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At least 235 records · Page 13

Polarized photoelectrons from converging vector waves

Abstract This paper investigates the spin characteristics of photoelectrons when hydrogen-like ions are centro-symmetrically irradiated with converging vector waves—a non-paraxial form of structured light. For a photon with given total angular momentum and third component thereof, photoelectrons with both helicities are obtained—in contrast to the fixed helicities produced by left- or right-circularly polarized light. The angular distribution of photoelectrons is broadly tunable through the radiation mode numbers, and opposite helicities can be extracted in synchronism.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The congenital APOA1 K107del mutation disrupts the lipid-free conformation of monomeric APOA1 and impairs oligomerization

Apolipoprotein A-I (APOA1) oligomerization is thought to be essential for high-density lipoprotein (HDL) formation and metabolism. Naturally occurring mutations can disrupt normal APOA1 folding and self-association, leading to dysfunctional HDL formation and cardiovascular disease. The congenital APOA1 variant p.K131del (APOA1 K107del ) has been associated with cardiovascular pathologies such as low HDL-cholesterol levels and aortic amyloidosis, and multiple studies indicate structural changes in APOA1 conformation underlie associated dysfunction. In the current study, we confirmed that APOA1 K107del exhibits no notable defect in lipid-binding. However, using polyacrylamide gel electrophoresis (PAGE) and size-exclusion chromatography (SEC), we found that loss of lysine 107 resulted in a remarkable shift in the distribution of APOA1 oligomers with a much higher proportion of monomers present in APOA1 K107del compared to wild-type APOA1. Further investigation using quantitative cross-linking revealed a major disruption of interactions in helical regions reported to participate in domain swaps necessary for proper self-association. This structural disruption appears to impair N- and C-termini interactions and dynamics that lead to non-specific aggregation. In conclusion, these findings support the hypothesis that lysine 107 is critical for proper folding and self-association of lipid-free APOA1 which could impact HDL biogenesis.

APOA1 (p.K131del)↗

Multimodal Approach Reveals the Symmetry-Breaking Pathway to the Broken Helix in EuIn 2 ⁢As 2

Understanding and manipulating emergent phases, which are themes at the forefront of quantum-materials research, rely on identifying their underlying symmetries. This general principle has been particularly prominent in materials with coupled electronic and magnetic degrees of freedom, in which magnetic order influences the electronic band structure and can lead to exotic topological effects. However, identifying symmetry of a magnetically ordered phase can pose a challenge, particularly in the presence of small domains. Here we introduce a multimodal approach for determining magnetic structures, which combines symmetry-sensitive optical probes, scattering, and group-theoretical analysis. We apply it to EuIn 2 ⁢As 2 , a material that has received attention as a candidate axion insulator. While first-principles calculations predict this state on the assumption of a simple collinear antiferromagnetic structure, subsequent neutron-scattering measurements reveal a much more intricate magnetic ground state characterized by two coexisting magnetic wave vectors reached by successive thermal phase transitions. The proposed high- and low-temperature phases are a spin helix and a state with interpenetrating helical and Néel antiferromagnetic order termed a “broken helix,” respectively. Employing a multimodal approach, we identify the magnetic structure associated with these two phases of EuIn 2 ⁢As 2 . We find that the higher-temperature phase is characterized by a variation of the magnetic moment amplitude from layer to layer, with the moment vanishing entirely in every third Eu layer. The lower-temperature structure is similar to the broken helix, with one important difference: Because of local strain, the relative orientation of the magnetic structure and the lattice is not fixed. Consequently, the symmetry required to protect the axion phase is not generically protected in EuIn 2 ⁢As 2 , but we show that it can be restored if the magnetic structure is tuned with uniaxial strain. Finally, we present a spin Hamiltonian that identifies the spin interactions that account for the complex magnetic order in EuIn 2 ⁢As 2 . Our work highlights the importance of a multimodal approach in determining the symmetry of complex order parameters.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Cellulose assembles into helical bundles of uniform handedness in cell walls with abnormal pectin composition

