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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

A Bayesian desmearing algorithm for Bonse–Hart USANS with anisotropic scattering

Ultra-small-angle neutron scattering (USANS) using Bonse–Hart optics provides micrometer-scale structural insights but suffers from severe slit-geometry smearing. While well-established for isotropic systems, quantitative desmearing of anisotropic data remains a challenge because conventional corrections break down for non-radial scattering. In this work, we address this by developing a resolution-aware Bayesian framework that explicitly incorporates anisotropy via an affine deformation to the scattering pattern, guided by the principle of parsimony. This results in orientation-resolved point-spread functions that enable a self-consistent determination of both the resolution and deformation parameters. Using Gaussian process regression with uncertainty quantification and a probabilistic correction for multiple scattering, we demonstrate the framework’s effectiveness through numerical benchmarks and experimental studies of a stretched polymer melt. Our approach enables the seamless integration of SANS and USANS data, facilitating quantitative structural analysis of deformed materials at nanometer to micrometer scales.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Enhanced coercivity in Fe5C2/SiO2 core/shell nanocrystals

Rod-shaped Fe5C2 and core/shell Fe5C2/SiO2 nanocrystals were synthesized via a solution-based chemical method. Structural analysis confirmed the monoclinic phase of Fe5C2 with space group C2/c. Zero-field-cooling (ZFC) and field-cooling (FC) magnetization curves revealed distinct magnetic behaviors: uncoated Fe5C2 exhibited a low-temperature FC plateau indicative of strong dipolar interactions, while Fe5C2/SiO2 showed a monotonic increase in FC magnetization, suggesting reduced dipolar interactions due to SiO2 surface passivation. Isothermal remanent magnetization (IRM) and DC demagnetization (DCD) measurements supported this trend, with δM plots confirming weaker dipolar interactions in the coated sample. Bloch’s law fitting of temperature-dependent saturation magnetization showed a smaller Bloch’s constant for pure Fe5C2 and a larger value for Fe5C2/SiO2, reflecting enhanced surface disorder and reduced exchange coupling in the latter. Notably, Fe5C2/SiO2 demonstrated increased coercivity, attributed to decreased dipolar interaction and elevated surface anisotropy. Kneller’s law fitting yielded higher blocking temperatures for Fe5C2 (476 K) than Fe5C2/SiO2 (456 K), highlighting the impact of dipolar interactions on magnetic relaxation. These findings illustrate how SiO2 coatings effectively modulate dipolar interactions and enhance coercivity in Fe5C2 nanocrystals.

Joshi, Pramanand [Department of Physics, Universit↗
DOE OSTI2020

Direct functionalization of C-H bonds by electrophilic anions

Bond formation between two of the most inert molecules, alkanes and [B12X12]2- (X = Cl, Br), is performed in a two step process. Fragmentation of [B12X12]2- in the gas phase generates highly reactive [B12X11]- ions which spontaneously react with alkanes. The reaction mechanism was investigated using tandem mass spectrometry and gas-phase vibrational spectroscopy combined with electronic structure calculations. This effort revealed the unprecedented and counterintuitive electrophilic substitution of a proton in an alkane by a negatively charged ion resulting in a B-C bond formation. The product is a dianionic [B12X11CnH2n+1]2- species, in which H+ is electrostatically bound to the dianion. High flux ion soft-landing was performed to co-deposit [B12X11]- and complex organic molecules (phthalates) in thin layers on surfaces. Molecular structure analysis of the product films revealed that C-H functionalization by [B12X11]- occured in the presence of other more reactive functional groups. This observation demonstrates the utility of highly reactive fragment ions for defined bond formation processes and may pave the way to the use of gas phase ion chemistry for chemical synthesis in the condensed phase.

