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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,135 records · Page 63
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structural basis of Gabija anti-phage defence and viral immune evasion

Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation. Gabija is one of the most prevalent anti-phage defence systems, occurring in more than 15% of all sequenced bacterial and archaeal genomes, but the molecular basis of how Gabija defends cells from viral infection remains poorly understood. Here we use X-ray crystallography and cryo-electron microscopy (cryo-EM) to define how Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA. Gabija protein A (GajA) is a DNA endonuclease that tetramerizes to form the core of the anti-phage defence complex. Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA–GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo. We show that a phage-encoded protein, Gabija anti-defence 1 (Gad1), directly binds to the Gabija GajAB complex and inactivates defence. A cryo-EM structure of the virally inhibited state shows that Gad1 forms an octameric web that encases the GajAB complex and inhibits DNA recognition and cleavage. Our results reveal the structural basis of assembly of the Gabija anti-phage defence complex and define a unique mechanism of viral immune evasion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structure-guided approach to modulate small molecule binding to a promiscuous ligand-activated protein

Ligand-binding promiscuity in detoxification systems protects the body from toxicological harm but is a roadblock to drug development due to the difficulty in optimizing small molecules to both retain target potency and avoid metabolic events. Immense effort is invested in evaluating metabolism of molecules to develop safer, more effective treatments, but engineering specificity into or out of promiscuous proteins and their ligands is a challenging task. To better understand the promiscuous nature of detoxification networks, we have used X-ray crystallography to characterize a structural feature of pregnane X receptor (PXR), a nuclear receptor that is activated by diverse molecules (with different structures and sizes) to up-regulate transcription of drug metabolism genes. We found that large ligands expand PXR’s ligand-binding pocket, and the ligand-induced expansion occurs through a specific unfavorable compound-protein clash that likely contributes to reduced binding affinity. Removing the clash by compound modification resulted in more favorable binding modes with significantly enhanced binding affinity. We then engineered the unfavorable ligand-protein clash into a potent, small PXR ligand, resulting in marked reduction in PXR binding and activation. Structural analysis showed that PXR is remodeled, and the modified ligands reposition in the binding pocket to avoid clashes, but the conformational changes result in less favorable binding modes. Thus, ligand-induced binding pocket expansion increases ligand-binding potential of PXR but is an unfavorable event; therefore, drug candidates can be engineered to expand PXR’s ligand-binding pocket and reduce their safety liability due to PXR binding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection

Broadly neutralizing antibodies (bnAbs) to coronaviruses (CoVs) are valuable in their own right as prophylactic and therapeutic reagents to treat diverse CoVs and as templates for rational pan-CoV vaccine design. We recently described a bnAb, CC40.8, from a CoV disease 2019 (COVID-19) convalescent donor that exhibits broad reactivity with human β-CoVs. Here, we showed that CC40.8 targets the conserved S2 stem helix region of the CoV spike fusion machinery. We determined a crystal structure of CC40.8 Fab with a SARS-CoV-2 S2 stem peptide at 1.6-Å resolution and found that the peptide adopted a mainly helical structure. Conserved residues in β-CoVs interacted with CC40.8 antibody, thereby providing a molecular basis for its broad reactivity. CC40.8 exhibited in vivo protective efficacy against SARS-CoV-2 challenge in two animal models. In both models, CC40.8-treated animals exhibited less weight loss and reduced lung viral titers compared to controls. Furthermore, we noted that CC40.8-like bnAbs are relatively rare in human COVID-19 infection, and therefore, their elicitation may require rational structure-based vaccine design strategies. Overall, our study describes a target on β-CoV spike proteins for protective antibodies that may facilitate the development of pan–β-CoV vaccines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

When Do Band Gap Calculations Agree with Experiments in Monolayer-Protected Cu 14 and Au 20 Atomically Precise Nanoclusters? A (TD)-DFT Comparison of HOMO–LUMO, Fundamental, Optical, and Electrochemical Energy Gaps

