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At least 1,423 records · Page 79

Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA

The interbacterial deaminase toxin DddA catalyzes cytosine-to-uracil conversion in double-stranded (ds) DNA and enables CRISPR-free mitochondrial base editing, but the molecular mechanisms underlying its unique substrate selectivity have remained elusive. Here, we report crystal structures of DddA bound to a dsDNA substrate containing the 5'-TC target motif. These structures show that DddA binds to the minor groove of a sharply bent dsDNA and engages the target cytosine extruded from the double helix. DddA Phe1375 intercalates in dsDNA and displaces the 5' (-1) thymine, which in turn replaces the target (0) cytosine and forms a noncanonical T–G base pair with the juxtaposed guanine. This tandem displacement mechanism allows DddA to locate a target cytosine without flipping it into the active site. Biochemical experiments demonstrate that DNA base mismatches enhance the DddA deaminase activity and relax its sequence selectivity. On the basis of the structural information, we further identified DddA mutants that exhibit attenuated activity or altered substrate preference. Our studies may help design new tools useful in genome editing or other applications.

59 BASIC BIOLOGICAL SCIENCES↗

Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains

Abstract Type IA topoisomerases interact with G-strand and T-strand ssDNA to regulate DNA topology. However, simultaneous binding of two ssDNA segments to a type IA topoisomerase has not been observed previously. We report here the crystal structure of a type IA topoisomerase with ssDNA segments bound in opposite polarity to the N- and C-terminal domains. Titration of small ssDNA oligonucleotides to Mycobacterium smegmatis topoisomerase I with progressive C-terminal deletions showed that the C-terminal region has higher affinity for ssDNA than the N-terminal active site. This allows the C-terminal domains to capture one strand of underwound negatively supercoiled DNA substrate first and position the N-terminal domains to bind and cleave the opposite strand in the relaxation reaction. Efficiency of negative supercoiling relaxation increases with the number of domains that bind ssDNA primarily with conserved aromatic residues and possibly with assistance from polar/basic residues. A comparison of bacterial topoisomerase I structures showed that a conserved transesterification unit (N-terminal toroid structure) for cutting and rejoining of a ssDNA strand can be combined with two different types of C-terminal ssDNA binding domains to form diverse bacterial topoisomerase I enzymes that are highly efficient in their physiological role of preventing excess negative supercoiling in the genome.

59 BASIC BIOLOGICAL SCIENCES↗

Flux Synthesis of A-site Disordered Perovskite La 0.5 M 0.5 TiO 3 (M$=$Li, Na, K) Nanorods Tailored for Solid Composite Electrolytes

Inorganic fillers play an important role in improving the ionic conductivity of solid composite electrolytes (SCEs) for Li-ion batteries. Among inorganic fillers, perovskite-type lithium lanthanum titanate (LLTO) stands out for its high bulk Li + conductivity on the order of 10 -3 S cm -1 at room temperature. According to a literature survey, the optimal LLTO filler should possess the following characteristics: i) a single-crystal structure to minimize grain boundaries; ii) a small particle size to increase the filler/polymer interface area; iii) a 1D morphology for efficient interface channels; and iv) cubic symmetry to facilitate rapid bulk Li + diffusion within the filler. However, the synthesis of single crystal, 1D LLTO nanomaterials with cubic symmetry is challenging. Herein, a flux strategy is developed to synthesize La 0.5 M 0.5 TiO 3 (LMTO, M$=$Li, Na, and K) single-crystal nanorods with an A-site-disordered, cubic perovskite phase. The flux media promotes the oriented growth of nanorods, prevents nanorods from sintering, and provides multiple alkali metal ion doping at M sites to stabilize the cubic phase. SCEs compositing the Li + -conducting LMTO nanorods as fillers and poly[vinylene carbonate- co -lithium sulfonyl(trifluoromethane sulfonyl)imide methacrylate] matrix exhibit more than twice the conductivity of the neat polymer electrolyte (30.6 vs 14.0 µS cm -1 at 303 K).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular-dynamics simulation methods for macromolecular crystallography

It is investigated whether molecular-dynamics (MD) simulations can be used to enhance macromolecular crystallography (MX) studies. Historically, protein crystal structures have been described using a single set of atomic coordinates. Because conformational variation is important for protein function, researchers now often build models that contain multiple structures. Methods for building such models can fail, however, in regions where the crystallographic density is difficult to interpret, for example at the protein–solvent interface. To address this limitation, a set of MD–MX methods that combine MD simulations of protein crystals with conventional modeling and refinement tools have been developed. In an application to a cyclic adenosine monophosphate-dependent protein kinase at room temperature, the procedure improved the interpretation of ambiguous density, yielding an alternative water model and a revised protein model including multiple conformations. The revised model provides mechanistic insights into the catalytic and regulatory interactions of the enzyme. The same methods may be used in other MX studies to seek mechanistic insights.