Warneke, Jonas↗
DOE OSTI2022

ENPP1’s regulation of extracellular cGAMP is a ubiquitous mechanism of attenuating STING signaling

The metazoan innate immune second messenger 2'3'-cGAMP is present both inside and outside cells. However, only extracellular cGAMP can be negatively regulated by the extracellular hydrolase ENPP1. Here, we determine whether ENPP1’s regulation of extracellular cGAMP is a ubiquitous mechanism of attenuating stimulator of interferon genes (STING) signaling. We identified ENPP1 H362A , a point mutation that cannot degrade the 2'-5' linkage in cGAMP while maintaining otherwise normal function. The selectivity of this histidine is conserved down to bacterial nucleotide pyrophosphatase/phosphodiesterase (NPP), allowing structural analysis and suggesting an unexplored ancient history of 2'-5' cyclic dinucleotides. Enpp1 H362A mice demonstrated that extracellular cGAMP is not responsible for the devastating phenotype in ENPP1-null humans and mice but is responsible for antiviral immunity and systemic inflammation. Our data define extracellular cGAMP as a pivotal STING activator, identify an evolutionarily critical role for ENPP1 in regulating inflammation, and suggest a therapeutic strategy for viral and inflammatory conditions by manipulating ENPP1 activity.

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 OSTI2025

Blocking C-terminal processing of KRAS4b via a direct covalent attack on the CaaX-box cysteine

RAS is the most frequently mutated oncogene in cancer. RAS proteins show high sequence similarities in their G-domains but are significantly different in their C-terminal hypervariable regions (HVR). These regions interact with the cell membrane via lipid anchors that result from posttranslational modifications (PTM) of cysteine residues. KRAS4b is unique as it has only one cysteine that undergoes PTM, C185. Small molecule covalent modification of C185 would block any form of prenylation and subsequently inhibit attachment of KRAS4b to the cell membrane, blocking its biological activity. We translated this concept to the discovery and development of disulfide tethering screen hits into irreversible covalent modifiers of C185. These compounds inhibited proliferation of KRAS4b-driven mouse embryonic fibroblasts, but not cells driven by N-myristoylated KRAS4b that harbor a C185S mutation and are not dependent on C185 prenylation. Top–down proteomics was used to confirm target engagement in cells. These compounds bind in a pocket formed when the HVR folds back between helix 3 and 4 in the G-domain (HVR-α3-α4). This interaction can happen in the absence of small molecules as predicted by molecular dynamics simulations and is stabilized in the presence of C185 binders as confirmed by small-angle X-ray scattering and solution NMR. NOESY-HSQC, an NMR approach that measures internuclear distances of 6 Å or less, and structure analysis identified the critical residues and interactions that define the HVR-α3-α4 pocket. Further development of compounds that bind to this pocket could be the basis of a new approach to targeting KRAS cancers.

C185↗
DOE OSTI2024

Mechanism-guided engineering of a minimal biological particle for genome editing

The widespread application of genome editing to treat and cure disease requires the delivery of genome editors into the nucleus of target cells. Enveloped delivery vehicles (EDVs) are engineered virally derived particles capable of packaging and delivering CRISPR-Cas9 ribonucleoproteins (RNPs). However, the presence of lentiviral genome encapsulation and replication proteins in EDVs has obscured the underlying delivery mechanism and precluded particle optimization. Here, we show that Cas9 RNP nuclear delivery is independent of the native lentiviral capsid structure. Instead, EDV-mediated genome editing activity corresponds directly to the number of nuclear localization sequences on the Cas9 enzyme. EDV structural analysis using cryo-electron tomography and small molecule inhibitors guided the removal of ~80% of viral residues, creating a minimal EDV (miniEDV) that retains full RNP delivery capability. MiniEDVs are 25% smaller yet package equivalent amounts of Cas9 RNPs relative to the original EDVs and demonstrated increased editing in cell lines and therapeutically relevant primary human T cells. These results show that virally derived particles can be streamlined to create efficacious genome editing delivery vehicles with simpler production and manufacturing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Engineering a protease-stable, oral single-domain antibody to inhibit IL-23 signaling

Interleukin (IL)-23 is a validated therapeutic target in inflammatory bowel disease. While antibodies targeting IL23 demonstrate clinical efficacy, they face challenges such as high costs, safety risks, and the necessity of parenteral administration. Here, we present a workflow to simultaneously enhance the affinity and protease stability of an inhibitory anti-IL23R VHH for oral use. Cocrystal structure analysis reveals that the anti-IL23R VHH employs both CDR and framework residues to achieve picomolar affinity for IL23R. The engineered VHH remains stable for over 8 h in intestinal fluid and 24 h in fecal samples. Oral administration of this VHH achieves deep pathway inhibition in a murine colitis model. Furthermore, a single pill provides sustained IL23R inhibition in nonhuman primate blood for over 24 h. With high potency, gut stability, high production yield, and favorable drug-like properties, oral VHHs offer a promising approach for inflammatory bowel diseases.

