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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2

SARS-CoV-2 Nsp15 is a uridine-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family that is highly conserved in coronaviruses. As endoribonuclease activity seems to be responsible for the interference with the innate immune response, Nsp15 emerges as an attractive target for therapeutic intervention. Here we report the first structures with bound nucleotides and show how the enzyme specifically recognizes uridine moiety. In addition to a uridine site we present evidence for a second base binding site that can accommodate any base. The structure with a transition state analog, uridine vanadate, confirms interactions key to catalytic mechanisms. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. This acquired knowledge was instrumental in identifying Tipiracil, an FDA approved drug that is used in the treatment of colorectal cancer, as a potential anti-COVID-19 drug. Using crystallography, biochemical, and whole-cell assays, we demonstrate that Tipiracil inhibits SARS-CoV-2 Nsp15 by interacting with the uridine binding pocket in the enzyme’s active site. Our findings provide new insights for the development of uracil scaffold-based drugs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Regulation of sarcomere formation and function in the healthy heart requires a titin intronic enhancer

Heterozygous truncating variants in the sarcomere protein titin (TTN) are the most common genetic cause of heart failure. To understand mechanisms that regulate abundant cardiomyocyte (CM) TTN expression, we characterized highly conserved intron 1 sequences that exhibited dynamic changes in chromatin accessibility during differentiation of human CMs from induced pluripotent stem cells (hiPSC-CMs). Homozygous deletion of these sequences in mice caused embryonic lethality, whereas heterozygous mice showed an allele-specific reduction in Ttn expression. A 296 bp fragment of this element, denoted E1, was sufficient to drive expression of a reporter gene in hiPSC-CMs. Deletion of E1 downregulated TTN expression, impaired sarcomerogenesis, and decreased contractility in hiPSC-CMs. Site-directed mutagenesis of predicted binding sites of NK2 homeobox 5 (NKX2-5) and myocyte enhancer factor 2 (MEF2) within E1 abolished its transcriptional activity. In embryonic mice expressing E1 reporter gene constructs, we validated in vivo cardiac-specific activity of E1 and the requirement for NKX2-5- and MEF2-binding sequences. Moreover, isogenic hiPSC-CMs containing a rare E1 variant in the predicted MEF2-binding motif that was identified in a patient with unexplained dilated cardiomyopathy (DCM) showed reduced TTN expression. Together, these discoveries define an essential, functional enhancer that regulates TTN expression. Manipulation of this element may advance therapeutic strategies to treat DCM caused by TTN haploinsufficiency.

Kim, Yuri↗
DOE OSTI2024

Structural insights into GABA A receptor potentiation by Quaalude

Methaqualone, a quinazolinone marketed commercially as Quaalude, is a central nervous system depressant that was used clinically as a sedative-hypnotic, then became a notorious recreational drug in the 1960s-80s. Due to its high abuse potential, medical use of methaqualone was eventually prohibited, yet it persists as a globally abused substance. Methaqualone principally targets GABA A receptors, which are the major inhibitory neurotransmitter-gated ion channels in the brain. The restricted status and limited accessibility of methaqualone have contributed to its pharmacology being understudied. Here, we use cryo-EM to localize the GABA A receptor binding sites of methaqualone and its more potent derivative, PPTQ, to the same intersubunit transmembrane sites targeted by the general anesthetics propofol and etomidate. Both methaqualone and PPTQ insert more deeply into subunit interfaces than the previously-characterized modulators. Binding of quinazolinones to this site results in widening of the extracellular half of the ion-conducting pore, following a trend among positive allosteric modulators in destabilizing the hydrophobic activation gate in the pore as a mechanism for receptor potentiation. These insights shed light on the underexplored pharmacology of quinazolinones and further elucidate the molecular mechanisms of allosteric GABA A receptor modulation through transmembrane binding sites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural Interconversion between Agglomerated Palladium Domains and Mononuclear Pd(II) Cations in Chabazite Zeolites

