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Results for “structure determination”

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 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA

Abstract In selected Campylobacter species, the biosynthesis of N‐linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane‐associated GT‐B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N ‐acetylgalatosamine (GalNAc) from uridine 5′‐diphospho‐ N ‐acetylgalactosamine (UDP‐GalNAc) to undecaprenyl‐diphospho‐ N , N ′‐diacetylbacillosamine (UndPP‐diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane‐embedded acceptor and the structural analysis of the complex together with bioinformatics and site‐directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″‐OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate‐specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.

Vuksanovic, Nemanja↗
DOE OSTI2023

Size-Dependent Lattice Symmetry Breaking Determines the Exciton Fine Structure of Perovskite Nanocrystals

The order of bright and dark excitonic states in lead-halide perovskite nanocrystals is debated. It has been proposed that the Rashba effect, driven by lattice-induced symmetry breaking, causes a bright excitonic ground state. Direct measurements of excitonic spectra, however, show the signatures of a dark ground state, bringing the role of the Rashba effect into question. We use an atomistic theory to model the exciton fine structure of perovskite nanocrystals, accounting for realistic lattice distortions. We calculate optical gaps and excitonic features that compare favorably with experimental works. The exciton fine structure splittings show a nonmonotonic size dependence due to a structural transition between cubic and orthorhombic phases. Additionally, the excitonic ground state is found to be dark with spin triplet character, exhibiting a small Rashba coupling. Here we additionally explore the effects of nanocrystal shape on the fine structure, clarifying observations on polydisperse nanocrystals.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Growth of PdCoO 2 films with controlled termination by molecular-beam epitaxy and determination of their electronic structure by angle-resolved photoemission spectroscopy

Utilizing the powerful combination of molecular-beam epitaxy (MBE) and angle-resolved photoemission spectroscopy (ARPES), we produce and study the effect of different terminating layers on the electronic structure of the metallic delafossite PdCoO 2 . Attempts to introduce unpaired electrons and synthesize new antiferromagnetic metals akin to the isostructural compound PdCrO 2 have been made by replacing cobalt with iron in PdCoO 2 films grown by MBE. Using ARPES, we observe similar bulk bands in these PdCoO 2 films with Pd-, CoO 2 -, and FeO 2 -termination. Nevertheless, Pd- and CoO 2 -terminated films show a reduced intensity of surface states. Additionally, we are able to epitaxially stabilize PdFe x Co 1– x O 2 films that show an anomaly in the derivative of the electrical resistance with respect to temperature at 20 K, but do not display pronounced magnetic order.

36 MATERIALS SCIENCE↗
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 OSTI2025

Experimental determination of energy-level structures of diamond silicon-vacancy centers in off-axis magnetic fields

Here, we report the development of an experimental approach to efficiently determine the energy level structure of an individual silicon vacancy (SiV) center in a magnetic field along an arbitrary direction. This approach uses two coupling rates (one each for the ground and the excited states) to characterize the combined effects of static strain and dynamic Jahn-Teller coupling and exploits the fact that orbital Zeeman effects vanish when the magnetic field is normal to the SiV axis. With an analytical expression for the energy level structure of the SiV under a transverse magnetic field, the two coupling rates can be directly derived from two measurements: one on the frequency separation between two spin-conserved transitions and the other on the coherent population trapping resonance of the SiV ground spin states. A detailed comparison between the numerical calculation and the experimental result on the dependence of the spin-conserved splitting on both the amplitude and direction of the magnetic field further reveals unequal orbital magnetic coupling for the ground and excited states, indicating that unequal orbital quenching factors are needed for an accurate description of the SiV energy level structure in a magnetic field.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data

In this work, we have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 Å 2 , a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 Å2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (S CD ) profiles calculated from the simulations were in relatively good agreement with S CD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 Å 2 resulted in good agreement between the simulation and experimental scattering form factors, but not with S CD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.

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

Polymer-based microfluidic device for on-chip counter-diffusive crystallization and in situ X-ray crystallography at room temperature

Proteins are long chains of amino acid residues that perform a myriad of functions in living organisms, including enzymatic reactions, signalling, and maintaining structural integrity. Protein function is determined directly by the protein structure. X-ray crystallography is the primary technique for determining the 3D structure of proteins, and facilitates understanding the effects of protein structure on function. The first step towards structure determination is crystallizing the protein of interest. We have developed a centrifugally-actuated microfluidic device that incorporates the fluid handling and metering necessary for protein crystallization. Liquid handling takes advantage of surface forces to control fluid flow and enable metering, without the need for any fluidic or pump connections. Our approach requires only the simple steps of pipetting the crystallization reagents into the device followed by either spinning or shaking to set up counter-diffusive protein crystallization trials. The use of thin, UV-curable polymers with a high level of X-ray transparency allows for in situ X-ray crystallography, eliminating the manual handling of fragile protein crystals and streamlining the process of protein structure analysis. We demonstrate the utility of our device using hen egg white lysozyme as a model system, followed by the crystallization and in situ, room temperature structural analysis of the hub domain of calcium–calmodulin dependent kinase II (CaMKIIβ).

