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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 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Spectrally selective fundamental core mode suppression in optical fibre containing absorbing rods

The feasibility of making a wavelength-selective fibre filter using fibre with absorbing rods in its silica cladding has been demonstrated theoretically for the first time. The technique described in this paper is of great practical interest for designing fibre lasers and amplifiers emitting at wavelengths where lasing is impeded by the presence of more energetically favourable radiative transitions in the active medium. In addition, the approach proposed here can be used for stimulated Raman scattering suppression. The unique feature of the fundamental core mode suppression mechanism examined is that there is a (bending) controlled spectral width of a region where excess losses are produced. (selection of papers presented at the international workshop on fibre lasers (20 – 24 September 2020, Novosibirsk))

36 MATERIALS SCIENCE↗
DOE OSTI2021

First-order antiferromagnetic transitions of SrMn 2 P 2 and CaMn 2 P 2 single crystals containing corrugated-honeycomb Mn sublattices

Significance With rare exceptions, an antiferromagnetic (AFM) transition in zero magnetic field is thermodynamically of second order where the thermal-average magnetic moments of the magnetic atoms (ordered moments) vary continuously on cooling through the AFM ordering temperature T N with no latent heat at the transition. Such materials include the AFM pnictides CaMn 2 As 2 , SrMn 2 As 2 , CaMn 2 Sb 2 , SrMn 2 Sb 2 , and CaMn 2 Bi 2 . Here we demonstrate that the closely related SrMn 2 P 2 and CaMn 2 P 2 insulators instead exhibit first-order AFM transitions at T N = 53 and 70 K, respectively, where the heat capacity exhibits a latent heat at T N . The mechanism causing these first-order transitions remains to be explained, but its understanding may lead to the development of novel magnetic materials of technological interest.

36 MATERIALS SCIENCE↗
DOE OSTI2022

De novo design of protein homodimers containing tunable symmetric protein pockets

Function follows form in biology, and the binding of small molecules requires proteins with pockets that match the shape of the ligand. For design of binding to symmetric ligands, protein homo-oligomers with matching symmetry are advantageous as each protein subunit can make identical interactions with the ligand. Here, we describe a general approach to designing hyperstable C2 symmetric proteins with pockets of diverse size and shape. We first designed repeat proteins that sample a continuum of curvatures but have low helical rise, then docked these into C2 symmetric homodimers to generate an extensive range of C2 symmetric cavities. We used this approach to design thousands of C2 symmetric homodimers, and characterized 101 of them experimentally. Of these, the geometry of 31 were confirmed by small angle X-ray scattering and 2 were shown by crystallographic analyses to be in close agreement with the computational design models. These scaffolds provide a rich set of starting points for binding a wide range of C2 symmetric compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Toward a glycyl radical enzyme containing synthetic bacterial microcompartment to produce pyruvate from formate and acetate

Formate has great potential to function as a feedstock for biorefineries because it can be sustainably produced by a variety of processes that don’t compete with agricultural production. However, naturally formatotrophic organisms are unsuitable for large-scale cultivation, difficult to engineer, or have inefficient native formate assimilation pathways. Thus, metabolic engineering needs to be developed for model industrial organisms to enable efficient formatotrophic growth. Here, we build a prototype synthetic formate utilizing bacterial microcompartment (sFUT) encapsulating the oxygen-sensitive glycyl radical enzyme pyruvate formate lyase and a phosphate acyltransferase to convert formate and acetyl-phosphate into the central biosynthetic intermediate pyruvate. This metabolic module offers a defined environment with a private cofactor coenzyme A that can cycle efficiently between the encapsulated enzymes. To facilitate initial design-build-test-refine cycles to construct an active metabolic core, we used a “wiffleball” architecture, defined as an icosahedral bacterial microcompartment (BMC) shell with unoccupied pentameric vertices to freely permit substrate and product exchange. The resulting sFUT prototype wiffleball is an active multi enzyme synthetic BMC functioning as platform technology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The bacterial copper resistance protein CopG contains a cysteine-bridged tetranuclear copper cluster

