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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Screening and Characterization of Novel Polyesterases from Environmental Metagenomes with High Hydrolytic Activity against Synthetic Polyesters

The continuous growth of global plastics production, including polyesters, has resulted in increasing plastic pollution and subsequent negative environmental impacts. Therefore, enzyme-catalyzed depolymerization of synthetic polyesters as a plastics recycling approach has become a focus of research. In this study, we screened over 200 purified uncharacterized hydrolases from environmental metagenomes and sequenced microbial genomes and identified at least 10 proteins with high hydrolytic activity against synthetic polyesters. These include the metagenomic esterases MGS0156 and GEN0105, which hydrolyzed polylactic acid (PLA), polycaprolactone, as well as bis-(benzoyloxyethyl)-terephthalate. With solid PLA as a substrate, both enzymes produced a mixture of lactic acid monomers, dimers, and higher oligomers as products. The crystal structure of MGS0156 was determined at 1.95 angstrom resolution and revealed a modified alpha/beta hydrolase fold, with a lid domain and highly hydrophobic active site. Mutational studies of MGS0156 identified the residues critical for hydrolytic activity against both polyester and monoester substrates, with two-times higher polyesterase activity in the MGS0156 L169A mutant protein. Thus, our work identified novel, highly active polyesterases in environmental metagenomes and provided molecular insights into their activity, thereby augmenting our understanding of enzymatic polyester hydrolysis.

Hajighasemi, Mahbod↗
DOE OSTI2018

Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases

Polyphosphate (polyP) kinases are widely conserved enzymes with importance in basic bacterial metabolism and virulence in many pathogens. However, the molecular mechanisms of their substrate specificity and catalysis remain unknown. Here, we present the results of comprehensive biochemical and structural studies of three polyP kinases from different bacteria, which belong to different clusters of the PPK2 class III family. Purified PPK2 proteins catalyzed polyP-dependent phosphorylation of AMP, ADP, GMP, and GDP to corresponding nucleoside di- and triphosphates. Crystal structures of these proteins in complex with substrates, products, Mg 2+ , and inhibitors revealed the binding sites for the nucleotide and polyP substrates overlapping at the Walker A and B loops. The Walker A loop is involved in the binding of polyP and the Mg 2+ ion, whereas the Walker B loop coordinates the nucleotide phosphate groups. Structure-based site-directed mutagenesis of CHU0107 from Cytophaga hutchinsonii demonstrated the critical role of several conserved residues from the PPK2 core and lid domains, involved in the coordination of both substrates and two Mg 2+ ions. Additionally, a two-times higher activity was observed following deletion of the C-terminal tail in the CHU0107 mutant protein L285Stop. Crystal structures of PPK2 in complex with three aryl phosphonate inhibitors indicated the presence of at least two binding pockets for inhibitors located close to the Walker A loop and the catalytic residues Lys81 and Arg208. Our findings provide a molecular framework for understanding the molecular mechanisms of PPK2 kinases and have implications for future drug design and biocatalytic applications

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Engineering and Application of a Thermostable MHETase for PET Depolymerization

Enzymatic hydrolysis of poly(ethylene terephthalate) (PET) releases mono(2-hydroxyethyl) terephthalate (MHET) as a major product, the accumulation of which can prolong reactor residence times and complicate downstream monomer separations. The use of a MHETase enzyme can enable MHET hydrolysis to the monomers, terephthalic acid and ethylene glycol, but industrial PETases typically operate at thermophilic temperatures and the well-known MHETase from Ideonella sakaiensis is a mesophilic enzyme, thus warranting the development of thermophilic MHETases. Here, we characterize thermostable MHET-active enzymes from a natural diversity screen by applying a hidden Markov model based on the previously reported, archaeal ferulic acid esterase, PET46. We identified enzymes with higher thermostability than PET46 and quantified their MHETase activity in reactions at 70 °C. The crystal structure of MHT077, the homologue with the highest MHETase activity and an apparent melting temperature (T m,app ) of 94.6 °C, informed site saturation mutagenesis in the active site and lid-domain interface. MHT077 exhibited a ∼100-fold slower unfolding rate at 65 °C than PET46, indicating substantially greater kinetic stability. In parallel, we applied evolution-informed design, a probabilistic model that leverages coevolutionary patterns in large multiple sequence alignments, to improve the activity and thermostability of five ferulic acid esterases. One design, EV-MHT043–5 was identified with a comparable thermostability (T m,app = 96.1 °C) and a 3-fold improvement in its MHETase activity relative to the wildtype enzyme, MHT043. Combination variants of beneficial mutations were screened and afforded a variant, MHT077 LFK , which reduced MHET accumulation in bioreactor experiments with postconsumer PET waste. Overall, this study expands the known MHET-hydrolyzing protein scaffolds available for enzymatic PET recycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2010

