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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 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
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 OSTI2020

Device-quality, reconfigurable metamaterials from shape-directed nanocrystal assembly

Significance Colloidal nanocrystals with defined sizes and shapes are ideal building blocks for nanofabrication. However, the ability to arbitrarily arrange them on surfaces with control over their orientation remains elusive. Here we report a shallow-template-assisted DNA-mediated assembly strategy to precisely arrange colloidal nanocrystals on surfaces, with single-particle control across submillimeter areas. In addition, the oligonucleotide bonds between the nanocrystals and substrate can be reversibly expanded and contracted enabling postsynthetic tunability of the assembled structures. Using this approach, we synthesized a nanocrystal-based, dynamically tunable metasurface (an anomalous reflector), thereby illustrating the potential for unique device construction via DNA programmable assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Ground-state phase diagram of the t-t ′ -J model

Significance Theoretical efforts to understand the superconducting cuprates have focused on a few simplified but challenging models: notably the Hubbard and the t - t ′ - J models. Using density matrix renormalization group (DMRG) simulations on width-8 cylinders, we study the ground-state phase diagram of the t - t ′- J model. The next nearest-neighbor hopping t ′ allows one to distinguish between hole ( t ′ < 0 ) and electron doping ( t ′ > 0 ). We find for the magnetic, charge, and single-particle properties that this model roughly captures the differences between the electron- and hole-doped cuprates. However, the superconducting properties differ. For hole doping ( t ′ < 0 ), there is an absence of superconductivity, while for electron doping ( t ′ > 0), we find d -wave superconductivity coexisting with antiferromagnetism and a secondary triplet p -wave pairing component.

Jiang, Shengtao↗
DOE OSTI2021

Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies)

We describe a general method that allows structure determination of small proteins by single-particle cryo-electron microscopy (cryo-EM). The method is based on the availability of a target-binding nanobody, which is then rigidly attached to two scaffolds: 1) a Fab fragment of an antibody directed against the nanobody and 2) a nanobody-binding protein A fragment fused to maltose binding protein and Fab-binding domains. The overall ensemble of ~120 kDa, called Legobody, does not perturb the nanobody–target interaction, is easily recognizable in EM images due to its unique shape, and facilitates particle alignment in cryo-EM image processing. The utility of the method is demonstrated for the KDEL receptor, a 23-kDa membrane protein, resulting in a map at 3.2-Å overall resolution with density sufficient for de novo model building, and for the 22-kDa receptor-binding domain (RBD) of SARS-CoV-2 spike protein, resulting in a map at 3.6-Å resolution that allows analysis of the binding interface to the nanobody. The Legobody approach thus overcomes the current size limitations of cryo-EM analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Single molecule tracking of bacterial cell surface cytochromes reveals dynamics that impact long-distance electron transport

Using a series of multiheme cytochromes, the metal-reducing bacterium Shewanella oneidensis MR-1 can perform extracellular electron transfer (EET) to respire redox-active surfaces, including minerals and electrodes outside the cell. While the role of multiheme cytochromes in transporting electrons across the cell wall is well established, these cytochromes were also recently found to facilitate long-distance (micrometer-scale) redox conduction along outer membranes and across multiple cells bridging electrodes. Recent studies proposed that long-distance conduction arises from the interplay of electron hopping and cytochrome diffusion, which allows collisions and electron exchange between cytochromes along membranes. However, the diffusive dynamics of the multiheme cytochromes have never been observed or quantified in vivo, making it difficult to assess their hypothesized contribution to the collision-exchange mechanism. Here, we use quantum dot labeling, total internal reflection fluorescence microscopy, and single-particle tracking to quantify the lateral diffusive dynamics of the outer membrane-associated decaheme cytochromes MtrC and OmcA, two key components of EET in S. oneidensis. We observe confined diffusion behavior for both quantum dot-labeled MtrC and OmcA along cell surfaces (diffusion coefficients D MtrC = 0.0192 ± 0.0018 µm 2 /s, D OmcA = 0.0125 ± 0.0024 µm 2 /s) and the membrane extensions thought to function as bacterial nanowires. We find that these dynamics can trace a path for electron transport via overlap of cytochrome trajectories, consistent with the long-distance conduction mechanism. The measured dynamics inform kinetic Monte Carlo simulations that combine direct electron hopping and redox molecule diffusion, revealing significant electron transport rates along cells and membrane nanowires.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants

