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Results for “structural characterization”

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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structural characterization of protective non-neutralizing antibodies targeting Crimean-Congo hemorrhagic fever virus

Crimean-Congo Hemorrhagic Fever Virus (CCHFV) causes a life-threatening disease with up to a 40% mortality rate. With no approved medical countermeasures, CCHFV is considered a public health priority agent. The non-neutralizing mouse monoclonal antibody (mAb) 13G8 targets CCHFV glycoprotein GP38 and protects mice from lethal CCHFV challenge when administered prophylactically or therapeutically. Here, we reveal the structures of GP38 bound with a human chimeric 13G8 mAb and a newly isolated CC5-17 mAb from a human survivor. These mAbs bind overlapping epitopes with a shifted angle. The broad-spectrum potential of c13G8 and CC5-17 and the practicality of using them against Aigai virus, a closely related nairovirus were examined. Binding studies demonstrate that the presence of non-conserved amino acids in Aigai virus corresponding region prevent CCHFV mAbs from binding Aigai virus GP38. This information, coupled with in vivo efficacy, paves the way for future mAb therapeutics effective against a wide swath of CCHFV strains.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Synthesis and structural characterization of 2,2’-bipyridine zinc formate: Analysis of formate bonding and hydrosilylation of CO 2 and carbonyl compounds

The zinc formate compound (bipy)Zn(O 2 CH) 2 is obtained via the reaction of Zn(O 2 CH) 2 with 2,2’-bipyridine (bipy). In addition, (bipy)Zn(O 2 CH) 2 may be formed from zinc hydride via addition of bipy followed by addition of (i) HCO 2 H and (ii) CO 2 . The molecular structure of (bipy)Zn(O 2 CH) 2 has been determined by X-ray diffraction, thereby demonstrating that it exists as a monomeric species with a distorted tetrahedral zinc center and monodentate formate ligands. Analysis of the bonding within the formate ligand indicates that the zinc–formate moiety is not best represented by a Zn–O–C(=O)H resonance structure, but instead possesses a significant ionic component that reduces the C=O bond order and increases the C–O bond order. The formate compound (bipy)Zn(O 2 CH) 2 participates in hydrosilylation transformations involving CO 2 and carbonyl compounds.

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

Structural Characterization of Linker Shielding in ADC Site-Specific Conjugates

Background/Objectives: Antibody–Drug Conjugates (ADCs) have rapidly evolved from early, rudimentary conjugates to highly targeted and precisely engineered molecules. Despite notable clinical successes, ADCs continue to face significant challenges, including aggregation and high hydrophobicity driven by high drug-to-antibody ratios (DARs), premature payload release, dose-limiting toxicities, and suboptimal pharmacokinetics. While site-specific linker–payload conjugation has improved ADC homogeneity and stability, the structural basis of antibody–linker interactions at specific sites remains underexplored. Methods: In this work, we present the crystal structures of trastuzumab Fab and Fc domains site-specifically conjugated with a cleavable linker–payload. Results: Our findings suggest that pockets within both Fab and Fc regions may interact with and shield the linker portion of the conjugate. Conclusions: These insights highlight the previously underappreciated potential of structure-based design to drive the optimization of ADC linker chemistry and facilitate the co-design of bespoke linker–payloads tailored to individual antibody conjugation sites.

Jaime-Garza, Maru [Discovery Chemistry, Merck & Co↗
DOE OSTI2021

Structural Characterization of Two CO Molecules Bound to the Nitrogenase Active Site

As an approach towards unraveling the nitrogenase mechanism, we have studied the binding of CO to the activesite FeMo-cofactor. CO is not only an inhibitor of nitrogenase, but it is also a substrate, undergoing reduction to hydrocarbons (Fischer–Tropsch-type chemistry). The CC bond forming capabilities of nitrogenase suggest that multiple CO or COderived ligands bind to the active site. Herein, we report a crystal structure with two CO ligands coordinated to the FeMo-cofactor of the molybdenum nitrogenase at 1.33 resolution. In addition to the previously observed bridging CO ligand between Fe2 and Fe6 of the FeMo-cofactor, a new ligand binding mode is revealed through a second CO ligand coordinated terminally to Fe6. While the relevance of this state to nitrogenase-catalyzed reactions remains to be established, it highlights the privileged roles for Fe2 and Fe6 in ligand binding, with multiple coordination modes available depending on the ligand and reaction conditions.

