Structural elucidation of full-length Pfs48/45 in complex with potent monoclonal antibodies isolated from a naturally exposed individual
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Biochemistry & Molecular Biology↗
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Structural architecture of TolQ-TolR inner membrane protein complex from opportunistic pathogen Acinetobacter baumannii
Gram-negative bacteria harness the proton motive force (PMF) within their inner membrane (IM) to uphold cell envelope integrity, an indispensable aspect for both division and survival. The IM TolQ-TolR complex is the essential part of the Tol-Pal system, serving as a conduit for PMF energy transfer to the outer membrane. Here we present cryo–electron microscopy reconstructions ofAcinetobacter baumanniiTolQ in apo and TolR-bound forms at atomic resolution. The apo TolQ configuration manifests as a symmetric pentameric pore, featuring a transmembrane funnel leading toward a cytoplasmic chamber. In contrast, the TolQ-TolR complex assumes a proton nonpermeable stance, characterized by the TolQ pentamer’s flexure to accommodate the TolR dimer, where two protomers undergo a translation-based relationship. Our structure-guided analysis and simulations support the rotor-stator mechanism of action, wherein the rotation of the TolQ pentamer harmonizes with the TolR protomers’ interplay. These findings broaden our mechanistic comprehension of molecular stator units empowering critical functions within the Gram-negative bacterial cell envelope.
Science & Technology - Other Topics↗
Crystal structure of MutYX: a novel clusterless adenine DNA glycosylase with a distinct C-terminal domain and 8-oxoguanine recognition sphere
Abstract The [4Fe–4S] cluster is an important cofactor of the base excision repair (BER) adenine DNA glycosylase MutY to prevent mutations associated with 8-oxoguanine (OG). Several MutYs lacking the [4Fe–4S] cofactor have been identified. Phylogenetic analysis shows that clusterless MutYs are distributed in two clades suggesting cofactor loss has occurred in multiple independent evolutionary events. Herein, we determined the first crystal structure of a clusterless MutY complexed with DNA. On the basis of the dramatic structural divergence from canonical MutYs, we refer to this as representative of a clusterless MutY subgroup “MutYX.” Interestingly, MutYX compensates for the missing [4Fe–4S] cofactor to maintain positioning of catalytic residues by expanding a pre-existing α-helix and acquisition of a new α-helix. Surprisingly, MutYX also acquired a new C-terminal domain that uniquely recognizes OG using residues Gln201 and Arg209. Adenine glycosylase assays and binding affinity measurements indicate that Arg209 is the primary residue responsible for OG:A lesion specificity, while Gln201 assists by bridging OG and Arg209. Surprisingly, replacement of Arg209 and Gln201 with Ala increased activity toward G:A mismatches. The MutYX structure serves as an example of devolution, capturing structural features required to retain function in the absence of a metal cofactor considered indispensable.
Trasviña-Arenas, Carlos H [University of Californi↗
Spectroscopic and Theoretical Studies of Ruthenium Complexes with a Noninnocent N 2 S 2 Ligand in Different Redox States
Herein we report an electronic structure investigation of neutral and oxidized Ru complexes containing a redox noninnocent N 2 S 2 ligand derived from o-phenylenediamide (L1). UV–vis spectroelectrochemistry (SEC) studies were conducted on the square pyramidal complex [Ru I I(L1)(PPh 3 )] (1) and the six-coordinate complexes [Ru I I(μ-BH 3 )(L1)(PPh 3 )] (2) – which has BH 3 bound in a metal–ligand cooperative (MLC) fashion across Ru and L1 – and [Ru II (L1)(PPh 3 )(MeCN)] (3). The SEC results yielded spectra assigned to singly and doubly oxidized 1 and 3, revealing electronic structure changes as a function of oxidation state and in response to the presence and absence of bound MeCN. By contrast, the SEC results of 2 showed that it rapidly loses MLC-bound BH 3 upon oxidation. The SEC results for 1 and 3 were compared to single-crystal XRD data and UV–vis, EPR, and P K-edge, S K-edge, and Ru L 3 -edge X-ray absorption spectroscopy (XAS) data collected on isolated samples of chemically oxidized 3. The data revealed that the first two oxidations are primarily localized on the ligand, which was supported by DFT and TDDFT calculations. DFT calculations for the doubly oxidized species revealed a singlet ground state with a singlet–triplet gap of 8.9 kcal/mol. CASPT2 calculations corroborated the DFT calculations and further revealed that the singlet ground state is multiconfigurational with 21% radical character. Collectively, the results establish redox formalisms and the underlying electronic structure of Ru complexes containing a noninnocent tetradentate ligand in different oxidation states.