Plant cells and organs grow into a remarkable diversity of shapes, as directed by cell walls composed primarily of polysaccharides such as cellulose and multiple structurally distinct pectins. The properties of the cell wall that allow for precise control of morphogenesis are distinct from those of the individual polysaccharide components. For example, cellulose, the primary determinant of cell morphology, is a chiral macromolecule that can self-assemble in vitro into larger-scale structures of consistent chirality, and yet most plant cells do not display consistent chirality in their growth. One interesting exception is the Arabidopsis thaliana rhm1 mutant, which has decreased levels of the pectin rhamnogalacturonan-I and causes conical petal epidermal cells to grow with a left-handed helical twist. Here, we show that in rhm1 the cellulose is bundled into large macrofibrils, unlike the evenly distributed microfibrils of the wild type. This cellulose bundling becomes increasingly severe over time, consistent with cellulose being synthesized normally and then self-associating into macrofibrils. We also show that in the wild type, cellulose is oriented transversely, whereas in rhm1 mutants, the cellulose forms right-handed helices that can account for the helical morphology of the petal cells. Furthermore, our results indicate that when the composition of pectin is altered, cellulose can form cellular-scale chiral structures in vivo, analogous to the helicoids formed in vitro by cellulose nano-crystals. We propose that an important emergent property of the interplay between rhamnogalacturonan-I and cellulose is to permit the assembly of nonbundled cellulose structures, providing plants flexibility to orient cellulose and direct morphogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

Skeletides: A Modular, Simplified Physical Model of Protein Secondary Structure

Three-dimensional (3D) models are essential for visualization and conceptual understanding of complex architectures such as protein structure. Although there is a plethora of software platforms that allow digital depictions of protein structure at an atomic level in silico, physical models are needed to convey an intuitive understanding of biomolecular architecture. However, it is a challenge to represent all the relevant features of proteins in a single physical model due to their sheer structural complexity. Here, we describe a modular protein model that focuses only on representation of the secondary structure—the underlying structural skeleton. The simplified model consists of amino acid units, which can be linked together to reproduce the two most fundamental structural features of protein secondary structure: the relative positions of the amino acid alpha carbon atoms, and the intra-main chain hydrogen bonding pattern. We use 3D printing and magnets to create a set of three modular amino acid building blocks, which when linked together into a chain, can faithfully represent alpha helices, beta sheets, and turns. These simple to make models can be used to quickly assemble the alpha carbon trace of an entire protein domain, which conveys a tactile experience of the complexity of protein skeletal architecture. These models highlight the modularity of protein structure: where a single structural unit, the amino acid, can be linked together to form a larger, regular secondary structure. These models also have a propensity to spontaneously organize into alpha helices and beta sheets, as demonstrated by their ability to autonomously assemble when placed in a circulating water tank. These models provide a missing educational tool to expand knowledge of protein structure, foster deeper insight into protein folding, and inspire greater interest in biomacromolecular architecture.

36 MATERIALS SCIENCE↗

Design of light- and chemically responsive protein assemblies through host-guest interactions

Host-guest (HG) interactions have been widely used to build responsive materials and molecular machines owing to their inherently dynamic nature, interaction specificity, and responsiveness to diverse stimuli. Here, in this work, we have set out to exploit these advantages of HG chemistry in the design of dynamic protein assemblies, using a C 4 symmetric protein, C98 RhuA, as a building block. We show that a C98 RhuA variant individually modified with β-cyclodextrin (βCD) (host) or azobenzene (guest) functionalities can specifically pair with each other to form highly ordered 1D and 2D assemblies. Association and dissociation of βCD RhuA- azo RhuA assemblies can be controlled by UV and visible light as well as by small-molecule modulators of βCD-azobenzene interactions. Kinetics analyses reveal that βCD RhuA- azo RhuA nanotubes assemble without a nucleation barrier, a highly unusual occurrence for helical supramolecular systems. Taken together, our findings provide a compelling example for achieving complex structural and dynamic outcomes in protein assembly through simple chemical design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sawtooth suppression by flux pumping on HBT-EP