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

Synthesis and Structural Characterization of 2′‐Deoxy‐2′‐Methoxy‐ L ‐Cytidine Nucleic Acids

Abstract We report here for the first time the synthesis of a novel 2′‐methoxy‐modified L‐cytidine analog and its phosphoramidite, as well as its incorporation into oligonucleotides via solid‐phase synthesis. Our measure the thermostability of the modified L‐nucleic acids by UV‐melting studies, and find out the 2′‐methoxy‐derivatization enhances the thermostability of the L‐duplexes. Consistent with the thermostability result, our X‐ray crystal structure study reveals that the 2′‐methoxy‐L‐deoxycytidine forms the Watson‐Crick base pair with L‐guanosine virtually as the mirror‐image fashion of native pair. This novel chemically modified L‐cytidine provides a useful biochemical and structural strategy to create mirror‐image nucleic acid molecules with expanded functionalities.

2′-Methoxy↗
DOE OSTI2025

Structural characterization of influenza group 1 chimeric hemagglutinins as broad vaccine immunogens

Chimeric hemagglutinins (cHA) appear to be promising for the design and development of universal influenza vaccines. Influenza A group 1 cHAs, cH5/1, cH8/1, and cH11/1, comprising an H1 stem attached to either an H5, H8, or H11 globular head, have been used sequentially as vaccine immunogens in human clinical trials and induced high levels of broadly protective antibodies. Using X-ray crystallography and negative-stain electron microscopy, we determined structures of cH5/1, cH8/1, and cH11/1 HAs in their apo (unliganded) and antibody Fab-bound states. Stem-reactive antibodies 3E1 and 31.b.09 recognize their cognate epitopes in cH5/1, cH8/1, and cH11/1 HAs. However, with cH5/1, the head domains are rotated by 35 to 45° around the threefold axis of the HA trimer compared to native HA with a more splayed-open conformation at the stem base. cH11/1 with 3E1 is structurally more native-like but resembles cH5/1 with 31.b.09, whereas cH8/1 with 31.b.09 exhibited a range of closed-to-open stem configurations with some separation of head and stem domains. Furthermore, all of these group 1 cHAs effectively bound a broad head trimer interface antibody and other broad stem antibodies. Thus, the cHAs exhibit structural plasticity without compromising the stem and head trimer interface epitopes for elicitation of influenza A group 1 cross-reactive antibodies.

Science & Technology - Other Topics↗
DOE OSTI2025

The Importance of Solution Studies for the Structural Characterization of the Enterovirus 5’ Cloverleaf

Enteroviruses initiate genomic replication via a highly conserved mechanism that is controlled by an RNA platform, also known as the 5’ cloverleaf (5’CL). Here, we present a biophysical analysis of the 5’CL conformation of three enterovirus serotypes under various ionic conditions, utilizing CD spectroscopy, size-exclusion chromatography, and small-angle X-ray scattering. In general, a tendency toward a smaller monomeric hydrodynamic radius in the presence of salts was observed, but the exact structural signature of each 5’CL varied depending upon the serotype. Rhinovirus B14 (RVB14) exhibited at least two monomeric conformations and a low propensity for dimerization, while poliovirus 1 (PV1) showed a high propensity for dimerization, which was enhanced by the presence of salts. Enterovirus D70 was observed to be somewhat intermediate, with primarily a monomeric structure, but possessing some potential for dimerization. The equilibrium between the two monomeric and the dimeric conformations is also discussed. These results indicate that the 5’CL conformation may be more complex than the current literature suggests, thus underscoring the need for a combined crystal and solution approach for the accurate representation of the 5’CL conformation, and the conformation of other RNA structural elements, under native conditions.

Virology↗
DOE OSTI2022

Structural Characterization of Uranium Tetrafluoride Hydrate (UF 4 ·2.5H 2 O)

