upon Na + extraction and insertion in the cathode materials. Here, we report that the large-sized K + is riveted in the prismatic Na + sites of P2-Na 0.612 K 0.056 MnO 2 to enable more thermodynamically favorable Na + vacancies. The Mn-O bonds are reinforced to reduce phase transition during charge and discharge. 0.901 Na + per formula are reversibly extracted and inserted, in which only the two-phase transition of P2 ↔ P’2 occurs at low voltages. It exhibits the highest specific capacity of 240.5 mAh g -1 and energy density of 654 Wh kg -1 based on the redox of Mn 3+ /Mn 4+ , and a capacity retention of 98.2% after 100 cycles. This investigation will shed lights on the tuneable chemical environments of transition-metal oxides for advanced cathode materials and promote the development of sodium-ion batteries.

25 ENERGY STORAGE↗
DOE OSTI2021

Structural basis of LAIR1 targeting by polymorphic Plasmodium RIFINs

RIFIN, a large family of Plasmodium variant surface antigens, plays a crucial role in malaria pathogenesis by mediating immune suppression through activation of inhibitory receptors such as LAIR1, and antibodies with LAIR1 inserts have been identified that bind infected erythrocytes through RIFIN. However, details of RIFIN-mediated LAIR1 recognition and receptor activation have been unclear. Here, we use negative-stain EM to define the architecture of LAIR1-inserted antibodies and determine crystal structures of RIFIN-variable 2 (V2) domain in complex with a LAIR1 domain. These structures reveal the LAIR1-binding region of RIFIN to be hydrophobic and membrane-distal, to exhibit extensive structural diversity, and to interact with RIFIN-V2 in a one-to-one fashion. Through structural and sequence analysis of various LAIR1 constructs, we identify essential elements of RIFIN-binding on LAIR1. Furthermore, a structure-derived LAIR1-binding sequence signature ascertained >20 LAIR1-binding RIFINs, including some from P. falciparum field strains and Plasmodium species infecting gorillas and chimpanzees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase

PrimPol is a human DNA polymerase-primase that localizes to mitochondria and nucleus and bypasses the major oxidative lesion 7,8-dihydro-8-oxoguanine (oxoG) via translesion synthesis, in mostly error-free manner. We present structures of PrimPol insertion complexes with a DNA template-primer and correct dCTP or erroneous dATP opposite the lesion, as well as extension complexes with C or A as a 3'–terminal primer base. We show that during the insertion of C and extension from it, the active site is unperturbed, reflecting the readiness of PrimPol to accommodate oxoG(anti). The misinsertion of A opposite oxoG(syn) also does not alter the active site, and is likely less favorable due to lower thermodynamic stability of the oxoG(syn)•A base-pair. During the extension step, oxoG(syn) induces an opening of its base-pair with A or misalignment of the 3'-A primer terminus. Together, the structures show how PrimPol accurately synthesizes DNA opposite oxidatively damaged DNA in human cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Au-activated N motifs in non-coherent cupric porphyrin metal organic frameworks for promoting and stabilizing ethylene production

Direct implementation of metal-organic frameworks as the catalyst for CO 2 electroreduction has been challenging due to issues such as poor conductivity, stability, and limited > 2e - products. In this study, Au nanoneedles are impregnated into a cupric porphyrin-based metal-organic framework by exploiting ligand carboxylates as the Au 3+ -reducing agent, simultaneously cleaving the ligand-node linkage. Surprisingly, despite the lack of a coherent structure, the Au-inserted framework affords a superb ethylene selectivity up to 52.5% in Faradaic efficiency, ranking among the best for metal-organic frameworks reported in the literature. Through operando X-ray, infrared spectroscopies and density functional theory calculations, the enhanced ethylene selectivity is attributed to Au-activated nitrogen motifs in coordination with the Cu centers for C-C coupling at the metalloporphyrin sites. Furthermore, the Au-inserted catalyst demonstrates both improved structural and catalytic stability, ascribed to the altered charge conduction path that bypasses the incoherent framework. This study underlines the modulation of reticular metalloporphyrin structure by metal impregnation for steering the CO 2 reduction reaction pathway.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Biosensor Guided Polyketide Synthases Engineering for Optimization of Domain Exchange Boundaries