Science & Technology - Other Topics↗
DOE OSTI2020

Mutations in penicillin-binding protein 2 from cephalosporin-resistant Neisseria gonorrhoeae hinder ceftriaxone acylation by restricting protein dynamics

The global incidence of the sexually transmitted disease gonorrhea is expected to rise due to the spread of Neisseria gonorrhoeae strains with decreased susceptibility to extended-spectrum cephalosporins (ESCs). ESC resistance is conferred by mosaic variants of penicillin-binding protein 2 (PBP2) that have diminished capacity to form acylated adducts with cephalosporins. To elucidate the molecular mechanisms of ESC resistance, we conducted a biochemical and high-resolution structural analysis of PBP2 variants derived from the decreased-susceptibility N. gonorrhoeae strain 35/02 and ESC-resistant strain H041. Our data reveal that mutations both lower affinity of PBP2 for ceftriaxone and restrict conformational changes that normally accompany acylation. Specifically, we observe that a G545S substitution hinders rotation of the β3 strand necessary to form the oxyanion hole for acylation and also traps ceftriaxone in a noncanonical configuration. In addition, F504L and N512Y substitutions appear to prevent bending of the β3–β4 loop that is required to contact the R1 group of ceftriaxone in the active site. Other mutations also appear to act by reducing flexibility in the protein. Overall, our findings reveal that restriction of protein dynamics in PBP2 underpins the ESC resistance of N. gonorrhoeae.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Csx3 is a cyclic oligonucleotide phosphodiesterase associated with type III CRISPR–Cas that degrades the second messenger cA 4

Cas10 is the signature gene for type III CRISPR–Cas surveillance complexes. Unlike type I and type II systems, type III systems do not require a protospacer adjacent motif and target nascent RNA associated with transcriptionally active DNA. Further, target RNA recognition activates the cyclase domain of Cas10, resulting in the synthesis of cyclic oligoadenylate second messengers. These second messengers are recognized by ancillary Cas proteins harboring CRISPR-associated Rossmann fold (CARF) domains and regulate the activities of these proteins in response to invading nucleic acid. Csx3 is a distant member of the CARF domain superfamily previously characterized as a Mn 2+ -dependent deadenylation exoribonuclease. However, its specific role in CRISPR–Cas defense remains to be determined. Here we show that Csx3 is strongly associated with type III systems and that Csx3 binds cyclic tetra-adenylate (cA 4 ) second messenger with high affinity. Further, Csx3 harbors cyclic oligonucleotide phosphodiesterase activity that quickly degrades this cA 4 signal. In addition, structural analysis identifies core elements that define the CARF domain fold, and the mechanistic basis for ring nuclease activity is discussed. Overall, the work suggests that Csx3 functions within CRISPR–Cas as a counterbalance to Cas10 to regulate the duration and amplitude of the cA 4 signal, providing an off ramp from the programmed cell death pathway in cells that successfully cure viral infection.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Comparison of human poly-N-acetyl-lactosamine synthase structure with GT-A fold glycosyltransferases supports a modular assembly of catalytic subsites

Poly-N-acetyl-lactosamine (poly-LacNAc) structures are composed of repeating [-Galβ(1,4)-GlcNAcβ(1,3)-]n glycan extensions. They are found on both N- and O-glycoproteins and glycolipids and play an important role in development, immune function, and human disease. The majority of mammalian poly-LacNAc is synthesized by the alternating iterative action of β1,3-N-acetylglucosaminyltransferase 2 (B3GNT2) and β1,4-galactosyltransferases. B3GNT2 is in the largest mammalian glycosyltransferase family, GT31, but little is known about the structure, substrate recognition, or catalysis by family members. Here we report the structures of human B3GNT2 in complex with UDP:Mg 2+ and in complex with both UDP:Mg 2+ and a glycan acceptor, lacto-N-neotetraose. The B3GNT2 structure conserves the GT-A fold and the DxD motif that coordinates a Mg 2+ ion for binding the UDP-GlcNAc sugar donor. The acceptor complex shows interactions with only the terminal Galβ(1,4)-GlcNAcβ(1,3)- disaccharide unit, which likely explains the specificity for both N- and O-glycan acceptors. Modeling of the UDP-GlcNAc donor supports a direct displacement inverting catalytic mechanism. Comparative structural analysis indicates that nucleotide sugar donors for GT-A fold glycosyltransferases bind in similar positions and conformations without conserving interacting residues, even for enzymes that use the same donor substrate. In contrast, the B3GNT2 acceptor binding site is consistent with prior models suggesting that the evolution of acceptor specificity involves loops inserted into the stable GT-A fold. These observations support the hypothesis that GT-A fold glycosyltransferases employ coevolving donor, acceptor, and catalytic subsite modules as templates to achieve the complex diversity of glycan linkages in biological systems.