Conformational Changes and Substrate Recognition in Pseudomonas aeruginosa d-Arginine Dehydrogenase

DADH catalyzes the flavin-dependent oxidative deamination of D-amino acids to the corresponding {alpha}-keto acids and ammonia. Here we report the first X-ray crystal structures of DADH at 1.06 {angstrom} resolution and its complexes with iminoarginine (DADH{sub red}/iminoarginine) and iminohistidine (DADH{sub red}/iminohistidine) at 1.30 {angstrom} resolution. The DADH crystal structure comprises an unliganded conformation and a product-bound conformation, which is almost identical to the DADH{sub red}/iminoarginine crystal structure. The active site of DADH was partially occupied with iminoarginine product (30% occupancy) that interacts with Tyr53 in the minor conformation of a surface loop. This flexible loop forms an 'active site lid', similar to those seen in other enzymes, and may play an essential role in substrate recognition. The guanidinium side chain of iminoarginine forms a hydrogen bond interaction with the hydroxyl of Thr50 and an ionic interaction with Glu87. In the structure of DADH in complex with iminohistidine, two alternate conformations were observed for iminohistidine where the imidazole groups formed hydrogen bond interactions with the side chains of His48 and Thr50 and either Glu87 or Gln336. The different interactions and very distinct binding modes observed for iminoarginine and iminohistidine are consistent with the 1000-fold difference in k{sub cat}/K{sub m} values for D-arginine and D-histidine. Comparison of the kinetic data for the activity of DADH on different D-amino acids and the crystal structures in complex with iminoarginine and iminohistidine establishes that this enzyme is characterized by relatively broad substrate specificity, being able to oxidize positively charged and large hydrophobic D-amino acids bound within a flask-like cavity.

08 HYDROGEN↗
DOE OSTI2014

Structural and Functional Consequences of Circular Permutation on the Active Site of Old Yellow Enzyme

Circular permutation of the NADPH-dependent oxidoreductase Old Yellow Enzyme from Saccharomyces pastorianus (OYE1) can significantly enhance the enzyme’s catalytic performance. Termini relocation into four regions of the protein (sectors I–IV) near the active site has proven effective in altering enzyme function. To better understand the structural consequences and rationalize the observed functional gains in these OYE1 variants, we selected representatives from sectors I–III for further characterization by biophysical methods and X-ray crystallography. These investigations not only show trends in enzyme stability and quaternary structure as a function of termini location but also provide a possible explanation for the catalytic gains in our top-performing OYE variant (new N-terminus at residue 303; sector III). Crystallographic analysis indicates that termini relocation into sector III affects the loop β6 region (amino acid positions: 290–310) of OYE1, which forms a lid over the active site. Peptide backbone cleavage greatly enhances local flexibility, effectively converting the loop into a tether and consequently increasing the environmental exposure of the active site. Interestingly, such an active site remodeling does not negatively impact the enzyme’s activity and stereoselectivity; neither does it perturb the conformation of other key active site residues with the exception of Y375. These observations were confirmed in truncation experiments, deleting all residues of the loop β6 region in our OYE variant. Intrigued by the finding that circular permutation leaves most of the key catalytic residues unchanged, we also tested OYE permutants for possible additive or synergistic effects of amino acid substitutions. Distinct functional changes in these OYE variants were detected upon mutations at W116, known in native OYE1 to cause inversion of diastereoselectivity for (S)-carvone reduction. In conclusion, our findings demonstrate the contribution of loop β6 toward determining the stereoselectivity of OYE1, an important insight for future OYE engineering efforts.

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

Design and Evaluation of Pyridinyl Sulfonyl Piperazine LpxH Inhibitors with Potent Antibiotic Activity Against Enterobacterales