Abstract This study examines the mechanisms underlying sawtooth suppression in the High Beta Tokamak-Extended Pulse (HBT-EP) device. It is observed that strong-intensity sawtooth activities correlate with reduced-amplitude magnetohydrodynamics (MHD) edge modes which are identified as m / n = 3 / 1 external kink modes, while sawtooth suppression correlates with larger and saturated edge mode amplitudes. To further investigate these correlations, the plasma–wall coupling was manipulated by adjusting the positions of the conducting walls in HBT-EP. It was found that strong sawtooth events occur when the normalized wall radius b / a is within a critical value. This implies that the plasma–wall distance must be sufficiently small to ensure effective stabilization of the edge mode. Even slight differences in major radius result in significantly different discharge styles, categorized as ‘sawtoothing discharges’ and ‘sawtooth-suppressed discharges’ respectively. Through a series of mode structure analyses, we confirm the coexistence and coupling of the m / n = 1 / 1 helical core, m / n = 2 / 1 tearing mode, and m / n = 3 / 1 external kink mode during sawtooth-suppression, and that this coupling induces anomalous current broadening. Based on these findings, we conclude that sawtooth suppression in the HBT-EP tokamak is consistent with the process of magnetic flux pumping.

Physics↗

The myosin interacting-heads motif present in live tarantula muscle explains tetanic and posttetanic phosphorylation mechanisms

Striated muscle contraction involves sliding of actin thin filaments along myosin thick filaments, controlled by calcium through thin filament activation. In relaxed muscle, the two heads of myosin interact with each other on the filament surface to form the interacting-heads motif (IHM). A key question is how both heads are released from the surface to approach actin and produce force. Here we used time-resolved synchrotron X-ray diffraction to study tarantula muscle before and after tetani. The patterns showed that the IHM is present in live relaxed muscle. Tetanic contraction produced only a very small backbone elongation, implying that mechanosensing—proposed in vertebrate muscle—is not of primary importance in tarantula. Rather, thick filament activation results from increases in myosin phosphorylation that release a fraction of heads to produce force, with the remainder staying in the ordered IHM configuration. After the tetanus, the released heads slowly recover toward the resting, helically ordered state. During this time the released heads remain close to actin and can quickly rebind, enhancing the force produced by posttetanic twitches, structurally explaining posttetanic potentiation. Taken together, these results suggest that, in addition to stretch activation in insects, two other mechanisms for thick filament activation have evolved to disrupt the interactions that establish the relaxed helices of IHMs: one in invertebrates, by either regulatory light-chain phosphorylation (as in arthropods) or Ca 2+ -binding (in mollusks, lacking phosphorylation), and another in vertebrates, by mechanosensing.

59 BASIC BIOLOGICAL SCIENCES↗

Structural basis for a highly conserved RNA-mediated enteroviral genome replication

Abstract Enteroviruses contain conserved RNA structures at the extreme 5′ end of their genomes that recruit essential proteins 3CD and PCBP2 to promote genome replication. However, the high-resolution structures and mechanisms of these replication-linked RNAs (REPLRs) are limited. Here, we determined the crystal structures of the coxsackievirus B3 and rhinoviruses B14 and C15 REPLRs at 1.54, 2.2 and 2.54 Å resolution, revealing a highly conserved H-type four-way junction fold with co-axially stacked sA-sD and sB-sC helices that are stabilized by a long-range A•C•U base-triple. Such conserved features observed in the crystal structures also allowed us to predict the models of several other enteroviral REPLRs using homology modeling, which generated models almost identical to the experimentally determined structures. Moreover, our structure-guided binding studies with recombinantly purified full-length human PCBP2 showed that two previously proposed binding sites, the sB-loop and 3′ spacer, reside proximally and bind a single PCBP2. Additionally, the DNA oligos complementary to the 3′ spacer, the high-affinity PCBP2 binding site, abrogated its interactions with enteroviral REPLRs, suggesting the critical roles of this single-stranded region in recruiting PCBP2 for enteroviral genome replication and illuminating the promising prospects of developing therapeutics against enteroviral infections targeting this replication platform.

