Force transmission and SUN-KASH higher-order assembly in the LINC complex models
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Biophysics↗
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Antibodies Raised Against an Aβ Oligomer Mimic Recognize Pathological Features in Alzheimer’s Disease and Associated Amyloid-Disease Brain Tissue
Antibodies that target the β-amyloid peptide (Aβ) and its associated assemblies are important tools in Alzheimer’s disease research and have emerged as promising Alzheimer’s disease therapies. This paper reports the creation and characterization of a triangular Aβ trimer mimic composed of Aβ 17–36 β-hairpins and the generation and study of polyclonal antibodies raised against the Aβ trimer mimic. The Aβ trimer mimic is covalently stabilized by three disulfide bonds at the corners of the triangular trimer to create a homogeneous oligomer. Structural, biophysical, and cell-based studies demonstrate that the Aβ trimer mimic shares characteristics with oligomers of full-length Aβ. X-ray crystallography elucidates the structure of the trimer and reveals that four copies of the trimer assemble to form a dodecamer. SDS-PAGE, size exclusion chromatography, and dynamic light scattering reveal that the trimer also forms higher-order assemblies in solution. Cell-based toxicity assays show that the trimer elicits LDH release, decreases ATP levels, and activates caspase-3/7 mediated apoptosis. Immunostaining studies on brain slices from people who lived with Alzheimer’s disease and people who lived with Down syndrome reveal that the polyclonal antibodies raised against the Aβ trimer mimic recognize pathological features including different types of Aβ plaques and cerebral amyloid angiopathy.
60 APPLIED LIFE SCIENCES↗
Nucleic acid mediated activation of a short prokaryotic Argonaute immune system
A short prokaryotic Argonaute (pAgo) TIR-APAZ (SPARTA) defense system, activated by invading DNA to unleash its TIR domain for NAD(P) + hydrolysis, was recently identified in bacteria. We report the crystal structure of SPARTA heterodimer in the absence of guide-RNA/target-ssDNA (2.66 Å) and a cryo-EM structure of the SPARTA oligomer (tetramer of heterodimers) bound to guide-RNA/target-ssDNA at nominal 3.15–3.35 Å resolution. The crystal structure provides a high-resolution view of SPARTA, revealing the APAZ domain as equivalent to the N, L1, and L2 regions of long pAgos and the MID domain containing a unique insertion (insert57). Cryo-EM structure reveals regions of the PIWI (loop10-9) and APAZ (helix αN) domains that reconfigure for nucleic-acid binding and decrypts regions/residues that reorganize to expose a positively charged pocket for higher-order assembly. The TIR domains amass in a parallel-strands arrangement for catalysis. We visualize SPARTA before and after RNA/ssDNA binding and uncover the basis of its active assembly leading to abortive infection.
59 BASIC BIOLOGICAL SCIENCES↗
Probing the Self-Assembly dynamics of cellulose nanocrystals by X-ray photon correlation spectroscopy
Charge-stabilized colloidal cellulose nanocrystals (CNCs) can self-assemble into higher-ordered chiral nematic structures by varying the volume fraction. The assembly process exhibits distinct dynamics during the isotropic to liquid crystal phase transition, which can be elucidated using X-ray photon correlation spectroscopy (XPCS). Anionic CNCs were dispersed in propylene glycol (PG) and water spanning a range of volume fractions, encompassing several phase transitions. Coupled with traditional characterization techniques, XPCS was conducted to monitor the dynamic evolution of the different phases. Additionally, simulated XPCS results were obtained using colloidal rods and compared with the experimental data, offering additional insights into the dynamic behavior of the system. The results indicate that the particle dynamics of CNCs undergo a stepped decay in three stages during the self-assembly process in PG, coinciding with the observed phases. The phase transitions are associated with a total drop of Brownian diffusion rates by four orders of magnitude, a decrease of more than a thousand times slower than expected in an ideal system of repulsive Brownian rods. Given the similarity in the phase behaviors in CNCs dispersed in PG and in water, we hypothesize that these dynamic behaviors can be extrapolated to other polar solvent environments. Importantly, these findings represent the direct measurement of CNC dynamics using XPCS, underscoring the feasibility of directly assessing the dynamic behavior of other rod-like colloidal suspensions.
