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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 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Structure of the GH1 domain of guanylate kinase-associated protein from Rattus norvegicus

Graphical abstract: - Highlights: • The crystal structure of GKAP homology domain 1 (GH1) was determined. • GKAP GH1 is a three-helix bundle connected by short flexible loops. • The predicted helix α4 associates weakly with the helix α3, suggesting dynamic nature of the GH1 domain. - Abstract: Guanylate-kinase-associated protein (GKAP) is a scaffolding protein that links NMDA receptor-PSD-95 to Shank–Homer complexes by protein–protein interactions at the synaptic junction. GKAP family proteins are characterized by the presence of a C-terminal conserved GKAP homology domain 1 (GH1) of unknown structure and function. In this study, crystal structure of the GH1 domain of GKAP from Rattus norvegicus was determined in fusion with an N-terminal maltose-binding protein at 2.0 Å resolution. The structure of GKAP GH1 displays a three-helix bundle connected by short flexible loops. The predicted helix α4 which was not visible in the crystal structure associates weakly with the helix α3 suggesting dynamic nature of the GH1 domain. The strict conservation of GH1 domain across GKAP family members and the lack of a catalytic active site required for enzyme activity imply that the GH1 domain might serve as a protein–protein interaction module for the synaptic protein clustering.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Terminal Sinking Velocity for Waste Packages Falling in a Deep Borehole - 17063

This evaluation of terminal velocity for a waste package sinking in a deep borehole filled with emplacement fluid was done to support concept development for the Deep Borehole Field Test (DBFT). The DBFT objective is to evaluate the safety and feasibility of the deep borehole disposal (DBD) concept for certain radioactive wastes. The DBD concept calls for emplacing waste packages in the lower 2 km of a borehole drilled into crystalline basement rock to a depth of 5 km. Previous studies identified that accidentally dropping one or more waste packages during emplacement could be an important risk, particularly if a waste package is breached. This study evaluated the range of terminal sinking velocity, which can be used to design waste packages and impact limiters to ensure that breach does not occur. Based on an analytical model of a sinking container, a highly turbulent flow is expected to develop in the emplacement fluid. Turbulence is a complex three-dimensional phenomenon and the applicability of analytical models is limited. To backstop the analytical model and to extend predictions to other package dimensions and fluid properties, numerical simulation was performed using the ANSYS Fluent computational fluid dynamics code. Terminal velocity was calculated for downhole temperatures up to 1200 C, and three emplacement fluids (water, NaCl brine, and NaBr brine). Simulation results confirmed that flow around the sinking container is highly turbulent (Reynolds number 5.6 x 10{sup 4} to 7.3 x 10{sup 5}). Turbulence increases with temperature and decreases with density. Calculated terminal velocity ranges from 1.95 (200 C) to 2.13 m/s (1200 C) in water; 1.61 (200 C) to 1.79 m/s (1200 C) in NaCl; and 1.30 (200 C) to 1.46 m/s (1200 C) in NaBr. Terminal velocity is inversely related to fluid density, and the temperature effect on density appears to have a stronger effect on terminal velocity than the temperature effect on viscosity. The foregoing results are for non-perforated casing, but in practice the casing may be perforated to prepare for cementing, and to allow relief of fluid pressure from thermal expansion after emplacement of heat generating waste, and after final borehole closure. To represent the effect from perforations, the analytical solution was modified to include bypass flow through perforations and in the annulus. A workable perforation scheme is identified, consistent with borehole construction and closure requirements, using 2-cm and 5-cm diameter perforations. This scheme is estimated to limit the terminal velocity to 3 m/s, for reference waste packages falling in water at 400 C. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects

SARS-CoV-2 is one of three coronaviruses that have crossed the animal-to-human barrier and caused widespread disease in the past two decades. The development of a universal human coronavirus vaccine could prevent future pandemics. We characterize 198 antibodies isolated from four COVID-19+ subjects and identify 14 SARS-CoV-2 neutralizing antibodies. One targets the N-terminal domain (NTD), one recognizes an epitope in S2, and 11 bind the receptor-binding domain (RBD). Three anti-RBD neutralizing antibodies cross-neutralize SARS-CoV-1 by effectively blocking binding of both the SARS-CoV-1 and SARS-CoV-2 RBDs to the ACE2 receptor. Using the K18-hACE transgenic mouse model, we demonstrate that the neutralization potency and antibody epitope specificity regulates the in vivo protective potential of anti-SARS-CoV-2 antibodies. All four cross-neutralizing antibodies neutralize the B.1.351 mutant strain. Thus, our study reveals that epitopes in S2 can serve as blueprints for the design of immunogens capable of eliciting cross-neutralizing coronavirus antibodies.

