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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 91 records · Page 5
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DOE OSTI2025

Acetylcholinesterase: Structure, dynamics, and interactions with organophosphorus compounds

Acetylcholinesterase (AChE) is an enzyme that hydrolyzes the neurotransmitter acetylcholine (ACh), removing it from the synaptic cleft after the transmission of an electrical signal, making it an essential component of chemical neurotransmission. AChE is a serine hydrolase, containing a catalytic triad of Ser/His/Glu. AChE is a prime target for pharmaceuticals treating a variety of neurological disorders. It is also the target of synthetic organophosphorus (OP) compounds that have been used as pesticides and chemical warfare agents. OP compounds contain a potent leaving group, such as fluorine, and act by forming a covalent adduct with the catalytic serine of the AChE active site. A wealth of structural information is available for AChE, including over 300 structures, including a subset of structures in complex with drugs as well as OP compounds. This review will highlight the interactions between OP compounds and AChE from a structural and computational perspective, with a discussion of access to the active site, as well as side reactions that lead to dealkylation of the OP-catalytic serine adduct, a process known as aging. We conclude that while the majority of the conformational changes needed to accommodate the OP compounds are localized to the acyl loop in the crystal structures, molecular dynamics simulations highlight the potential for a far more dynamic enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The crystal structure of bacteriophage λ RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins

Abstract RexA and RexB function as an exclusion system that prevents bacteriophage T4rII mutants from growing on Escherichia coli λ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here, we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron–electron spin resonance spectroscopy support a DNA-dependent conformational change. In vivo phenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNA in vitro. Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain

Epidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of the Arabidopsis thaliana SPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Circular dichroism in hard X-ray photoelectron diffraction observed by time-of-flight momentum microscopy

X-ray photoelectron diffraction (XPD) is a powerful technique that yields detailed structural information of solids and thin films that complements electronic structure measurements. Among the strongholds of XPD we can identify dopant sites, track structural phase transitions, and perform holographic reconstruction. High-resolution imaging of k ll -distributions (momentum microscopy) presents a new approach to core-level photoemission. It yields full-field k x -k y XPD patterns with unprecedented acquisition speed and richness in details. Here, we show that beyond the pure diffraction information, XPD patterns exhibit pronounced circular dichroism in the angular distribution (CDAD) with asymmetries up to 80%, alongside with rapid variations on a small k ll -scale (0.1 Å -1 ). Measurements with circularly-polarized hard X-rays (hν = 6 keV) for a number of core levels, including Si, Ge, Mo and W, prove that core-level CDAD is a general phenomenon that is independent of atomic number. The fine structure in CDAD is more pronounced compared to the corresponding intensity patterns. Additionally, they obey the same symmetry rules as found for atomic and molecular species, and valence bands. Further, the CD is antisymmetric with respect to the mirror planes of the crystal, whose signatures are sharp zero lines. Calculations using both the Bloch-wave approach and one-step photoemission reveal the origin of the fine structure that represents the signature of Kikuchi diffraction. To disentangle the roles of photoexcitation and diffraction, XPD has been implemented into the Munich SPRKKR package to unify the one-step model of photoemission and multiple scattering theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Modeling Heterogeneity in UO 2 Nanoparticles Using X‐ray Absorption Spectroscopy

Abstract EXAFS provides the capability to interrogate nanoparticle (NP) structure in atomistic detail without relying on long‐range crystallinity. There is a limitation in that EXAFS provides averaged structural information, making it difficult to separate a small amount of heterogeneous structure from bulk. In this work, models were developed to extract surface‐specific information from conventional EXAFS measurements collected on UO 2 NPs of varying size. Specifically, the surface terminating species of UO 2 NPs was determined from comparison of coordination numbers with geometric models while the origin of static disorder was interrogated from user‐defined simulations. Results show that the degree of oxygenation on the NP surface does not significantly deviate from bulk surface and that static disorder is highly enhanced in NP surface layers but cannot be attributed to surface relaxation effects alone. The approach described herein has the potential to be adapted to a range of inorganic NP systems to interrogate surface structure.