Enterobacterales, a large order of Gram-negative bacteria, including Escherichia coli and Klebsiella pneumoniae, are major causes of urinary tract and gastrointestinal infections, pneumonia, and other diseases in healthcare settings and communities. ESBL-producing Enterobacterales and carbapenem-resistant Enterobacterales can break down commonly used antibiotics, with some strains being resistant to all available antibiotics. This public health threat necessitates the development of novel antibiotics, ideally targeting new pathways in these bacteria. Gram-negative bacteria possess an outer membrane enriched with lipid A, a saccharolipid that serves as the membrane anchor of lipopolysaccharides and the active component of the bacterial endotoxin, causing septic shock. The biosynthesis of lipid A is crucial for the viability of Gram-negative bacteria, and as an essential enzyme in this process, LpxH has emerged as a promising target for developing novel antibiotics against multidrugresistant Gram-negative pathogens. Here, we report the development of pyridinyl sulfonyl piperazine LpxH inhibitors. Among them, ortho-substituted pyridinyl compounds significantly boost LpxH inhibition and antibiotic activity over the original phenyl series. Structural and QM/MM analyses reveal that these improved activities are primarily due to the enhanced interaction between F141 of the LpxH insertion lid and the pyridinyl group. Incorporation of the N-methyl-N-phenyl-methanesulfonamide moiety into the pyridinyl sulfonyl piperazine backbone results in JHLPH- 106 and JH-LPH-107, both of which exhibit potent antibiotic activity against wild-type Enterobacterales such as K. pneumoniae and E. coli. JH-LPH-107 exhibits a low rate of spontaneous resistance and a high safety window in vitro, rendering it an excellent lead for further clinical development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Delayed deglaciation or extreme Arctic conditions 21-16 cal. kyr at southeastern Laurentide Ice Sheet margin?

The conventionally accepted ages of the Last Glacial Maximum (LGM) retreat of the southeastern Laurentide Ice Sheet (LIS) are 26–21 cal. kyr (derived from bulk-sediment radiocarbon ages) and 28–23 cal. kyr (varve estimates). By utilizing accelerator mass spectrometry (AMS) 14 C dating of earliest macrofossils in 13 lake/bog inorganic clays, we find that vegetation first appeared on the landscape at 16–15 cal. kyr, suggesting ice had not retreated until that time. The gap between previous age estimates and ours is significant and has large implications for our understanding of ocean-atmosphere linkages. Older ages imply extreme Arctic conditions for 9–5 cal kyr; a landscape with no ice, yet no deposition in lakes. Also, our new AMS chronology of LIS retreat is consistent with marine evidence of deglaciation from the N. Atlantic, showing significant freshwater input and sea level rise only after 19 cal kyr with a cold meltwater lid, perhaps delaying ice melt.

58 GEOSCIENCES↗
DOE OSTI2017

A hydrophobic anchor mechanism defines a deacetylase family that suppresses host response against YopJ effectors

Several Pseudomonas<\em> and Xanthomonas<\em> species are plant pathogens that infect the model organism Arabidopsis<\em> thaliana<\em> and important crops such as Brassica<\em>. Resistant plants contain the infection by rapid cell death of the infected area through the hypersensitive response (HR). A family of highly related α/β hydrolases is involved in diverse processes in all domains of life. Functional details of their catalytic machinery, however, remained unclear. We report the crystal structures of α/β hydrolases representing two different clades of the family, including the protein SOBER1, which suppresses AvrBsT-incited HR in Arabidopsis<\em>. Our results reveal a unique hydrophobic anchor mechanism that defines a previously unknown family of protein deacetylases. Furthermore, this study identifies a lid-loop as general feature for substrate turnover in acyl-protein thioesterases and the described family of deacetylases. Furthermore, we found that SOBER1’s biological function is not restricted to Arabidopsis<\em> thaliana<\em> and not limited to suppress HR induced by AvrBsT.

Bürger, Marco↗
DOE OSTI2019

Bacterial cGAS-like enzymes synthesize diverse nucleotide signals

Cyclic dinucleotides (CDNs) have central roles in bacterial homeostasis and virulence by acting as nucleotide second messengers. Bacterial CDNs also elicit immune responses during infection when they are detected by pattern-recognition receptors in animal cells. Here we perform a systematic biochemical screen for bacterial signalling nucleotides and discover a large family of cGAS/DncV-like nucleotidyltransferases (CD-NTases) that use both purine and pyrimidine nucleotides to synthesize a diverse range of CDNs. Here, a series of crystal structures establish CD-NTases as a structurally conserved family and reveal key contacts in the enzyme active-site lid that direct purine or pyrimidine selection. CD-NTase products are not restricted to CDNs and also include an unexpected class of cyclic trinucleotide compounds. Biochemical and cellular analyses of CD-NTase signalling nucleotides demonstrate that these cyclic di- and trinucleotides activate distinct host receptors and thus may modulate the interaction of both pathogens and commensal microbiota with their animal and plant hosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Conformational flexibility related to enzyme activity: evidence for a dynamic active-site gatekeeper function of Tyr 215 in Aerococcus viridans lactate oxidase

