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DOE OSTI2020

Architecture of a catalytically active homotrimeric plant cellulose synthase complex

Cellulose is an essential plant cell wall component and represents the most abundant biopolymer on Earth. Supramolecular plant cellulose synthase complexes organize multiple linear glucose polymers into microfibrils as load-bearing wall components. We determined the structure of a poplar cellulose synthase CesA homotrimer that suggests a molecular basis for cellulose microfibril formation. This complex, stabilized by cytosolic plant-conserved regions and helical exchange within the transmembrane segments, forms three channels occupied by nascent cellulose polymers. Secretion steers the polymers toward a common exit point, which could facilitate protofibril formation. CesA’s N-terminal domains assemble into a cytosolic stalk that interacts with a microtubule-tethering protein and may thus be involved in CesA localization. Here, our data suggest how cellulose synthase complexes assemble and provide the molecular basis for plant cell wall engineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Proton spin from small-x with constraints from the valence quark model

We apply the valence quark model [1] to constrain the non-perturbative initial condition for the small-x helicity evolution. The remaining free parameters are constrained by performing a global analysis akin to [2] to the available polarized small-x deep inelastic scattering data. A good description of the world data is obtained with only 8 free parameters. The model parameters are tightly constrained by the data, allowing us to predict the proton polarized structure function $g^p_1$ to be negative at small x. Furthermore, we obtain the small-x quark and gluon spins to give a contribution $\int^{0.1}_{10^{-5}} dx (\frac{1}{2}\Delta\Sigma + \Delta{G}) = 0.63 ± 0.10$ or $1.35 ± 0.16$ (or to the proton spin, depending on the applied running coupling prescription.

Color-class condensate↗

DOE OSTI2020

Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA

Nop9 is an essential factor in the processing of preribosomal RNA. Its absence in yeast is lethal, and defects in the human ortholog are associated with breast cancer, autoimmunity, and learning/language impairment. PUF family RNA-binding proteins are best known for sequence-specific RNA recognition, and most contain eight α-helical repeats that bind to the RNA bases of single-stranded RNA. Nop9 is an unusual member of this family in that it contains eleven repeats and recognizes both RNA structure and sequence. Here we report a crystal structure of Saccharomyces cerevisiae Nop9 in complex with its target RNA within the 20S preribosomal RNA. This structure reveals that Nop9 brings together a carboxy-terminal module recognizing the 5' single-stranded region of the RNA and a bifunctional amino-terminal module recognizing the central double-stranded stem region. We further show that the 3' single-stranded region of the 20S target RNA adds sequence-independent binding energy to the RNA–Nop9 interaction. Both the amino- and carboxy-terminal modules retain the characteristic sequence-specific recognition of PUF proteins, but the amino-terminal module has also evolved a distinct interface, which allows Nop9 to recognize either single-stranded RNA sequences or RNAs with a combination of single-stranded and structured elements.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Helical allophycocyanin nanotubes absorb far-red light in a thermophilic cyanobacterium

To compete in certain low-light environments, some cyanobacteria express a paralog of the light-harvesting phycobiliprotein, allophycocyanin (AP), that strongly absorbs far-red light (FRL). Using cryo–electron microscopy and time-resolved absorption spectroscopy, we reveal the structure-function relationship of this FRL-absorbing AP complex (FRL-AP) that is expressed during acclimation to low light and that likely associates with chlorophyll a–containing photosystem I. FRL-AP assembles as helical nanotubes rather than typical toroids due to alterations of the domain geometry within each subunit. Spectroscopic characterization suggests that FRL-AP nanotubes are somewhat inefficient antenna; however, the enhanced ability to harvest FRL when visible light is severely attenuated represents a beneficial trade-off. The results expand the known diversity of light-harvesting proteins in nature and exemplify how biological plasticity is achieved by balancing resource accessibility with efficiency.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Structural basis for severe pain caused by mutations in the S4-S5 linkers of voltage-gated sodium channel Na V 1.7