Type I modular polyketide synthases (PKSs) are multi-domain enzymes functioning like assembly lines. Many engineering attempts have been made for the last three decades to replace, delete and insert new functional domains into PKSs to produce novel molecules. However, inserting heterologous domains often destabilize PKSs, causing loss of activity and protein misfolding. To address this challenge, here we develop a fluorescence-based solubility biosensor that can quickly identify engineered PKSs variants with minimal structural disruptions. Using this biosensor, we screen a library of acyltransferase (AT)-exchanged PKS hybrids with randomly assigned domain boundaries, and we identify variants that maintain wild type production levels. We then probe each position in the AT linker region to determine how domain boundaries influence structural integrity and identify a set of optimized domain boundaries. Overall, we have successfully developed an experimentally validated, high-throughput method for making hybrid PKSs that produce novel molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Correlative operando microscopy of oxygen evolution electrocatalysts

Transition metal (oxy)hydroxides are promising electrocatalysts for the oxygen evolution reaction.1–3 The properties of these materials evolve dynamically and heterogeneously4 with applied voltage through ion insertion redox reactions, converting inactive materials at open-circuit into active electrocatalysts during operation.5 Thus, the catalytic state is inherently far-from-equilibrium, complicating its direct observation. Here, we establish the link between the oxygen evolution activity and the local operational chemical, physical, and electronic nanoscale structure of single-crystalline β-Co(OH)2 platelet particles through a suite of newly developed correlative operando scanning probe and X-ray microscopy techniques. At pre-catalytic voltages, the particles swell to form an α-CoO2H1.5·0.5H2O-like structure with associated Co2.5+ oxidation state produced through hydroxide intercalation. With increasing voltage to drive oxygen evolution, interlayer water and protons de-intercalate to form contracted β-CoOOH particles with Co3+ species. While these transformations manifest heterogeneously through the bulk of the particles, the electrochemical current is primarily restricted to the particle edge facets. The observed Tafel behavior is correlated to the local concentration of Co3+ at these reactive edge sites, demonstrating the link between bulk ion-insertion and surface catalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production

Abstract Optimizing microbial hosts for the large-scale production of valuable metabolites often requires multiple mutations and modifications to the host’s genome. We describe a three-round screen for increased L-DOPA production in S. cerevisiae using FACS enrichment of an enzyme-coupled biosensor for L-DOPA. Multiple rounds of screening were enabled by a single build of a barcoded in vitro transposon-mediated disruption library. New background strains for screening were built for each iteration using results from previous iterations. The same in vitro transposon-mediated disruption library was integrated by homologous recombination into new background strains in each round of screening. Compared with creating new transposon insertions in each round, this method takes less time and saves the cost of additional sequencing to characterize transposon insertion sites. In the first two rounds of screening, we identified deletions that improved biosensor compartmentalization and, consequently, improved our ability to screen for L-DOPA production. In a final round, we discovered that deletion of heme oxygenase (HMX1) increases total heme concentration and increases L-DOPA production, using dopamine measurement as a proxy. We further demonstrated that deleting HMX1 may represent a general strategy for P450 function improvement by improving activity of a second P450 enzyme, BM3, which performs a distinct reaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase η

