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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 OSTI2023

The smallest functional antibody fragment: Ultralong CDR H3 antibody knob regions potently neutralize SARS-CoV-2

Cows produce antibodies with a disulfide-bonded antigen-binding domain embedded within ultralong heavy chain third complementarity determining regions. This “knob” domain is analogous to natural cysteine-rich peptides such as knottins in that it is small and stable but can accommodate diverse loops and disulfide bonding patterns. We immunized cattle with SARS-CoV-2 spike and found ultralong CDR H3 antibodies that could neutralize several viral variants at picomolar IC 50 potencies in vitro and could protect from disease in vivo. The independent CDR H3 peptide knobs were expressed and maintained the properties of the parent antibodies. The knob interaction with SARS-CoV-2 spike was revealed by electron microscopy, X-ray crystallography, NMR spectroscopy, and mass spectrometry and established ultralong CDR H3-derived knobs as the smallest known recombinant independent antigen-binding fragment. Unlike other vertebrate antibody fragments, these knobs are not reliant on the immunoglobulin domain and have potential as a new class of therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Structure of native four-repeat satellite III sequence with non-canonical base interactions

Abstract Tandem-repetitive DNA (where two or more DNA bases are repeated numerous times) can adopt non-canonical secondary structures. Many of these structures are implicated in important biological processes. Human Satellite III (HSat3) is enriched for tandem repeats of the sequence ATGGA and is located in pericentromeric heterochromatin in many human chromosomes. Here, we investigate the secondary structure of the four-repeat HSat3 sequence 5′-ATGGA ATGGA ATGGA ATGGA-3′ using X-ray crystallography, NMR, and biophysical methods. Circular dichroism spectroscopy, thermal stability, native PAGE, and analytical ultracentrifugation indicate that this sequence folds into a monomolecular hairpin with non-canonical base pairing and B-DNA characteristics at concentrations below 0.9 mM. NMR studies at 0.05–0.5 mM indicate that the hairpin is likely folded-over into a compact structure with high dynamics. Crystallographic studies at 2.5 mM reveal an antiparallel self-complementary duplex with the same base pairing as in the hairpin, extended into an infinite polymer. The non-canonical base pairing includes a G–G intercalation sandwiched by sheared A–G base pairs, leading to a cross-strand four guanine stack, so called guanine zipper. The guanine zippers are spaced throughout the structure by A–T/T–A base pairs. Our findings lend further insight into recurring structural motifs associated with the HSat3 and their potential biological functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Applying Crystallography and 19 F NMR to investigate dynamics and partner protein interactions in a long chain Flavodoxin

Flavodoxin (Fld) is a small FMN containing protein that is involved in single electron transfer. The long‐chain flavodoxin in Rhodopseudomonas palustris bacteria replaces ferredoxin as a low‐potential electron carrier when iron is scarce. Thus it is proposed to interact with the bifurcating electron transfer flavoprotein (ETF) that yields low‐potential electrons. A surface loop on Fld interacts with another of Fld's partner proteins, so we hypothesize that it also mediates Fld's interaction with ETF. To monitor interactions with ETF directly and investigate dynamics in this loop, we are using 19 F NMR in solution. 19 F is hyperresponsive to changes in its chemical environment with a chemical shift range of >300 ppm. To provide a static reference point and assess structural heterogeneity, we are also exploiting X‐ray crystallography. In this study we selectively fluorinated the five tyrosine residues in Fld. We obtained resonance assignments from 19 F spectra of Fld variants in which individual tyrosine residues have been replaced. We obtain well resolved signals for each residue, but the resonances' linewidths indicate dynamics that affects some resonances more than others. Y90 residue displays two resonances demonstrating two different conformations that interconvert slowly on an NMR time scale. Meanwhile the crystal structure solved at 2.1Å resolution reveals two molecules per asymmetric unit providing two perspectives on the details of the structure. The crystal symmetry is monoclinic in contrast to most of the other Flds, which are orthorhombic. Interestingly, the long loop bearing Y121 and Y123 is not well resolved in chain B of the crystal structure, and the NMR line of Y123 is exceptionally broad, both indicating that the loop is dynamic and capable of altering its conformation to accomodate binding to a partner protein. Future directions include monitoring the changes in the 19 F NMR of the Fld when titrated with the partner protein, temperature dependence of the NMR spectrum and relaxation studies to evaluate time scales of motions.