Gain-of-function mutations in voltage-gated sodium channel Na V 1.7 cause severe inherited pain syndromes, including inherited erythromelalgia (IEM). The structural basis of these disease mutations, however, remains elusive. Here, we focused on three mutations that all substitute threonine residues in the alpha-helical S4-S5 intracellular linker that connects the voltage sensor to the pore: Na V 1.7/I234T, Na V 1.7/I848T, and Na V 1.7/S241T in order of their positions in the amino acid sequence within the S4-S5 linkers. Introduction of these IEM mutations into the ancestral bacterial sodium channel Na V Ab recapitulated the pathogenic gain-of-function of these mutants by inducing a negative shift in the voltage dependence of activation and slowing the kinetics of inactivation. Remarkably, our structural analysis reveals a common mechanism of action among the three mutations, in which the mutant threonine residues create new hydrogen bonds between the S4-S5 linker and the pore-lining S5 or S6 segment in the pore module. Because the S4-S5 linkers couple voltage sensor movements to pore opening, these newly formed hydrogen bonds would stabilize the activated state substantially and thereby promote the 8 to 18 mV negative shift in the voltage dependence of activation that is characteristic of the Na V 1.7 IEM mutants. Our results provide key structural insights into how IEM mutations in the S4-S5 linkers may cause hyperexcitability of Na V 1.7 and lead to severe pain in this debilitating disease.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Non-Covalent Interactions and Helical Packing in Thiophene-Phenylene Copolymers: Tuning Solid-State Ordering and Charge Transport for Organic Field-Effect Transistors

In this study, we introduce two thiophene-phenylene-thiophene (TPT) polymers designed to leverage noncovalent intramolecular interactions to regulate main-chain conformation and enhance solid-state ordering. By incorporating unsubstituted thiophene (T) or bithiophene (2T) units, we reveal striking divergence in the thermal, morphological, and optoelectronic properties of the resulting films, facilitated by these noncovalent interactions. Using a combination of computational and experimental approaches, we show that annealing yields remarkably different polymer conformations and, consequently, charge transport properties. TPT-T undergoes a significant structural transformation, adopting a more planar backbone conformation and a highly crystalline, edge-on molecular orientation. In contrast, the introduction of a single additional thiophene unit in TPT-2T leads to a more isotropic molecular orientation with a slight preference for face-on alignment, resulting in a heterogeneous film structure that hinders charge transport despite achieving tighter molecular packing. Remarkably, despite being composed of achiral components, TPT-2T develops chirality upon annealing, indicating the formation of a helical conformation. Organic field-effect transistor measurements reveal that the well-ordered alignment in annealed TPT-T films results in higher charge carrier mobility and a narrower distribution of mobility values than in TPT-2T. These findings provide critical insights into the structure−property relationships of conjugated polymers, offering guidance for optimizing molecular design and processing strategies for highperformance organic electronic materials.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Correlated conformational dynamics of the human GluN1-GluN2A type N-methyl-D-aspartate (NMDA) receptor

N-Methyl-D-aspartate receptors (NMDARs) are glutamate-gated ion channels found in the nerve cell membranes. As a result of overexcitation of NMDARs, neuronal death occurs and may lead to diseases such as epilepsy, stroke, Alzheimer’s disease, and Parkinson’s disease. In this study, human GluN1- GluN2A type NMDAR structure is modeled based on the X-ray structure of the Xenopus laevis template and missing loops are added by ab-initio loop modeling. The final structure is chosen according to two different model assessment scores. To be able to observe the structural changes upon ligand binding, glycine and glutamate molecules are docked into the corresponding binding sites of the receptor. Subsequently, molecular dynamics simulations of 1.3 μs are performed for both apo and ligand-bound structures. Structural parameters, which have been considered to show functionally important changes in previous NMDAR studies, are monitored as conformational rulers to understand the dynamics of the conformational changes. Moreover, principal component analysis (PCA) is performed for the equilibrated part of the simulations. Additionally, from these analyses, the differences in between apo and ligand-bound simulations can be summarized as the following: The girdle right at the beginning of the pore loop, which connects M2 and M3 helices of the ion channel, partially opens. Ligands act like an adhesive for the ligand-binding domain (LBD) by keeping the bi-lobed structure together and consequently this is reflected to the overall dynamics of the protein as an increased correlation of the LBD with especially the amino-terminal domain (ATD) of the protein.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The Helicity Sign of Flux Transfer Event Flux Ropes and Its Relationship to the Guide Field and Hall Physics in Magnetic Reconnection at the Magnetopause