electronic structure↗
Structural insights into transcriptional regulation by the helicase RECQL5
Abstract Transcription poses a major challenge for genome stability. The RECQL5 helicase helps safeguard genome integrity and is the only member of the human RecQ helicase family that directly binds to RNA polymerase II (Pol II) and affects its progression. While RECQL5 mitigates transcription stress in cells, the molecular mechanism underlying this phenomenon is unclear. Here, we use cryo-electron microscopy to determine the structures of stalled human Pol II elongation complexes (ECs) bound to RECQL5. Our structures reveal the molecular interactions stabilizing RECQL5 binding to the Pol II EC and highlight its role as a transcriptional roadblock. Additionally, we find that, in its nucleotide-free state, RECQL5 twists the downstream DNA in the EC and, upon nucleotide binding, undergoes a conformational change that allosterically induces Pol II toward a post-translocation state. We propose that this mechanism may help restart Pol II elongation and, therefore, contribute to reducing transcription stress.
Biochemistry & Molecular Biology↗
Ferromagnetism and structural phase transition in rhombohedral PrI r 3
The synthesis, structural, magnetic, thermal, and transport properties are reported for polycrystalline PrIr 3 . At room temperature PrIr 3 displays the rhombohedral space group R–3m and a PuNi 3 -type structure. At around 70 K a phase transition to a monoclinic C2/m structure is observed and continued cooling reveals temperature independent behavior of the unit cell volume. Further, PrIr 3 undergoes a paramagnetic to ferromagnetic transition with T c =7.5K. The temperature dependent magnetic susceptibility follows the Curie-Weiss law with a positive Curie-Weiss temperature, and an effective moment that is close to the theoretical effective moment for a free Pr +3 ion. Finally, the structural transition introduces further complexity into the behavior of PuNi 3 -type materials and highlights the importance of temperature-dependent structural studies to complement physical property measurements in intermetallic compounds.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Alkali Counterion-Dependent Crystallization of Uranium(IV)–Chloro Structural Units
The synthesis, structural characterization, and spectroscopic properties of five tetravalent uranium (U) phases including Li 6 [U 4 (μ 3 -O) 2 Cl 18 (H 2 O) 2 ]·10H 2 O (1), [U(H 2 O) 4 Cl 4 ] (2), [U(H 2 O) 4 Cl 4 ]·KCl (3), Rb 2 UCl 6 (4), and Cs 2 UCl 6 (5) are reported. Notably, a change in the U 4+ solid-state structural unit was observed based on the identity of the alkali counterion used in the synthesis. Li 1+ yielded a tetranuclear oxo-bridged cluster, [U 4 (μ 3 -O) 2 Cl 18 (H 2 O) 2 ] 6– , Na 1+ and K 1+ yielded two structurally distinct [U(H 2 O) 4 Cl 4 ] complexes, and Rb 1+ and Cs 1+ resulted in [UCl 6 ] 2– as the dominant phases. The spectroscopic properties of the compounds were analyzed using Raman and UV–vis–NIR absorption spectroscopy. The UV–vis–NIR spectra of compounds 1–5 exhibited transitions consistent with uranium in the +4 oxidation state. Clear differences in the absorption band splitting were observed and are likely attributed to differences in metal ion coordination, crystal field effects, and outer sphere interactions Overall, this work demonstrates the utility of noncovalent interactions in tuning the crystallization of various metal complexes from otherwise identical reaction solutions and provides further evidence that counterions impact the composition and structure of actinide complexes isolated in the solid state. In this way, this work affords important insight into directing and controlling the structure of actinide complexes and clusters.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Screening a knowledge‐based library of low molecular weight compounds against the proline biosynthetic enzyme 1‐pyrroline‐5‐carboxylate 1 ( PYCR1)
Abstract Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 1 (PYCR1) is the last enzyme of proline biosynthesis and catalyzes the NAD(P)H‐dependent reduction of Δ 1 ‐pyrroline‐5‐carboxylate toL‐proline. High PYCR1 gene expression is observed in many cancers and linked to poor patient outcomes and tumor aggressiveness. The knockdown of thePYCR1gene or the inhibition of PYCR1 enzyme has been shown to inhibit tumorigenesis in cancer cells and animal models of cancer, motivating inhibitor discovery. We screened a library of 71 low molecular weight compounds (average MW of 131 Da) against PYCR1 using an enzyme activity assay. Hit compounds were validated with X‐ray crystallography and kinetic assays to determine affinity parameters. The library was counter‐screened against human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3 and proline dehydrogenase (PRODH) to assess specificity/promiscuity. Twelve PYCR1 and one PRODH inhibitor crystal structures were determined. Three compounds inhibit PYCR1 with competitive inhibition parameter of 100 μM or lower. Among these, (S)‐tetrahydro‐2H‐pyran‐2‐carboxylic acid (70 μM) has higher affinity than the current best tool compoundN‐formyl‐l‐proline, is 30 times more specific for PYCR1 over human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3, and negligibly inhibits PRODH. Structure‐affinity relationships suggest that hydrogen bonding of the heteroatom of this compound is important for binding to PYCR1. The structures of PYCR1 and PRODH complexed with 1‐hydroxyethane‐1‐sulfonate demonstrate that the sulfonate group is a suitable replacement for the carboxylate anchor. This result suggests that the exploration of carboxylic acid isosteres may be a promising strategy for discovering new classes of PYCR1 and PRODH inhibitors. The structure of PYCR1 complexed withl‐pipecolate and NADH supports the hypothesis that PYCR1 has an alternative function in lysine metabolism.