Uranium tetrafluoride is an important intermediate in the nuclear fuel cycle. Facile synthesis of its hydrate, uranium tetrafluoride hydrate (UF 4 ·2.5H 2 O), has recently been reported. The hydrate forms by contacting anhydrous UF 4 with neat H 2 O at room temperature for 24 h or by exposing anhydrous UF 4 to high relative humidity (>90%) conditions for several weeks. These pathways are of clear environmental relevance. Further understanding of the structure and optical spectra of UF 4 ·2.5H 2 O, especially of the water molecules, is therefore necessary. Herein, the structure of UF 4 ·2.5H 2 O was probed using time-of-flight neutron powder diffraction to improve understanding of the crystalline water environments in the structure. The complete structure was elucidated and compared to a previously reported partial structure for UF 4 ·2.5H 2 O and a predicted complete structure from density functional theory. The crystalline structure exhibits three distinct water environments: two of the three water sites are bound to uranium, and the third water is unbound or “free”. Furthermore, the completed structure reveals an extensive hydrogen bonding network involving water–fluorine and water–water interactions. One bound water site participates in hydrogen bonding with nearby fluoride ligands (O–H···F–U), and the second bound water site participates in hydrogen bonding with the unbound water (O–H···O) and a nearby fluoride ligand (O–H···F–U); the unbound water participates in hydrogen bonding with bound water (O–H···O–U). Low-temperature experiments and thermal analysis indicate UF 4 ·2.5H 2 O is thermally stable from 10 to 358 K, undergoes dehydration at higher temperatures, and is nearly dehydrated at 473 K. Structural measurements provide foundational understanding and will inform future investigations of the thermal and environmental stability of UF 4 ·2.5H 2 O.

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

Contrast Matching Biopolymers: A SANS-Based Approach to Structural Characterization of Chitosan

Immobilizing enzymes in polysaccharide-based matrices has been shown to improve both their stability and their catalytic efficiency. Among available materials, chitosan was selected for its abundance, biocompatibility, and versatility in a range of applications. While the broader aim of this work is to study chitosan as a matrix for immobilizing carbonic anhydrase (CA) for CO₂ capture, this study focused on determining the contrast match point (CMP) of hydrogenated and deuterated chitosan in D₂O:H₂O mixtures to enable future structural investigations using small-angle neutron scattering (SANS). Previous work successfully synthesized deuterated chitosan from Rhizopus oryzae mycelia and assessed the degree of deuteration using Fourier-transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (NMR). Building on this foundation, the current study determined the CMPs of both H-chitosan and D-chitosan by performing SANS measurements across a range of D₂O:H₂O solvent contrasts. The extracted CMPs for both forms correlated well with their respective calculated scattering length densities (SLDs), validating the experimental approach. These results establish a critical reference for selective contrast matching in future SANS studies of carbonic anhydrase immobilized in chitosan matrices, enabling detailed structural analysis of enzyme–matrix interactions.

Kosgallana, Chathurika J [ORNL] (ORCID:00000002851↗
DOE OSTI2023

Characterization, Structure, and Reactivity of Hydroxyl Groups on Metal‐Oxide Cluster Nodes of Metal–Organic Frameworks: Structural Diversity and Keys to Reactivity and Catalysis

Among the most stable metal–organic frameworks (MOFs) are those incorporating nodes that are metal oxide clusters with frames such as Zr 6 O 8 . This review is a summary of the structure, bonding, and reactivity of MOF node hydroxyl groups, emphasizing those bonded to nodes containing aluminum and zirconium ions. Hydroxyl groups are often present on these nodes, sometimes balancing the charges of the metal ions. They arise during MOF syntheses in aqueous media or in post-synthesis treatments. They are identified with infrared and 1 H nuclear magnetic resonance spectroscopies and characterized by their reactivities with polar compounds such as alcohols. Terminal OH, paired µ 2 -OH, and aqua groups on nodes are catalytic sites in numerous reactions. Relatively unreactive hydroxyl groups (such as isolated µ 2 -OH groups) may replace reactive groups and inhibit catalysis; some node hydroxyl groups (e.g., µ 3 -OH) are mere spectators in catalysis. There are similarities between MOF node hydroxyl groups and those on the surfaces of bulk metal oxides, zeolites, and enzymes, but the comparisons are mostly inexact, and much remains to be understood about MOF node hydroxyl group chemistry. It is posited that understanding and controlling this chemistry will lead to tailored MOFs and improved adsorbents and catalysts.

36 MATERIALS SCIENCE↗
NASA NTRS2011

High-Throughput Processes and Structural Characterization of Single-Nanotube Based Devices for 3D Electronics

We have developed manufacturable approaches to form single, vertically aligned carbon nanotubes, where the tubes are centered precisely, and placed within a few hundred nm of 1-1.5 micron deep trenches. These wafer-scale approaches were enabled by chemically amplified resists and inductively coupled Cryo-etchers to form the 3D nanoscale architectures. The tube growth was performed using dc plasmaenhanced chemical vapor deposition (PECVD), and the materials used for the pre-fabricated 3D architectures were chemically and structurally compatible with the high temperature (700 C) PECVD synthesis of our tubes, in an ammonia and acetylene ambient. The TEM analysis of our tubes revealed graphitic basal planes inclined to the central or fiber axis, with cone angles up to 30 deg. for the particular growth conditions used. In addition, bending tests performed using a custom nanoindentor, suggest that the tubes are well adhered to the Si substrate. Tube characteristics were also engineered to some extent, by adjusting growth parameters, such as Ni catalyst thickness, pressure and plasma power during growth.