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

Broad and potent neutralizing human antibodies to tick-borne flaviviruses protect mice from disease

Tick-borne encephalitis virus (TBEV) is an emerging human pathogen that causes potentially fatal disease with no specific treatment. Mouse monoclonal antibodies are protective against TBEV, but little is known about the human antibody response to infection. Here, we report on the human neutralizing antibody response to TBEV in a cohort of infected and vaccinated individuals. Expanded clones of memory B cells expressed closely related anti-envelope domain III (EDIII) antibodies in both groups of volunteers. However, the most potent neutralizing antibodies, with IC50s below 1 ng/ml, were found only in individuals who recovered from natural infection. These antibodies also neutralized other tick-borne flaviviruses, including Langat, louping ill, Omsk hemorrhagic fever, Kyasanur forest disease, and Powassan viruses. Structural analysis revealed a conserved epitope near the lateral ridge of EDIII adjoining the EDI–EDIII hinge region. Prophylactic or early therapeutic antibody administration was effective at low doses in mice that were lethally infected with TBEV.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Observation of a new pedestal stability regime in MAST Upgrade H-mode plasmas

Abstract The first pedestal stability and structure analysis on the new MAST Upgrade (MAST-U) spherical tokamak H-mode plasmas is presented. Our results indicate that MAST-U pedestals are close to the low toroidal mode number ( n ) peeling branch of the peeling-ballooning instability, in contrast with MAST H-mode pedestals which were deeply in the high- n ballooning branch. This offers the possibility of reaching the ELM-free quiescent H-mode (Burrell et al 2005 Plasma Phys. Control. Fusion 47 B37–B52) or high-performance super H-mode (Snyder et al 2015 Nucl. Fusion 55 083026; Snyder et al 2019 Nucl. Fusion 59 086017) regimes. In addition, the coupling between the peeling and ballooning branches is weak in MAST-U, suggesting that a path to very high pedestal pressure gradient at high density may exist with sufficient heating power. A possible explanation for the differences between MAST and MAST-U pedestal stability is given in terms of plasma shaping parameters, in particular squareness and elongation, as well as the pedestal top temperature and collisionality.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Structural Characteristics and Phase Evolution of Calcium-Reduced (Sm,Zr)(Fe,Co,Ti) 12 Particles

Magnetic materials are essential for applications in electronics, energy conversion and many other industrial and technological sectors. Among the permanent magnets, rare-earth magnets exhibit the strongest properties and dominate the market shares in related applications. However, due to the increasing cost and unstable supply, the research on reducing the rare-earth elements in magnets attracts significant increasing interest. Rare-earth-lean samarium transition metal (TM) compounds (SmTM 12 or 1:12 for short) have made breakthroughs in 2020 and the (Sm,Zr)(Fe,Co,Ti) 12 monocrystalline particles synthesized by a Ca reduction of elemental oxides at high temperature demonstrated an order of magnitude improvement in coercivity at room temperature. In this study, we made structural analysis of (Sm,Zr)(Fe,Co,Ti) 12 particles to elucidate the impact of synthesis conditions, microstructure and phase transformation on the evolution of magnetic properties.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1