L-Lactate oxidase (LOX) belongs to a large family of flavoenzymes that catalyze oxidation of α-hydroxy acids. How in these enzymes the protein structure controls reactivity presents an important but elusive problem. LOX contains a prominent tyrosine in the substrate binding pocket (Tyr 215 in Aerococcus viridans LOX) hat is partially responsible for securing a flexible loop which sequesters the active site. To characterize the role of Tyr 215 , effects of substitutions of the tyrosine (Y215F, Y215H) were analyzed kinetically, crystallographically and by molecular dynamics simulations. Enzyme variants showed slowed flavin reduction and oxidation by up to 33-fold. Pyruvate release was also decelerated and in Y215F, it was the slowest step overall. A 2.6-Å crystal structure of Y215F in complex with pyruvate shows the hydrogen bond between the phenolic hydroxyl and the keto oxygen in pyruvate is replaced with a potentially stronger hydrophobic interaction between the phenylalanine and the methyl group of pyruvate. Residues 200 through 215 or 216 appear to be disordered in two of the eight monomers in the asymmetric unit suggesting that they function as a lid controlling substrate entry and product exit from the active site. Substitutions of Tyr 215 can thus lead to a kinetic bottleneck in product release.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2010

Spectroscopic diagnostics for liquid lithium divertor studies on National Spherical Torus Experiment

The use of lithium-coated plasma facing components for plasma density control is studied in the National Spherical Torus Experiment (NSTX). A recently installed liquid lithium divertor (LLD) module has a porous molybdenum surface, separated by a stainless steel liner from a heated copper substrate. Lithium is deposited on the LLD from two evaporators. Two new spectroscopic diagnostics are installed to study the plasma surface interactions on the LLD: (1) A 20-element absolute extreme ultraviolet (AXUV) diode array with a 6 nm bandpass filter centered at 121.6 nm (the Lyman-{alpha} transition) for spatially resolved divertor recycling rate measurements in the highly reflective LLD environment, and (2) an ultraviolet-visible-near infrared R=0.67 m imaging Czerny-Turner spectrometer for spatially resolved divertor D I, Li I-II, C I-IV, Mo I, D{sub 2}, LiD, CD emission and ion temperature on and around the LLD module. The use of photometrically calibrated measurements together with atomic physics factors enables studies of recycling and impurity particle fluxes as functions of LLD temperature, ion flux, and divertor geometry.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2010

Fluid Flow Characteristic Simulation of the Original TRIGA 2000 Reactor Design Using Computational Fluid Dynamics Code

Common energy crisis has modified the national energy policy which is in the beginning based on natural resources becoming based on technology, therefore the capability to understanding the basic and applied science is needed to supporting those policies. National energy policy which aims at new energy exploitation, such as nuclear energy is including many efforts to increase the safety reactor core condition and optimize the related aspects and the ability to build new research reactor with properly design. The previous analysis of the modification TRIGA 2000 Reactor design indicates that forced convection of the primary coolant system put on an effect to the flow characteristic in the reactor core, but relatively insignificant effect to the flow velocity in the reactor core. In this analysis, the lid of reactor core is closed. However the forced convection effect is still presented. This analysis shows the fluid flow velocity vector in the model area without exception. Result of this analysis indicates that in the original design of TRIGA 2000 reactor, there is still forced convection effects occur but less than in the modified TRIGA 2000 design.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2013

A transparent Pyrex μ-reactor for combined in situ optical characterization and photocatalytic reactivity measurements

A new Pyrex-based μ-reactor for photocatalytic and optical characterization experiments is presented. The reactor chamber and gas channels are microfabricated in a thin poly-silicon coated Pyrex chip that is sealed with a Pyrex lid by anodic bonding. The device is transparent to light in the UV-vis-near infrared range of wavelengths (photon energies between ∼0.4 and ∼4.1 eV). The absorbance of a photocatalytic film obtained with a light transmission measurement during a photocatalytic reaction is presented as a proof of concept of a photocatalytic reactivity measurement combined with in situ optical characterization. Diffuse reflectance measurements of highly scattering photocatalytic nanopowders in a sealed Pyrex μ-reactor are also possible using an integrating sphere as shown in this work. These experiments prove that a photocatalyst can be characterized with optical techniques after a photocatalytic reaction without removing the material from the reactor. The catalyst deposited in the cylindrical reactor chamber can be illuminated from both top and bottom sides and an example of application of top and bottom illumination is presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Stratified spin-up in a sliced, square cylinder