The serotonin transporter (SERT) is a member of the SLC6 neurotransmitter transporter family that mediates serotonin reuptake at presynaptic nerve terminals. SERT is the target of both therapeutic antidepressant drugs and psychostimulant substances such as cocaine and methamphetamines, which are small molecules that perturb normal serotonergic transmission by interfering with serotonin transport. Despite decades of studies, important functional aspects of SERT such as the oligomerization state of native SERT and its interactions with potential proteins remain unresolved. Here, we develop methods to isolate SERT from porcine brain (pSERT) using a mild, nonionic detergent, utilize fluorescence-detection size-exclusion chromatography to investigate its oligomerization state and interactions with other proteins, and employ single-particle cryo-electron microscopy to elucidate the structures of pSERT in complexes with methamphetamine or cocaine, providing structural insights into psychostimulant recognition and accompanying pSERT conformations. Methamphetamine and cocaine both bind to the central site, stabilizing the transporter in an outward open conformation. We also identify densities attributable to multiple cholesterol or cholesteryl hemisuccinate (CHS) molecules, as well as to a detergent molecule bound to the pSERT allosteric site. Under our conditions of isolation, we find that pSERT is best described as a monomeric entity, isolated without interacting proteins, and is ensconced by multiple cholesterol or CHS molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Identification of a carbonic anhydrase–Rubisco complex within the alpha-carboxysome

Carboxysomes are proteinaceous organelles that encapsulate key enzymes of CO 2 fixation—Rubisco and carbonic anhydrase—and are the centerpiece of the bacterial CO 2 concentrating mechanism (CCM). In the CCM, actively accumulated cytosolic bicarbonate diffuses into the carboxysome and is converted to CO 2 by carbonic anhydrase, producing a high CO 2 concentration near Rubisco and ensuring efficient carboxylation. Self-assembly of the α-carboxysome is orchestrated by the intrinsically disordered scaffolding protein, CsoS2, which interacts with both Rubisco and carboxysomal shell proteins, but it is unknown how the carbonic anhydrase, CsoSCA, is incorporated into the α-carboxysome. Here, we present the structural basis of carbonic anhydrase encapsulation into α-carboxysomes from Halothiobacillus neapolitanus . We find that CsoSCA interacts directly with Rubisco via an intrinsically disordered N-terminal domain. A 1.98 Å single-particle cryoelectron microscopy structure of Rubisco in complex with this peptide reveals that CsoSCA binding is predominantly mediated by a network of hydrogen bonds. CsoSCA's binding site overlaps with that of CsoS2, but the two proteins utilize substantially different motifs and modes of binding, revealing a plasticity of the Rubisco binding site. Our results advance the understanding of carboxysome biogenesis and highlight the importance of Rubisco, not only as an enzyme but also as a central hub for mediating assembly through protein interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

B56$δ$ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan’s syndrome mutations

Intrinsically disordered regions (IDR) and short linear motifs (SLiMs) play pivotal roles in the intricate signaling networks governed by phosphatases and kinases. B56δ (encoded by PPP2R5D) is a regulatory subunit of protein phosphatase 2A (PP2A) with long IDRs that harbor a substrate-mimicking SLiM and multiple phosphorylation sites. De novo missense mutations in PPP2R5D cause intellectual disabilities (ID), macrocephaly, Parkinsonism, and a broad range of neurological symptoms. Our single-particle cryo-EM structures of the PP2A-B56δ holoenzyme reveal that the long, disordered arms at the B56δ termini fold against each other and the holoenzyme core. This architecture suppresses both the phosphatase active site and the substrate-binding protein groove, thereby stabilizing the enzyme in a closed latent form with dual autoinhibition. The resulting interface spans over 190 Å and harbors unfavorable contacts, activation phosphorylation sites, and nearly all residues with ID-associated mutations. Our studies suggest that this dynamic interface is coupled to an allosteric network responsive to phosphorylation and altered globally by mutations. Furthermore, we found that ID mutations increase the holoenzyme activity and perturb the phosphorylation rates, and the severe variants significantly increase the mitotic duration and error rates compared to the normal variant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural and functional dynamics of human cone cGMP-phosphodiesterase important for photopic vision

Cone cGMP-phosphodiesterase (PDE6) is the key effector enzyme for daylight vision, and its properties are critical for shaping distinct physiology of cone photoreceptors. We determined the structures of human cone PDE6C in various liganded states by single-particle cryo-EM that reveal essential functional dynamics and adaptations of the enzyme. Our analysis exposed the dynamic nature of PDE6C association with its regulatory γ-subunit (Pγ) which allows openings of the catalytic pocket in the absence of phototransduction signaling, thereby controlling photoreceptor noise and sensitivity. We demonstrate evolutionarily recent adaptations of PDE6C stemming from residue substitutions in the Pγ subunit and the noncatalytic cGMP binding site and influencing the Pγ dynamics in holoPDE6C. Thus, our structural analysis sheds light on the previously unrecognized molecular evolution of the effector enzyme in cones that advances adaptation for photopic vision.

