NOVEL CHEMICALLY STABLE Ba3Ca1.18Nb1.82-xYxO9-bPROTON CONDUCTOR:IMPROVED PROTON CONDUCTIVITY THROUGH TAILORED CATION ORDERING
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carbon sequestration↗
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Results for “structural complexity”
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Structures of the CRISPR genome integration complex
CRISPR-Cas systems depend on the Cas1-Cas2 integrase to capture and integrate short foreign DNA fragments into the CRISPR locus, enabling adaptation to new viruses. In this paper, we present crystal structures of Cas1-Cas2 bound to both donor and target DNA in intermediate and product integration complexes, as well as a cryo–electron microscopy structure of the full CRISPR locus integration complex, including the accessory protein IHF (integration host factor). The structures show unexpectedly that indirect sequence recognition dictates integration site selection by favoring deformation of the repeat and the flanking sequences. IHF binding bends the DNA sharply, bringing an upstream recognition motif into contact with Cas1 to increase both the specificity and efficiency of integration. Lastly, these results explain how the Cas1-Cas2 CRISPR integrase recognizes a sequence-dependent DNA structure to ensure site-selective CRISPR array expansion during the initial step of bacterial adaptive immunity.
59 BASIC BIOLOGICAL SCIENCES↗
4,4′-Bipyridine-aided synthesis and characterization of Zn(II) and Cd(II) 2-sulfoterephthalate complexes
Six d{sup 10} complexes, [Zn{sub 1.5}(stp)(bpy){sub 0.5}(H{sub 2}O){sub 2}]·0.5H{sub 2}O (1), Cd{sub 1.5}(stp)(bpy){sub 0.5}(H{sub 2}O){sub 2} (2), [Cd{sub 1.5}(stp)(bpy)(H{sub 2}O)]·H{sub 2}O (3), [Zn{sub 0.5}(bpy){sub 0.5}(H{sub 2}O){sub 2}][Zn(stp)(bpy)(H{sub 2}O)]·0.5H{sub 2}O (4), Cd{sub 3}(stp){sub 2}(bpy){sub 3}(H{sub 2}O){sub 3} (5), Hbpy·[Zn{sub 0.5}(bpy)(H{sub 2}O){sub 2}][Zn{sub 0.5}(stp)(H{sub 2}O)]·H{sub 2}O (6) based on 2-sulfoterephthalate (stp{sup 3−}) and 4,4′-bipyridine (bpy) have been synthesized under hydro/solvo-thermal conditions and structurally characterized. Complex 1 exhibits a three-fold interpenetrated 3D porous architecture. Complexes 2 and 3 possess helices with different chirality arranging alternately. 4 and 6 are addition compounds, which compose of complex cation and complex anion. Complex 5 features a 3D layer-pillar framework in which a (4, 4) grid layer is constructed by stp{sup 3−} ligands and Cd(II) ions, and the layers are further connected by bpy pillars. The solid-state luminescent properties of the coordination polymers have also been investigated. - Graphical abstract: Display Omitted - Highlights: • Complexes 1–3 possess helices with different chirality arranging alternately. • The structural diversity can be attributed to various coordination modes of ligands. • The formation of helical structure is related to the adjacent carboxyl and sulfonate groups. • Bpy exhibits three roles: bridge, hydrogen bonding acceptor, and template.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Single-Molecule Fluorescence Spectroscopy of Photosynthetic Systems
Photosynthesis begins when a network of pigment–protein complexes captures solar energy and transports it to the reaction center, where charge separation occurs. When necessary (under low light conditions), photosynthetic organisms perform this energy transport and charge separation with near unity quantum efficiency. Remarkably, this high efficiency is maintained under physiological conditions, which include thermal fluctuations of the pigment–protein complexes and changing local environments. These conditions introduce multiple types of heterogeneity in the pigment–protein complexes, including structural heterogeneity, energetic heterogeneity, and functional heterogeneity. Understanding how photosynthetic light-harvesting functions in the face of these fluctuations requires understanding this heterogeneity, which, in turn, requires characterization of individual pigment–protein complexes. Single-molecule spectroscopy has the power to probe individual complexes. In this review, we present an overview of the common techniques for single-molecule fluorescence spectroscopy applied to photosynthetic systems and describe selected experiments on these systems. We discuss how these experiments provide a new understanding of the impact of heterogeneity on light harvesting and thus how these systems are optimized to capture sunlight under physiological conditions.