60 APPLIED LIFE SCIENCES↗
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 OSTI2017

Unveiling a Drift Resistant Cryptotope within Marburgvirus Nucleoprotein Recognized by Llama Single-Domain Antibodies

Marburg virus (MARV) is a highly lethal hemorrhagic fever virus that is increasingly re-emerging in Africa, has been imported to both Europe and the US, and is also a Tier 1 bioterror threat. As a negative sense RNA virus, MARV has error prone replication which can yield progeny capable of evading countermeasures. To evaluate this vulnerability, we sought to determine the epitopes of 4 llama single-domain antibodies (sdAbs or VHH) specific for nucleoprotein (NP), each capable of forming MARV monoclonal affinity reagent sandwich assays. Here, we show that all sdAb bound the C-terminal region of NP, which was produced recombinantly to derive X-ray crystal structures of the three best performing antibody-antigen complexes. The common epitope is a trio of alpha helices that form a novel asymmetric basin-like depression that accommodates each sdAb paratope via substantial complementarity-determining region (CDR) restructuring. Shared core contacts were complemented by unique accessory contacts on the sides and overlooks of the basin yielding very different approach routes for each sdAb to bind the antigen. The C-terminal region of MARV NP was unable to be crystallized alone and required engagement with sdAb to form crystals suggesting the antibodies acted as crystallization chaperones. While gross structural homology is apparent between the two most conserved helices of MARV and Ebolavirus, the positions and morphologies of the resulting basins were markedly different. Naturally occurring amino acid variations occurring in bat and human Marburgvirus strains all mapped to surfaces distant from the predicted sdAb contacts suggesting a vital role for the NP interface in virus replication. As an essential internal structural component potentially interfacing with a partner protein it is likely the C-terminal epitope remains hidden or “cryptic” until virion disruption occurs. Conservation of this epitope over 50 years of Marburgvirus evolution should make these sdAb useful foundations for diagnostics and therapeutics resistant to drift.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Minimax terminal approach problem in two-level hierarchical nonlinear discrete-time dynamical system

We consider a discrete–time dynamical system consisting of three controllable objects. The motions of all objects are given by the corresponding vector nonlinear or linear discrete–time recurrent vector relations, and control system for its has two levels: basic (first or I level) that is dominating and subordinate level (second or II level) and both have different criterions of functioning and united a priori by determined informational and control connections defined in advance. For the dynamical system in question, we propose a mathematical formalization in the form of solving a multistep problem of two-level hierarchical minimax program control over the terminal approach process with incomplete information and give a general scheme for its solving.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Full-length Gα q -phospholipase C-β3 structure reveals interfaces of the C-terminal coiled-coil domain

Phospholipase C-β (PLCβ) is directly activated by Gα q , but the molecular basis for how its distal C-terminal domain (CTD) contributes to maximal activity is poorly understood. Herein we present both the crystal structure and cryo-EM three-dimensional reconstructions of human full-length PLCβ3 in complex with mouse Gα q . The distal CTD forms an extended monomeric helical bundle consisting of three antiparallel segments with structural similarity to membrane-binding bin-amphiphysin-Rvs (BAR) domains. Sequence conservation of the distal CTD suggests putative membrane and protein interaction sites, the latter of which bind the N-terminal helix of Gα q in both the crystal structure and cryo-EM reconstructions. Functional analysis suggests that the distal CTD has roles in membrane targeting and in optimizing the orientation of the catalytic core at the membrane for maximal rates of lipid hydrolysis.

Lyon, Angeline M.↗
DOE OSTI2012

Ribonuclease A suggests how proteins self-chaperone against amyloid fiber formation

Genomic analyses have identified segments with high fiber-forming propensity in many proteins not known to form amyloid. Proteins are often protected from entering the amyloid state by molecular chaperones that permit them to fold in isolation from identical molecules; but, how do proteins self-chaperone their folding in the absence of chaperones? Here, we explore this question with the stable protein ribonuclease A (RNase A). We previously identified fiber-forming segments of amyloid-related proteins and demonstrated that insertion of these segments into the C-terminal hinge loop of nonfiber-forming RNase A can convert RNase A into the amyloid state through three-dimensional domain-swapping, where the inserted fiber-forming segments interact to create a steric zipper spine. In this study, we convert RNase A into amyloid-like fibers by increasing the loop length and hence conformational freedom of an endogenous fiber-forming segment, SSTSAASS, in the N-terminal hinge loop. This is accomplished by sandwiching SSTSAASS between inserted Gly residues. With these inserts, SSTSAASS is now able to form the steric zipper spine, allowing RNase A to form amyloid-like fibers. We show that these fibers contain RNase A molecules retaining their enzymatic activity and therefore native-like structure. Thus, RNase A appears to prevent fiber formation by limiting the conformational freedom of this fiber-forming segment from entering a steric zipper. Our observations suggest that proteins have evolved to self-chaperone by using similar protective mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Preparation and comparison of bulk and membrane hydrogels based on Kraft- and ionic-liquid-isolated lignins