Palladium-exchanged zeolites are candidate materials for passive NO x adsorption in automotive exhaust aftertreatment, where mononuclear Pd cations behave as precursors to the purported NO x adsorption sites. Yet, the structures of zeolite lattice binding sites capable of stabilizing mononuclear Pd 2+ ions, and the mechanisms that interconvert agglomerated PdO and Pd domains into mononuclear Pd 2+ ions during Pd redispersion treatments, remain incompletely understood. In this work, we use a suite of spectroscopic methods and quantitative site titration techniques to characterize mononuclear and agglomerated Pd species on zeolites with varying material properties and treatment history. Aqueous-phase methods to introduce Pd onto NH 4 -form zeolites initially form mononuclear [Pd(NH 3 ) 4 ] 2+ complexes, but subsequent thermal treatments (573–723 K; air) lead to in situ formation of H 2 that first reduces Pd 2+ to metallic Pd domains, which are then oxidized by air to PdO domains. Progressive treatment of Pd-zeolites in air to higher temperatures (723–1023 K) converts larger fractions of agglomerated PdO to mononuclear Pd 2+ , as quantified by H 2 temperature programmed reduction, because higher temperature treatments facilitate Pd redispersion toward deeper locations within chabazite (CHA) crystallites, which is corroborated by complementary titrimetric and spectroscopic data. Pd-CHA zeolites synthesized with similar bulk Pd and framework Al content, but varying framework Al arrangement, provide evidence that six-membered rings (6-MR) hosting paired Al sites (Al–O–(Si–O) x –Al, x = 1, 2) stabilize Pd 2+ ions and that otherwise isolated Al sites can stabilize [PdOH] + species, identifiable by an IR OH stretch at 3660 cm –1 . These findings clarify the underlying chemical processes and gas environments that cause Pd agglomeration in zeolites and their subsequent redispersion to mononuclear Pd 2+ ions, which prefer binding at 6-MR paired Al sites in CHA, and indicate that higher temperature air treatments lead to more uniform Pd spatial distributions throughout zeolite crystallites.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Energy coupling and stoichiometry of Zn 2+ /H + antiport by the prokaryotic cation diffusion facilitator YiiP

YiiP from Shewanella oneidensis is a prokaryotic Zn 2+ /H + antiporter that serves as a model for the Cation Diffusion Facilitator (CDF) superfamily, members of which are generally responsible for homeostasis of transition metal ions. Previous studies of YiiP as well as related CDF transporters have established a homodimeric architecture and the presence of three distinct Zn 2+ binding sites named A, B, and C. In this study, we use cryo-EM, microscale thermophoresis and molecular dynamics simulations to address the structural and functional roles of individual sites as well as the interplay between Zn 2+ binding and protonation. Structural studies indicate that site C in the cytoplasmic domain is primarily responsible for stabilizing the dimer and that site B at the cytoplasmic membrane surface controls the structural transition from an inward facing conformation to an occluded conformation. Binding data show that intramembrane site A, which is directly responsible for transport, has a dramatic pH dependence consistent with coupling to the proton motive force. A comprehensive thermodynamic model encompassing Zn 2+ binding and protonation states of individual residues indicates a transport stoichiometry of 1 Zn 2+ to 2–3 H + depending on the external pH. This stoichiometry would be favorable in a physiological context, allowing the cell to use the proton gradient as well as the membrane potential to drive the export of Zn 2+ .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Morphology Effects on Free Energies of Proton-Coupled Electron Transfer in Polyoxotungstates

Polyoxotungstates have previously been established to facilitate the hydrogenation of small molecule substrates via hydrogen atom transfer from reactive hydroxyl groups formed at the assembly surface. Understanding structure−function relationships that dictate the thermochemistry and kinetics of protoncoupled electron transfer is key to controlling this chemistry. In this work, we combine comprehensive electrochemical experiments and density functional theory calculations to address how different polyoxotungstate morphologies, specifically W 6 O 19 −2 , W 10 O 32 −4 , SiW 12 O 40 −4 , and P 2 W 18 O 62 −6 , affect the bond dissociation free energies of surface hydroxides (BDFE(O−H)) formed upon reduction of the assembly in acidic media. Our results reveal increasing hydroxide bond strengths with increasing cluster size, and that anisotropic cluster geometries result in substantial thermodynamic differentiation of H-binding sites. We demonstrate an excellent agreement between theory and experiments on the reported BDFE(O−H) values and, importantly, we elucidate how cluster size and shape affect electronic properties (local charges and frontier molecular orbitals), giving rise to sites with increased preference for hydrogen binding, demonstrated in higher BDFE(O−H). Overall, this work aids the understanding and design of polyoxometalates exhibiting surface sites with tailored interaction strengths.

anions↗
DOE OSTI2025

Computational Optimization of Room Temperature Usable Capacity for Hydrogen Storage in MFU-4-Type Metal–Organic Frameworks via Pairwise Metal Substitutions