14 SOLAR ENERGY↗
Influence of Steric and Electronic Properties of P2 Groups on Covalent Inhibitor Binding to SARS-CoV-2 Main Protease
The main protease (MPro) of SARS-CoV-2 is a critical enzyme required for viral replication, making it a prime target for antiviral drug development. Covalent inhibitors, which form a stable interaction with the catalytic C145, have demonstrated strong inhibition of MPro, but the influence of steric and electronic properties of P2 substituents, designed to engage the S2 substrate-binding subsite within the MPro active site, on inhibitor binding affinity remains underexplored. Here, in this study, we design and characterize two hybrid covalent inhibitors, BBH-3 and BBH-4, and present their X-ray crystallographic structures in complex with MPro, providing molecular insights into how their distinct P2 groups, a dichlorobenzyl moiety in BBH-3 and an adamantyl substituent in BBH-4, affect binding conformation and active site adaptability. Comparative structural analyses with previously characterized inhibitors, including BBH-2 and Mcule-5948770040, reveal how the P2 bulkiness and electronic properties influence active site dynamics, particularly through interactions with the S2 and S5 subsites. The P2 group of BBH-3 induces conformational shifts in the S2 helix and the S5 loop, while BBH-4 displaces M49, stabilizing its binding through hydrophobic interactions. Isothermal titration calorimetry further elucidates the impact of P2 modifications on inhibitor affinity, revealing a delicate balance between enthalpic and entropic contributions. The data demonstrate that BBH-3 exhibits less favorable binding, affirming that dichlorobenzyl substitution at the P2 position has a more negative impact on the affinity for MPro than bulky saturated cyclic groups. This underscores the feature that MPro active site malleability may be accompanied by a conformational strain.
SARS-CoV-2↗
Improving Ligand Geometry in Protein Data Bank Structures Computationally
Information about the three‐dimensional structures of complex biological molecules is an indispensable research tool for many fields of study, including biology, chemistry, pharmacology, and computer science. The Protein Data Bank (PDB) is an public digital archive providing access to structures of nucleic acids, proteins, and large macromolecular machines determined experimentally by X‐ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and 3‐dimensional electron microscopy (3DEM). PDB structures undergo validation for structural plausibility upon their deposition into the PDB using the program Mogul, which cross references each deposited structure against similar data in the Cambridge Structural Database (CSD). Ligands associated with PDB structures are a common source of structural inaccuracy. In this study, a programmatic pipeline was developed to determine if ligand geometric accuracy could be improved using known computational tools. Ligands with dubious geometry were identified through a Python mining code. A sample set of the identified structures was remodeled into minimum energy conformations using the molecular dynamics program AMBER and then fit to the original experimental density maps using the molecular modeling program Coot. The refined models were compared to the original models in the PDB as well as to similar structures in the CSD using the deposition statistical validation server. Preliminary results suggest that the pipeline effectively identifies and improves ligand structures that possess inaccurate geometry. This method can be used to evaluate and improve the accuracy of specific ligands in structures both archived and pending deposition. Support or Funding Information This work was supported by an NSF REU and the RCSB PDB [NSF (DBI‐1338415), NIH, and DOE.] This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Miller, Beck↗
Insulating ground state and 2−𝑘 magnetic structure of candidate Weyl hydrogen-atom K2Mn3(AsO4)3
