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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 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Quantitative Non-Destructive Evaluation of Fatigue Damage Based on Multi-Sensor Fusion

Based on sensor fusion and machine learning, this project developed a novel non-destructive evaluation (NDE) methodology, which consists of a remaining useful life (RUL) prediction framework and regression models for predicting residual stress and full width at half maximum (FWHM). A series of fatigue testing experiments were conducted using 5052-H32 aluminum alloy specimens. All specimens were measured using linear ultrasonic (LU) and nonlinear ultrasonic (NLU) testing methods non-destructively. Machine learning models were developed to use LU and NLU measurements to predict loading condition, fatigue level, residual stress, and FWHM. It was demonstrated that the developed methodology could distinguish new and fatigue specimens with an accuracy of 97.53%. Also, the prediction errors for residual stress and FWHM were as low as 4.73% and 1.62%, respectively. An interactive database was created to publicly share the data generated from the project. It is envisioned that the developed NDE technology will equip manufacturers with a responsive screening system for incoming used metallic components, and potentially lead to a significant increase in using used metallic components for remanufacturing.

42 ENGINEERING↗
NASA NTRS2009

Computational Study on Full-length Human Ku70 with Double Stranded DNA: Dynamics, Interactions and Functional Implications

The Ku70/80 heterodimer is the first repair protein in the initial binding of double-strand break (DSB) ends following DNA damage, and is a component of nonhomologous end joining repair, the primary pathway for DSB repair in mammalian cells. In this study we constructed a full-length human Ku70 structure based on its crystal structure, and performed 20 ns conventional molecular dynamic (CMD) simulations on this protein and several other complexes with short DNA duplexes of different sequences. The trajectories of these simulations indicated that, without the topological support of Ku80, the residues in the bridge and C-terminal arm of Ku70 are more flexible than other experimentally identified domains. We studied the two missing loops in the crystal structure and predicted that they are also very flexible. Simulations revealed that they make an important contribution to the Ku70 interaction with DNA. Dislocation of the previously studied SAP domain was observed in several systems, implying its role in DNA binding. Targeted molecular dynamic (TMD) simulation was also performed for one system with a far-away 14bp DNA duplex. The TMD trajectory and energetic analysis disclosed detailed interactions of the DNA-binding residues during the DNA dislocation, and revealed a possible conformational transition for a DSB end when encountering Ku70 in solution. Compared to experimentally based analysis, this study identified more detailed interactions between DNA and Ku70. Free energy analysis indicated Ku70 alone is able to bind DNA with relatively high affinity, with consistent contributions from various domains of Ku70 in different systems. The functional implications of these domains in the processes of Ku heterodimerization and DNA damage recognition and repair can be characterized in detail based upon this analysis.

Hu, Shaowen↗
DOE OSTI2017

Two alternative binding mechanisms connect the protein translocation Sec71-Sec72 complex with heat shock proteins

The biosynthesis of many eukaryotic proteins requires accurate targeting to and translocation across the endoplasmic reticulum membrane. Post-translational protein translocation in yeast requires both the Sec61 translocation channel, and a complex of four additional proteins: Sec63, Sec62, Sec71, and Sec72. The structure and function of these proteins are largely unknown. This pathway also requires the cytosolic Hsp70 protein Ssa1, but whether Ssa1 associates with the translocation machinery to target protein substrates to the membrane is unclear. Here, we use a combined structural and biochemical approach to explore the role of Sec71-Sec72 subcomplex in post-translational protein translocation. To this end, we report a crystal structure of the Sec71-Sec72 complex, which revealed that Sec72 contains a tetratricopeptide repeat (TPR) domain that is anchored to the endoplasmic reticulum membrane by Sec71. We also determined the crystal structure of this TPR domain with a C-terminal peptide derived from Ssa1, which suggests how Sec72 interacts with full-length Ssa1. Surprisingly, Ssb1, a cytoplasmic Hsp70 that binds ribosome-associated nascent polypeptide chains, also binds to the TPR domain of Sec72, even though it lacks the TPR-binding C-terminal residues of Ssa1. We demonstrate that Ssb1 binds through its ATPase domain to the TPR domain, an interaction that leads to inhibition of nucleotide exchange. Taken together, our results suggest that translocation substrates can be recruited to the Sec71-Sec72 complex either post-translationally through Ssa1 or co-translationally through Ssb1.