The efficient storage of hydrogen is a critical challenge in the quest for sustainable energy solutions. Current adsorbent-based methods achieve satisfactory storage densities predominantly under cryogenic temperatures and/or high pressures, which imposes problems with cost-efficient and safe implementation of this technology. Materials that can bind hydrogen gas reversibly at ambient temperatures and more moderate pressures could play a pivotal role in enabling hydrogen-powered technologies. In this study, we use reliable computational modeling to investigate two synthetically feasible paths for tuning the enthalpy of H2 binding in MFU-4-type metal–organic frameworks (MOFs), aiming to maximize usable capacity. This study examines MIM4 IICl3(bta)6 (bta– = benzotriazolate) Kuratowski-type clusters as a model for strong binding sites in MFU-4l frameworks. We systematically evaluate the impact of separately tuning the central MII metal ion (which plays a structural role) and the peripheral MI metal ion (which binds the substrate) on the energetics of H2 binding. Our computational study reveals that H2 binding at an MI site mostly follows the trend AgI < CuI < NiI < CoI < AuI while a larger central MII site generally weakens the H2 binding at a MI site. Importantly, we have identified three new combinations of MI and MII to achieve high fractional usable capacities of the total H2 adsorbed under a pressure swing from 5 to 100 bar at room temperature. Additionally, we examine the nature of the binding interaction between the peripheral metal atom and the hydrogen molecule. While charge transfer predominantly induces this interaction, for several atom combinations, a change in the polarization (associated with variations in the ionic radius of the MI binding atom) is another important factor for adjusting the strength of the interaction. We suggest that the proposed compositions of Kuratowski-type clusters are highly desirable synthetic targets for future laboratory study.

Tkachenko, Nikolay V↗
DOE OSTI2023

Synthesis of Zwitterionic CsPbBr 3 Nanocrystals with Controlled Anisotropy using Surface‐Selective Ligand Pairs

Abstract Mechanistic studies of the morphology of lead halide perovskite nanocrystals (LHP‐NCs) are hampered by a lack of generalizable suitable synthetic strategies and ligand systems. Here, the synthesis of zwitterionic CsPbBr 3 NCs is presented with controlled anisotropy using a proposed “surface‐selective ligand pairs” strategy. Such a strategy provides a platform to systematically study the binding affinity of capping ligand pairs and the resulting LHP morphologies. By using zwitterionic ligands (ZwL) with varying structures, majority ZwL‐capped LHP NCs with controlled morphology are obtained, including anisotropic nanoplatelets and nanorods, for the first time. Combining experiments with density functional theory calculations, factors that govern the ligand binding on the different surface facets of LHP‐NCs are revealed, including the steric bulkiness of the ligand, the number of binding sites, and the charge distance between binding moieties. This study provides guidance for the further exploration of anisotropic LHP‐NCs.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Rational design of a genetically encoded NMR zinc sensor

Elucidating the biochemical roles of the essential metal ion, Zn 2+ , motivates detection strategies that are sensitive, selective, quantitative, and minimally invasive in living systems. Fluorescent probes have identified Zn 2+ in cells but complementary approaches employing nuclear magnetic resonance (NMR) are lacking. Recent studies of maltose binding protein (MBP) using ultrasensitive 129 Xe NMR spectroscopy identified a switchable salt bridge which causes slow xenon exchange and elicits strong hyperpolarized 129 Xe chemical exchange saturation transfer (hyper-CEST) NMR contrast. To engineer the first genetically encoded, NMR-active sensor for Zn 2+ , we converted the MBP salt bridge into a Zn 2+ binding site, while preserving the specific xenon binding cavity. The zinc sensor (ZS) at only 1 μM achieved ‘turn-on’ detection of Zn 2+ with pronounced hyper-CEST contrast. This made it possible to determine different Zn 2+ levels in a biological fluid via hyper-CEST. ZS was responsive to low-micromolar Zn 2+ , only modestly responsive to Cu 2+ , and nonresponsive to other biologically important metal ions, according to hyper-CEST NMR spectroscopy and isothermal titration calorimetry (ITC). Protein X-ray crystallography confirmed the identity of the bound Zn 2+ ion using anomalous scattering: Zn 2+ was coordinated with two histidine side chains and three water molecules. Penta-coordinate Zn 2+ forms a hydrogen-bond-mediated gate that controls the Xe exchange rate. Metal ion binding affinity, 129 Xe NMR chemical shift, and exchange rate are tunable parameters via protein engineering, which highlights the potential to develop proteins as selective metal ion sensors for NMR spectroscopy and imaging.