The ideal Weyl "hydrogen-atom" semimetal exhibits only a single pair of Weyl nodes and no other trivial states at the Fermi energy. Such a material would be a panacea in the study of Weyl quasi-particles, allowing direct unambiguous observation of their topological properties. The alluaudite-like K2Mn3(AsO4)3 compound was recently proposed as such a material. Here, we use comprehensive experimental work and first-principle calculations to assess this prediction. We find K2Mn3(AsO4)3 crystallizes in the 𝐶2/𝑐 symmetry with a quasi-one-dimensional Mn sublattice, growing as small needle-like crystals. Bulk property measurements reveal magnetic transitions at ≈8 and ≈4 K, which neutron scattering experiments show correspond to two distinct magnetic orders, first a partially ordered ferrimagnetic 𝐤𝟏=(0,0,0) structure at 8 K and a second transition of 𝐤𝟐=(1,0,0) at 4 K to a fully ordered state. Below the second transition, both ordering vectors are necessary to describe the complex magnetic structure with modulated spin magnitudes. Both of the best-fit magnetic structures in this work are found to break the symmetry necessary for the generation of Weyl nodes, though one of the magnetic structures allowed by 𝐤𝟏 does preserve this symmetry. However, the crystals are optically transparent and ellipsometry measurements reveal a large band gap, undermining expectations of semimetallic behavior. Density functional theory calculations predict an insulating antiferromagnetic ground state, in contrast to previous reports, and suggest potential frustration on the magnetic sublattice. Given the wide tunability of the alluaudite structure, we consider ways to push the system closer to a semimetallic state.
Taddei, Keith M [Argonne National Laboratory]↗
Resonant X-ray scattering of biological assemblies
Understanding the relationship between structure and function for biological assemblies can guide identification of new therapeutics, design of biomaterials, and development of biotechnological processes. Resonant X-ray scattering provides a chemically-specific approach to characterize complex biological structures based on anomalous or resonant scattering from a specific element or chemical moiety. Anomalous or resonant diffraction can provide structural details with high atomic resolution, while resonant X-ray scattering can provide structural details with lower resolution through tender or soft X-rays. Furthermore, we review applications, challenges, and opportunities for resonant X-ray scattering in the field of structural biology.
36 MATERIALS SCIENCE↗
Mechanical Response of Additively Manufactured Stainless Steel 304L Across a Wide Range of Loading Conditions
The mechanical response of additively manufactured (AM) stainless steel 304L has been investigated across a broad range of loading conditions, covering 11 decades of strain rate, and compared with the behaviors of traditional ingot-derived (wrought) material. In general, the AM material exhibits a greater strength and reduced ductility compared with the baseline wrought form. These differences are consistently found from quasi-static and high strain rate tests. A detailed investigation of the microstructure, the defect structure, the phase, and the composition of both forms reveals differences that may contribute to the differing mechanical behaviors. Compared with the baseline wrought material, dense AM stainless steel 304L has a more complex grain structure with substantial sub-structure, a fine dispersion of ferrite, increased dislocation density, oxide dispersions and larger amounts of nitrogen. In-situ neutron diffraction studies conducted during quasi-static loading suggest that the increased strength of AM material is due to its initially greater dislocation density. The flow strength of both forms is correlated with dislocation density through a square root dependence akin to a Taylor-like relationship. Neutron diffraction measurements of lattice strains also correlate with a crystal plasticity finite element simulations of the tensile test. Other simulations predict a significant degree of elastic and plastic anisotropy due to crystallographic texture. Hopkinson tests at higher strain rates $\dot{ε}$ = 500 and 2500 s -1 ) also show a greater strength for AM stainless steel 304L; although, the differences compared with wrought are reduced at higher strain rates. Gas gun impact tests, including reverse ballistic, forward ballistic and spall tests, consistently reveal a larger dynamic strength in the AM material. The Hugoniot Elastic Limit (HEL) of AM SS 304L exceeds that of wrought material although considerable variability is observed with the AM material. Forward ballistic testing demonstrates spall strengths of AM material (3.27 -- 3.91 GPa) that exceed that of the wrought material (2.63 -- 2.88 GPa). The Hugoniot equation-of-state for AM samples matches archived data for this metal alloy.