We previously reported experimental and theoretical results on the linear spin-up of a linearly stratified, rotating fluid in a uniform-depth square cylinder [M. R. Foster and R. J. Munro, “The linear spin-up of a stratified, rotating fluid in a square cylinder,” J. Fluid Mech. 712, 7–40 (2012)]. Here we extend that analysis to a “sliced” square cylinder, which has a base-plane inclined at a shallow angle α. Asymptotic results are derived that show the spin-up phase is achieved by a combination of the Ekman-layer eruptions (from the perimeter region of the cylinder's lid and base) and cross-slope-propagating stratified Rossby waves. The final, steady state limit for this spin-up phase is identical to that found previously for the uniform depth cylinder, but is reached somewhat more rapidly on a time scale of order E{sup −1/2}Ω{sup −1}/log (α/E{sup 1/2}) (compared to E{sup −1/2}Ω{sup −1} for the uniform-depth cylinder), where Ω is the rotation rate and E the Ekman number. Experiments were performed for Burger numbers, S, between 0.4 and 16, and showed that for S≳O(1), the Rossby modes are severely damped, and it is only at small S, and during the early stages, that the presence of these wave modes was evident. These observations are supported by the theory, which shows the damping factors increase with S and are numerically large for S≳O(1)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Performance evaluation of OpenFOAM on many-core architectures

In this article application of Open Source Field Operation and Manipulation (OpenFOAM) C++ libraries for solving engineering problems on many-core architectures is presented. Objective of this article is to present scalability of OpenFOAM on parallel platforms solving real engineering problems of fluid dynamics. Scalability test of OpenFOAM is performed using various hardware and different implementation of standard PCG and PBiCG Krylov iterative methods. Speed up of various implementations of linear solvers using GPU and MIC accelerators are presented in this paper. Numerical experiments of 3D lid-driven cavity flow for several cases with various number of cells are presented.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

The spin physics results from COMPASS

COMPASS (COmmon Muon and Proton Apparatus for Structure and Spectroscopy) is a fixed target experiment at CERN dedicated to studies of the spin structure of the nucleon and of the spectroscopy of hadrons. During the years 2002-2004, 2006-2007 and 2010-2011 the COMPASS collaboration has collected a large amount of data by scattering polarized 160(200) GeV/c muons on polarized {sup 6}LiD and NH{sub 3} targets. The COMPASS results on quark and gluon helicities are discussed, as well as results on transverse spin and transverse momentum effects in semi-inclusive deeply inelastic scattering.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

Lagrangian flows within reflecting internal waves at a horizontal free-slip surface

In this paper sequel to Zhou and Diamessis [“Reflection of an internal gravity wave beam off a horizontal free-slip surface,” Phys. Fluids 25, 036601 (2013)], we consider Lagrangian flows within nonlinear internal waves (IWs) reflecting off a horizontal free-slip rigid lid, the latter being a model of the ocean surface. The problem is approached both analytically using small-amplitude approximations and numerically by tracking Lagrangian fluid particles in direct numerical simulation (DNS) datasets of the Eulerian flow. Inviscid small-amplitude analyses for both plane IWs and IW beams (IWBs) show that Eulerian mean flow due to wave-wave interaction and wave-induced Stokes drift cancels each other out completely at the second order in wave steepness A, i.e., O(A{sup 2}), implying zero Lagrangian mean flow up to that order. However, high-accuracy particle tracking in finite-Reynolds-number fully nonlinear DNS datasets from the work of Zhou and Diamessis suggests that the Euler-Stokes cancelation on O(A{sup 2}) is not complete. This partial cancelation significantly weakens the mean Lagrangian flows but does not entirely eliminate them. As a result, reflecting nonlinear IWBs produce mean Lagrangian drifts on O(A{sup 2}) and thus particle dispersion on O(A{sup 4}). The above findings can be relevant to predicting IW-driven mass transport in the oceanic surface and subsurface region which bears important observational and environmental implications, under circumstances where the effect of Earth rotation can be ignored.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Vortex breakdown in closed containers with polygonal cross sections

The vortex breakdown bubble in the confined flow generated by a rotating lid in closed containers with polygonal cross sections was analysed both experimentally and numerically for the height/radius aspect ratio equal to 2. The stagnation point locations of the breakdown bubble emergence and the corresponding Reynolds number were determined experimentally and in addition computed numerically by STAR-CCM+ CFD software for square, pentagonal, hexagonal, and octagonal cross section configurations. The flow pattern and the velocity were observed and measured by combining the seeding particle visualization and the temporal accuracy of laser Doppler anemometry. The vortex breakdown size and position on the container axis were determined for Reynolds numbers, ranging from 1450 to 2400. The obtained results were compared with the flow structure in the closed container of cubical and cylindrical configurations. It is shown that the measured evolution of steady vortex breakdown is in close agreement with the numerical results.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