Khan, Sharique↗
DOE OSTI2023

Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation

Post-translational modification of proteins with polyubiquitin chains is a critical cellular signaling mechanism in eukaryotes with implications in various cellular states and processes. Unregulated ubiquitin-mediated protein degradation can be detrimental to cellular homeostasis, causing numerous diseases including cancers. Recently, macrocyclic peptides were developed that selectively target long Lysine-48-linked polyubiquitin chains (tetra-ubiquitin) to inhibit ubiquitin-proteasome system, leading to attenuation of tumor growth in vivo. However, structural determinants of the chain length and linkage selectivity by these cyclic peptides remained unclear. Here, we uncover the mechanism underlying cyclic peptide’s affinity and binding selectivity by combining X-ray crystallography, solution NMR, and biochemical studies. We found that the peptide engages three consecutive ubiquitins that form a ring around the peptide and determined requirements for preferential selection of a specific trimer moiety in longer polyubiquitin chains. The structural insights gained from this work will guide the development of next-generation cyclic peptides with enhanced anti-cancer activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

One-bond 13 C– 13 C spin-coupling constants in saccharides: a comparison of experimental and calculated values by density functional theory using solid-state 13 C NMR and X-ray crystallography

Methyl aldohexopyranosides were 13 C-labeled at contiguous carbons, crystallized, and studied by single-crystal X-ray crystallography and solid-state 13 C nuclear magnetic resonance (NMR) spectroscopy to examine the degree to which density functional theory (DFT) can calculate one-bond 13C–13C spin-coupling constants ( 1 J CC ) in saccharides with sufficient accuracy to permit their use in MA'AT analysis, a newly-reported hybrid DFT/NMR method that provides probability distributions of molecular torsion angles in solution (Zhang et al., J. Phys. Chem. B, 2017, 121, 3042–3058; Meredith et al., J. Chem. Inf. Model., 2022, 62, 3135–3141). Experimental 1 J CC values in crystalline samples of the doubly 13 C-labeled compounds were measured by solid-state 13 C NMR and compared to those calculated from five different DFT models: (1) 1 J CC values calculated from single structures identical to those observed in crystalline samples by X-ray crystallography (all atom refinement); (2) 1 J CC values calculated from the single structures in (1) but after Hirshfeld atom refinement (HAR); (3) 1 J CC values calculated from the single structures in (1) after DFT-optimization of hydrogen atoms only; and (4 and 5) 1 J CC values calculated in rotamers of torsion angle θ 2 (C1–C2–O2–O2H) or ω(C4–C5–C6–O6) from which either specific or generalized parameterized equations were obtained and used to calculate 1 J CC values in the specific θ 2 or ω rotamers observed in crystalline samples. Good qualitative agreement was observed between calculated 1 J CC values and those measured by solid-state 13 C NMR regardless of the DFT model, but in no cases were calculated 1 J CC values quantitative, differing (over-estimated) on average by 4–5% from experimental values. These findings, and those reported recently from solution NMR studies (Tetrault et al., J. Phys. Chem. B 2022, 126, 9506–9515), indicate that improvements in DFT calculations are needed before calculated 1 J CC values can be used directly as reliable constraints in MA'AT analyses of saccharides in solution.

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

The Structure of Boron Monoxide

Boron monoxide (BO), prepared by the thermal condensation of tetrahydroxydiboron, was first reported in 1955; however, its structure could not be determined. With the recent attention on boron-based two-dimensional materials, such as borophene and hexagonal boron nitride, there is renewed interest in BO. A large number of stable BO structures have been computationally identified, but none are supported by experiments. The consensus is that the material likely forms a boroxine-based two-dimensional material. Herein, we apply advanced 11 B NMR experiments to determine the relative orientations of B(B)O 2 centers in BO. We find that the material is composed of D 2h -symmetric O 2 B–BO 2 units that organize to form larger B 4 O 2 rings. Further, powder diffraction experiments additionally reveal that these units organize to form two-dimensional layers with a random stacking pattern. This observation is in agreement with earlier density functional theory (DFT) studies that showed B 4 O 2 -based structures to be the most stable.