36 MATERIALS SCIENCE↗
Holographic Fabrication of 3D Moiré Photonic Crystals Using Circularly Polarized Laser Beams and a Spatial Light Modulator
A moiré photonic crystal is an optical analog of twisted graphene. A 3D moiré photonic crystal is a new nano-/microstructure that is distinguished from bilayer twisted photonic crystals. Holographic fabrication of a 3D moiré photonic crystal is very difficult due to the coexistence of the bright and dark regions, where the exposure threshold is suitable for one region but not for the other. In this paper, we study the holographic fabrication of 3D moiré photonic crystals using an integrated system of a single reflective optical element (ROE) and a spatial light modulator (SLM) where nine beams (four inner beams + four outer beams + central beam) are overlapped. By modifying the phase and amplitude of the interfering beams, the interference patterns of 3D moiré photonic crystals are systemically simulated and compared with the holographic structures to gain a comprehensive understanding of SLM-based holographic fabrication. We report the holographic fabrication of phase and beam intensity ratio-dependent 3D moiré photonic crystals and their structural characterization. Superlattices modulated in the z-direction of 3D moiré photonic crystals have been discovered. This comprehensive study provides guidance for future pixel-by-pixel phase engineering in SLM for complex holographic structures.
42 ENGINEERING↗
Study of the structural features of ε-Co nanoparticles synthesized by cobalt carbonyl decomposition in the presence of surfactant
Cobalt nanoparticles (3–7 nm in size) obtained by cobalt carbonyl decomposition in 1,2-dichlorobenzene in the presence of surfactants (trioctylphosphine oxide and oleic acid) have been studied by a complex of structural methods: small-angle X-ray scattering, electron diffraction, and transmission electron microscopy. The nanoparticles synthesized are found to consist of the cubic ε-Со phase; their crystal structure is described within the sp. gr. P4{sub 1}32, a = 6.097 Å. Using small-angle X-ray scattering, the size and shape of nanoparticles have been determined directly in the liquid dispersion. Most of the particles have a spherical shape; their average size is ≈3.5 ± 0.5 nm, which agrees with the electron microscopy data. Possible factors causing the ε-phase formation during synthesis of metallic Co nanoparticles are discussed.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Synthesis, structure, and luminescent properties of lanthanide complexes containing 1,10-phenanthroline and perfluorinated 2-mercaptobenzothiazolate ligands
Mononuclear terbium and erbium complexes of the composition Ln(mbt{sup F}){sub 3}phen and the dinuclear complex Tb{sub 2}(mbt{sup F}){sub 4}(OH){sub 2}(phen){sub 2} (mbt{sup F} is 4,5,6,7-tetrafluoro-2-mercaptobenzothiazolate, phen is 1,10-phenanthroline) were synthesized. The structures of the complexes Er(mbt{sup F}){sub 3}phen and Tb{sub 2}(mbt{sup F}){sub 4}(OH){sub 2}(phen){sub 2} were determined by X-ray diffraction. In the solid state, the terbium and erbium complexes exhibit intense metal-centered photoluminescence. Based on the complexes Ln(mbt{sup F}){sub 3}phen, double-layer organic light-emitting diodes (OLEDs) were assembled. These OLEDs exhibit electroplex emission with a band maximum at 630 nm.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Extended hierarchical solvent perturbations from curved surfaces of mesoporous silica particles in a deep eutectic solvent
Here, many applications of deep eutectic solvents (DES) rely on exploitation of their unique yet complex liquid structures. Due to the ionic nature of the DES components, their diffuse structures are perturbed in the presence of a charged surface. We hypothesize that it is possible to perturb the bulk DES structure far (> 100 nm) from a curved, charged surface with mesoscopic dimensions. We performed in situ, synchrotron-based ultra-small angle X-ray scattering (USAXS) experiments to study the solvent distribution near the surface of charged mesoporous silica particles (MPS) (≈ 0.5 µm in diameter) suspended in both water and a common type of DES (1:2 choline Cl-:ethylene glycol). A careful USAXS analysis reveals that the perturbation of electron density distribution within the DES extends ≈ 1 μm beyond the particle surface, and that this perturbation can be manipulated by the addition of salt ions (AgCl). The concentration of the pore-filling fluid is greatly reduced in the DES. Notably, we extracted the real-space structures of these fluctuations from the USAXS data using a simulated annealing approach that does not require a priori knowledge about the scattering form factor, and can be generalized to a wide range of complex small-angle scattering problems.