In view of the tremendous progress in atomically precise metal nanoclusters where electrochemical and optical energetics are routinely supported by computations to establish structure−function correlations, we explore the relationship between different protocols for measuring and computing band gaps of two distinct organic ligand-protected nanoclusters: [Cu 14 H 10 (MBN) 3 (PPh 3 ) 8 ] + and Au 20 (TBBT) 16 . Through UV/visible spectroscopy and differential pulse voltammetry, we measure optical and electrochemical band gaps in those systems. We then compare these experimentally determined gaps to HOMO−LUMO gaps, fundamental gaps, vertical excitation energies, and E o ox − E o red potentials computed using different density functional theory (DFT) or time-dependent DFT (TDDFT) methods. Specifically, in both copper and gold nanoclusters, we test the effect of truncating inert ligands from the model and compare density functionals with varying degrees of Hartree−Fock (HF) exchange from 0 to 50%, range-separated hybrids with a varying long-range tuning parameter, different correlation functionals, basis sets, and (equilibrium and nonequilibrium) continuum solvation models. Despite having different frontier orbital characters (the copper nanocluster has a metal-to-ligand charge transfer character while the gold nanocluster has metal-centered frontier orbitals), both nanoclusters display a similar sensitivity of the HOMO−LUMO gap to the HF exchange that is partially mitigated when computing the fundamental, optical, and electrochemical gaps. Other factors, such as the nature of the correlation functional, basis set, and geometry relaxation, have a considerably smaller effect on computed band gaps in these systems. Overall, this work provides guidelines for factors of varied importance for correlating computed and experimental band gap values.

Chemical calculations↗
DOE OSTI2026

EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks

Exonuclease/endonuclease/phosphatase (EEP)-fold hydrolases are canonically monomeric phosphodiesterases exemplified by APE1, DNase I, and TDP2 nucleases. While EEP family domain containing protein 1 (EEPD1) acts in DNA stress responses, its proposed nuclease activities are enigmatic. Here, we integrate hybrid structural methods, evolution, biochemistry, cancer genomics, plus molecular and cell biology to define EEPD1 structure, assembly, and function at stalled DNA replication forks. Results imply EEPD1 surprisingly requires both unique EEP domain dimer and distinctive tandem Helix-hairpin-Helix [(HhH) 2 ] domains to clamp double-stranded (ds) DNA at reversed DNA replication forks for fork protection. Small-angle X-ray Scattering (SAXS), crystal, and cryo-EM structures unveil an unprecedented tryptophan handshake dimer, conserved interface di-Trp-Pro pocket, and adjustable “wrist” enabling an open-closed conformational switch. EEPD1 dimer cooperatively binds complex dsDNA replication fork intermediates but alone lacks nuclease activity due to loss of key EEP catalytic residues during Metazoan evolution and atmospheric oxygen buildup. Instead, EEPD1 prevents nucleolytic degradation of reversed replication forks by MRE11. Furthermore, cancer bioinformatics support oxidative damage-dependent EEPD1 association as a significant modulator of overall patient survival. Collective findings uncover unexpected EEP dimer and fork protection function in clamping, not cleaving, reversed replication forks for metazoan oxidative stress responses controlling genome stability and cancer outcomes.

Shen, Runze [Univ. of Texas, Houston, TX (United S↗
DOE OSTI2021

The unique Phe–His dyad of 2-ketopropyl coenzyme M oxidoreductase/carboxylase selectively promotes carboxylation and S–C bond cleavage

The 2-ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC) enzyme is the only member of the disulfide oxidoreductase (DSOR) family of enzymes, which are important for reductively cleaving S–S bonds, to have carboxylation activity. 2-KPCC catalyzes the conversion of 2-ketopropyl-coenzyme M to acetoacetate, which is used as a carbon source, in a controlled reaction to exclude protons. A conserved His–Glu motif present in DSORs is key in the protonation step; however, in 2-KPCC, the dyad is substituted by Phe–His. Here, we propose that this difference is important for coupling carboxylation with C–S bond cleavage. We substituted the Phe–His dyad in 2-KPCC to be more DSOR like, replacing the phenylalanine with histidine (F501H) and the histidine with glutamate (H506E), and solved crystal structures of F501H and the double variant F501H_H506E. We found that F501 protects the enolacetone intermediate from protons and that the F501H variant strongly promotes protonation. We also provided evidence for the involvement of the H506 residue in stabilizing the developing charge during the formation of acetoacetate, which acts as a product inhibitor in the WT but not the H506E variant enzymes. Finally, we determined that the F501H substitution promotes a DSOR-like charge transfer interaction with flavin adenine dinucleotide, eliminating the need for cysteine as an internal base. Taken together, these results indicate that the 2-KPCC dyad is responsible for selectively promoting carboxylation and inhibiting protonation in the formation of acetoacetate.