Biochemistry & Molecular Biology↗

3D-printed mirror-less helicity preserving metasurface “mirror” for THz applications

Stimulated by seminal works on generalized reflection and refraction laws, metasurfaces have evolved to a highly promising research direction, as they allow a multitude of different functionalities by optically thin wave-control elements/structures. Among them, structures functioning in the low THz regime are of extensive research interest, due to their high potential in communication and sensing applications. In this paper we propose a simple THz metasurface design that exhibits ideally perfect cross-polarized reflection for linear polarization and perfect helicity-preserving reflection with a geometric (Pancharatnam–Berry) phase for circular polarization, without the presence of any back-reflector. Numerical calculations demonstrating the structure response are justified by analytical models, which provide physical insights on this response. The designed metasurfaces are fabricated using the direct laser writing 3D-printing technology, metallized with electroless silver plating, and are characterized by THz time domain spectroscopy, with the experimental results validating the corresponding theoretical ones. Applications including beam steering and focusing, exploring the Pancharatnam–Berry phase, are also demonstrated numerically. Besides those applications, the helicity preserving mirror response of our metasurfaces can be valuable, among others, also in molecular chirality sensing applications, an issue that is also highlighted here.

3D-printed metasurfaces↗

Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation

Effective gene regulation by the tetrahydrofolate riboswitch depends not only on ligand affinity but also on the kinetics of ligand association, which involves two cooperative binding sites. Here, we have determined a 1.9-Å resolution crystal structure of the ligand-free THF riboswitch aptamer. The pseudoknot binding site ‘unwinds’ in the absence of ligand, whereby the adjacent helical domains (P1, P2, and P3) become disjointed, resulting in rotation and misalignment of the gene-regulatory P1 helix with respect to P3. In contrast, the second binding site at the three-way junction, which is the first to fold, is structurally conserved between apo and holo forms. This suggests a kinetic role for this site, in which binding of the first ligand molecule to the stably folded three-way junction promotes formation of the regulatory pseudoknot site and subsequent binding of the second molecule. As such, these findings provide a molecular basis for both conformational switching and kinetic control.

59 BASIC BIOLOGICAL SCIENCES↗

Structural basis for the subtype-selectivity of K Ca 2.2 channel activators

Small-conductance (K Ca 2.2) and intermediate-conductance (K Ca 3.1) Ca 2+ -activated K + channels are gated by a Ca 2+ -calmodulin dependent mechanism. NS309 potentiates the activity of both K Ca 2.2 and K Ca 3.1, while rimtuzalcap selectively activates K Ca 2.2. Rimtuzalcap has been used in clinical trials for the treatment of spinocerebellar ataxia and essential tremor. We report cryo-electron microscopy structures of NS309-bound K Ca 2.2 and K Ca 3.1, in addition to structures of rimtuzalcap-bound K Ca 2.2 and mutant K Ca 3.1_R355K. The different conformations of calmodulin and the cytoplasmic HC helices in the two channels underlie the subtype-selectivity of rimtuzalcap for K Ca 2.2. NS309 binds to pre-existing pockets in both channels, while the bulkier rimtuzalcap binds in an induced-fit pocket in K Ca 2.2 requiring conformational changes. In K Ca 2.2, calmodulin’s N-lobes are sufficiently far apart to enable conformational changes to accommodate either NS309 or rimtuzalcap. In K Ca 3.1, calmodulin’s N-lobes are closer to each other and constrained by K Ca 3.1’s HC helices, which allows binding of NS309 but not rimtuzalcap. Replacement of arginine-355 in K Ca 3.1’s HB helix with lysine (K Ca 3.1_R355K) allows the binding of rimtuzalcap and renders the mutant channel sensitive to rimtuzalcap. These structures provide a framework for structure-based drug design targeting K Ca 2.2 channels.