top-down fabrication↗
DOE OSTI2022

Biochemical and structural characterization of an aromatic ring–hydroxylating dioxygenase for terephthalic acid catabolism

Significance More than 400 million tons of plastic waste is produced each year, the overwhelming majority of which ends up in landfills. Bioconversion strategies aimed at plastics have emerged as important components of enabling a circular economy for synthetic plastics, especially those that exhibit chemically similar linkages to those found in nature, such as polyesters. The enzyme system described in this work is essential for mineralization of the xenobiotic components of poly(ethylene terephthalate) (PET) in the biosphere. Our description of its structure and substrate preferences lays the groundwork for in vivo or ex vivo engineering of this system for PET upcycling.

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

Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

Chitin is an abundant biopolymer and pathogen-associated molecular pattern that stimulates a host innate immune response. Mammals express chitin-binding and chitin-degrading proteins to remove chitin from the body. One of these proteins, Acidic Mammalian Chitinase (AMCase), is an enzyme known for its ability to function under acidic conditions in the stomach but is also active in tissues with more neutral pHs, such as the lung. Here, we used a combination of biochemical, structural, and computational modeling approaches to examine how the mouse homolog (mAMCase) can act in both acidic and neutral environments. We measured kinetic properties of mAMCase activity across a broad pH range, quantifying its unusual dual activity optima at pH 2 and 7. We also solved high-resolution crystal structures of mAMCase in complex with oligomeric GlcNAcn, the building block of chitin, where we identified extensive conformational ligand heterogeneity. Leveraging these data, we conducted molecular dynamics simulations that suggest how a key catalytic residue could be protonated via distinct mechanisms in each of the two environmental pH ranges. These results integrate structural, biochemical, and computational approaches to deliver a more complete understanding of the catalytic mechanism governing mAMCase activity at different pH. Engineering proteins with tunable pH optima may provide new opportunities to develop improved enzyme variants, including AMCase, for therapeutic purposes in chitin degradation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2020

Prochlorococcus phage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases

Marine cyanobacteria are infected by phages whose genomes encode ferredoxin (Fd) electron carriers. These Fds are thought to redirect the energy harvested from light to phage-encoded oxidoreductases that enhance viral fitness, but it is unclear how the biophysical properties and partner specificities of phage Fds relate to those of photosynthetic organisms. Here, results of a bioinformatics analysis using a sequence similarity network revealed that phage Fds are most closely related to cyanobacterial Fds that transfer electrons from photosystems to oxidoreductases involved in nutrient assimilation. Structural analysis of myovirus P-SSM2 Fd (pssm2-Fd), which infects the cyanobacterium Prochlorococcus marinus, revealed high levels of similarity to cyanobacterial Fds (root mean square deviations of ≤0.5 Å). Additionally, pssm2-Fd exhibited a low midpoint reduction potential (–336 mV versus a standard hydrogen electrode), similar to other photosynthetic Fds, although it had lower thermostability (Tm = 28 °C) than did many other Fds. When expressed in an Escherichia coli strain deficient in sulfite assimilation, pssm2-Fd complemented bacterial growth when coexpressed with a P. marinus sulfite reductase, revealing that pssm2-Fd can transfer electrons to a host protein involved in nutrient assimilation. The high levels of structural similarity with cyanobacterial Fds and reactivity with a host sulfite reductase suggest that phage Fds evolved to transfer electrons to cyanobacterially encoded oxidoreductases.

cyanobacteria↗
DOE OSTI2023

Structural Characterization of TRAF6 N-Terminal for Therapeutic Uses and Computational Studies on New Derivatives