36 MATERIALS SCIENCE↗
Unraveling the Dynamics of Nucleosome Arrays
The organization of genomic DNA into chromatin is a fundamental determinant of genome stability, regulation, and cellular function. Nucleosomes, the basic repeating units of chromatin, assemble into higher-order structures whose organization and heterogeneity remain difficult to characterize using conventional ensemble-averaged techniques. A key need in the field is the development of experimental approaches capable of directly visualizing nucleosome assemblies and their structural variability at the single-molecule level. This LDRD Lab-Wide project focused on establishing and evaluating atomic force microscopy (AFM)–based approaches for the characterization of nucleosome assemblies. The work emphasized experimental workflows for preparing, imaging, and assessing multi-nucleosome systems, rather than isolated single nucleosomes. Through method development and exploratory measurements, the project demonstrated the feasibility of applying scanning probe microscopy to investigate chromatin-relevant assemblies and provided preliminary insight into the strengths and limitations of this approach for future quantitative studies. Results and lessons learned from this effort were disseminated to the broader scientific community through multiple national conference presentations, helping to position LLNL for continued work in chromatin and genome organization research.
59 BASIC BIOLOGICAL SCIENCES↗
Site-specific photo-crosslinking in a double crossover DNA tile facilitated by squaraine dye aggregates: advancing thermally stable and uniform DNA nanostructures
We investigated the role of dichloro-squaraine (SQ) dye aggregates in facilitating thymine–thymine interstrand photo-crosslinking within double crossover (DX) tiles, to develop thermally stable and structurally uniform two-dimensional (2D) DNA-based nanostructures. By strategically incorporating SQ modified thymine pairs, we enabled site-selective [2 + 2] photocycloaddition under 310 nm UV light. Strong dye–dye interactions, particularly through the formation of aggregates, facilitated covalent bond formation between proximal thymines. To evaluate the impact of dye aggregation on crosslinking efficiency, ten DX tile variants with varying SQ-modified thymine positions were tested. Our results demonstrated that SQ dye aggregates significantly enhanced crosslinking, driven by precise SQ-modified thymine dimer placement within the DNA tiles. Analytical techniques, including denaturing PAGE and UV-visible spectroscopy, validated successful crosslinking in DNA tiles with multiple SQ-modified thymine pairs. This non-phototoxic method offers a potential route for creating thermally stable, homogeneous higher-order DNA–dye assemblies with potential applications in photoactive and exciton-based fields such as optoelectronics, nanoscale computing, and quantum computing. Furthermore, the insights from this study establish a foundation for further exploration of advanced DNA–dye systems, enabling the design of next-generation DNA nanostructures with enhanced functional properties.
2D DNA template↗
Cryo-EM structure of a methanogen nitrogenase-PII protein supercomplex
Abstract Nitrogenases are metalloenzymes that catalyze the reduction of atmospheric dinitrogen to ammonia, sustaining the global nitrogen cycle. While bacterial nitrogenase has been extensively characterized, the architecture and regulation of archaeal nitrogenases remain unknown despite longstanding evidence of nitrogen fixation in methanogens. Here we report a 3.1 Å cryo-electron microscopy structure of a native nitrogenase–PII protein supercomplex from Methanosarcina acetivorans. The structure reveals an unprecedented assembly of three NifDK heterotetramers bridged by six NifI1,2 heterotrimeric PII complexes, which sterically block NifH association and lock the enzyme in an inactive state. The NifI complexes display asymmetric binding of ADP and 2-oxoglutarate, coupling nitrogenase inhibition directly to cellular energy and nitrogen status. Addition of 2-oxoglutarate and ATP releases the NifI complexes, stimulating a threefold increase in NifDK activity in vitro. This higher-order architecture uncovers a previously unrecognized regulatory strategy in methanogens, in which PII proteins drive nitrogenase oligomerization to control activity. The discovery that nitrogenase activity may be modulated through direct assembly into higher-order structures opens new avenues for exploring nitrogenase evolution, regulation, and biotechnological applications. One sentence summary Discovery of a nitrogenase-PII protein supercomplex in methanogens, uncovering a metabolite-gated assembly mechanism for nitrogenase inhibition.