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

Ion pair extractant selective for LiCl and LiBr

Improved methods for achieving the selective extraction of lithium salts from lithium sources, including rocky ores, salt-lake brines, and end-of-life lithium-ion batteries, could help address projected increases in the demand for lithium. Here, we report an ion pair receptor (2) capable of extracting LiCl and LiBr into an organic receiving phase both from the solid state and from aqueous solutions. Ion pair receptor 2 consists of a calix[4]pyrrole framework, which acts as an anion binding site, linked to a phenanthroline cation binding motif via ether linkages. Receptor 2 binds MgBr 2 and CaCl 2 with high selectivity over the corresponding lithium salts in a nonpolar aprotic solvent. The preference for Mg 2+ and Ca 2+ salts is reversed in polar protic media, allowing receptor 2 to complex LiCl and LiBr with high selectivity and affinity in organic media containing methanol or water. The effectiveness of receptor 2 as an extractant for LiCl and LiBr under liquid–liquid extraction (LLE) conditions was found to be enhanced by the presence of other potentially competitive salts in the aqueous source phase.

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

A structural framework for unidirectional transport by a bacterial ABC exporter

The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from Novosphingobium aromaticivorans (NaAtm1) can export glutathione derivatives and confer protection against heavy-metal toxicity. To establish the structural framework underlying the NaAtm1 transport mechanism, we determined eight structures by X-ray crystallography and single-particle cryo-electron microscopy in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. As NaAtm1 progresses through the transport cycle, conformational changes in transmembrane helix 6 (TM6) alter the glutathione-binding site and the associated substrate-binding cavity. Significantly, kinking of TM6 in the post-ATP hydrolysis state stabilized by MgADPVO4 eliminates this cavity, precluding uptake of glutathione derivatives. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provide an elegant and conceptually simple mechanism for enforcing the export directionality of transport by NaAtm1. One of the disulfide crosslinked NaAtm1 variants characterized in this work retains significant glutathione transport activity, suggesting that ATP hydrolysis and substrate transport by Atm1 may involve a limited set of conformational states with minimal separation of the nucleotide-binding domains in the inward-facing conformation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Production and Improved Separation of Therapeutic Radionuclides Tb-161, Er-165, and Lu-177

This project resulted in the synthesis and utility of new solid-phase extractants using diglycolamide (DGA) extractants grafted onto mesoporous silica. We used DGA ligands that offer multidentate coordination sites for lanthanides and offer pre-arranged binding sites that may facilitate radiolanthanide metal binding. Also, the Hunter graduate student worked at University of Utah on production and separation of 161 Tb with high specific activity resulting in a publication. These are reported in the full text upload.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2022

Cholesterol-induced suppression of Kir2 channels is mediated by decoupling at the inter-subunit interfaces

Cholesterol is a major regulator of multiple types of ion channels. Although there is increasing information about cholesterol binding sites, the molecular mechanisms through which cholesterol binding alters channel function are virtually unknown. In this study, we used a combination of Martini coarse-grained simulations, a network theory-based analysis, and electrophysiology to determine the effect of cholesterol on the dynamic structure of the Kir2.2 channel. We found that increasing membrane cholesterol reduced the likelihood of contact between specific regions of the cytoplasmic and transmembrane domains of the channel, most prominently at the subunit-subunit interfaces of the cytosolic domains. This decrease in contact was mediated by pairwise interactions of specific residues and correlated to the stoichiometry of cholesterol binding events. The predictions of the model were tested by site-directed mutagenesis of two identified residues—V265 and H222—and high throughput electrophysiology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies

Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To understand how this glycan can be recognized, here we isolate two lineages of glycan276-dependent CD4bs antibodies. Antibody CH540-VRC40.01 (named for donor-lineage.clone) neutralizes 81% of a panel of 208 diverse strains, while antibody CH314-VRC33.01 neutralizes 45%. Cryo-electron microscopy (cryo-EM) structures of these two antibodies and 179NC75, a previously identified glycan276-dependent CD4bs antibody, in complex with HIV-envelope trimer reveal substantially different modes of glycan276 recognition. Despite these differences, binding of glycan276-dependent antibodies maintains a glycan276 conformation similar to that observed in the absence of glycan276-binding antibodies. By contrast, glycan276-independent CD4bs antibodies, such as VRC01, displace glycan276 upon binding. These results provide a foundation for understanding antibody recognition of glycan276 and suggest its presence may be crucial for priming immunogens seeking to initiate broad CD4bs recognition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal structure of the kinase domain of a receptor tyrosine kinase from a choanoflagellate, Monosiga brevicollis