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

Strong Turbulent Alfvén Wave Interactions in a Laboratory Plasma (Final Scientific/Technical Report)

Turbulence is a fundamental and widespread aspect of plasma behavior, occurring in nearly every natural plasma system that is observed, from clusters of distant galaxies to plasmas within the solar system. Plasma continuously streaming from the sun, known as the solar wind, has been particularly fruitful in understanding plasma turbulence due to the availability of spacecraft data. An ensuring mystery in solar wind turbulence is the unexpected observation of residual energy – there is excess energy in the magnetic fluctuations compared to the velocity fluctuations even though an Alfvén wave in Magnetohydrodynamics has equal amounts of energy in each. The project studied strong non-linear interaction between counter-propagating Alfvén waves in the lab for the first time. Dr. Mel Abler, who was hired as a postdoctoral researcher under this grant, obtained the first observation of residual energy in a counter-propagating Alfvén wave interaction. Dr. Abler showed experimentally that the interaction of two counter-propagating Alfvén waves produces daughter modes that are not not normal modes of the system and only exist in the presence of the nonlinear drive. These Alfvén quasimodes contain either negative residual energy (more energy in magnetic fluctuations) or positive residual energy (more energy in velocity fluctuations).

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2012

Novel Ganglioside-mediated Entry of Botulinum Neurotoxin Serotype D into Neurons

Botulinum Neurotoxins (BoNTs) are organized into seven serotypes, A-G. Although several BoNT serotypes enter neurons through synaptic vesicle cycling utilizing dual receptors (a ganglioside and a synaptic vesicle-associated protein), the entry pathway of BoNT/D is less well understood. Although BoNT/D entry is ganglioside-dependent, alignment and structural studies show that BoNT/D lacks key residues within a conserved ganglioside binding pocket that are present in BoNT serotypes A, B, E, F, and G, which indicate that BoNT/D-ganglioside interactions may be unique. In this study BoNT/D is shown to have a unique association with ganglioside relative to the other BoNT serotypes, utilizing a ganglioside binding loop (GBL, residues Tyr-1235-Ala-1245) within the receptor binding domain of BoNT/D (HCR/D) via b-series gangliosides, including GT1b, GD1b, and GD2. HCR/D bound gangliosides and entered neurons dependent upon the aromatic ring of Phe-1240 within the GBL. This is the first BoNT-ganglioside interaction that is mediated by a phenylalanine. In contrast, Trp-1238, located near the N terminus of the ganglioside binding loop, was mostly solvent-inaccessible and appeared to contribute to maintaining the loop structure. BoNT/D entry and intoxication were enhanced by membrane depolarization via synaptic vesicle cycling, where HCR/D colocalized with synaptophysin, a synaptic vesicle marker, but immunoprecipitation experiments did not detect direct association with synaptic vesicle protein 2. Thus, BoNT/D utilizes unique associations with gangliosides and synaptic vesicles to enter neurons, which may facilitate new neurotoxin therapies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Involvement of viral envelope GP2 in Ebola virus entry into cells expressing the macrophage galactose-type C-type lectin

Highlights: {yields} Ebola virus infection is mediated by binding to and fusion with the target cells. {yields} Structural feature of the viral glycoprotein determines the infectivity. {yields} Surface C-type lectin, MGL, of macrophages and dendritic cells mediate the infection. {yields} GP2, one of glycoprotein subunits, plays an essential role in MGL-mediated infection. {yields} There is a critical amino acid residue involved in high infectivity. -- Abstract: Ebola virus (EBOV) infection is initiated by the interaction of the viral surface envelope glycoprotein (GP) with the binding sites on target cells. Differences in the mortality among different species of the Ebola viruses, i.e., Zaire ebolavirus (ZEBOV) and Reston ebolavirus (REBOV), correspond to the in vitro infectivity of the pseudo-typed virus constructed with the GPs in cells expressing macrophage galactose-type calcium-type lectin (MGL/CD301). Through mutagenesis of GP2, the transmembrane-anchored subunit of GP, we found that residues 502-527 of the GP2 sequence determined the different infectivity between VSV-ZEBOV GP and -REBOV GP in MGL/CD301-expressing cells and a histidine residue at position 516 of ZEBOV GP2 appeared essential in the differential infectivity. These findings may provide a clue to clarify a molecular basis of different pathogenicity among EBOV species.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Acetylation of lysine residues in the recombinant nucleoprotein and VP40 matrix protein of Zaire Ebolavirus by eukaryotic histone acetyltransferases