Cytarabine (AraC) is the mainstay chemotherapy for acute myeloid leukemia (AML). Whereas initial treatment with AraC is usually successful, most AML patients tend to relapse, and AraC treatment-induced mutagenesis may contribute to the development of chemo-resistant leukemic clones. We show here that whereas the high-fidelity replicative polymerase Polδ is blocked in the replication of AraC, the lower-fidelity translesion DNA synthesis (TLS) polymerase Polη is proficient, inserting both correct and incorrect nucleotides opposite a template AraC base. Furthermore, we present high-resolution crystal structures of human Polη with a template AraC residue positioned opposite correct (G) and incorrect (A) incoming deoxynucleotides. We show that Polη can accommodate local perturbation caused by the AraC via specific hydrogen bonding and maintain a reaction-ready active site alignment for insertion of both correct and incorrect incoming nucleotides. Taken together, the structures provide a novel basis for the ability of Polη to promote AraC induced mutagenesis in relapsed AML patients.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural and functional analyses of the echinomycin resistance conferring protein Ecm16 from Streptomyces lasalocidi

Echinomycin is a natural product DNA bisintercalator antibiotic. The echinomycin biosynthetic gene cluster in Streptomyces lasalocidi includes a gene encoding the self-resistance protein Ecm16. Here, we present the 2.0 Å resolution crystal structure of Ecm16 bound to adenosine diphosphate. The structure of Ecm16 closely resembles that of UvrA, the DNA damage sensor component of the prokaryotic nucleotide excision repair system, but Ecm16 lacks the UvrB-binding domain and its associated zinc-binding module found in UvrA. Mutagenesis study revealed that the insertion domain of Ecm16 is required for DNA binding. Furthermore, the specific amino acid sequence of the insertion domain allows Ecm16 to distinguish echinomycin-bound DNA from normal DNA and link substrate binding to ATP hydrolysis activity. Expression of ecm16 in the heterologous host Brevibacillus choshinensis conferred resistance against echinomycin and other quinomycin antibiotics, including thiocoraline, quinaldopeptin, and sandramycin. Our study provides new insight into how the producers of DNA bisintercalator antibiotics fend off the toxic compounds that they produce.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Mitigating mechanical failure of crystalline silicon electrodes for lithium batteries by morphological design [Morphological design of silicon electrode with anisotropic interface reaction rate for lithium ion batteries]

Although crystalline silicon (c-Si) anodes promise very high energy densities in Li-ion batteries, their practical use is complicated by amorphization, large volume expansion and severe plastic deformation upon lithium insertion. Recent experiments have revealed the existence of a sharp interface between crystalline Si (c-Si) and the amorphous Li x Si alloy during lithiation, which propagates with a velocity that is orientation dependent; the resulting anisotropic swelling generates substantial strain concentrations that initiate cracks even in nanostructured Si. Here we describe a novel strategy to mitigate lithiation-induced fracture by using pristine c-Si structures with engineered anisometric morphologies that are deliberately designed to counteract the anisotropy in the crystalline/amorphous interface velocity. This produces a much more uniform volume expansion, significantly reducing strain concentration. Based on a new, validated methodology that improves previous models of anisotropic swelling of c-Si, we propose optimal morphological designs for c-Si pillars and particles. The advantages of the new morphologies are clearly demonstrated by mesoscale simulations and verified by experiments on engineered c-Si micropillars. The results of this study illustrate that morphological design is effective in improving the fracture resistance of micron-sized Si electrodes, which will facilitate their practical application in next-generation Li-ion batteries. In conclusion, the model and design approach present in this paper also have general implications for the study and mitigation of mechanical failure of electrode materials that undergo large anisotropic volume change upon ion insertion and extraction.

25 ENERGY STORAGE↗
DOE OSTI2016

The effect of a Ta oxygen scavenger layer on HfO 2 -based resistive switching behavior: Thermodynamic stability, electronic structure, and low-bias transport