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

A Trichomonas vaginalis C2-XYPPX-repeat protein with a structured C2 domain displaying dampened flexibility upon binding calcium

C2 domains are ubiquitous membrane-binding modules of ∼130 residues in eukaryotes that are often associated with proteins involved in membrane trafficking and lipid modification. The genome of Trichomonas vaginalis, the most common, non-viral, sexually transmitted human pathogen, encodes eight genes that contain a N-terminal C2 module linked to a XYPPX-repeat domain of more than four XYPPX repeats (C2-XYPPX). While the function of the XYPPX-repeat domain remains unknown, its multiple association with C2 domains in T. vaginalis suggests it is important. Here, the C2 domain from one of these C2-XYPPX-repeat proteins, Tv-C2-1, was structurally and physically characterized using X-ray crystallography and NMR spectroscopy. The crystal structure for Tv-C2-1 shows that this domain shares a fold common to all C2 domains, a compact Greek-key motif composed of eight anti-parallel β-strands in the type-2 topology. An NMR chemical shift perturbation study with Ca 2+ showed that Tv-C2-1 bound two Ca 2+ atoms primarily via two loops (loop-1 and loop-3) on the predicted calcium binding face of the protein with K d s of 58.0 ± 0.1 μM and 232 ± 6 μM. Estimations of the overall rotational correlation time, τ c , in the apo (11.1 ns) and Ca 2+ -bound (9.2 ns) state suggests the protein becomes more compact upon Ca 2+ binding, consistent with a decrease in dynamics in loop-3 and marginally in loop-1 suggested by amide 15 N heteronuclear steady-state { 1 H}- 15 N NOEs. Showing Tv-C2-1 binds calcium and adopts a compact Greek-key motif structure, two primary features of C2 domains, suggests understanding the function of the XYPPX-repeat domain may be warranted.

NMR spectroscopy↗
DOE OSTI2023

Quantifying Actinide–Carbon Bond Covalency in a Uranyl–Aryl Complex Utilizing Solution 13 C NMR Spectroscopy

Reaction of [UO 2 Cl 2 (THF) 2 ] 2 with in situ generated LiFmes (FmesH = 1,3,5-(CF 3 ) 3 C 6 H 3 ) in Et 2 O resulted in the formation of the uranyl aryl complexes [Li(THF) 3 ][UO 2 (Fmes) 3 ] ([Li(THF) 3 ][1]) and [Li(Et 2 O) 3 (THF)][UO 2 (Fmes) 3 ] ([Li(Et 2 O) 3 (THF)][1]) in good to moderate yields after crystallization from hexanes and Et 2 O, respectively. Both complexes were characterized by X-ray crystallography and NMR spectroscopy. DFT calculations reveal that the C ispo resonance in [1] – exhibits a deshielding of 51 ppm from spin–orbit coupling effects originating at uranium, which indicates an appreciable covalency in the U–C bonding interaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Picolinate-based acyclic ligand for rare earth element extraction and separation

The rare earth elements (REEs) play an important role in many modern technologies, particularly those relevant to clean energy. Despite their increasing importance, obtaining them in elementally pure forms suitable for downstream applications is challenging due to their similar chemical properties. This problem has impeded efforts to efficiently and selectively extract them from end-of-life materials and electronic waste. Here, we report a cost-efficient acyclic picolinate-based chelator H 4 aapa. The REE stability constants (log K ML ) of this chelator were measured via pH potentiometric and UV-Visible spectrophotometric titrations, revealing it to preferably bind light over heavy REEs like many recently reported 18-membered macrocycles. Its REE complexes were characterized by X-ray crystallography and NMR spectroscopy, demonstrating that this chelator can attain different conformations. The unique properties of aapa were subsequently used to separate REEs via the dissolution of insoluble REE oxalate mixtures. This dissolution-based separation led to large separation factors, the most significant being that for the Ce 3+ /Lu 3+ pair (38.6) at pH 4. Leveraging the strong REE binding affinity of aapa, we further demonstrated this chelator can leach REEs from authentic end-of-life materials in the form of magnet waste and autocatalyst smelting (autocat) slag. With this approach, exposure of these materials to a 20 mM solution of aapa at neutral pH generates a metal-containing solution enriched in Nd 3+ and Dy 3+ by 56.9 wt% and 3.0 wt%, marking a 4-fold improvement over the use of 4 M HNO 3 .