Biochemistry & Molecular Biology↗
Complex-Concentrated Anion Doping Enables Ultra-Stable Lattice Oxygen and Structural Integrity in Lithium-Rich Layered Oxide Cathodes
Lithium- and manganese-rich layered oxides (LMR) stand out as next-generation lithium-ion cathode chemistries, which harness both transition-metal and lattice-oxygen redox processes to deliver exceptional capacity and energy density. However, their full potential is hindered by intrinsic oxygen instability and structural degradation, resulting in pronounced voltage fade and capacity decay. Here, we present a complex-concentrated anion-doping paradigm in which multiple anions, F, Br, and S, are incorporated into the oxygen sublattice to enhance oxygen-redox and structural stability. X-ray absorption spectroscopy and aberration-corrected scanning transmission electron microscopy confirm ultra-stable local oxygen coordination environments during long-term cycling, with detrimental phase transformations and oxygen-loss-induced cavitation dramatically inhibited. Notably, we show that the characteristic LiTM6 transition metal (TM) honeycomb ordering is preserved even after electrochemical cycling. Concurrently, this strategy yields an unprecedented volume change of only 0.63% upon charging to 4.8 V vs. Li+/Li, achieving the first zero-strain LMR cathode. The resulting LMR cathode delivers ultralow voltage fade (1 mV per cycle during the first 100 cycles and becomes negligible in subsequent cycles) and outstanding energy retention (93% after 200 cycles) in a pouch cell configuration. Our complex-concentrated anion-doping concept establishes a broadly applicable strategy for resolving chemo-mechanical failure mechanisms in ceramic intercalation electrodes for next-generation energy storage.
Li-ion batteries↗
Anti-idiotype isolation of a broad and potent influenza A virus-neutralizing human antibody
The VH6-1 class of antibodies includes some of the broadest and most potent antibodies that neutralize influenza A virus. Here, we elicit and isolate anti-idiotype antibodies against germline versions of VH6-1 antibodies, use these to sort human leukocytes, and isolate a new VH6-1-class member, antibody L5A7, which potently neutralized diverse group 1 and group 2 influenza A strains. While its heavy chain derived from the canonical IGHV6-1 heavy chain gene used by the class, L5A7 utilized a light chain gene, IGKV1-9, which had not been previously observed in other VH6-1-class antibodies. The cryo-EM structure of L5A7 in complex with Indonesia 2005 hemagglutinin revealed a nearly identical binding mode to other VH6-1-class members. The structure of L5A7 bound to the isolating anti-idiotype antibody, 28H6E11, revealed a shared surface for binding anti-idiotype and hemagglutinin that included two critical L5A7 regions: an FG motif in the third heavy chain-complementary determining region (CDR H3) and the CDR L1 loop. Surprisingly, the chemistries of L5A7 interactions with hemagglutinin and with anti-idiotype were substantially different. Overall, we demonstrate anti-idiotype-based isolation of a broad and potent influenza A virus-neutralizing antibody, revealing that anti-idiotypic selection of antibodies can involve features other than chemical mimicry of the target antigen.
59 BASIC BIOLOGICAL SCIENCES↗
Isolation of a new polyoxometalate complex of plutonium
We report the synthesis, plus structural and spectroscopic characterization, of a plutonium(IV) complex with the polyoxometalate W 5 O 18 6− . The complex was isolated as Cs 8 [Pu(W 5 O 18 ) 2 ]·CsCl·6.5H 2 O, with the tetravalent actinide cation sandwiched between two lacunary polyoxotungstate anions. It represents a rare case of a POM compound with plutonium and also the first Peacock–Weakley type complex of plutonium.