Tumor necrosis factor receptor-associated factors (TRAFs) are a protein family with a wide variety of roles and binding partners. Among them, TRAF6, a ubiquitin ligase, possesses unique receptor binding specificity and shows diverse functions in immune system regulation, cellular signaling, central nervous system, and tumor formation. TRAF6 consists of an N-terminal Really Interesting New Gene (RING) domain, multiple zinc fingers, and a C-terminal TRAF domain. TRAF6 is an important therapeutic target for various disorders and structural studies of this protein are crucial for the development of next-generation therapeutics. Here, we presented a TRAF6 N-terminal structure determined at the Turkish light source “Turkish DeLight” to be 3.2 Å resolution at cryogenic temperature (PDB ID: 8HZ2). This structure offers insight into the domain organization and zinc-binding, which are critical for protein function. Since the RING domain and the zinc fingers are key targets for TRAF6 therapeutics, structural insights are crucial for future research. Separately, we rationally designed numerous new compounds and performed molecular docking studies using this template (PDB ID:8HZ2). According to the results, 10 new compounds formed key interactions with essential residues and zinc ion in the N-terminal region of TRAF6. Molecular dynamic (MD) simulations were performed for 300 ns to evaluate the stability of three docked complexes (compounds 256, 322, and 489). Compounds 256 and 489 was found to possess favorable bindings with TRAF6. These new compounds also showed moderate to good pharmacokinetic profiles, making them potential future drug candidates as TRAF6 inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Using Multiple Isotope-Labeled Infrared Spectra for the Structural Characterization of an Intrinsically Disordered Peptide

Intrinsically disordered proteins (IDPs) rapidly interconvert between conformers, requiring an ensemble description. This complicates their experimental characterization, and force field limitations pose challenges for their simulation. Here, in this work, we use isotope-labeled and unlabeled infrared (IR) spectra to reweight simulated ensembles of the elastin-like peptide GVGVPGVG, a paradigmatic disordered peptide. By comparing the results obtained with different spectra, we explicitly show that the weights are underdetermined by the ensemble averaged data. We identify which labels and frequency regions maximize structural information while minimizing sensitivity to simulation error and show that these regions report on whether the peptide makes specific interactions. Our work shows the importance of incorporating simulations and simulated spectra at the planning stages of isotope-labeled IR experiments and more generally provides a framework for interpreting IR data for IDPs.

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

Electrical and structural characterization of nano-carbon–aluminum composites fabricated by electro-charging-assisted process

Incorporating nano-carbon phases into metal-matrix composites is a promising strategy for simultaneously enhancing electrical conductivity and mechanical properties of metals. Here, we describe the manufacture of novel nano-carbonaluminum composites by an electro-charge-assisted process (EAP) that show 5.6% ± 1.7% increase in electrical conductivity compared to the base metal alloy. The source of nano-carbon that we used in this study is activated carbon with particle size less than 100 nm. The enhancement is attributed to nano-graphitic structures that extend through the lattice of the metal. Through electron transfer from the metal to the nanostructures the electron density at the interface of nano-crystalline graphite and the metal lattice increases thereby enhancing the bulk electrical conductivity. We identify the important fabrication parameters of the EAP for a reaction system employing a tapered graphite cathode. Here, a high current density of 100 A/cm 2 causes ionization and crystallization of the carbon in the liquid metal. The increase in electrical conductivity of the composite are directly related to the incorporation of the nanocrystalline carbon in the metal lattice. The superior performance of these nano-carbon aluminum composites makes them promising candidates for power transmission lines and other applications.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis

Abstract Identification of the molecular networks that facilitated the evolution of multicellular animals from their unicellular ancestors is a fundamental problem in evolutionary cellular biology. Choanoflagellates are recognized as the closest extant nonmetazoan ancestors to animals. These unicellular eukaryotes can adopt a multicellular‐like “rosette” state. Therefore, they are compelling models for the study of early multicellularity. Comparative studies revealed that a number of putative human orthologs are present in choanoflagellate genomes, suggesting that a subset of these genes were necessary for the emergence of multicellularity. However, previous work is largely based on sequence alignments alone, which does not confirm structural nor functional similarity. Here, we focus on the PDZ domain, a peptide‐binding domain which plays critical roles in myriad cellular signaling networks and which underwent a gene family expansion in metazoan lineages. Using a customized sequence similarity search algorithm, we identified 178 PDZ domains in the Monosiga brevicollis proteome. This includes 11 previously unidentified sequences, which we analyzed using Rosetta and homology modeling. To assess conservation of protein structure, we solved high‐resolution crystal structures of representative M. brevicollis PDZ domains that are homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains. To assess functional conservation, we calculated binding affinities for mbGIPC, mbSHANK1, mbSNX27, and mbDLG‐3 PDZ domains from M. brevicollis . Overall, we find that peptide selectivity is generally conserved between these two disparate organisms, with one possible exception, mbDLG‐3. Overall, our results provide novel insight into signaling pathways in a choanoflagellate model of primitive multicellularity.

Gao, Melody↗