Gao, Yangyang [University of California, Santa Bar↗
DOE OSTI2021

Synthesis of Non-Aqueous Neptunium(III) Halide Solvates from NpO 2

We report two Np(III) halides, NpI 3 (THF) 4 and NpBr 3 (THF) 4 , have been prepared and isolated in high yields as described in this work. Starting with neptunia (NpO 2 ), NpCl 4 (DME) 2 was first generated in an updated, higher yielding synthesis than what was previously reported by using HCl/HF. This material was then reduced with KC 8 , followed by subsequent ligand exchange, to generate NpBr 3 (THF) 4 and NpI 3 -(THF) 4 . Full characterization by single-crystal X-ray crystallography, 1 H NMR spectroscopy and electronic absorption spectroscopy confirmed the molecular formulas and oxidation states. These trivalent materials are straightforward to synthesize and can be used as starting materials for non-aqueous Np(III) chemistry, obviating the need for rare and restricted Np metal and elemental halogens.

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

The Monomeric Alanediyl : AlAr i Pr8 (Ar i Pr8 = C 6 H-2,6-(C 6 H 2 -2,4,6-Pr i 3 ) 2 -3,5-Pr i 2 ): An Organoaluminum(I) Compound with a One-Coordinate Aluminum Atom

Reduction of the aluminum iodide AlI 2 Ar i Pr8 ( 1 ; Ar i Pr8 = C 6 H-2,6-(C 6 H 2 -2,4,6-Pr i 3 ) 2 -3,5-Pr i 2 ) with 5% w/w Na/NaCl in hexanes gave a dark red solution from which the monomeric alanediyl : AlAr i Pr8 ( 2 ) was isolated in ca. 28% yield as yellow-orange crystals. Compounds 1 and 2 were characterized by X-ray crystallography, electronic and NMR spectroscopy, and theoretical calculations. The Al atom in 2 is one-coordinate, and the compound displays two absorptions in its electronic spectrum at 354 and 455 nm. It reacts with H 2 under ambient conditions to give the aluminum hydride {AlH(μ-H)Ar i Pr8 } 2 , probably via a weakly bound dimer of 2 as an intermediate.

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

Structural characterization of HIV-1 matrix mutants implicated in envelope incorporation

During the late phase of HIV-1 infection, viral Gag polyproteins are targeted to the plasma membrane (PM) for assembly. Gag localization at the PM is a prerequisite for the incorporation of the envelope protein (Env) into budding particles. Gag assembly and Env incorporation are mediated by the N-terminal myristoylated matrix (MA) domain of Gag. Nonconservative mutations in the trimer interface of MA (A45E, T70R, and L75G) were found to impair Env incorporation and infectivity, leading to the hypothesis that MA trimerization is an obligatory step for Env incorporation. Conversely, Env incorporation can be rescued by a compensatory mutation in the MA trimer interface (Q63R). The impact of these MA mutations on the structure and trimerization properties of MA is not known. In this study, we employed NMR spectroscopy, X-ray crystallography, and sedimentation techniques to characterize the structure and trimerization properties of HIV-1 MA A45E, Q63R, T70R, and L75G mutant proteins. NMR data revealed that these point mutations did not alter the overall structure and folding of MA but caused minor structural perturbations in the trimer interface. Analytical ultracentrifugation data indicated that mutations had a minimal effect on the MA monomer–trimer equilibrium. The high-resolution X-ray structure of the unmyristoylated MA Q63R protein revealed hydrogen bonding between the side chains of adjacent Arg-63 and Ser-67 on neighboring MA molecules, providing the first structural evidence for an additional intermolecular interaction in the trimer interface. These findings advance our knowledge of the interplay of MA trimerization and Env incorporation into HIV-1 particles.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

PDB ‐101: Educational resources supporting molecular explorations through biology and medicine

Abstract The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic‐level three‐dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB‐101 was launched to support teachers, students, and the general public in PDB archive exploration ( pdb101.rcsb.org ). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB‐101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popular Molecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB‐101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year‐on‐year. In addition, PDB‐101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB‐101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy.