Acetylation of histones and other proteins plays crucial roles in transcriptional regulation, chromatin organization, and other biological processes. It has been recently reported that the nucleoprotein (NP) of influenza virus is acetylated in infected cells, and this modification contributes to the RNA polymerization activity of the virus. As the influenza virus, the Ebolavirus contains single-stranded negative-sense RNA as its viral genome, which interacts with NP and other viral proteins. In this study, we performed a series of biochemical experiments and revealed that the recombinant Ebolavirus NP and the viral matrix protein VP40, which binds with NP, were acetylated by eukaryotic histone acetyltransferases, such as P300/CREB-binding protein (P300/CBP) and P300/CBP-associated factor (PCAF), in vitro. Mass spectrometry was used to identify the lysine residues that were potential acetylation targets in NP and VP40. The identified lysine residues in NP were located in the RNA-binding cleft and the VP35-binding domain. Potentially acetylated lysine targets in VP40 were identified in the basic patch, which is necessary for constructing oligomers. These results suggest that the acetylation of these lysine residues is involved in the interactions between viral proteins.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2002

Isolation and characterization of a novel calmodulin-binding protein from potato

Tuberization in potato is controlled by hormonal and environmental signals. Ca(2+), an important intracellular messenger, and calmodulin (CaM), one of the primary Ca(2+) sensors, have been implicated in controlling diverse cellular processes in plants including tuberization. The regulation of cellular processes by CaM involves its interaction with other proteins. To understand the role of Ca(2+)/CaM in tuberization, we have screened an expression library prepared from developing tubers with biotinylated CaM. This screening resulted in isolation of a cDNA encoding a novel CaM-binding protein (potato calmodulin-binding protein (PCBP)). Ca(2+)-dependent binding of the cDNA-encoded protein to CaM is confirmed by (35)S-labeled CaM. The full-length cDNA is 5 kb long and encodes a protein of 1309 amino acids. The deduced amino acid sequence showed significant similarity with a hypothetical protein from another plant, Arabidopsis. However, no homologs of PCBP are found in nonplant systems, suggesting that it is likely to be specific to plants. Using truncated versions of the protein and a synthetic peptide in CaM binding assays we mapped the CaM-binding region to a 20-amino acid stretch (residues 1216-1237). The bacterially expressed protein containing the CaM-binding domain interacted with three CaM isoforms (CaM2, CaM4, and CaM6). PCBP is encoded by a single gene and is expressed differentially in the tissues tested. The expression of CaM, PCBP, and another CaM-binding protein is similar in different tissues and organs. The predicted protein contained seven putative nuclear localization signals and several strong PEST motifs. Fusion of the N-terminal region of the protein containing six of the seven nuclear localization signals to the reporter gene beta-glucuronidase targeted the reporter gene to the nucleus, suggesting a nuclear role for PCBP.

NASA Discipline Plant Biology↗
DOE OSTI2024

Effects of Plume Targeted Cooling on Residual Stress in Controlled Atmosphere Plasma Sprayed Coatings

Thermal spray processes can benefit from cooling to maintain substrate temper, reduce processing times, and manage thermally induced residual stresses. “Plume quenching” is a plume-targeted cooling technique which has been shown to reduce substrate temperatures by redirection of hot plume gases using a lateral argon curtain injected into the plume, while limiting interaction with the substrate or affecting coating properties. Here, this study explores the use of this technique for residual stress management by reducing the thermally driven component in nickel and tantalum coatings on titanium and aluminum substrates. The in-situ residual stress profiles were measured for all substrate and coating pairings during spraying and cooling, and the deposition and thermal stresses recorded. For substrate and coating pairings where the predominant component of residual stress was thermal (driven by a large difference in coefficient of thermal expansion, Δα, between coating and substrate), plume quenching reduced both the thermal stress and the final stress state of the coating. This was seen primarily in tantalum on aluminum coatings where the Δα was -17 × 10 -6 /°C, and thermal stress was reduced by 7.5% and 22.4% for the plume quenching rates of 50 and 100 slpm, respectively.