59 BASIC BIOLOGICAL SCIENCES↗

Structural basis for Ca2+-dependent activation of a plant metacaspase

Abstract Plant metacaspases mediate programmed cell death in development, biotic and abiotic stresses, damage-induced immune response, and resistance to pathogen attack. Most metacaspases require Ca 2+ for their activation and substrate processing. However, the Ca 2+ -dependent activation mechanism remains elusive. Here we report the crystal structures of Metacaspase 4 from Arabidopsis thaliana ( At MC4) that modulates Ca 2+ -dependent, damage-induced plant immune defense. The At MC4 structure exhibits an inhibitory conformation in which a large linker domain blocks activation and substrate access. In addition, the side chain of Lys225 in the linker domain blocks the active site by sitting directly between two catalytic residues. We show that the activation of At MC4 and cleavage of its physiological substrate involve multiple cleavages in the linker domain upon activation by Ca 2+ . Our analysis provides insight into the Ca 2+ -dependent activation of At MC4 and lays the basis for tuning its activity in response to stresses for engineering of more sustainable crops for food and biofuels.

59 BASIC BIOLOGICAL SCIENCES↗

Structural basis for autophagy inhibition by the human Rubicon–Rab7 complex

Rubicon is a potent negative regulator of autophagy and a potential target for autophagy-inducing therapeutics. Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7–GTP. Here we report the 2.8-Å crystal structure of the Rubicon RH domain in complex with Rab7–GTP. Our structure reveals a fold for the RH domain built around four zinc clusters. The switch regions of Rab7 insert into pockets on the surface of the RH domain in a mode that is distinct from those of other Rab–effector complexes. Rubicon residues at the dimer interface are required for Rubicon and Rab7 to colocalize in living cells. Mutation of Rubicon RH residues in the Rab7-binding site restores efficient autophagic flux in the presence of overexpressed Rubicon, validating the Rubicon RH domain as a promising therapeutic target.

60 APPLIED LIFE SCIENCES↗

On the Phase with an Unreported Ternary Composition Found in the P-Pt-Rh System

This work reports a ternary structure in the P-Pt-Rh system, which has a composition not reported in the literature. The structure formed in the Pt-6 wt.% Rh alloy which was partially melted in a P-enriched CO environment near 1000 °C isothermally and non-isothermally as part of the type B thermocouple assembly. A composition and a crystal structure of this phase were investigated by utilizing SEM, EPMA, XRD and TEM techniques to discuss the potential of this structure being a true ternary phase. The EPMA indicated chemistries of the ternary structure from both isothermal and non-isothermal samples were about 23P-52Pt-25Rh (at.%) and, 22P-54Pt-24Rh (at.%) respectively. TEM diffraction patterns identified this ternary structure to be crystalline with a complex non-cubic structure, and confirmed it was not amorphous. Finally, by superimposing the compositions in the ternary phase diagram, it was concluded this phase was not extensions of any binary phases known in the respective binary systems.

36 MATERIALS SCIENCE↗

A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly

Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene (“BMIE”), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu ++ and Zn ++ in bidentate (N 2 ) and tridentate (N 2 S*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn ++ , Cu ++ , and Co ++ . EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu ++ coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (H 2 O/HO – , tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn ++ metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. Finally, these features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure and Negative Thermal Expansion in Zr 0.3 Sc 1.7 Mo 2.7 V 0.3 O 12

A 2 M 3 O 12 -based materials have received considerable attention owing to their wide range of negative thermal expansion (NTE) and chemical flexibility toward novel materials design. However, the structure and NTE mechanism remain challenging. In this paper, Zr 4+ and V 5+ are used as a unit to compensatorily replace Sc 3+ and Mo 6+ in Sc 2 Mo 3 O 12 to tune its thermal expansion. Its crystal structure, phase transition, NTE property, and corresponding mechanisms are studied by high-resolution synchrotron X-ray diffraction, powder X-ray diffraction, ultralow-frequency Raman spectroscopy, and density functional theory calculations. The results show that Zr 0.3 Sc 1.7 Mo 2.7 V 0.3 O 12 adopts an orthorhombic (Pbcn) structure at room temperature, with V atoms occupying the position of Mo1 atoms and Zr atoms occupying the position of Sc atoms, and transforms to monoclinic (P2 1 /a) structure at similar to ~133 K (45 K lower than that of Sc 2 Mo 3 O 12 ). It exhibits excellent NTE in a broader range. Most of the phonon modes below 350 cm -1 have negative Grüneisen parameters, of which the lowest and next-lowest frequency (38.5 and 45.8 cm -1 ) optical phonon modes arising from the translational vibrations of the Sc/Zr and Mo/V atoms in the plane of the nonlinear linkage Sc/Zr-O-Mo/V have the largest and next-largest negative Grüneisen parameters and positive total anharmonicity, and contribute most to the NTE.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structures of flavivirus RNA promoters suggest two binding modes with NS5 polymerase