Science & Technology - Other Topics↗
DOE OSTI2025

A distinct LHCI arrangement is recruited to photosystem I in Fe-starved green algae

Iron (Fe) availability limits photosynthesis at a global scale where Fe-rich photosystem (PS) I abundance is drastically reduced in Fe-poor environments. We used single-particle cryoelectron microscopy to reveal a unique Fe starvation-dependent arrangement of light-harvesting chlorophyll (LHC) proteins where Fe starvation–induced TIDI1 is found in an additional tetramer of LHC proteins associated with PSI in Dunaliella tertiolecta and Dunaliella salina . These cosmopolitan green algae are resilient to poor Fe nutrition. TIDI1 is a distinct LHC protein that co-occurs in diverse algae with flavodoxin (an Fe-independent replacement for the Fe-containing ferredoxin). The antenna expansion in eukaryotic algae we describe here is reminiscent of the iron-starvation induced (isiA-encoding) antenna ring in cyanobacteria, which typically co-occurs with isiB , encoding flavodoxin. Our work showcases the convergent strategies that evolved after the Great Oxidation Event to maintain PSI capacity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles

Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) spike proteins that recognize SARS-CoV-2 variants of concern and zoonotic sarbecoviruses, we developed mosaic-8b RBD nanoparticles presenting eight sarbecovirus RBDs arranged randomly on a 60-mer nanoparticle. Mosaic-8b immunizations protected animals from challenges from viruses whose RBDs were matched or mismatched to those on nanoparticles. Here, we describe neutralizing mAbs isolated from mosaic-8b-immunized rabbits, some on par with Pemgarda, the only currently FDA-approved therapeutic mAb. Deep mutational scanning, in vitro selection of spike resistance mutations, and single-particle cryo-electron microscopy structures of spike–antibody complexes demonstrated targeting of conserved RBD epitopes. Rabbit mAbs included critical D-gene segment RBD-recognizing features in common with human anti-RBD mAbs, despite rabbit genomes lacking an equivalent human D-gene segment, thus demonstrating that the immune systems of humans and other mammals can utilize different antibody gene segments to arrive at similar modes of antigen recognition. These results suggest that animal models can be used to elicit anti-RBD mAbs with similar properties to those raised in humans, which can then be humanized for therapeutic use, and that mosaic RBD nanoparticle immunization coupled with multiplexed screening represents an efficient way to generate and select broadly cross-reactive therapeutic pan-sarbecovirus and pan-SARS-CoV-2 variant mAbs.

Science & Technology - Other Topics↗
DOE OSTI2022

The X-ray Focusing System at the Time-Resolved AMO Instrument

The emergence of X-ray Free Electron Lasers (XFELs) in recent years has opened up new fields of research, with the merging of short wavelengths and ultrafast timescales. As XFEL facilities including the Linac Coherent Light Source (LCLS) have matured, there is renewed interest in pushing the performance boundaries of experimental endstations, as well as improving ease of operation for experiments. One of the major areas of improvement is that of X-ray micro- and nano-focusing. The focus quality is directly linked to the peak intensity at the interaction point with a sample, and is especially important for intensity-dependent (e.g. x-ray pump) studies and imaging efforts such as single particle imaging.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