CopG is an uncharacterized protein ubiquitous in Gram-negative bacteria whose gene frequently occurs in clusters of copper resistance genes and can be recognized by the presence of a conserved CxCC motif. To investigate its contribution to copper resistance, here we undertook a structural and biochemical characterization of the CopG protein from Pseudomonas aeruginosa . Results from biochemical analyses of CopG purified under aerobic conditions indicate that it is a green copper-binding protein that displays absorbance maxima near 411, 581, and 721 nm and is monomeric in solution. Determination of the three-dimensional structure by X-ray crystallography revealed that CopG consists of a thioredoxin domain with a C-terminal extension that contributes to metal binding. We noted that adjacent to the CxCC motif is a cluster of four copper ions bridged by cysteine sulfur atoms. Structures of CopG in two oxidation states support the assignment of this protein as an oxidoreductase. On the basis of these structural and spectroscopic findings and also genetic evidence, we propose that CopG has a role in interconverting Cu(I) and Cu(II) to minimize toxic effects and facilitate export by the Cus RND transporter efflux system.

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

Alternative pathways utilize or circumvent putrescine for biosynthesis of putrescine-containing rhizoferrin

The siderophore rhizoferrin (N 1 ,N 4 -dicitrylputrescine) is produced in fungi and bacteria to scavenge iron. Putrescine-producing bacterium Ralstonia pickettii synthesizes rhizoferrin and encodes a single nonribosomal peptide synthetase-independent siderophore (NIS) synthetase. From biosynthetic logic, we hypothesized that this single enzyme is sufficient for rhizoferrin biosynthesis. We confirmed this by expression of R. pickettii NIS synthetase in Escherichia coli, resulting in rhizoferrin production. This was further confirmed in vitro using the recombinant NIS synthetase, synthesizing rhizoferrin from putrescine and citrate. Heterologous expression of homologous lbtA from Legionella pneumophila, required for rhizoferrin biosynthesis in that species, produced siderophore activity in E. coli. Rhizoferrin is also synthesized by Francisella tularensis and Francisella novicida, but unlike R. pickettii or L. pneumophila, Francisella species lack putrescine biosynthetic pathways because of genomic decay. Francisella encodes a NIS synthetase FslA/FigA and an ornithine decarboxylase homolog FslC/FigC, required for rhizoferrin biosynthesis. Ornithine decarboxylase produces putrescine from ornithine, but we show here in vitro that FigA synthesizes N-citrylornithine, and FigC is an N-citrylornithine decarboxylase that together synthesize rhizoferrin without using putrescine. We co-expressed F. novicida figA and figC in E. coli and produced rhizoferrin. A 2.1 Å X-ray crystal structure of the FigC N-citrylornithine decarboxylase reveals how the larger substrate is accommodated and how active site residues have changed to recognize N-citrylornithine. FigC belongs to a new subfamily of alanine racemase-fold PLP-dependent decarboxylases that are not involved in polyamine biosynthesis. These data reveal a natural product biosynthetic workaround that evolved to bypass a missing precursor and re-establish it in the final structure.

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

Cyclic deformation and lattice strain distribution of high Nb containing TiAl alloy

Low cycle fatigue of lamellar TiAl with 8.5 at.-%Nb was studied with a total strain amplitude of 0.28% at three temperatures: room temperature, 750°C and 900°C. At room temperature, the material exhibited cyclic hardening and the fracture mode was mainly interlamellar. At 750°C and 900°C, the material showed cyclic softening and the fracture mode was translamellar. The lattice strain in γ phase was almost tensile and larger tensile lattice strain in γ phase seems detrimental. Besides, the opposite direction of {201} γ and {100} α2 lead to crack propagation along α 2 /γ interfaces. B2/β o phase always suffered compressive lattice strain in the tests. Finally, the destruction of lamellar microstructure was the reason for colony refinement at 750°C and 900°C.