36 MATERIALS SCIENCE↗
CryoEM structure of the low-complexity domain of hnRNPA2 and its conversion to pathogenic amyloid
hnRNPA2 is a human ribonucleoprotein (RNP) involved in RNA metabolism. It forms fibrils both under cellular stress and in mutated form in neurodegenerative conditions. Previous work established that the C-terminal low-complexity domain (LCD) of hnRNPA2 fibrillizes under stress, and missense mutations in this domain are found in the disease multisystem proteinopathy (MSP). However, little is known at the atomic level about the hnRNPA2 LCD structure that is involved in those processes and how disease mutations cause structural change. Here we present the cryo-electron microscopy (cryoEM) structure of the hnRNPA2 LCD fibril core and demonstrate its capability to form a reversible hydrogel in vitro containing amyloid-like fibrils. Whereas these fibrils, like pathogenic amyloid, are formed from protein chains stacked into β-sheets by backbone hydrogen bonds, they display distinct structural differences: the chains are kinked, enabling non-covalent cross-linking of fibrils and disfavoring formation of pathogenic steric zippers. Both reversibility and energetic calculations suggest these fibrils are less stable than pathogenic amyloid. Moreover, the crystal structure of the disease-mutation-containing segment (D290V) of hnRNPA2 suggests that the replacement fundamentally alters the fibril structure to a more stable energetic state. These findings illuminate how molecular interactions promote protein fibril networks and how mutation can transform fibril structure from functional to a pathogenic form.
59 BASIC BIOLOGICAL SCIENCES↗
Controlling Magnetism via Transition Metal Exchange in the Series of Intermetallics Eu( T 1, T 2)5In ( T = Cu, Ag, Au)
Three series of intermetallic compounds Eu( T 1, T 2) 5 In (T = Cu, Ag, Au) have been investigated in full compositional ranges. Single crystals of all compounds have been obtained by self-flux and were analyzed by single X-ray diffraction revealing the representatives to fall into two structure types: CeCu 6 ( oP 28, Pnma , a = 8.832(3)–9.121(2) Å, b = 5.306(2)–5.645(1) Å, c = 11.059(4)–11.437(3) Å, V = 518.3(3)–588.9(2) Å 3 ) and YbMo2Al4 ( t I 14, I 4/ mmm , a = 5.417(3)–5.508(1) Å, c = 7.139(2)– 7.199(2) Å, V = 276.1(2)–285.8(1) Å 3 ). The structural preference was found to depend on the cation/anion size ratio, while the positional preference within the CeCu 6 type structure shows an apparent correlation with the anion size. Chemical compression, hence, a change in cell volume, which occurs upon anion substitution appears to be the main driving force for the change of magnetic ordering. While EuAg 5 In shows antiferromagnetic behavior at low temperatures, mixing Cu and Au within the same type of structure results in considerable changes in the magnetism. The Eu(Cu,Au) 5 In alloys with CeCu 6 structure show complex magnetic behaviors and strong magnetic field-induced spin-reorientation transition with the critical field of the transition being dependent on Cu/Au ratio. The alloys adopting the YbMo 2 Al 4 type structure are ferromagnets exhibiting unusually high magnetic moments. The heat capacity of EuAu 2.66 Cu 2.34 In reveals a double-peak structure evolving with the magnetic field. Furthermore, low-temperature X-ray powder diffraction does not show a structural transition.