Colliard, Ian [Lawrence Livermore National Laborat↗
Multiconfigurational Electronic Structure of Nickel Cross-Coupling Catalysts Revealed by X-ray Absorption Spectroscopy
Ni II 2,2'-bipyridine complexes are commonly invoked intermediates in metallaphotoredox cross-coupling reactions. Despite their ubiquity, design principles targeting improved catalytic performance remain underdetermined. A series of Ni( R bpy)( R 'Ar)Cl (R = MeOOC, t-Bu, R' = CH 3 , CF 3 ) complexes were proposed to have multiconfigurational electronic structures on the basis of multiconfigurational/multireference calculations, with significant mixing of Ni → bpy metal-to-ligand charge transfer (MLCT) configurations into the ground-state wave function. Here, Ni K-edge and L 2,3 -edge X-ray absorption spectroscopies provide experimental support for the highly covalent and multiconfigurational electronic structures of these complexes. The pre-edge intensity in the K-edge spectrum reflects highly covalent Ni–aryl bonding. The L 3 -edge spectral shape is dependent on ligand functionalization, and a feature reflecting the MLCT character is assigned using prior ab initio and new semiempirical calculations. The results suggest the push/pull effects of the aryl/bpy ligands moderate the changes in electron density on Ni during the multiredox cross-coupling reaction cycle.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Heterogeneous Multilayer Nanopores via Chemically Tuned Dielectric Breakdown for Single‐Molecule Sensing
Solid-state nanopores are powerful platforms for single-molecule sensing, yet their performance is often constrained by fabrication complexity, noise, and limited control over surface properties. Here we report a direct method to fabricate heterogeneous multilayer nanopores using chemically tuned controlled dielectric breakdown (CT-CDB). We integrate hBN, MoS 2 , or graphene atop a silicon nitride membrane to form five distinct bilayer and tri-layer architectures, with bare SiN x nanopore as a control. CT-CDB achieves pore formation reproducibly through material-stacks with high efficiency, good pore size control, and strong yield, validated by various characterizations. Transferrin protein translocation experiments, supported by simulations, reveal that multilayer configurations modulate protein conformations, ionic current blockade and dwell time distributions, reflecting combined effects of membrane type, interfacial chemistry, and local electric field gradients. A supervised machine learning framework is implemented to assist identifying multilayer structure effects embedded in signal signatures, with over 96% accuracy. This work presents a modular and scalable framework for functional nanopore engineering with complex structural integration, thereby expanding the potential of 2D materials in single-molecule sensing applications.
2D materials↗
Improved deep learning prediction of antigen–antibody interactions
Identifying antibodies that neutralize specific antigens is crucial for developing effective immunotherapies, but this task remains challenging for many target antigens. The rise of deep learning–based computational approaches presents a promising avenue to address this challenge. Here, we assess the performance of a deep learning approach through two benchmark tests aimed at predicting antibodies for the receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Three different strategies for constructing input sequence alignments are employed for predicting structural models of antigen–antibody complexes. In our initial testing set, which comprises known experimental structures, these strategies collectively yield a significant top-ranked prediction for 61% of cases and a success rate of 47%. Notably, one strategy that utilizes the sequences of known antigen binders outperforms the other two, achieving a precision of 90% in a subsequent test set of ~1,000 antibodies, balanced between true and control antibodies for the antigen, albeit with a lower recall of 25%. Our results underscore the potential of integrating deep learning methods with single B cell sequencing techniques to enhance the prediction accuracy of antigen–antibody interactions.
Science & Technology - Other Topics↗
Designed Spin‐Texture‐Lattice to Control Anisotropic Magnon Transport in Antiferromagnets
Abstract Spin waves in magnetic materials are promising information carriers for future computing technologies due to their ultra‐low energy dissipation and long coherence length. Antiferromagnets are strong candidate materials due, in part, to their stability to external fields and larger group velocities. Multiferroic antiferromagnets, such as BiFeO 3 (BFO), have an additional degree of freedom stemming from magnetoelectric coupling, allowing for control of the magnetic structure, and thus spin waves, with the electric field. Unfortunately, spin‐wave propagation in BFO is not well understood due to the complexity of the magnetic structure. In this work, long‐range spin transport is explored within an epitaxially engineered, electrically tunable, 1D magnonic crystal. A striking anisotropy is discovered in the spin transport parallel and perpendicular to the 1D crystal axis. Multiscale theory and simulation suggest that this preferential magnon conduction emerges from a combination of a population imbalance in its dispersion, as well as anisotropic structural scattering. This work provides a pathway to electrically reconfigurable magnonic crystals in antiferromagnets.