42 ENGINEERING↗
DOE OSTI2013

X-Ray Diffraction Line Broadening in Shock Modified Pyrite [Book Chapter]

Powder compacts of a commercially-available pyrite, FeS 2 , have been subjected to controlled, quantitative high pressure shock loading at peak pressures from 7.5-22 GPa. The profiles of the x-ray diffraction lines have been examined to determine the reduction of the crystallite (domain) size and the introduction of residual microstrain due to defects and dislocations resulting from the transmission and interaction of the shockwave. Pyrite experience a surprisingly smaller profile broadening than observed for all other materials under similar shock conditions, suggesting a much more refractory character. Such small changes are consistent with low defect densities and with the relative low reaction activity (oxidation of sulfide to sulfate by humid air) observed on this material in the complementary studies.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Pentamidine blocks the interaction between mutant S100A5 and RAGE V domain and inhibits the RAGE signaling pathway

The human S100 protein family contains small, dimeric and acidic proteins that contain two EF-hand motifs and bind calcium. When S100A5 binds calcium, its conformation changes and promotes interaction with the target protein. The extracellular domain of RAGE (Receptor of Advanced Glycation End products) contain three domains: C1, C2 and V. The RAGE V domain is the target protein of S100A5 that promotes cell survival, growth and differentiation by activating several signaling pathways. Pentamidine is an apoptotic and antiparasitic drug that is used to treat or prevent pneumonia. Here, we found that pentamidine interacts with S100A5 using HSQC titration. We elucidated the interactions of S100A5 with RAGE V domain and pentamidine using fluorescence and NMR spectroscopy. We generated two binary models—the S100A5-RAGE V domain and S100A5-Pentamidine complex—and then observed that the pentamidine and RAGE V domain share a similar binding region in mS100A5. We also used the WST-1 assay to investigate the bioactivity of S100A5, RAGE V domain and pentamidine. These results indicated that pentamidine blocks the binding between S100A5 and RAGE V domain. This finding is useful for the development of new anti-proliferation drugs. - Highlights: • The interaction between mS100A5–RAGE V was investigated by fluorescence spectroscopy. • The interfacial residues on mS100A5–RAGE V and mS100A5–pentamidine contact surface were mapped by {sup 1}H-{sup 15}N HSQC experiments. • mS100A5–RAGE V and mS100A5–pentamidine complex models were generated from NMR restraints using HADDOCK program. • The bioactivity of the mS100A5–RAGE V and mS100A5–pentamidine complex was studied using WST-1 assay.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Effect of ethoxylation and lauryl alcohol on the self-assembly of sodium laurylsulfate: Significant structural and rheological transformation

Fatty alcohols are added to the surfactant solutions to modify foaming and lubrication properties, while the degree of ethoxylation is increased to improve mildness to the skin. However, it is envisioned that both parameters are capable of manipulating rheological and morphological properties. Therefore, an efficient control over the carbon chain length, amount of fatty alcohol and degree of ethoxylation could modify the surfactant self-assembly in an unprecedented way. The present work is focused on understanding the structural transformation, intermolecular interactions and rheological properties of the colloidal systems containing various amounts of lauryl alcohol (LA), and surfactant with varying degrees of ethoxylation. Additionally, combined small-angle neutron scattering (SANS), nuclear magnetic resonance (NMR) spectroscopy, rheological and morphological studies were performed to elucidate these properties. The results reveal that an increase in LA content increases the system viscosity ultimately forming a gel, and drives the assembly pattern of the surfactant from ellipsoidal micellar to lamellar via a vesicular and vesicular/lamellar mixed intermediates. Conversely, higher degrees of ethoxylation delay the onset of morphological transformation and gel formation. The interplay between hydrophobic and polar interactions coupled with hydrogen bonding interactions drive the overall rheological and morphological transformations. Therefore, fine-tuning residual chemicals can offer a novel tool for optimization of the product formulation.

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

Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins

Here, we demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D 3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β 1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Investigation of the role of 10 Li resonances in the halo structure of 11 Li through the 11 Li(p,d) 10 Li transfer reaction

Here, the first measurement of the one-neutron transfer reaction 11 Li(p,d) 10 Li performed using the IRIS facility at TRIUMF with a 5.7A MeV 11 Li beam interacting with a solid H 2 target is reported. The 10 Li residue was populated strongly as a resonance peak with energy E r = 0.62 ± 0.04 MeV having a total width Γ = 0.33 ± 0.07 MeV. The angular distribution of this resonance is characterized by neutron occupying the 1p 1/2 orbital. A DWBA analysis yields a spectroscopic factor of 0.67 ± 0.12 for p 1/2 removal strength from the ground state of 11 Li to the region of the peak.