Nitrogenase, Electron Transfer, Methanogen↗
Nanotubes Growth by Self-Assembly of DNA Strands at Room Temperature
Artificial biomolecular nanotubes are a promising approach to building materials mimicking the capacity of the cellular cytoskeleton to grow and self-organize dynamically. Nucleic acid nanotechnology has demonstrated a variety of self-assembling nanotubes with programmable, robust features and morphological similarities to actual cytoskeleton components. However, their production typically requires thermal annealing, which not only poses a general constraint on their potential applications but is also incompatible with physiological conditions. Here, we demonstrate that DNA nanotubes can self-assemble from a simple mixture of five short DNA strands at constant room temperature, growing for extended periods of time in bulk conditions as well as under confinement. Assembly is achieved using a monovalent salt buffer, which ensures a faithful nanoscale arrangement and avoids nanotube aggregation. We observe the formation of individual nanotubes up to 20 days with a diameter of 22 ± 4 nm and length of several tens of micrometers. We finally encapsulate the strands in microsized compartments, such as water-in-oil microdroplets and giant unilamellar vesicles serving as simple cell models. Notably, nanotubes not only isothermally self-assemble directly inside the microcompartments but also self-organize into dynamic higher-order structures resembling rings and dynamic networks. Our study provides an advantageous method for in situ assembly of programmable biomolecular scaffolds and materials using synthetic DNA strands without requirements of thermal treatment.
Chemistry↗
Structure of orthoreovirus RNA chaperone σNS, a component of viral replication factories
Abstract The mammalian orthoreovirus (reovirus) σNS protein is required for formation of replication compartments that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of a σNS mutant that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure shows that dimers interact with each other using N-terminal arms to form a helical assembly resembling WT σNS filaments in complex with RNA observed using cryo-EM. The interior of the helical assembly is of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same site as the N-terminal arm. This finding suggests that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS, which is supported by the structure of σNS lacking an N-terminal arm. We further observed that σNS has RNA chaperone activity likely essential for presenting mRNA to the viral polymerase for genome replication. This activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.
59 BASIC BIOLOGICAL SCIENCES↗
Galaxy-multiplet clustering from DESI DR2
We present an efficient estimator for higher-order galaxy clustering using small groups of nearby galaxies, or multiplets. Using the Luminous Red Galaxy (LRG) sample from the Dark Energy Spectroscopic Instrument (DESI) Data Release 2, we identify galaxy multiplets as discrete objects and measure their cross-correlations with the general galaxy field. Our results show that the multiplets exhibit stronger clustering bias as they trace more massive dark matter halos than individual galaxies. When comparing the observed clustering statistics with the mock catalogs generated from the N-body simulation AbacusSummit, we find that the mocks underpredict multiplet clustering despite reproducing the galaxy two-point auto-correlation reasonably well. This discrepancy indicates that the standard Halo Occupation Distribution (HOD) model is insufficient to describe the properties of galaxy multiplets, revealing the greater constraining power of this higher-order statistic on galaxy-halo connection and the possibility that multiplets are specific to additional assembly bias. We demonstrate that incorporating secondary biases into the HOD model improves agreement with the observed multiplet statistics, specifically by allowing galaxies to preferentially occupy halos in denser environments. Our results highlight the potential of utilizing multiplet clustering, beyond traditional two-point correlation measurements, to break degeneracies in models describing the galaxy-dark matter connection.
cosmology↗
CpoS-Inc interactions facilitate host cell modulation during Chlamydia trachomatis infection
ABSTRACT Chlamydia trachomatis ( C.t .), the leading bacterial cause of sexually transmitted infections, replicates within a unique intracellular compartment called the inclusion, which is modified by secreted proteins known as inclusion membrane (Inc) proteins. Here, we further characterize CpoS, an Inc protein previously shown to be critical for bacterial replication and inclusion development. We demonstrate that CpoS directly binds multiple coiled-coil region-containing Incs and engages Rab GTPases at a separate site. Notably, CpoS-InaC interactions facilitate the recruitment of select Arf GTPases to the inclusion membrane, while Rab recruitment occurs independently of these interactions. Biochemical and biophysical analyses revealed that Incs self-oligomerize to form higher-ordered structures, with CpoS adopting a tetrameric conformation resembling that of eukaryotic SNARE proteins. We propose that these assemblies serve as scaffolds to orchestrate vesicle docking, tethering, and fusion. Our findings highlight the intricate interplay between bacterial and host factors, revealing how C.t . leverages both Inc-Inc interactions and host protein engagement to manipulate vesicular trafficking and sustain infection.