Genomic analysis of the unicellular choanoflagellate, Monosiga brevicollis (MB), revealed the remarkable presence of cell signaling and adhesion protein domains that are characteristically associated with metazoans. Strikingly, receptor tyrosine kinases, one of the most critical elements of signal transduction and communication in metazoans, are present in choanoflagellates. We determined the crystal structure at 1.95 Å resolution of the kinase domain of the M . brevicollis receptor tyrosine kinase C8 (RTKC8, a member of the choanoflagellate receptor tyrosine kinase C family) bound to the kinase inhibitor staurospaurine. The chonanoflagellate kinase domain is closely related in sequence to mammalian tyrosine kinases (~ 40% sequence identity to the human Ephrin kinase domain EphA3) and, as expected, has the canonical protein kinase fold. The kinase is structurally most similar to human Ephrin (EphA5), even though the extracellular sensor domain is completely different from that of Ephrin. The RTKC8 kinase domain is in an active conformation, with two staurosporine molecules bound to the kinase, one at the active site and another at the peptide-substrate binding site. To our knowledge this is the first example of staurospaurine binding in the Aurora A activation segment (AAS). We also show that the RTKC8 kinase domain can phosphorylate tyrosine residues in peptides from its C-terminal tail segment which is presumably the mechanism by which it transmits the extracellular stimuli to alter cellular function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Two distinct rotations of bithiazole DNA intercalation revealed by direct comparison of crystal structures of Co(III)•bleomycin A 2 and B 2 bound to duplex 5'-TAGTT sites

Bleomycins constitute a family of anticancer natural products that bind DNA through intercalation of a C-terminal tail/bithiazole moiety and hydrogen-bonding interactions between the remainder of the drug and the minor groove. The clinical utility of the bleomycins is believed to result from single- and double-strand DNA cleavage mediated by the HOO-Fe(III) form of the drug. The bleomycins also serve as a model system to understand the nature of complex drug-DNA interactions that may guide future DNA-targeted drug discovery. In this study, the impact of the C-terminal tail on bleomycin-DNA interactions was investigated. Toward this goal, we determined two crystal structures of HOO-Co(III)•BLMA 2 “green” (a stable structural analogue of the active HOO-Fe(III) drug) bound to duplex DNA containing 5'-TAGTT, one in which the entire drug is bound (fully bound) and a second with only the C-terminal tail/bithiazole bound (partially bound). The structures reported here were captured by soaking HOO-Co(III)•BLMA 2 into preformed host–guest crystals including a preferred DNA-binding site. While the overall structure of DNA-bound BLMA 2 was found to be similar to those reported earlier at the same DNA site for BLMB 2 , the intercalated bithiazole of BLMB 2 is “flipped” 180° relative to DNA-bound BLMA 2 . Further, this finding highlights an unidentified role for the C-terminal tail in directing the intercalation of the bithiazole. In addition, these analyses identified specific bond rotations within the C-terminal domain of the drug that may be relevant for its reorganization and ability to carry out a double-strand DNA cleavage event.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Functional anatomy of zinc finger antiviral protein complexes

Abstract ZAP is an antiviral protein that binds to and depletes viral RNA, which is often distinguished from vertebrate host RNA by its elevated CpG content. Two ZAP cofactors, TRIM25 and KHNYN, have activities that are poorly understood. Here, we show that functional interactions between ZAP, TRIM25 and KHNYN involve multiple domains of each protein, and that the ability of TRIM25 to multimerize via its RING domain augments ZAP activity and specificity. We show that KHNYN is an active nuclease that acts in a partly redundant manner with its homolog N4BP1. The ZAP N-terminal RNA binding domain constitutes a minimal core that is essential for antiviral complex activity, and we present a crystal structure of this domain that reveals contacts with the functionally required KHNYN C-terminal domain. These contacts are remote from the ZAP CpG binding site and would not interfere with RNA binding. Based on our dissection of ZAP, TRIM25 and KHNYN functional anatomy, we could design artificial chimeric antiviral proteins that reconstitute the antiviral function of the intact authentic proteins, but in the absence of protein domains that are otherwise required for activity. Together, these results suggest a model for the RNA recognition and action of ZAP-containing antiviral protein complexes.

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