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

Spin splitting of dopant edge state in magnetic zigzag graphene nanoribbons

Spin-ordered electronic states in hydrogen-terminated zigzag nanographene give rise to magnetic quantum phenomena that have sparked renewed interest in carbon-based spintronics. Zigzag graphene nanoribbons (ZGNRs)-quasi one-dimensional semiconducting strips of graphene bounded by parallel zigzag edges-host intrinsic electronic edge states that are ferromagnetically ordered along the edges of the ribbon and antiferromagnetically coupled across its width. Despite recent advances in the bottom-up synthesis of GNRs featuring symmetry protected topological phases and even metallic zero mode bands, the unique magnetic edge structure of ZGNRs has long been obscured from direct observation by a strong hybridization of the zigzag edge states with the surface states of the underlying support. Here, we present a general technique to thermodynamically stabilize and electronically decouple the highly reactive spin-polarized edge states by introducing a superlattice of substitutional N-atom dopants along the edges of a ZGNR. First-principles GW calculations and scanning tunnelling spectroscopy reveal a giant spin splitting of low-lying nitrogen lone-pair flat bands by an exchange field (~850 tesla) induced by the ferromagnetically ordered edge states of ZGNRs. Finally, our findings directly corroborate the nature of the predicted emergent magnetic order in ZGNRs and provide a robust platform for their exploration and functional integration into nanoscale sensing and logic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Evidence of Au(111) topological states in a kagome analogue lattice and their robustness beyond ultra-low temperatures and defect-free conditions

The experimental realization of kagome lattices that exhibit the predicted coexistence of topological states with high electron kinetics and non-dispersing quantum states remains challenging. Additionally, the robustness of these states against structural perturbations has rarely been explored. Here, we report on the formation of an analogue kagome structure via the electrostatic self-assembly of 4,7-dibromobenzo[c]-1,2,5-thiadiazole (2Br-BTD) molecules on Au(111). Local spectroscopic measurements, supported by theoretical calculations, reveal that the weak molecular coupling reshapes the topological-induced Shockley surface state of Au(111) by imposing a (7 × 7) periodicity, resulting in new band crossings. The molecular overlayer favours the opening of electron gaps at these positions manifested as sharp peaks in dI/dV spectra and electron localization in either the hexagonal or triangular sublattices of the kagome structure. To explore the robustness of these topological states, we monitored their stability under varied conditions, including different temperatures, the unaltered herringbone reconstruction of the Au(111) surface and local structural relaxation of the molecular assembly. These results demonstrate the degree of topological protection of these states, which holds potential for fundamental and applied research.

Austin, Dave [University of Central Florida, Orlan↗
DOE OSTI2021

Understanding the interaction between carboxylates and coinage metals from first principles

Carboxylate groups have recently been explored as a new type of ligand to protect superatomic copper and silver nanoclusters, but little is known of the interfacial structure and bonding. Here, we employ density functional theory to investigate the interfaces of a model carboxylate group, CH3COO, on the coinage metal surfaces and clusters. We found that μ2-CH3COO is the most preferred binding mode on the three M(111) surfaces (M = Cu, Ag, and Au), while μ3-CH3COO is also stable on Cu(111) and Ag(111). The saturation coverage was found to be about seven CH3COO groups per nm2 for all surfaces. CH3COO has the strongest binding on Cu and weakest on Au. Moving from the flat surfaces to the icosahedral M13 clusters, we found that the eight-electron superatomic [M13(CH3COO)6]− nanoclusters also prefer the μ2-CH3COO mode on the surface. The icosahedral kernel in [Cu13(CH3COO)6]− and [Ag13(CH3COO)6]− was well maintained after geometry optimization, but a larger deformation was found in [Au13(CH3COO)6]−. Given the broad availability and variety of carboxylic acids including amino acids, our work suggests that carboxylate groups could be the next-generation ligands to further expand the universe of atomically precise metal clusters, especially for Cu and Ag.

Liu, Tongyu↗
DOE OSTI2022

Bifurcation Buckling Analysis and Non-Linear Collapse Analysis of Teardrop Shaped Vacuum Chamber

The Spallation Neutron Source (SNS) accelerator is being upgraded to increase the beam power from 1.4MW at 1GeV to 2.8MW at 1.3GeV. The currents in the middle two injection chicane magnets cannot simply be scaled up to accommodate the increased injection energy of 1.3GeV due to potential excessive H- stripping; the magnets must be replaced with longer, lower-field magnets and the associated vacuum chambers need to be redesigned. A new teardrop-shaped vacuum chamber was initially designed to accommodate the new magnets and the updated beam paths and instrumentation. This paper focuses on the structural stability study of the teardrop shape vacuum chamber based on buckling analysis. Protection against collapse from buckling according to the ASME BPVC requirement has been evaluated in depth. First, a Type-1 bifurcation buckling analysis using a linear eigenvalue solution to determine the critical load factor was performed. Subsequently, a Type-3 nonlinear collapse analysis was conducted using the static Riks method with elastic-plastic material properties and imperfections explicitly considered in the model geometry. The critical buckling load for the teardrop shape vacuum chamber was confidently estimated based upon this two-stage approach.