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

Atomically Dispersed Copper Sites in a Metal–Organic Framework for Reduction of Nitrogen Dioxide

Metal-organic framework (MOF) materials provide an excellent platform to fabricate single-atom catalysts due to their structural diversity, intrinsic porosity, and designable functionality. However, the unambiguous identification of atomically dispersed metal sites and the elucidation of their role in catalysis are challenging due to limited methods of characterization and lack of direct structural information. Here, we report a comprehensive investigation of the structure and the role of atomically dispersed copper sites in UiO-66 for the catalytic reduction of NO 2 at ambient temperature. The atomic dispersion of copper sites on UiO-66 is confirmed by high-angle annular dark-field scanning transmission electron microscopy, electron paramagnetic resonance spectroscopy, and inelastic neutron scattering, and their location is identified by neutron powder diffraction and solid-state nuclear magnetic resonance spectroscopy. The Cu/UiO-66 catalyst exhibits superior catalytic performance for the reduction of NO 2 at 25 °C without the use of reductants. A selectivity of 88% for the formation of N2 at a 97% conversion of NO 2 with a lifetime of >50 h and an unprecedented turnover frequency of 6.1 h-1 is achieved under nonthermal plasma activation. In situ and operando infrared, solid-state NMR, and EPR spectroscopy reveal the critical role of copper sites in the adsorption and activation of NO 2 molecules, with the formation of {Cu(I)···NO} and {Cu···NO 2 } adducts promoting the conversion of NO 2 to N 2 . This study will inspire the further design and study of new efficient single-atom catalysts for NO 2 abatement via detailed unravelling of their role in catalysis.

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

An approach to nearest neighbor analysis of pigment-protein complexes using chemical cross-linking in combination with mass spectrometry

Herein, protein cross-linking is the process of chemically joining two amino acids in a protein or protein complex by a covalent bond. When combined with mass spectrometry, it becomes one of the structural mass spectrometry techniques gaining in importance for deriving valuable three-dimensional structural information on proteins and protein complexes. This platform complements existing structural methods, such as NMR spectroscopy, X-ray crystallography, and cryo-EM. Photosynthetic pigment protein complexes serve as light-energy harvesting systems and perform photochemical conversion as part of the “early events” of photosynthesis. This chapter outlines how to prepare cross-linking pigment protein complex samples for LC-MS/MS analysis, including identification of the cross-linked species, network analysis in a protein complex, and structural modeling and justification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Charge Movement and Structural Changes in the Gas-Phase Unfolding of Multimeric Protein Complexes Captured by Native Top-Down Mass Spectrometry

The extent to which noncovalent protein complexes retain native structure in the gas phase is highly dependent on experimental conditions. Energetic collisions with background gas can cause structural changes ranging from unfolding to subunit dissociation. Additionally, recent studies have highlighted the role of charge in such structural changes, but the mechanism is not completely understood. In this study, native top down (native TD) mass spectrometry was used to probe gas-phase structural changes of alcohol dehydrogenase (ADH, 4mer) under varying degrees of in-source activation. Changes in covalent backbone fragments produced by electron capture dissociation (ECD) or 193 nm ultraviolet photodissociation (UVPD) were correlated to structural changes of the ADH 4mer. ECD fragments indicated unfolding started at the N-terminus, and the charge states of UVPD fragments enabled monitoring of charge migration to the unfolded regions. Interestingly, UVPD fragments also indicated that the charge at the “unfolding” N-terminus of ADH decreased at high in-source activation energies after the initial increase. We proposed a possible “refolding-after-unfolding” mechanism, as further supported by monitoring hydrogen elimination from radical a-ions produced by UVPD at the N-terminus of ADH. However, “refolding-after-unfolding” with increasing in-source activation was not observed for charge-reduced ADH, which likely adopted compact structures that are resistant to both charge migration and unfolding. Combined, these results support a charge-directed unfolding mechanism for protein complexes. Overall, an experimental framework was outlined for utilizing native TD to generate structure-informative mass spectral signatures for protein complexes that complement other structure characterization techniques, such as ion mobility spectrometry and computational modeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Bioremediation of Chlorinated Volatile Organic Compounds: DOE Experiences and Lessons Learned