UHRF1 is an important epigenetic regulator associated with apoptosis and tumour development. It is a multidomain protein that integrates readout of different histone modification states and DNA methylation with enzymatic histone ubiquitylation activity. Emerging evidence indicates that the chromatin-binding and enzymatic modules of UHRF1 do not act in isolation but interplay in a coordinated and regulated manner. Here, we compared two splicing variants (V1, V2) of murine UHRF1 (mUHRF1) with human UHRF1 (hUHRF1). We show that insertion of nine amino acids in a linker region connecting the different TTD and PHD histone modification-binding domains causes distinct H3K9me3-binding behaviour of mUHRF1 V1. Structural analysis suggests that in mUHRF1 V1, in contrast to V2 and hUHRF1, the linker is anchored in a surface groove of the TTD domain, resulting in creation of a coupled TTD-PHD module. This establishes multivalent, synergistic H3-tail binding causing distinct cellular localization and enhanced H3K9me3-nucleosome ubiquitylation activity. In contrast to hUHRF1, H3K9me3-binding of the murine proteins is not allosterically regulated by phosphatidylinositol 5-phosphate that interacts with a separate less-conserved polybasic linker region of the protein. Our results highlight the importance of flexible linkers in regulating multidomain chromatin binding proteins and point to divergent evolution of their regulation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation

RNA-guided endonucleases are involved in processes ranging from adaptive immunity to site-specific transposition and have revolutionized genome editing. CRISPR-Cas9, -Cas12 and related proteins use guide RNAs to recognize ~20-nucleotide target sites within genomic DNA by mechanisms that are not yet fully understood. We used structural and biochemical methods to assess early steps in DNA recognition by Cas12a protein-guide RNA complexes. We show here that Cas12a initiates DNA target recognition by bending DNA to induce transient nucleotide flipping that exposes nucleobases for DNA-RNA hybridization. Cryo-EM structural analysis of a trapped Cas12a–RNA–DNA surveillance complex and fluorescence-based conformational probing show that Cas12a-induced DNA helix destabilization enables target discovery and engagement. This mechanism of initial DNA interrogation resembles that of CRISPR-Cas9 despite distinct evolutionary origins and different RNA-DNA hybridization directionality of these enzyme families. Our findings support a model in which RNA-mediated DNA interference begins with local helix distortion by transient CRISPR-Cas protein binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

N-Terminal domain homologs of the orange carotenoid protein increase quenching of cyanobacterial phycobilisomes

Stress exerted by excess captured light energy in cyanobacteria is prevented by the photoprotective activity of the orange carotenoid protein (OCP). Under high light, the OCP converts from an orange, inactive form (OCP O ) into the red form (OCP R ) that binds to and quenches the phycobilisome (PBS). Structurally, the OCP consists of 2 domains: the N-terminal effector domain and a C-terminal regulatory domain. Structural analysis of the OCP-PBS complex showed that the N-terminal domains of an OCP dimer interact with the PBS core. These N-terminal OCP domains have single-domain protein paralogs known as helical carotenoid proteins (HCPs). Using PBS quenching assays, we show that the HCP4 and HCP5 homologs efficiently quench PBS fluorescence in vitro, surpassing the quenching ability of the OCP. This is consistent with computational quantum mechanics/molecular mechanics results. Interestingly, when using a maximum quenching concentration of OCP with PBSs, HCP5 addition further increases PBS quenching. Our results provide mechanistic insight into the quenching capacity and roles of HCP4 and HCP5 in cyanobacteria, suggesting that they are more than simply functionally redundant to the OCP.

Sheppard, Damien I.↗
DOE OSTI2021

Geometric frustration in the myosin superlattice of vertebrate muscle

Geometric frustration results from an incompatibility between minimum energy arrangements and the geometry of a system, and gives rise to interesting and novel phenomena. Here, we report geometric frustration in a native biological macromolecular system---vertebrate muscle. We analyse the disorder in the myosin filament rotations in the myofibrils of vertebrate striated (skeletal and cardiac) muscle, as seen in thin-section electron micrographs, and show that the distribution of rotations corresponds to an archetypical geometrically frustrated system---the triangular Ising antiferromagnet. Spatial correlations are evident out to at least six lattice spacings. The results demonstrate that geometric frustration can drive the development of structure in complex biological systems, and may have implications for the nature of the actin--myosin interactions involved in muscle contraction. Identification of the distribution of myosin filament rotations with an Ising model allows the extensive results on the latter to be applied to this system. It shows how local interactions (between adjacent myosin filaments) can determine long-range order and, conversely, how observations of long-range order (such as patterns seen in electron micrographs) can be used to estimate the energetics of these local interactions. Furthermore, since diffraction by a disordered system is a function of the second-order statistics, the derived correlations allow more accurate diffraction calculations, which can aid in interpretation of X-ray diffraction data from muscle specimens for structural analysis.

59 BASIC BIOLOGICAL SCIENCES↗