In this work, lignin obtained from two different sources, from the Kraft process (KF-lignin) and from dissolution of wood using ionic liquid (IL-lignin), was dissolved in alkaline solution and crosslinked with different methods, attempting to form bulk and membrane hydrogels. Without a chemical crosslinker, no physical lignin gels could be formed. When employing three different chemically crosslinking routes, epichlorohydrin (ECH), polyethylene glycol (PEG)/ECH, and epoxide-terminated PEG (ETPEG), only the third route produced “hydrogels” with excellent water absorbency. To form a hydrogel, lower IL-lignin concentration (15 wt%) was needed than for KF-lignin (20 wt%). Once air-dried, both of the dense lignin/ETPEG gels showed comparable high tensile strength, independent of the type of lignin. However, while in the wet state, the IL-lignin/ETPEG hydrogels were much stronger than those from KF-lignin, thus facilitating their preparation and utilization. High water uptake was observed for all lignin/ETPEG gels, although a smaller swelling was observed with IL-lignin gels. Additionally, water vapor transmission (WVT), antioxidant efficiency, and antimicrobial activity of the membranes were determined and these data suggest their potential application as food packaging or wound dressing materials, especially for the IL-lignin membranes considering their easier formation, higher WVT, antioxidant efficiency, and wet strength.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Shock-induced termination of reentrant cardiac arrhythmias: Comparing monophasic and biphasic shock protocols

In this article, we compare quantitatively the efficiency of three different protocols commonly used in commercial defibrillators. These are based on monophasic and both symmetric and asymmetric biphasic shocks. A numerical one–dimensional model of cardiac tissue using the bidomain formulation is used in order to test the different protocols. In particular, we performed a total of 4.8 × 10{sup 6} simulations by varying shock waveform, shock energy, initial conditions, and heterogeneity in internal electrical conductivity. Whenever the shock successfully removed the reentrant dynamics in the tissue, we classified the mechanism. The analysis of the numerical data shows that biphasic shocks are significantly more efficient (by about 25%) than the corresponding monophasic ones. We determine that the increase in efficiency of the biphasic shocks can be explained by the higher proportion of newly excited tissue through the mechanism of direct activation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut

Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating > 200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G–U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G–C base pairs (G3:C70 and G5:C68).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing

The Hop2–Mnd1 complex functions with the DMC1 recombinase in meiotic recombination. Hop2–Mnd1 stabilizes the DMC1-single-stranded DNA (ssDNA) filament and promotes the capture of the double stranded DNA partner by the recombinase filament to assemble the synaptic complex. Herein, we define the action mechanism of Hop2–Mnd1 in DMC1-mediated recombination. Small angle X-ray scattering analysis and electron microscopy reveal that the heterodimeric Hop2–Mnd1 is a V-shaped molecule. We show that the protein complex harbors three distinct DNA binding sites, and determine their functional relevance. Specifically, the N-terminal double-stranded DNA binding functions of Hop2 and Mnd1 co-operate to mediate synaptic complex assembly, whereas ssDNA binding by the Hop2 C-terminus helps stabilize the DMC1-ssDNA filament. A model of the Hop2-Mnd1-DMC1-ssDNA ensemble is proposed to explain how it mediates homologous DNA pairing in meiotic recombination.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

ELECTRON ACCELERATION IN PULSAR-WIND TERMINATION SHOCKS: AN APPLICATION TO THE CRAB NEBULA GAMMA-RAY FLARES

The γ -ray flares from the Crab Nebula observed by AGILE and Fermi -LAT reaching GeV energies and lasting several days challenge the standard models for particle acceleration in pulsar-wind nebulae because the radiating electrons have energies exceeding the classical radiation-reaction limit for synchrotron. Previous modeling has suggested that the synchrotron limit can be exceeded if the electrons experience electrostatic acceleration, but the resulting spectra do not agree very well with the data. As a result, there are still some important unanswered questions about the detailed particle acceleration and emission processes occurring during the flares. We revisit the problem using a new analytical approach based on an electron transport equation that includes terms describing electrostatic acceleration, stochastic wave-particle acceleration, shock acceleration, synchrotron losses, and particle escape. An exact solution is obtained for the electron distribution, which is used to compute the associated γ -ray synchrotron spectrum. We find that in our model the γ -ray flares are mainly powered by electrostatic acceleration, but the contributions from stochastic and shock acceleration play an important role in producing the observed spectral shapes. Our model can reproduce the spectra of all the Fermi -LAT and AGILE flares from the Crab Nebula, using magnetic field strengths in agreement with the multi-wavelength observational constraints. We also compute the spectrum and duration of the synchrotron afterglow created by the accelerated electrons, after they escape into the region on the downstream side of the pulsar-wind termination shock. The afterglow is expected to fade over a maximum period of about three weeks after the γ -ray flare.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Changes in the C-terminal, N-terminal, and histidine regions of amelogenin reveal the role of oligomer quaternary structure on adsorption and hydroxyapatite mineralization