From the mid-1980s to the present, the Department of Energy (DOE) has developed, tested, and deployed diverse bioremediation strategies for chlorinated volatile organic compounds (cVOCs). A systematic review of these projects after decades of activity provides an opportunity to identify crosscutting themes and lessons learned. The knowledge provided by a DOE bioremediation retrospective represents a resource to support current and future bioremediation operations, and future decisions related to cVOC bioremediation. This systematic review examined the design, objectives, performance and outcomes for remediation projects at DOE sites including Savannah River, Hanford, Idaho, Mound and Pinellas. The results were used to identify emergent themes to provide actionable insights. The bioremediation retrospective technical team first developed standardized criteria to support the systematic review. Then, the evaluation was performed using a sequential process that was informed by local technical experts who identified and provided the structured information that served as the basis for the evaluation. The participation of these experts was invaluable to the effort. Importantly, DOE cVOC bioremediation efforts were implemented based on the foundational knowledge developed by U.S. Department of Defense (DoD) strategic and applied environmental technology development and certification programs, as well as technical, policy and regulatory guidance from the U.S. Environmental Protection Agency (EPA), Interstate Technology and Regulatory Council (ITRC), U.S. Geological Survey (USGS), industry, and universities. To maximize the value of the DOE cVOC bioremediation retrospective, the systematic review strategy focused on identifying important DOE-specific experiences, trends and lessons learned that would extend the knowledge available from these other key entities.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes

Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein–FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a “closed” FakB1 state to an “open” state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic α-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.

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

Differentiating Three-Dimensional Molecular Structures Using Laser-Induced Coulomb Explosion Imaging

Coulomb explosion imaging (CEI) with x-ray free electron lasers has recently been shown to be a powerful method for obtaining detailed structural information of gas-phase planar ring molecules [R. Boll et al., X-ray multiphoton-induced Coulomb explosion images complex single molecules, Nat. Phys. 18, 423 (2022).]. In this Letter, we investigate the potential of CEI driven by a tabletop laser and extend this approach to differentiating three-dimensional structures. We study the static CEI patterns of planar and nonplanar organic molecules that resemble the structures of typical products formed in ring-opening reactions. Here, our results reveal that each molecule exhibits a well-localized and distinctive pattern in three-dimensional fragment-ion momentum space. We find that these patterns yield direct information about the molecular structures and can be qualitatively reproduced using a classical Coulomb explosion simulation. Our findings suggest that laser-induced CEI can serve as a robust method for differentiating molecular structures of organic ring and chain molecules. As such, it holds great promise as a method for following ultrafast structural changes, e.g., during ring-opening reactions, by tracking the motion of individual atoms in pump-probe experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Supramolecular Support of Cuprophilic Network Bonding in 2-D Copper n -Alkanethiolates

Here, the development of heterogeneous materials, catalysts, and semiconductors is often reliant on precise control of self-assembly and crystal packing. Many new materials are initially synthesized as microcrystalline powders, making them incompatible with typical methods of structure determination, such as single-crystal X-ray diffraction. This resultant lack of structural information has made thorough investigation into the effect of metal substitution on crystal structure in metal-organic chalcogenolates (MOChas) challenging. Here, we use small molecule serial femtosecond crystallography (smSFX) to present the structures of four copper n-alkanethiolates: CuSC4, CuSC5, CuSC6, and CuSC7. Divergent patterns of alkyl chain packing are identified from microcrystalline powders via smSFX. An odd-even effect in crystal packing has been identified and attributed to different orientations of symmetry elements in the even- and odd-numbered chains. This results in minute changes in the azimuthal organization of the even-numbered chains and the network of cuprophilic interactions. Additionally, we present a synthesis of crystalline gold n-alkanethiolates to provide the first comparison between three d 10 coinage metals (Cu, Ag, and Au) and their resultant n-alkanethiolates.