Tijerina, Xavier [Department of Microbiology and I↗
Higher-order tails and RG flows due to scattering of gravitational radiation from binary inspirals
Abstract We establish and develop a novel methodology to treat higher-order non-linear effects of gravitational radiation that is scattered from binary inspirals, which employs modern scattering-amplitudes methods on the effective picture of the binary as a composite particle. We spell out our procedure to study such effects: assembling tree amplitudes via generalized-unitarity methods and employing the closed-time-path formalism to derive the causal effective actions, which encompass the full conservative and dissipative dynamics. We push through to a new state of the art for these higher-order effects, up to the third subleading tail effect, at order$$ {G}_N^5 $$ G N 5 and the 5-loop level, which corresponds to the 8.5PN order. We formulate the consequent dissipated energy for these higher-order corrections, and carry out a renormalization analysis, where we uncover new subleading RG flow of the quadrupole coupling. For all higher-order tail effects we find perfect agreement with partial observable results in PN and self-force theories, where available.
Physics↗
Interpreting scattered neutron spectra on omega cryogenic implosions with measured backgrounds and higher-order scattering
Measurements of the areal density (ρR) of inertially confined implosions are critical to evaluate their performance. On OMEGA, ρR is inferred from measurements of the scattered neutron spectrum via neutron-time-of-flight (nTOF) and magnetic recoil spectrometer detectors. The nTOF measurements, in particular, have the ability to measure a wide range of neutron energies and thus scattering angles, with high precision. However, the neutrons that are backscattered into the detector must transit through the entire dense fuel assembly, and as a result are subject to rescattering effects, which have been heretofore neglected in the interpretation of OMEGA neutron spectra. At the backscatter edge, neglecting rescattering on OMEGA can lead to a ~10 to 20% reduction of the apparent areal density and therefore must be included in the analysis. The low ρR s on OMEGA also mean that backgrounds from non-target physics effects, such as scattering in the target chamber or slow scintillator decays, can significantly alter the measured signal. Here, we discuss how the Monte Carlo neutron spectrum postprocessor IRIS is used to include second-order scattering effects in the interpretation of the scattered neutron spectrum in OMEGA implosion experiments, and how dedicated implosion experiments are used to measure nTOF backgrounds in order to infer backscattered areal densities on OMEGA.
Deuterium↗
Investigations on the multiple-sector hard-copper X-band accelerating structures
The development of advanced, high gradient accelerating structures is one of the leading activity of the particle accelerator community. In the technological research of new construction methods for these devices, high-power testing is a critical step for the verification of their viability. Recent experiments showed that accelerating cavities made out of hard copper, fabricated without high-temperature processes, can achieve better performance as compared with soft copper ones. Recently, we have built cavities using Tungsten Inert Gas welding and the high-power experiments confirmed that this joining process is a robust and low-cost alternative to brazing or diffusion bonding. This is a good solution for high-gradient operation, with a gradient of about 150 MV/m in X-band, at a breakdown rate of 10 -3 /pulse/meter using a shaped RF pulse with a 150 ns flat part. We continue the design, construction and high power tests of three-cells standing-wave X-band accelerating cavities fabricated with a split-open geometry, made of hard copper and vacuum-sealed by welding. Our aim is the fabrication of accelerating structures made out of hard copper alloys by using innovative cost-effective technologies. Moreover, our method of multiple-sector structures opens the way to new technological approaches and design methods, for example providing the possibility of placing dampers of the parasitic higher-order modes. Such structures with dampers allow for acceleration of multi-bunch beams, both in standing and in travelling-wave accelerating modality. Here, this paper describes the design of two cavities made of multiple sectors that were fabricated at the Italian Institute for Nuclear Physics in Frascati, Italy (INFN-LNF), assembled by means of clamping and then joined with the Tungsten Inert Gas welding in order to preserve the hardness of the metal. These are three-cell standing-wave X-band accelerating cavities, to be operated in the π-mode. We report the low-power RF tests of the first one, made of two halves, and the RF design of the second one, made of four quadrants. Both structures were built for high-gradient tests at SLAC National Accelerator Laboratory.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Capacitor Design for Self-Resonant Coils for Long-Distance Wireless Power Transfer System
In this paper, an integrated capacitor design is proposed for higher-order resonant tank topologies for self-resonant coils, such as series, parallel, LCC, LLC, etc. The capacitor is one of the large, lossy, and thermally vulnerable components of a high-frequency resonant tank, and designing a high-voltage, thermally stable resonant capacitor can be highly challenging. Designing the extremely high-voltage capacitor as an integral part of the coil reduces the size and complexity of the coil assembly. This paper proposes a low-loss PCB-based high-voltage capacitor design to achieve that target, which can be implemented as an integral part of the coil. The proposed capacitor designs are simulated using Multiphysics FEA and tested experimentally. A 23 kV, 133 pF capacitor prototype was built and tested as part of a 1 kW long-distance wireless charging system. The test results verify the capacitor’s voltage, current, and thermal resiliency performance.