Nam, Young-Woo [Chapman Univ., Irvine, CA (United ↗

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.

Methanosarcina acetivorans↗

Moments of nucleon isovector structure functions in 2+1+1-flavor QCD

We present results on the isovector momentum fraction, $\langle x \rangle_{u–d}$ , helicity moment, $\langle x \rangle_{Δ u–Δd}$ , and the transversity moment, $\langle x \rangle_{δu–δd}$, of the nucleon obtained using nine ensembles of gauge configurations generated by the MILC Collaboration using 2 + 1 + 1 -flavors of dynamical highly improved staggered quarks. The correlation functions are calculated using the Wilson-Clover action, and the renormalization of the three operators is carried out nonperturbatively on the lattice in the RI'–MOM scheme. The data have been collected at lattice spacings a ≈ 0.15 , 0.12, 0.09, and 0.06 fm and $M_π$ ≈ 310 , 220, and 135 MeV, which are used to obtain the physical values using a simultaneous chiral-continuum-finite-volume fit. The final results, in the $\overline{\text{MS}}$ scheme at 2 GeV, are $\langle$ x $\rangle$ u – d = 0.173 ( 14 ) ( 07 ) , $\langle x \rangle_{Δu–Δd}$ = 0.213 ( 15 ) ( 22 ) , and $\langle x \rangle_{δu–δd}$ = 0.208 ( 19 ) ( 24 ) , where the first error is the overall analysis uncertainty and the second is an additional systematic uncertainty due to possible residual excited-state contributions. These results are consistent with other recent lattice calculations and phenomenological global fit values.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Flat-band tuning and emergent itinerant magnetism in Sr(Co 1− x Pd x ) 2 As 2

The interplay between magnetism and flat-band (FB) instability is a central theme in quantum materials research. A striking example is the emergence of magnetic order in a nominally nonmagnetic compound when a flat band is tuned near the Fermi energy (E F ). Here, in this study, we investigate this phenomenon in the Pauli paramagnet SrCo 2 As 2 , where an FB associated with Co e g orbitals lies close to E F . Remarkably, a minute substitution of the nonmagnetic element Pd onto the Co site (~2%) induces antiferromagnetic order with a transition temperature as high as T N = 25 K. Temperature- and magnetic-field-dependent magnetic and transport measurements, complemented by zero-field neutron diffraction, reveal a helical magnetic order for x ≤ 0.10 in Sr(Co 1−x Pd x ) 2 As 2 , transitioning to a complex ferromagnetic state at higher Pd concentrations. Spectroscopic evidence and theoretical band structure calculations demonstrate that electron doping shifts the flat band closer to E F , significantly enhancing the Stoner parameter. This enhancement drives a strong ferromagnetic instability, leading to helical magnetic ordering dominated by in-plane ferromagnetic interactions. The emergence of robust magnetic ordering through substitution with nonmagnetic elements is a unique phenomenon that underscores the pivotal role of flat-band instability in tuning magnetism in itinerant systems.

36 MATERIALS SCIENCE↗

The Nucleoid-Associated Protein GapR Uses Conserved Structural Elements To Oligomerize and Bind DNA

Nucleoid-associated proteins (NAPs) are DNA binding proteins critical for the organization and function of the bacterial chromosome. A newly discovered NAP in Caulobacter crescentus, GapR, is thought to facilitate the movement of the replication and transcription machines along the chromosome by stimulating type II topoisomerases to remove positive supercoiling. Here, utilizing genetic, biochemical, and biophysical studies of GapR in light of a recently published DNA-bound crystal structure of GapR, we identified the structural elements involved in oligomerization and DNA binding. Moreover, we show that GapR is maintained as a tetramer upon its dissociation from DNA and that tetrameric GapR is capable of binding DNA molecules in vitro. Analysis of protein chimeras revealed that two helices of GapR are functionally conserved in H-NS, demonstrating that two evolutionarily distant NAPs with distinct mechanisms of action utilize conserved structural elements to oligomerize and bind DNA.