Willson, Maggie C. [Univ. of Connecticut, Storrs, ↗
DOE OSTI2020

Structural basis for divergent C–H hydroxylation selectivity in two Rieske oxygenases

Biocatalysts that perform C–H hydroxylation exhibit exceptional substrate specificity and site-selectivity, often through the use of high valent oxidants to activate these inert bonds. Rieske oxygenases are examples of enzymes with the ability to perform precise mono- or dioxygenation reactions on a variety of substrates. Understanding the structural features of Rieske oxygenases responsible for control over selectivity is essential to enable the development of this class of enzymes for biocatalytic applications. Decades of research has illuminated the critical features common to Rieske oxygenases, however, structural information for enzymes that functionalize diverse scaffolds is limited. Here, we report the structures of two Rieske monooxygenases involved in the biosynthesis of paralytic shellfish toxins (PSTs), SxtT and GxtA, adding to the short list of structurally characterized Rieske oxygenases. Based on these structures, substrate-bound structures, and mutagenesis experiments, we implicate specific residues in substrate positioning and the divergent reaction selectivity observed in these two enzymes.

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

Rapid sensing of hidden objects and defects using a single-pixel diffractive terahertz sensor

Abstract Terahertz waves offer advantages for nondestructive detection of hidden objects/defects in materials, as they can penetrate most optically-opaque materials. However, existing terahertz inspection systems face throughput and accuracy restrictions due to their limited imaging speed and resolution. Furthermore, machine-vision-based systems using large-pixel-count imaging encounter bottlenecks due to their data storage, transmission and processing requirements. Here, we report a diffractive sensor that rapidly detects hidden defects/objects within a 3D sample using a single-pixel terahertz detector, eliminating sample scanning or image formation/processing. Leveraging deep-learning-optimized diffractive layers, this diffractive sensor can all-optically probe the 3D structural information of samples by outputting a spectrum, directly indicating the presence/absence of hidden structures or defects. We experimentally validated this framework using a single-pixel terahertz time-domain spectroscopy set-up and 3D-printed diffractive layers, successfully detecting unknown hidden defects inside silicon samples. This technique is valuable for applications including security screening, biomedical sensing and industrial quality control.

Li, Jingxi (ORCID:0000000165958680)↗
DOE OSTI2020

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world’s largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Density Functional Tight-Binding Models for Band Structures of Transition-Metal Alloys and Surfaces across the d -Block

First-principles electronic structure simulations are an invaluable tool for understanding chemical bonding and reactions. While machine-learning models such as interatomic potentials significantly accelerate the exploration of potential energy surfaces, electronic structure information is generally lost. Particularly in the field of heterogeneous catalysis, simulated electron band structures provide fundamental insights into catalytic reactivity. This ab initio knowledge is preserved in semiempirical methods such as density functional tight binding (DFTB), which extend the accessible computational length and time scales beyond first-principles approaches. In this paper here we present Shell-Optimized Atomic Confinement (SOAC) DFTB electronic-part-only parametrizations for bulk and surface band structures of all d-block transition metals that enable efficient predictions of electronic descriptors for large structures or high-throughput studies on complex systems outside the computational reach of density functional theory.

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

Structure-aware annotation of leucine-rich repeat domains

Protein domain annotation is typically done by predictive models such as HMMs trained on sequence motifs. However, sequence-based annotation methods are prone to error, particularly in calling domain boundaries and motifs within them. These methods are limited by a lack of structural information accessible to the model. With the advent of deep learning-based protein structure prediction, existing sequenced-based domain annotation methods can be improved by taking into account the geometry of protein structures. We develop dimensionality reduction methods to annotate repeat units of the Leucine Rich Repeat solenoid domain. The methods are able to correct mistakes made by existing machine learning-based annotation tools and enable the automated detection of hairpin loops and structural anomalies in the solenoid. The methods are applied to 127 predicted structures of LRR-containing intracellular innate immune proteins in the model plant Arabidopsis thaliana and validated against a benchmark dataset of 172 manually-annotated LRR domains.

Xu, Boyan↗