Mohammad, Mostak [ORNL] (ORCID:0000000256388783)↗
Atomistic, macromolecular model of the Populus secondary cell wall informed by solid-state NMR
Plant secondary cell walls (SCWs) are composed of a heterogeneous interplay of three major biopolymers: cellulose, hemicelluloses, and lignin. Details regarding specific intermolecular interactions and higher-order architecture of the SCW superstructure remain ambiguous. Here, we use solid-state nuclear magnetic resonance (ssNMR) measurements to infer refined details about the structural configuration, intermolecular interactions, and relative proximity of all three major biopolymers within air-dried Populus wood. To enhance the utility of these findings and enable evaluation of hypotheses in a physics-based environment in silico, the NMR observables are articulated into an atomistic, macromolecular model for biopolymer assemblies within the plant SCW. Through molecular dynamics simulation, we quantitatively evaluate several variations of atomistic models to determine structural details that are corroborated by ssNMR measurements.
09 BIOMASS FUELS↗
Opto-twistronic Hall effect in a three-dimensional spiral lattice
Studies of moire systems have elucidated the exquisite effect of quantum geometry on the electronic bands and their properties, leading to the discovery of new correlated phases. However, most experimental studies have been confined to a few layers in the 2D limit. The extension of twistronics to its 3D limit, where the twist is extended into the third dimension between adjacent layers, remains underexplored due to the challenges in precisely stacking layers. Here, in this study, we focus on 3D twistronics on a platform of self-assembled spiral superlattice of multilayered WS 2 . Our findings reveal an opto-twistronic Hall effect in the spiral superlattice. This mesoscopic response is an experimental manifestation of the noncommutative geometry that arises when translational symmetry is replaced by a non-symmorphic screw operation. We also discover signatures of altered laws of optical excitation, manifested as an unconventional photon momentum-lattice interaction owing to moire of moire modulations in the 3D twistronic system. Crucially, our findings mark the initial identification of higher-order quantum geometrical tensors in light-matter interactions. This breakthrough opens new avenues for designing quantum materials-based optical lattices with large nonlinearities, paving the way for the development of advanced quantum nanophotonic devices.
Ji, Zhurun↗
Effects of N -glycans on the structure of human IgA2
The transition of IgA antibodies into clinical development is crucial because they have the potential to create a new class of therapeutics with superior pathogen neutralization, cancer cell killing, and immunomodulation capacity compared to IgG. However, the biological role of IgA glycans in these processes needs to be better understood. This study provides a detailed biochemical, biophysical, and structural characterization of recombinant monomeric human IgA2, which varies in the amount/locations of attached glycans. Monomeric IgA2 antibodies were produced by removing the N-linked glycans in the CH1 and CH2 domains. The impact of glycans on oligomer formation, thermal stability, and receptor binding was evaluated. In addition, we performed a structural analysis of recombinant IgA2 in solution using Small Angle X-Ray Scattering (SAXS) to examine the effect of glycans on protein structure and flexibility. Our results indicate that the absence of glycans in the Fc tail region leads to higher-order aggregates. SAXS, combined with atomistic modeling, showed that the lack of glycans in the CH2 domain results in increased flexibility between the Fab and Fc domains and a different distribution of open and closed conformations in solution. When binding with the Fcα-receptor, the dissociation constant remains unaltered in the absence of glycans in the CH1 or CH2 domain, compared to the fully glycosylated protein. These results provide insights into N-glycans’ function on IgA2, which could have important implications for developing more effective IgA-based therapeutics in the future.
59 BASIC BIOLOGICAL SCIENCES↗