Flaviviruses use a ~70 nucleotide stem-loop structure called stem-loop A (SLA) at the 5' end of the RNA genome as a promoter for RNA synthesis. Flaviviral polymerase NS5 specifically recognizes SLA to initiate RNA synthesis and methylate the 5' guanosine cap. We report the crystal structures of dengue (DENV) and Zika virus (ZIKV) SLAs. DENV and ZIKV SLAs differ in the relative orientations of their top stem-loop helices to bottom stems, but both form an intermolecular three-way junction with a neighboring SLA molecule. To understand how NS5 engages SLA, we determined the SLA-binding site on NS5 and modeled the NS5-SLA complex of DENV and ZIKV. Our results show that the gross conformational differences seen in DENV and ZIKV SLAs can be compensated by the differences in the domain arrangements in DENV and ZIKV NS5s. We describe two binding modes of SLA and NS5 and propose an SLA-mediated RNA synthesis mechanism.

59 BASIC BIOLOGICAL SCIENCES↗

Structural and biochemical insights into NEIL2’s preference for abasic sites

Cellular DNA is subject to damage from a multitude of sources and repair or bypass of sites of damage utilize an array of context or cell cycle dependent systems. The recognition and removal of oxidatively damaged bases is the task of DNA glycosylases from the base excision repair pathway utilizing two structural families that excise base lesions in a wide range of DNA contexts including duplex, single-stranded and bubble structures arising during transcription. The mammalian NEIL2 glycosylase of the Fpg/Nei family excises lesions from each of these DNA contexts favoring the latter two with a preference for oxidized cytosine products and abasic sites. We have determined the first liganded crystal structure of mammalian NEIL2 in complex with an abasic site analog containing DNA duplex at 2.08 Å resolution. Comparison to the unliganded structure revealed a large interdomain conformational shift upon binding the DNA substrate accompanied by local conformational changes in the C-terminal domain zinc finger and N-terminal domain void-filling loop necessary to position the enzyme on the DNA. The detailed biochemical analysis of NEIL2 with an array of oxidized base lesions indicates a significant preference for its lyase activity likely to be paramount when interpreting the biological consequences of variants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring the Structural Behavior of Hydrophilic Diglycolamide Complexes with the Lanthanides and Actinides

In the ongoing effort to meet the anticipated rise in energy demand while maintaining the full-scale abandonment of natural gas and coal, a substantial shift in our considerations of green energy is required through the wider adoption of nuclear power. However, the advantages of nuclear power are hindered by the challenges of safely managing nuclear waste. Hydrophilic diglycolamides (DGA) ligands have been explored for use as stripping agents in various lanthanide and actinide partitioning processes. Additionally, the separation of lanthanide fission products and transplutonic actinides can serve multifaceted advantages in that the separation neutron poisoning rare earth element (REE) fission products from minor actinides from used nuclear fuel (UNF) can be mutually beneficial to the fundamental research behind REE separations and UNF separations. With this in mind, understanding the bonding differences between the Ln3+ and An3+ ions as a function of DGA structure, such as varying the alkyl groups on each of the amide functional groups, has an influence on the molecule’s selectivity and solubility and whose changes in molecular architecture also impact the radiolytic behavior of these molecules. As such, crystal structures of (Y3+, La-Lu3+, excl. Pm, Pu3+/4+, Am3+, Bk3+, and Cf3+) with hydrophilic diglycolamides show the systematic progression, and changes in coordination habits, as a function of a f-element ions. These coordination complexes see a consistent decrease in bond lengths and changes in the coordination environment while traversing across the f-elements, owing to the effects of the lanthanide contraction as well as local geometry around the metal centers. Direct comparisons of lanthanide with actinide DGA structures display both striking similarities in coordination with earlier actinides of Pu and Am, while later actinides of Bk and Cf display a complete breakdown of these observed trends. This work has also presented the rare opportunity to study homoleptic DGA compounds across multiple oxidation states have provided insight into their nuanced differences in structural chemistry.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Spin and lattice dynamics of the two-dimensional van der Waals ferromagnet CrI3