Jiang, Hao↗
DOE OSTI2023

Improved Biofuel Production through Discovery and Engineering of Terpene Metabolism in Switchgrass

Project Objectives - Of the myriad specialized metabolites that plants deploy to adapt to environmental challenges, terpenes form the largest group. In many major crops, unique terpene blends serve as key stress defenses that directly impact plant fitness and yield. In addition, terpenes, such as bisabolene and pinene, are used for producing renewable biofuels. Essential to advancing a broader use of terpenes for biofuel feedstock engineering is a system-wide knowledge of the diverse biosynthetic machinery and defensive potential of often species-specific terpene blends. The proposed project would merge genome-wide enzyme discovery with comparative –omics, protein structural and plant microbiome studies to define the biosynthesis and stress-defensive functions of the switchgrass (Panicum virgatum) terpene network. These insights would be combined with developing and applying non-transgenic genome editing tools to design plants with desirable terpene blends for higher productivity and biofuel production on marginal lands. As a dedicated lignocellulosic feedstock for U.S. biofuel production with high net energy yield, stress tolerance, and available genome resources, switchgrass is well-suited for devising new avenues for biofuel production. Project Description – The diversity of plant terpene defenses is governed by species-specific families of terpene synthase (TPS) and cytochrome P450 monooxygenase (P450) enzymes. Mining of the switchgrass genome (genotype Alamo) identified ~100 TPS and P450 candidate genes, and combinatorial biochemical analysis of synthesized TPSs and P450s revealed more than a dozen enzymes with common and novel activities. In addition, several identified terpene metabolites and the corresponding transcripts were up-regulated in response to abiotic stressors. These findings demonstrate a unique switchgrass terpene network with probable importance to abiotic stress tolerance, thus providing a large chemical portfolio for optimizing crop resistance, yield, and biofuel composition. Leveraging these preliminary data, we propose to generate a genome-wide map of the switchgrass terpene metabolic network through multi-gene co-expression analyses that allow the efficient cross-validation of TPS and P450 functions. Key enzymes would further be applied to structure-function studies via X-ray protein crystallography, homology modeling and site-directed mutagenesis to gain mechanistic insight into the catalytic specificity of switchgrass terpene metabolism and provide gene and amino acid targets for genome editing. In tandem with terpene pathway discovery, system-wide metabolomics, transcriptomics and proteomics studies in switchgrass accessions of contrasting drought tolerance would define the role of switchgrass terpene metabolism in conferring abiotic stress resilience. Metabolic changes would be assessed in a combined approach of targeted (terpenes) and untargeted metabolite profiling using a high-resolution LC-MS/MS approach, differential gene expression analyses through multiplexed Illumina RNA sequencing, and quantitative analysis of high-priority pathway enzymes using multiple reaction monitoring (MRM). Drawing on these insights, knock-down/out mutants of stress-associated pathway nodes would be generated by optimizing transient virus-induced gene silencing (VIGS) and CRISPR/Cas9 systems under control of the Tobacco Rattle Virus (TRV). The resulting mutant lines would then be analyzed for stress susceptibility and the impact on the root microbiome to define gene functions in planta. Knowledge of terpene pathways, enzyme mechanisms and bioactivities would be applied to enhance switchgrass stress resilience and to tailor-make terpene blends for biofuel production. Here, TRV-enabled CRISPR/Cas9 genome editing, including allele-specific knock-out of redundant genes, engineering of enzyme specificity via structure-guided point mutations, and overexpression of terpene genes relevant to stress-protection or biofuel production, would be used to increase metabolic flux toward desired pathways. Broader Impacts - Integrating the system-wide discovery, mechanistic analysis and non-transgenic genome engineering of the switchgrass terpene network aligns the required steps to unlock the chemical potential of this important metabolite class to generate crops that are more resistant to stress and provide advanced biofuel production in light of rising climate pressures as foreseeable challenges for bioenergy crop cultivation. The proposed project would further offer interdisciplinary student training through active involvement in the project and integration of research concepts and outcomes into newly-developed graduate and undergraduate courses on Plant Biotechnology.