Adsorption interactions between amelogenin and calcium phosphate minerals are believed to be important to amelogenin’s function in enamel formation, however, the role of specific amino acid residues and domains within the protein in controlling adsorption is not well known. We synthesized “mechanistic probes” by systematically removing charged regions of amelogenin in order to elucidate their roles. The probes included amelogenin without the charged residues in the N-terminus (SEKR), without two, three, or eight histidines (H) in the central protein region (H2, H3, H8), or without the C-terminal residues (Delta). In-situ atomic force microscopy (AFM) adsorption studies onto hydroxyapatite (HAP) single crystals confirmed that the C-terminus was the dominant domain in promoting adsorption. We propose that subtle changes in protein-protein interactions for proteins with histidines and N-terminal residues removed resulted in changes in the oligomer quaternary size and structure that also affected protein adsorption. HAP mineralization studies revealed that the oligomer-HAP binding energy and protein layer thickness were factors in controlling the amorphous calcium phosphate (ACP) to HAP induction time. Our studies with mechanistic probes reveal the importance of the oligomer quaternary structure in controlling amelogenin adsorption and HAP mineralization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

PLASMA NEAR THE HELIOSHEATH: OBSERVATIONS AND MODELING

Sound numerical modeling is capable of providing important predictive information about the solar wind interaction with the local interstellar medium. The results of our three-dimensional simulation show a good agreement with Voyager observations from 2007 to 2010. We analyze the termination shock properties at the Voyager crossing points and juxtapose them with the observed data. The heliospheric current sheet structure in the inner heliosheath is examined.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Enhancement to the conductivity of surface transfer-doped (111) diamond through thermochemical surface etching

The use of a transition metal catalyzed thermochemical etching method for improving the carrier transport properties of the near-surface two-dimensional (2D) hole gas in surface transfer-doped hydrogen-terminated (111) diamond is demonstrated. Using Ni 0.8 Cr 0.2 films deposited and annealed to a temperature of 900 °C, with up to three etch cycles, preferential (111) surface etching produces large terraces exceeding 10 μm in size with a surface microroughness, σ 2 RMS λ, that is two orders of magnitude lower than for the pre-etched (111) surface. Magnetotransport measurements on hydrogen-terminated Hall bars engineered on the pre- and post-etched surfaces and rendered conductive by the adsorbed water layer formed on exposure to ambient conditions demonstrate that this etching causes an improvement in the hole mobility by an order of magnitude, resulting in a measured sheet resistivity of 1.04 kΩ/sq at a temperature of 4.2 K without gating.

42 ENGINEERING↗
DOE OSTI2018

The Ups and Downs of Repeated Cleavage and Internal Fragment Production in Top-Down Proteomics

Analysis of whole proteins by mass spectrometry, or top-down proteomics, has several advantages over methods relying on proteolysis. For example, proteoforms can be unambiguously identified and examined. However, from a gas-phase ion-chemistry perspective, proteins are enormous molecules that present novel challenges relative to peptide analysis. Herein, the statistics of cleaving the peptide backbone multiple times are examined to evaluate the inherent propensity for generating internal versus terminal ions. The raw statistics reveal an inherent bias favoring production of terminal ions, which holds true regardless of protein size. Importantly, even if the full suite of internal ions is generated by statistical dissociation, terminal ions are predicted to account for at least 50% of the total ion current, regardless of protein size, if there are three backbone dissociations or fewer. Top-down analysis should therefore be a viable approach for examining proteins of significant size. Comparison of the purely statistical analysis with actual top-down data derived from ultraviolet photodissociation (UVPD) and higher-energy collisional dissociation (HCD) reveals that terminal ions account for much of the total ion current in both experiments. Terminal ion production is more favored in UVPD relative to HCD, which is likely due to differences in the mechanisms controlling fragmentation. Importantly, internal ions are not found to dominate from either the theoretical or experimental point of view. .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