36 MATERIALS SCIENCE↗
Discovering Elusive Dynamics Across Frontiers (Final Technical Report)
Profound puzzles, such as the nature of dark matter, the origins of the electroweak scale, the mechanism behind the small neutrino mass, and the strong CP problem, suggested new physics beyond the Standard Model and drove the particle physics program in search of the associated new particles. Despite extensive searches, conventional realizations of new physics have not yet provided conclusive evidence. This raised the serious possibility that new dynamics might be more elusive, perhaps due to a richer gauge and matter structure than previously considered. Notably, the existence of dark matter and advancements in understanding the naturalness problem urged exploration into sectors with complex gauge and matter structures. Through experiments like the LHC, DUNE, and small-scale experiments, the robust US HEP program played a critical role in pursuing these well-motivated but under-explored scenarios for new physics. I explored these physics opportunities in depth, focusing on novel searches and significant improvements in parameter space coverage. The elusive dynamics revealed rich information about the underlying theory and were essential in identifying observable opportunities. Understanding the observable consequences required a deep comprehension of the theory, which I also developed. The proposal included essential components aimed at coherently increasing our knowledge in well-motivated elusive dynamics models. Through research on high-quality axions, composite neutrinos, the Higgs boson as a portal to hidden strong dynamics, and new scalar potentials to generate alternative electroweak phase transitions, I focused on identifying new signatures and parameter regions in plausible elusive dynamics models. The exploration emphasized generic possibilities motivated by broad classes of elusive dynamics models. These signatures were not effectively probed previously due to various challenges such as triggering, background suppression, or experimental design. My research involved close interaction with experimental colleagues to overcome these difficulties, leveraging new theoretical and experimental possibilities. These efforts included identifying new observables such as timing information and substructure in calorimetries, new multiple-hit techniques, new scattering events, and new resonance searches in liquid argon detectors. This work created a positive feedback loop: theory and experimental work inspired each other, revealing new exciting opportunities that supported both programs.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Complex Adsorption Behavior of Neodymium and Ytterbium on Structurally-Distinct Alumina Surfaces
New sources of rare earth elements (REEs) are needed to support a green energy transition. REEs adsorbed to aluminum-rich clays in weathering deposits represent important resources but the mechanisms responsible for their retention and ease of extraction are unresolved. Disordered coordination and co-occurrence of multiple species pose challenges to investigating REE adsorption processes via established spectroscopic methods. In this study, we applied element-specific surface crystallography methods to obtain a new perspective on the complexity of REE adsorption mechanisms and affinities. Alumina (001) and (012) crystal surfaces were utilized to evaluate surface-specific controls on Nd(III) and Yb(III) adsorption behavior. The REEs displayed similar total adsorption to alumina (001) as a mixture of inner- and outer-sphere complexes, but Nd displayed a greater proportion of inner-sphere binding. Adsorption of ordered inner- and outer-sphere REE species was substantially lower on alumina (012). These distinct behaviors reflect differences in the surface functional group charging and topography of the two surfaces. However, alumina (012) also hosted a substantial population of disordered adsorbed species, especially for Nd, potentially associated with Al vacancy surface defects. Here, the accumulation of light versus heavy REEs via adsorption in weathering deposits likely results from multiple, competing reactions affected by clay particle morphology. Leaching procedures for resource recovery should account for differential rates of desorption by coexisting inner- and outer-sphere REE surface complexes.
58 GEOSCIENCES↗
Learning a general model of single phase flow in complex 3D porous media
Modeling effective transport properties of 3D porous media, such as permeability, at multiple scales is challenging as a result of the combined complexity of the pore structures and fluid physics—in particular, confinement effects which vary across the nanoscale to the microscale. While numerical simulation is possible, the computational cost is prohibitive for realistic domains, which are large and complex. Although machine learning (ML) models have been proposed to circumvent simulation, none so far has simultaneously accounted for heterogeneous 3D structures, fluid confinement effects, and multiple simulation resolutions. By utilizing numerous computer science techniques to improve the scalability of training, we have for the first time developed a general flow model that accounts for the pore-structure and corresponding physical phenomena at scales from Angstrom to the micrometer. Using synthetic computational domains for training, our ML model exhibits strong performance (R 2 = 0.9) when tested on extremely diverse real domains at multiple scales.
36 MATERIALS SCIENCE↗