36 MATERIALS SCIENCE↗
THE POPULATION OF COMPACT RADIO SOURCES IN THE ORION NEBULA CLUSTER
We present a deep centimeter-wavelength catalog of the Orion Nebula Cluster (ONC), based on a 30 hr single-pointing observation with the Karl G. Jansky Very Large Array in its high-resolution A-configuration using two 1 GHz bands centered at 4.7 and 7.3 GHz. A total of 556 compact sources were detected in a map with a nominal rms noise of 3 μ Jy bm{sup −1}, limited by complex source structure and the primary beam response. Compared to previous catalogs, our detections increase the sample of known compact radio sources in the ONC by more than a factor of seven. The new data show complex emission on a wide range of spatial scales. Following a preliminary correction for the wideband primary-beam response, we determine radio spectral indices for 170 sources whose index uncertainties are less than ±0.5. We compare the radio to the X-ray and near-infrared point-source populations, noting similarities and differences.
79 ASTRONOMY AND ASTROPHYSICS↗
Plant-specific features of respiratory supercomplex I + III2 from Vigna radiata
Abstract The last steps of cellular respiration—an essential metabolic process in plants—are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane protein complexes (complexes I–V) that form higher-order assemblies called supercomplexes. Although supercomplexes are the most physiologically relevant form of the oxidative phosphorylation complexes, their functions and structures remain mostly unknown. Here we present the cryogenic electron microscopy structure of the supercomplex I + III 2 from Vigna radiata (mung bean). The structure contains the full subunit complement of complex I, including a newly assigned, plant-specific subunit. It also shows differences in the mitochondrial processing peptidase domain of complex III 2 relative to a previously determined supercomplex with complex IV. The supercomplex interface, while reminiscent of that in other organisms, is plant specific, with a major interface involving complex III 2 ’s mitochondrial processing peptidase domain and no participation of complex I’s bridge domain. The complex I structure suggests that the bridge domain sets the angle between the enzyme’s two arms, limiting large-scale conformational changes. Moreover, complex I’s catalytic loops and its response in active-to-deactive assays suggest that, in V. radiata , the resting complex adopts a non-canonical state and can sample deactive- or open-like conformations even in the presence of substrate. This study widens our understanding of the possible conformations and behaviour of complex I and supercomplex I + III 2 . Further studies of complex I and its supercomplexes in diverse organisms are needed to determine the universal and clade-specific mechanisms of respiration.
59 BASIC BIOLOGICAL SCIENCES↗
Structural mapping and tuning of mixed halide ions in amorphous sulfides for fast Li-ion conduction and high deformability
Amorphous sulfides are among the most promising candidates for solid electrolytes (SEs) owing to their excellent deformability and acceptable Li-ion conductivity (σion) at room temperature. However, the complex atomic structure of these amorphous materials without long-range ordering results in a lack of structural understanding and difficulties in tuning material properties. Here, in this study, we performed structural mapping of glassy sulfide SEs composed of various anion clusters using a combinatorial atomic level analysis of synchrotron X-ray-based pair distribution function (PDF) and reverse Monte-Carlo (RMC) methods, demonstrating the potential to tune σ ion in glass SEs. First, we prepared a new glassy sulfide with a mixed anion framework of two halogens (Br and I) as atomic anions, with PS 4 3- molecular anions in a Li 2 S–P 2 S 5 -based glass SE. At a specific Br content, [(Li 2 S) 0.658 (LiI 0.9 LiBr 0.1 ) 0.342 ] 0.825 [P 2 S 5 ] 0.175 recorded a σ ion of 2.27 mS cm -1 , the highest value for any glass sulfides reported to date; however, its elastic modulus was still suppressed to 14.48 GPa. PDF and RMC calculations successfully provided structural mapping of anion clusters, including two halogens. Molecular dynamics simulations of each composition confirmed that flexible coordination caused by the rattling of small polarizable Br ions in the mixed halogens of glassy SEs contributed to the superior σ ion . Our results may provide new insights into the design of superior glassy SEs that play key roles in all-solid-state batteries requiring fast Li-ion conduction and high deformability.
36 MATERIALS SCIENCE↗