Chromium tri-iodide (CrI 3 ) is a prototypical ferromagnetic van der Waals insulator with its genuinely two-dimensional (2D) long-range magnetic order below 45 K demonstrated recently. The underlying magnetic anisotropy has not been completely understood while both the Dzyaloshinskii-Moriya (DM) interaction and the Kitaev—Γ type interaction have been considered as the relevant magnetic Hamiltonian. In addition, the relation between the crystal structure and the magnetic order needs to be further elucidated concerning their possible coupling in few-layer samples and in the topmost surface layers of bulk samples. Here, we investigate these issues via temperature- and magnetic field-dependent terahertz spectroscopy on bulk CrI 3 single crystals, focusing on the dynamics of ferromagnetic resonances (FMRs) and optical phonons in the terahertz (THz) region from 4 to 120 cm -1 (from 0.5 to 15 meV). We narrow down the possible ranges of the interaction parameters such as the off-diagonal symmetric terms and the single-ion anisotropy. The accurate values of these parameters significantly constrain the magnitude of possible Kitaev—Γ exchange interaction and the topological magnon gap. Moreover, the structure-magnetism relationship was critically analyzed based on the temperature- and field-dependences of two E u in-plane optical phonon modes, which shows that the commonly believed structural phase diagram of CrI 3 , derived from surface-preferential data, has to be seriously modified.

36 MATERIALS SCIENCE↗

Li 21 Ge 8 P 3 S 34 : New Lithium Superionic Conductor with Unprecedented Structural Type

Abstract Lithium superionic conductors are pivotal for enabling all‐solid‐state batteries, which aim to replace liquid electrolytes and enhance safety. Herein, we report the discovery of an unprecedented lithium superionic conductor, Li 21 Ge 8 P 3 S 34 , featuring a novel structural type and a new composition in the Li–Ge–P–S system. This material exhibits high lithium ionic conductivity of approximately 1.0 mS cm −1 at 303 K with a low activation energy of 0.20(1) eV. It's unique crystal structure was elucidated using three‐dimensional electron diffraction (3D ED) and further refined through combined powder X‐ray and neutron diffraction analyses. The structure consists of alternating two‐dimensional slabs: one of corner‐sharing GeS 4 tetrahedra and the other of isolated PS 4 tetrahedra, enabling efficient lithium‐ion transport through a tetrahedrally interconnected network of 1D, 2D, and 3D diffusion pathways. This distinctive structural motif provides a novel design strategy for next‐generation solid electrolytes, broadening the structural landscape of lithium superionic conductors. With further advancements in compositional tuning and interfacial engineering, Li 21 Ge 8 P 3 S 34 could contribute to the development of high‐performance all‐solid‐state batteries.

Chemistry↗

The Water-Fe-Pressure dependent single-crystal elastic properties of wadsleyite: Implications for the seismic anisotropy in the upper Mantle Transition Zone

Recent seismic studies suggest an anisotropic Mantle Transition Zone (MTZ) in areas adjacent to subducted slabs. Wadsleyite is the main anisotropy contributor in the upper MTZ, therefore the interpretation of these seismic observations requires the knowledge of single-crystal elastic moduli (C ij s) and the deformation-induced lattice preferred orientation (LPO) of wadsleyite. Wadsleyite can host up to 3 wt% water in its crystal structure as point defects in the form of hydroxyl groups, however, the combined effect of water content, Fe content, and pressure on the C ij s of wadsleyite remains unclear. In this study, we measured the high-pressure single-crystal elasticity of a synthetic hydrous Fe-bearing wadsleyite (0.14(5) wt% water, Fe#=9.4, Fe 3+ /ΣFe=0.3) up to 18.2 (2) GPa. In combination with previous experimental data, we separated the effects of pressure, water, and Fe contents on the Cijs and intrinsic elastic anisotropy of wadsleyite. Overall, our results suggest that the intrinsic elastic anisotropy of wadsleyite decreases with pressure, water, and Fe contents. At 15 GPa, increasing the water content by 0.1 wt% or Fe# by 1 decreases the V P and V S anisotropy of wadsleyite by ~1.1-1.3%, and ~0.8-1.3% in average, respectively. Combined with the LPO determined in previous deformation experiments, we modeled the seismic anisotropy in the upper MTZ generated by a sub-vertical mantle flow near cold subducted slabs and a sub-horizontal mantle flow in the ambient mantle. In both scenarios, the LPO of wadsleyite leads to V SV (vertically polarized shear wave velocity) > V SH (horizontally polarized shear wave velocity). Our results suggest that wadsleyite may account for a weak anisotropic MTZ (<1%) on the global scale. Considering the fact that water decreases the elastic anisotropy but promotes LPO of wadsleyite, seismic anisotropy may not be a good water sensor.