10,11Li↗
DOE OSTI2012

Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA

During DNA synthesis, base stacking and Watson-Crick (WC) hydrogen bonding increase the stability of nascent base pairs when they are in a ternary complex. To evaluate the contribution of base stacking to the incorporation efficiency of dNTPs when a DNA polymerase encounters an abasic site, we varied the penultimate base pairs (PBs) adjacent to the abasic site using all 16 possible combinations. We then determined pre-steady-state kinetic parameters with an RB69 DNA polymerase variant and solved nine structures of the corresponding ternary complexes. The efficiency of incorporation for incoming dNTPs opposite an abasic site varied between 2- and 210-fold depending on the identity of the PB. We propose that the A rule can be extended to encompass the fact that DNA polymerase can bypass dA/abasic sites more efficiently than other dN/abasic sites. Crystal structures of the ternary complexes show that the surface of the incoming base was stacked against the PB's interface and that the kinetic parameters for dNMP incorporation were consistent with specific features of base stacking, such as surface area and partial charge-charge interactions between the incoming base and the PB. Without a templating nucleotide residue, an incoming dNTP has no base with which it can hydrogen bond and cannot be desolvated, so that these surrounding water molecules become ordered and remain on the PB's surface in the ternary complex. When these water molecules are on top of a hydrophobic patch on the PB, they destabilize the ternary complex, and the incorporation efficiency of incoming dNTPs is reduced.

08 HYDROGEN↗
DOE OSTI2013

DAXX envelops a histone H3.3-H4 dimer for H3.3-specific recognition

Histone chaperones represent a structurally and functionally diverse family of histone-binding proteins that prevent promiscuous interactions of histones before their assembly into chromatin. DAXX is a metazoan histone chaperone specific to the evolutionarily conserved histone variant H3.3. Here we report the crystal structures of the DAXX histone-binding domain with a histone H3.3–H4 dimer, including mutants within DAXX and H3.3, together with in vitro and in vivo functional studies that elucidate the principles underlying H3.3 recognition specificity. Occupying 40% of the histone surface-accessible area, DAXX wraps around the H3.3–H4 dimer, with complex formation accompanied by structural transitions in the H3.3–H4 histone fold. DAXX uses an extended α-helical conformation to compete with major inter-histone, DNA and ASF1 interaction sites. Our structural studies identify recognition elements that read out H3.3-specific residues, and functional studies address the contributions of Gly90 in H3.3 and Glu225 in DAXX to chaperone-mediated H3.3 variant recognition specificity.

Elsässer, Simon J↗
DOE OSTI2016

Surface, structural and mechanical properties of zirconium ablated by KrF excimer laser radiation

We study the effect of the ambient – dry (air) and wet (propanol) – environment on the surface, structural and mechanical properties of zirconium samples after irradiation with a KrF excimer laser (wavelength of 248 nm, pulse duration of 20 ns and repetition rate of 20 Hz). The samples are exposed to an increasing number of laser pulses varying from 500 to 2000 in both media. Various features of the treated targets such as surface morphology, chemical composition, crystalline structure and hardness are analysed by complementary characterisation techniques, such as scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), X-ray diffraction (XRD), Raman spectroscopy and Vickers hardness tester, respectively. Surface morphology and hardness are explained on the basis of modifications in crystalinity, residual pressures and chemical properties of the sample surface after its irradiation. (interaction of laser radiation with matter)

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2012

A Salmonella typhimurium-translocated Glycerophospholipid:Cholesterol Acyltransferase Promotes Virulence by Binding to the RhoA Protein Switch Regions

Salmonella enterica serovar typhimurium translocates a glycerophospholipid: cholesterol acyltransferase (SseJ) into the host cytosol after its entry into mammalian cells. SseJ is recruited to the cytoplasmic face of the host cell phagosome membrane where it is activated upon binding the small GTPase, RhoA. SseJ is regulated similarly to cognate eukaryotic effectors, as only the GTP-bound form of RhoA family members stimulates enzymatic activity. Using NMR and biochemistry, this work demonstrates that SseJ competes effectively with Rhotekin, ROCK, and PKN1 in binding to a similar RhoA surface. The RhoA surface that binds SseJ includes the regulatory switch regions that control activation of mammalian effectors. These data were used to create RhoA mutants with altered SseJ binding and activation. This structure-function analysis supports a model in which SseJ activation occurs predominantly through binding to residues within switch region II. We further defined the nature of the interaction between SseJ and RhoA by constructing SseJ mutants in the RhoA binding surface. These data indicate that SseJ binding to RhoA is required for recruitment of SseJ to the endosomal network and for full Salmonella virulence for inbred susceptible mice, indicating that regulation of SseJ by small GTPases is an important virulence strategy of this bacterial pathogen. The dependence of a bacterial effector on regulation by a mammalian GTPase defines further how intimately host pathogen interactions have coevolved through similar and divergent evolutionary strategies.

Environmental Molecular Sciences Laboratory↗