59 BASIC BIOLOGICAL SCIENCES↗

Coherently coupled carrier and phonon dynamics in elemental tellurium probed by extreme ultraviolet transient absorption

The narrow band-gap semiconductor elemental tellurium (Te) has a unique electronic structure due to strong spin-orbit splitting and a lack of inversion symmetry of its helical lattice. Using broadband extreme ultraviolet core-level transient absorption, we simultaneously measure the coherently coupled photoinduced carrier and lattice dynamics at the Te N4,5 edge initiated by a few-cycle NIR pulse. Ultrafast excitation of carriers leads to a coherently excited A1 phonon oscillation and the generation of a hot carrier population distribution that oscillates in temperature, and the phonon excursion and hot carrier temperature are π out of phase with respect to each other. The depths of modulation suggest a significant coupling between the electronic and lattice degrees of freedom in Te. A long-lived shift of the absorption edge suggests an excited state of Te in another equilibrium potential energy surface that lives on the order of the carrier recombination timescale. The observed phonon-induced oscillations of the hot carriers are supportive of a change in the metallicity, whereby Te becomes more metallic with increasing phonon-induced displacement. Additionally, near the Fermi level we observe an energy-dependent phase of the displacive excitation of the A1 phonon mode. The discovery of coherent coupling between the lattice and hot carriers in Te provides the basis to investigate coherent interactions between spin and orbital degrees of freedom. The results spectrally and temporally resolve the correlation between photoexcited hot carriers and coherent lattice excitations, providing insight on the optical manipulation of the Te electronic structure at high carrier densities exceeding 1021cm−3.

Adelman, Jonah R↗

An explainable variational autoencoder model for three-dimensional acoustic emission source localization in hollow cylindrical structures

We introduce an explainable variational autoencoder for three-dimensional (3D) localization of acoustic emission sources in hollow cylindrical structures, with an unsupervised approach. This research capitalizes on multi-arrival waveforms generated by helical path propagation in cylindrical geometries to enable efficient two-receiver localization. By integrating the modal characteristics of Lamb modes under multi-path conditions, we demonstrate that two sets of time-of-arrival differences and peak amplitudes extracted from one receiver can serve as effective localization features. This initial approach identifies four potential source locations, highlighting the feasibility of two-receiver source localization using traditional feature extraction methods. However, direct extraction can be challenging when mode overlaps occur, complicating the localization process. To address this, our work proposes a novel waveform-based method. This method leverages the consistent dispersion characteristics within isotropic materials, where each unique combination of mode arrival times and peak amplitudes constructs a distinct waveform. This distinctiveness overcomes the ambiguities associated with mode overlaps, significantly enhancing the method’s precision and robustness. Our approach adopts a data-driven strategy for waveform-based localization using variational autoencoder (VAE). VAE discerns waveform patterns for localization, while also addressing data uncertainties. The VAE’s encoder and decoder networks capture the localization process and the source’s influence on waveform generation, respectively, guiding latent variables to segregate waveforms by source in the latent space. The design of the learning process focuses on specific localization characteristics to enhance result explainability. Localization predictions are generated by projecting test waveforms, not included in the training set, onto a trained latent space. The prediction is determined using a nearest-neighbor approach based on the closest latent representation of a source. Validation with pencil-lead-break tests on a metallic pipe confirmed our method’s effectiveness, achieving an averaged 3D localization accuracy of 0.84.

Lee, Guan-Wei↗