phase transformation↗
DOE OSTI2021

Absence of long-range magnetic order in lithium-containing honeycombs in the Li–Cr–Sb(Te)–O phases

Li 3 ((LiCr)(Te/Sb))O 6 compounds where Cr atoms along with Li and Te or Sb are part of a honeycomb and are studied using magnetic susceptibility, specific heat, x-ray photoelectron spectroscopy and neutron diffraction. The oxides stoichiometries as determined from the neutron diffraction studies are Li 4.47 Cr 0.53 TeO 6 and Li 3.88 Cr 1.12 SbO 6 with a stable oxidation state of +3 for Cr. Both the compounds crystallize in space group C2/m with intermixing of cations at the 4g sites leaving the 2a sites preferentially for Te or Sb. Again, the Li + ions alone predominantly occur in the interlayer sites. Both the compounds show a broad anomaly in specific heat at 8 K, which is robust against 8 T. A corresponding anomaly is absent in the magnetic susceptibility but recovers from its derivative, dχ(T)/dT. Here, we ascertain the magnetic anomaly temperatures (T a ) of Li 4.47 Cr 0.53 TeO 6 and Li 3.88 Cr 1.12 SbO 6 as 5.9 K and 6.7 K respectively from specific heat. Although the physical properties indicated a low temperature anomaly, neutron diffraction data did not reveal a magnetic signal or a structural anomaly down to 1.5 K. This rules out a conventional long-range ordered magnetic ground state in either compounds. Combining the results from specific heat, neutron diffraction and electron paramagnetic resonance, we put forth a scenario of depleted honeycomb lattice of Cr 3+ with predominant short-range magnetic correlations as the magnetic ground states of the title compounds.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes

Interpreting changes in patient genomes, understanding how viruses evolve and engineering novel protein function all depend on accurately predicting the functional outcomes that arise from amino acid substitutions. To that end, the development of first-generation prediction algorithms was guided by historic experimental datasets. However, these datasets were heavily biased toward substitutions at positions that have not changed much throughout evolution (i.e. conserved). Although newer datasets include substitutions at positions that span a range of evolutionary conservation scores, these data are largely derived from assays that agglomerate multiple aspects of function. To facilitate predictions from the foundational chemical properties of proteins, large substitution databases with biochemical characterizations of function are needed. We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family—pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization—including quantitative evaluation of allosteric regulation—of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predictions. We trust that the collected dataset will be useful for the broader scientific community in the further development of prediction algorithms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site

Transcription regulators play central roles in orchestrating responses to changing environmental conditions. Recently the Caulobacter crescentus transcription activator DriD, which belongs to the newly defined WYL-domain family, was shown to regulate DNA damage responses independent of the canonical SOS pathway. However, the molecular mechanisms by which DriD and other WYL-regulators sense environmental signals and recognize DNA are not well understood. We showed DriD DNA-binding is triggered by its interaction with ssDNA, which is produced during DNA damage. Here we describe the structure of the full-length C. crescentus DriD bound to both target DNA and effector ssDNA. DriD consists of an N-terminal winged-HTH (wHTH) domain, linker region, three-helix bundle, WYL-domain and C-terminal WCX-dimer domain. Strikingly, DriD binds DNA using a novel, asymmetric DNA-binding mechanism that results from different conformations adopted by the linker. Although the linker does not touch DNA, our data show that contacts it makes with the wHTH are key for specific DNA binding. The structure indicates how ssDNA-effector binding to the WYL-domain impacts wHTH DNA binding. In conclusion, we present the first structure of a WYL-activator bound to both effector and target DNA. The structure unveils a unique, asymmetric DNA binding mode that is likely conserved among WYL-activators.

59 BASIC BIOLOGICAL SCIENCES↗