09 BIOMASS FUELS↗
NASA NTRS1975

The effects of lightning on digital flight control systems

Present practices in lightning protection of aircraft deal primarily with the direct effects of lightning, such as structural damage and ignition of fuel vapors. There is increasing evidence of troublesome electromagnetic effects, however, in aircraft employing solid-state microelectronics in critical navigation, instrumentation and control functions. The potential impact of these indirect effects on critical systems such as digital fly-by-wire (DFBW) flight controls has been studied by several recent research programs, including an experimental study of lightning-induced voltages in the NASA F8 DFBW airplane. The results indicate a need for positive steps to be taken during the design of future fly-by-wire systems to minimize the possibility of hazardous effects from lightning.

Plumer, J. A.↗
NASA NTRS1976

The effects of lightning on digital flight control systems

Present practices in lightning protection of aircraft deal primarily with the direct effects of lightning, such as structural damage and ignition of fuel vapors. There is increasing evidence of troublesome electromagnetic effects, however, in aircraft employing solid-state microelectronics in critical navigation, instrumentation and control functions. The potential impact of these indirect effects on critical systems such as digital fly by wire (DFBW) flight controls was studied. The results indicate a need for positive steps to be taken during the design of future fly by wire systems to minimize the possibility of hazardous effects from lightning.

Plumer, J. A.↗
NASA NTRS1982

Tool Preloads Screw and Applies Locknut

Special tool reaches through structural members inside Space Shuttle fasten nut on preloaded screw that holds thermal protection tile against outside skin of vehicle. Tool attaches tiles with accuratelycontrolled tensile loading.

Wood, K. E.↗
NASA NTRS1985

Material interactions with the low earth orbital environment Accurate reaction rate measurements

Interactions between spacecraft surfaces and atomic oxygen within the low earth orbital (LEO) environment have been observed and measured during Space Shuttle flights over the past 3 yr. The results of these experiments have demonstrated that interaction rates for many materials proposed for spacecraft applications are high and that protective coatings must be developed to enable long-lived operation of spacecraft structures in the LEO environment. A flight experiment discussed herein uses the Space Shuttle as an orbiting exposure laboratory to obtain accurate reaction rate measurements for materials typically used in spacecraft construction. An ion-neutral mass spectrometer, installed in the Orbiter cargo bay, will measure diurnal ambient oxygen densities while material samples are exposed at low altitude (222 km) to the orbital environment. From in situ atomic oxygen density information and postflight material recession measurements, accurate reaction rates can be derived to update the Space Station materials interaction data base. Additionally, gases evolved from a limited number of material surfaces subjected to direct oxygen impingement will be identified using the mass spectrometer. These measurements will aid in mechanistic definitions of chemical reactions which cause atom-surface interactions and in validating results of upcoming degradation studies conducted in ground-based neutral beam laboratories.

Visentine, J. T.↗
NASA NTRS1987

Thermally Insulating Support for Cryogenic Tanks

Passive alternate-load-path support scheme keeps weight low while conserving cryogenic liquid. Method of supporting inner vessel of large Dewar container minimizes heat conductance and weight but ensures high strength and impact resistance. Accommodates thermal expansion and contraction of vessel while introducing minimal stresses in structure. Inner vessel hangs from struts in outer vessel. Thin wall graphite/epoxy tube protected from high loads by close tolerance stops.

Parmley, Richard T.↗
NASA NTRS1989

Views on the impact of HOST

The Hot Section Technology (HOST) Project, which was initiated by NASA Lewis Research Center in 1980 and concluded in 1987, was aimed at improving advanced aircraft engine hot section durability through better technical understanding and more accurate design analysis capability. The project was a multidisciplinary, multiorganizational, focused research effort that involved 21 organizations and 70 research and technology activities and generated approximately 250 research reports. No major hardware was developed. To evaluate whether HOST had a significant impact on the overall aircraft engine industry in the development of new engines, interviews were conducted with 41 participants in the project to obtain their views. The summarized results of these interviews are presented. Emphasis is placed on results relative to three-dimensional inelastic structural analysis, thermomechanical fatigue testing, constitutive modeling, combustor aerothermal modeling, turbine heat transfer, protective coatings, computer codes, improved engine design capability, reduced engine development costs, and the impacts on technology transfer and the industry-government partnership.

J B Esgar↗
NASA NTRS1990

Self-Aligning Coupler

Joint reduces assembly time and eliminates fumbling. Self-aligning coupler easy to use for people wearing heavy gloves or other restrictive clothing. Consists of two threaded sections, one with blade, other with slot - joined by threaded collar. Blade fits precisely in slot. Notch in blade engages pin in slot to form temporary attachment. Collar turned on continuous thread of joined sections to form tight, rigid joint. Designed for assembly of structures by astronauts in space suits, coupler used on Earth by firefighters wearing protective garments, technicians handling hazardous materials, and others working underwater or in other difficult environments.

Cooney, Earl T.↗