Zardecki, Christine↗
DOE OSTI2022

Capture Instead of Release: Defect-Modulated Radionuclide Leaching Kinetics in Metal–Organic Frameworks

Comparison of defect-controlled leaching-kinetics modulation of metal–organic frameworks (MOFs) and porous functionalized silica-based materials was performed on the example of a radionuclide and radionuclide surrogate for the first time, revealing an unprecedented readsorption phenomenon. On a series of zirconium-based MOFs as model systems, we demonstrated the ability to capture and retain >99% of the transuranic 241 Am radionuclide after 1 week of storage. Here, we report the possibility of tailoring radionuclide release kinetics in MOFs through framework defects as a function of postsynthetically installed organic ligands including cation-chelating crown ether-based linkers. Based on comprehensive analysis using spectroscopy (EXAFS, UV–vis, FTIR, and NMR), X-ray crystallography (single crystal and powder), and theoretical calculations (nine kinetics models and structure simulations), we demonstrated the synergy of radionuclide integration methods, topological restrictions, postsynthetic scaffold modification, and defect engineering. This combination is inaccessible in any other material and highlights the advantages of using well-defined frameworks for gaining fundamental knowledge necessary for the advancement of actinide-based material development, providing a pathway for addressing upcoming challenges in the nuclear waste administration sector.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
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 OSTI2022

Chelating Rare-Earth Metals (Ln 3+ ) and 225 Ac 3+ with the Dual-Size-Selective Macrocyclic Ligand Py 2 -Macrodipa

Radioisotopes of metallic elements, or radiometals, are widely employed in both therapeutic and diagnostic nuclear medicine. For this application, chelators that efficiently bind the radiometal of interest and form a stable metal–ligand complex with it are required. Toward the development of new chelators for nuclear medicine, we recently reported a novel class of 18-membered macrocyclic chelators that is characterized by their ability to form stable complexes with both large and small rare-earth metals (Ln 3+ ), a property referred to as dual size selectivity. A specific chelator in this class called py-macrodipa, which contains one pyridyl group within its macrocyclic core, was established as a promising candidate for 135 La 3+ , 213 Bi 3+ , and 44 Sc 3+ chelation. Building upon this prior work, here we report the synthesis and characterization of a new chelator called py 2 -macrodipa with two pyridyl units fused into the macrocyclic backbone. Its coordination chemistry with the Ln 3+ series was investigated by NMR spectroscopy, X-ray crystallography, density functional theory (DFT) calculations, analytical titrations, and transchelation assays. These studies reveal that py 2 -macrodipa retains the expected dual size selectivity and possesses an enhanced thermodynamic affinity for all Ln 3+ compared to py-macrodipa. By contrast, the kinetic stability of Ln 3+ complexes with py 2 -macrodipa is only improved for the light, large Ln 3+ ions. Based upon these observations, we further assessed the suitability of py 2 -macrodipa for use with 225 Ac 3+ , a large radiometal with valuable properties for targeted α therapy. Radiolabeling and stability studies revealed py 2 -macrodipa to efficiently incorporate 225 Ac 3+ and to form a complex that is inert in human serum over 3 weeks. Although py 2 -macrodipa does not surpass the state-of-the-art chelator macropa for 225 Ac 3+ chelation, it does provide another effective 225 Ac 3+ chelator. Furthermore, these studies shed light on the fundamental coordination chemistry of the Ln 3+ series and may inspire future chelator design efforts.

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

A Dicopper Platform that Stabilizes the Formation of Pentanuclear Coinage Metal Hydride Complexes

Abstract Reduction of a dicopper(II) bis(hydroxide) complex with silanes in the presence of external copper or silver cations results in the formation of multinuclear hydride clusters, which were characterized by a variety of NMR spectroscopic experiments and X‐ray crystallography. In particular, the pentanuclear complexes adopt an unusual planar “bow tie” configuration. The copper hydride complexes are efficient catalysts for the dehydrogenation of formic acid to H 2 and CO 2 .

Desnoyer, Addison N.↗