The Electron Spectro-Microscopy (ESM) Beamline at NSLS-II

Photoelectron spectroscopy is a primary tool for the study of the electronic structure of materials and the chemical composition of surfaces. High-resolution angle-resolved photoemission spectroscopy (ARPES) has the unique ability to map the energy bands in momentum space. Furthermore, going beyond the single particle picture, the self-energy corrections caused by correlations in solids can be extracted from the analysis of the emission line shape. The current level of refinement, in terms of energy and angular resolution (ΔE < 1 meV, Δθ < 0.1°), makes the technique sensitive to the lowest energy excitations and the dynamics of electrons, which in turn virtually determine all the macroscopic properties of any system and govern the chemical, electrical, magnetic, and physical processes. Similarly important, X-ray photoelectron microscopy (XPEEM), combined with the low-energy electron microscopy (LEEM), is indispensable in probing the complexity of chemical, structural, electronic and magnetic properties of surfaces and shallow interfaces, with the spatial resolution of few tens of nanometer (nm). The Electron-Spectro-Microscopy beamline (ESM) has been recently commissioned at NSLS-II and is now in operation. The primary spectroscopic technique is photoemission, performed over a wide energy range with control of light polarization and in a variety of flux/resolution conditions. The beamline has two experimental end stations that allow to perform ARPES and XPEEM/LEEM, separately. The ARPES end station focuses on high energy-resolution work, with spot-size of a few microns. The XPEEM/LEEM end station is a full-field microscope (XPEEM) operating either with the synchrotron generated X-rays (XPEEM), or with an internal electron gun (LEEM). Spatial resolution is crucial in studies of newly synthesized complex materials since they are often initially available only as small specimens (typically micron size). Furthermore, chemical inhomogeneities on surfaces are often an integral part of surface chemical processes. Finally, the ESM beamline with X-ray spots of few microns is optimized to study the electronic structure of novel materials with microscopy capabilities.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP

YiiP is a secondary transporter that couples Zn 2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn 2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn 2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn 2+ . To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn 2+ and validated its performance with known Zn 2+ -binding proteins. Using these tools, we find that, in the presence of Zn 2+ , YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn 2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn 2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn 2+ binding sites and their role in the conformational dynamics that govern the transport cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cooper minima in high-Z atoms: effects of correlation and relativity on np photoionization

Abstract Photoionization dipole transition matrix elements pass through a zero or attain a minimum that leaves imprints on photoionization parameters like the cross-section, angular distribution asymmetry parameter, phase shift, and photoionization time delay. This minimum is commonly known as the ‘Cooper minimum’ (CM). The CM, in general, is strongly affected by relativistic and correlation effects. Previous works investigated CM in the 6pand 5psubshell photoionization up toZ= 100 using the single-particle Dirac-Slater (DS) method. The present work extends the earlier work toZup to 120 using more accurate methods; Dirac–Hartree–Fock (DHF) which includes the relativistic effects and exchange correlations, and the relativistic random phase approximation (RRPA) which includes both initial and final state electron-electron correlations along with relativistic effects. In addition to the study of photoionization from the 6pand 5psubshells, the 4psubshell has also been investigated in the present work. To demonstrate the prominent effects in the high-Z atoms, Rn (Z= 86), Ra (Z= 88), No (Z= 102), Cn (Z = 112), Og (Z= 118), and Ubn (Z= 120) are investigated.

Optics↗
DOE OSTI2020

Intrinsic operators for the translationally-invariant many-body problem

Abstract The need to enforce fermionic antisymmetry in the nuclear many-body problem commonly requires use of single-particle coordinates, defined relative to some fixed origin. To obtain physical operators which nonetheless act on the nuclear many-body system in a Galilean-invariant fashion, thereby avoiding spurious center-of-mass contributions to observables, it is necessary to express these operators with respect to the translational intrinsic frame. Several commonly-encountered operators in nuclear many-body calculations, including the magnetic dipole and electric quadrupole operators (in the impulse approximation) and generators of U(3) and Sp ( 3 , R ) symmetry groups, are bilinear in the coordinates and momenta of the nucleons and, when expressed in intrinsic form, become two-body operators. To work with such operators in a second-quantized many-body calculation, it is necessary to relate three distinct forms: the defining intrinsic-frame expression, an explicitly two-body expression in terms of two-particle relative coordinates, and a decomposition into one-body and separable two-body parts. We establish the relations between these forms, for general (non-scalar and non-isoscalar) operators bilinear in coordinates and momenta.

Physics↗
DOE OSTI2023

Proton-neutron entanglement in the nuclear shell model

Abstract We compute the proton-neutron entanglement entropy in the interacting nuclear shell model for a variety of nuclides and interactions. Some results make intuitive sense, for example, that the shell structure, as governed by single-particle and monopole energies, strongly affects the energetically available space and thus the entanglement entropy. We also find a surprising result: that the entanglement entropy at low excitation energy tends to decrease for nuclides when N ≠ Z . While we provide evidence this arises from the physical nuclear force by contrasting with random two-body interactions which shows no such decrease, the exact mechanism is unclear. Nonetheless, the low entanglement suggests that in models of neutron-rich nuclides, the coupling between protons and neutrons may be less computationally demanding than one might otherwise expect.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