Reversible resistive switching between high-resistance and low-resistance states in metal-oxide-metal heterostructures makes them very interesting for applications in random access memories. While recent experimental work has shown that inserting a metallic "oxygen scavenger layer'' between the positive electrode and oxide improves device performance, the fundamental understanding of how the scavenger layer modifies the heterostructure properties is lacking. We use density functional theory to calculate thermodynamic properties and conductance of TiN/HfO 2 /TiN heterostructures with and without a Ta scavenger layer. First, we show that Ta insertion lowers the formation energy of low-resistance states. Second, while the Ta scavenger layer reduces the Schottky barrier height in the high-resistance state by modifying the interface charge at the oxide-electrode interface, the heterostructure maintains a high resistance ratio between high-and low-resistance states. Lastly, we show that the low-bias conductance of device on-states becomes much less sensitive to the spatial distribution of oxygen removed from the HfO 2 in the presence of the Ta layer. By providing a fundamental understanding of the observed improvements with scavenger layers, we open a path to engineer interfaces with oxygen scavenger layers to control and enhance device performance. In turn, this may enable the realization of a non-volatile low-power memory technology with concomitant reduction in energy consumption by consumer electronics and offering significant benefits to society.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

The electrochemical storage mechanism in oxy-hydroxyfluorinated anatase for sodium-ion batteries

Replacing lithium ions with sodium ions as the charge carriers in rechargeable batteries can induce noticeable differences in the electrochemical storage mechanisms of electrode materials. Many material parameters, such as particle size, morphology, and the presence of defects, are known to further affect the storage mechanism. Here, we report an investigation of how the introduction of titanium vacancies into anatase TiO 2 affects the sodium storage mechanism. From pair distribution function analysis, we observe that sodium ions are inserted into titanium vacancies at the early stage of the discharge process. This is supported by density functional theory calculations, which predict that sodium insertion is more favourable at vacancies than at interstitial sites. Our calculations also show that the intercalation voltage is sensitive to the anion coordination environment of the vacancy. Sodiation to higher concentrations induces a phase transition toward a disordered rhombohedral structure, similar to that observed in defect-free TiO 2 . Finally, we find that the X-ray diffraction pattern of the rhombohedral phase drastically changes depending on the composition and degree of disorder, providing further comprehension on the sodium storage mechanism of anatase.

25 ENERGY STORAGE↗
DOE OSTI2019

The molecular mechanism of robust macrophage immune responses induced by PEGylated molybdenum disulfide

Molybdenum disulfide (MoS 2 ), a representative hexagonal transition metal dichalcogenide (TMD), has been extensively exploited in biomedical applications due to its unique physicochemical properties and biocompatibility. However, the lack of adequate data regarding how MoS 2 activates immunological responses of macrophages remains a key concern for its risk assessment. Here, we employ a combined theoretical and experimental approach to investigate the interactions of MoS 2 and PEGylated MoS 2 (MoS 2 -PEG) with macrophages. We first perform molecular dynamics simulations to examine the atomic-detailed interactions of MoS 2 and MoS 2 -PEG nanoflakes with a realistic model of the macrophage membrane. We show that a small MoS 2 nanoflake (edge length of 2.86 nm) is capable of penetrating the macrophage membrane independent of its concentration. We also demonstrate that when initiated with a corner point-on configuration, the surface-bound PEG chains of MoS 2 -PEG hinder its membrane insertion process, leading to a prolonged passage through the membrane. Moreover, when placed in a face-on arrangement initially, the MoS 2 -PEG exhibits a lower binding free energy than pristine MoS 2 after its adsorption on the membrane surface. The PEG chains can even insert and get buried in the outer leaflet of the membrane, providing additional contact for membrane adsorption. Our flow cytometric experiments then show that the responses of macrophages to either MoS 2 -PEG or MoS 2 are significantly higher than that of the control (no nanomaterial stimulus), with MoS 2 -PEG eliciting stronger cytokine secretion than the pristine MoS 2 . The characteristics of slower/prolonged membrane penetration and stronger membrane adsorption of MoS 2 -PEG compared to pristine MoS 2 explain why it triggers more sustained stimulation and higher cytokine secretion in macrophages as observed in our experiments. Our findings reveal the underlying molecular mechanism of how MoS 2 -PEG influences the immune responses and suggest its potential applications in nanomedicine involving immune stimulation.

59 BASIC BIOLOGICAL SCIENCES↗