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

Insights from Femtosecond Transient Absorption Spectroscopy into the Structure–Function Relationship of Glyceline Deep Eutectic Solvents

This study aimed to determine the structure–function relationship (SFR) for ChCl–glycerol mixtures, a deep eutectic solvent (DES), by investigating their microscopic solvation dynamics and how it relates to their macroscopic properties across varying concentrations of ChCl. Femtosecond transient absorption (fs-TA) spectroscopy revealed two distinct solvation dynamics time constants: τ 1 , governed by glycerol–glycerol interactions, and τ 2 , dominated by the choline response. The τ 2 minimum at 25–30 mol % ChCl closely aligned with the eutectic composition (~33.33 mol % ChCl), where the glycerol network was the most organized and the choline ions exhibited the fastest relaxation. The viscosity decreased sharply up to ~25 mol % ChCl and then plateaued, while the conductivity increased monotonically with ChCl concentration, reflecting enhanced ionic mobility. The density decreased with both increasing ChCl concentration and temperature, indicating disrupted hydrogen bonding and reduced molecular packing. The polarity, measured using betaine-30 (B30) and the E T (30) polarity scale, increased steeply up to approximately 25 mol % ChCl before reaching a plateau. These findings identified the eutectic composition as the optimal concentration range for balancing stability, fluidity, conductivity, and enhanced dynamics within the glycerol system.

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

Electrolyte/Dye/TiO 2 Interfacial Structures of Dye-Sensitized Solar Cells Revealed by In Situ Neutron Reflectometry with Contrast Matching

The nature of an interfacial structure buried within a device assembly is often critical to its function. For example, the dye/TiO 2 interfacial structure that comprises the working electrode of a dye-sensitized solar cell (DSC) governs its photovoltaic output. These structures have been determined outside of the DSC device, using ex situ characterization methods; yet, they really should be probed while held within a DSC since they are modulated by the device environment. Dye/TiO 2 structures will be particularly influenced by a layer of electrolyte ions that lies above the dye self-assembly. We show that electrolyte/dye/TiO 2 interfacial structures can be resolved using in situ neutron reflectometry with contrast matching. Here, we find that electrolyte constituents ingress into the self-assembled monolayer of dye molecules that anchor onto TiO 2 . Some dye/TiO 2 anchoring configurations are modulated by the formation of electrolyte/dye intermolecular interactions. These electrolyte-influencing structural changes will affect dye-regeneration and electron-injection DSC operational processes. This underpins the importance of this in situ structural determination of electrolyte/dye/TiO 2 interfaces within representative DSC device environments.

14 SOLAR ENERGY↗
DOE OSTI2025

Potent HIV‑1 protease inhibitors containing oxabicyclo octanol-derived P2-ligands: Design, synthesis, and X‑ray structural studies of inhibitor-HIV-1 protease complexes

Here, we describe here the design, synthesis, and X-ray structural studies of a new class of HIV-1 protease inhibitors containing 8-oxabicyclo[3.2.1]octanol-derived P2 ligands. We investigated the functional effect of these stereochemically defined fused-poly cyclic ligands on enzyme inhibition and antiviral activity in MT-2 cells. The tricyclic core of 8-oxabicyclo[3.2.1]octan-6-ol is designed to interact with the residues in the S2 subsite of HIV-1 protease. The syntheses of the ligands were carried out using the [5+2]-cycloaddition as the key step. Several inhibitors exhibited potent enzyme inhibitory activity. High resolution room-temperature X-ray structures of inhibitor-bound HIV-1 protease were determined. These structures provided important molecular insights for further design and optimization of inhibitor potency.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Exploration of imatinib and nilotinib-derived templates as the P2-Ligand for HIV-1 protease inhibitors: Design, synthesis, protein X-ray structural studies, and biological evaluation

Structure-based design, synthesis, X-ray structural studies, and biological evaluation of a new series of potent HIV-1 protease inhibitors are described. Here, these inhibitors contain various pyridyl-pyrimidine, aryl thiazole or alkylthiazole derivatives as the P2 ligands in combination with darunavir-like hydroxyethylamine sulfonamide isosteres. These heterocyclic ligands are inherent to kinase inhibitor drugs, such as nilotinib and imatinib. These ligands are designed to make hydrogen bonding interactions with the backbone atoms in the S2 subsite of HIV-1 protease. Various benzoic acid derivatives have been synthesized and incorporation of these ligands provided potent inhibitors that exhibited subnanomolar level protease inhibitory activity and low nanomolar level antiviral activity. Two high resolution X-ray structures of inhibitor-bound HIV-1 protease were determined. These structures provided important ligand-binding site interactions for further optimization of this class of protease inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Structure-based decoupling of the pro- and anti-inflammatory functions of interleukin-10

Interleukin-10 (IL-10) is an immunoregulatory cytokine with both anti-inflammatory and immunostimulatory properties and is frequently dysregulated in disease. We used a structure-based approach to deconvolute IL-10 pleiotropy by determining the structure of the IL-10 receptor (IL-10R) complex by cryo–electron microscopy at a resolution of 3.5 angstroms. The hexameric structure shows how IL-10 and IL-10Rα form a composite surface to engage the shared signaling receptor IL-10Rβ, enabling the design of partial agonists. IL-10 variants with a range of IL-10Rβ binding strengths uncovered substantial differences in response thresholds across immune cell populations, providing a means of manipulating IL-10 cell type selectivity. Some variants displayed myeloid-biased activity by suppressing macrophage activation without stimulating inflammatory CD8 + T cells, thereby uncoupling the major opposing functions of IL-10. These results provide a mechanistic blueprint for tuning the pleiotropic actions of IL-10.

60 APPLIED LIFE SCIENCES↗