36 MATERIALS SCIENCE↗

Application of the core shell model for strengthening polymer filament interfaces

While surface segregation has been intensively studied in thin films, relatively little has been investigated in filament geometries. In contrast to thin films, the filament surface forms a continuum, with interactions both at the free air and internal filament interface, which makes it difficult to achieve an equilibrium configuration. This asymmetry has become particularly apparent with the increasing use of additive manufacturing where entire structures are constructed via layered deposition of filamentous layers from a moving thermal nozzle. In addition, this process is highly non-equilibrated with poor thermal retention and is responsible for insufficient filament–filament interfacial fusion and internal pore formation along the printing direction. These features all contribute to poor mechanical and structural properties, which are exacerbated in semi-crystalline polymers, such as Polylactic Acid (PLA), where the melting point, T m , is much higher than the glass transition, T g . Even though system is liquid the molecules become ordered within the crystal structure and this ordering interferes with interdiffusion, which in turn prevents proper interfacial fusion. Capitalizing on the differential in surface tension, we show that addition of less than 1%, or trace amounts, of longer chain polymers, an oriented core shell structure, will be formed with a self-limiting thickness of three time the radius of gyration, R g , of the tracer chains. The lower T g of the tracers and their orientation makes them poised for interdiffusion when subsequent layers are deposited producing structures with significant improvement of the mechanical properties and internal structural integrity.

36 MATERIALS SCIENCE↗

Structures of Vanadium-Containing Silicate and Borosilicate Glasses: Vanadium Potential Development and MD Simulations

Vanadium-containing multi-component glasses have been found with widely interests in various applications. However, the complex compositions, thus structures, lead to the challenges in experiments to understand the structural origin of the property change of these glasses. In this work, we developed compatible vanadium-related parameters for a widely used pair wise potential set to enable the simulations of the vanadium-containing multi-component glasses. Various crystal structures and glass compositions (with vanadium in different oxidation states) have been tested using the newly developed parameters, and structural information of cell parameters, pair distribution function, estimated bond distance, and coordination number have been obtained. The results are in good agreement with available experimental data, which indicates the new vanadium parameters can be used to simulate the vanadium-containing multi-component glasses and thus help study those applications with wide interests.

Deng, Lu↗

As–Se Pentagonal Linkers to Induce Chirality and Polarity in Mixed-Valent Fe–Se Tetrahedral Chains Resulting in Hidden Magnetic Ordering

A novel mixed-valent hybrid chiral and polar compound, Fe 7 As 3 Se 12 (en) 6 (H 2 O), has been synthesized by a single-step solvothermal method. The crystal structure consists of 1D [Fe 5 Se 9 ] chains connected via [As 3 Se 2 ]–Se pentagonal linkers and charge-balancing interstitial [Fe(en) 3 ] 2+ complexes (en = ethylenediamine). Neutron powder diffraction verified that interstitial water molecules participate in the crystal packing. Magnetic polarizability of the produced compound was confirmed by X-ray magnetic circular dichroism (XMCD) spectroscopy. X-ray absorption spectroscopy (XAS) and 57 Fe Mössbauer spectroscopy showed the presence of mixed-valent Fe 2+ /Fe 3+ in the Fe–Se chains. Magnetic susceptibility measurements reveal strong antiferromagnetic nearest neighbor interactions within the chains with no apparent magnetic ordering down to 2 K. Hidden short-range magnetic ordering below 70 K was found by 57 Fe Mössbauer spectroscopy, showing that a fraction of the Fe 3+ /Fe 2+ in the chains are magnetically ordered. Nevertheless, complete magnetic ordering is not achieved even at 6 K. Analysis of XAS spectra demonstrates that the fraction of Fe 3+ in the chain increases with decreasing temperature. Computational analysis points out several competing ferrimagnetic ordered models within a single chain. Here, this competition, together with variation in the Fe oxidation state and additional weak intrachain interactions, is hypothesized to prevent long-range magnetic ordering.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