Flux Transfer Events (FTEs) are transient magnetic flux ropes typically found at the Earth's magnetopause on the dayside. While it is known that FTEs are generated by magnetic reconnection, it remains unclear how the details of magnetic reconnection controls their properties. A recent study showed that the helicity sign of FTEs positively correlates with the east-west (B y ) component of the Interplanetary Magnetic Field (IMF). With data from the Cluster and Magnetospheric Multiscale missions, we performed a statistical study of 166 quasi force-free FTEs. We focus on their helicity sign and possible association with upstream solar wind conditions and local magnetic reconnection properties. Using both in situ data and magnetic shear modeling, we find that FTEs whose helicity sign corresponds to the IMF B y are associated with moderate magnetic shears while those that do not correspond to the IMF B y are associated with higher magnetic shears. While uncertainty in IMF propagation to the magnetopause may lead to randomness in the determination of the flux rope core field and helicity, we rather propose that for small IMF B y , which corresponds to high shear and low guide field, the Hall pattern of magnetic reconnection determines the FTE core field and helicity sign. In that context we explain how the temporal sequence of multiple X-line formation and the reconnection rate are important in determining the flux rope helicity sign. This work highlights a fundamental connection between kinetic processes at work in magnetic reconnection and the macroscale structure of FTEs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Directing polymorph specific calcium carbonate formation with de novo protein templates

Biomolecules modulate inorganic crystallization to generate hierarchically structured biominerals, but the atomic structure of the organic-inorganic interfaces that regulate mineralization remain largely unknown. We hypothesized that heterogeneous nucleation of calcium carbonate could be achieved by a structured flat molecular template that pre-organizes calcium ions on its surface. To test this hypothesis, we design helical repeat proteins (DHRs) displaying regularly spaced carboxylate arrays on their surfaces and find that both protein monomers and protein-C a2+ supramolecular assemblies directly nucleate nano-calcite with non-natural {110} or {202} faces while vaterite, which forms first in the absence of the proteins, is bypassed. These protein-stabilized nanocrystals then assemble by oriented attachment into calcite mesocrystals. We find further that nanocrystal size and polymorph can be tuned by varying the length and surface chemistry of the designed protein templates. Thus, bio-mineralization can be programmed using de novo protein design, providing a route to next-generation hybrid materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Evidence for a single-layer van der Waals multiferroic

Here we searched for signatures of type-II multiferroic order in ultrathin van der Waals materials, to determine if such a state, comprising coexisting electrical polarization and spin order with strong magnetoelectric effects, could persist down to a single-atomic layer. We reported the first observation of such a state in triangular lattice material NiI 2 . This system has a layered structure and built-in magnetic frustration that promotes a complex magnetic ground state with proper-screw spin helices. The spin helix pattern breaks inversion symmetry and induces electrical polarization via magnetoelectric coupling. We use circular dichroic Raman measurements to directly probe the magneto-chiral ground state and its electromagnon modes originating from dynamic magnetoelectric coupling. Using birefringence and second-harmonic generation measurements, we detect a highly anisotropic electronic state simultaneously breaking three-fold rotational and inversion symmetry. The evolution of the optical signatures as a function of temperature and layer number surprisingly revealed a multiferroic state that persists down to the ultrathin limit of monolayer NiI 2 . These observations establish NiI 2 and transition metal dihalides as a new platform for studying emergent multiferroic phenomena, chiral magnetic textures and ferroelectricity in the 2D limit.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Tad and toxin-coregulated pilus structures reveal unexpected diversity in bacterial type IV pili

<Type IV pili (T4P) are ubiquitous in both bacteria and archaea. They are polymers of the major pilin protein, which has an extended and protruding N-terminal helix, α1, and a globular C-terminal domain. Cryo-EM structures have revealed key differences between the bacterial and archaeal T4P in their C-terminal domain structure and in the packing and continuity of α1. This segment forms a continuous α-helix in archaeal T4P but is partially melted in all published bacterial T4P structures due to a conserved helix breaking proline at position 22. The tad (tight adhesion) T4P are found in both bacteria and archaea and are thought to have been acquired by bacteria through horizontal transfer from archaea. Tad pilins are unique among the T4 pilins, being only 40 to 60 residues in length and entirely lacking a C-terminal domain. They also lack the Pro22 found in all high-resolution bacterial T4P structures. We show using cryo-EM that the bacterial tad pilus from Caulobacter crescentus is composed of continuous helical subunits that, like the archaeal pilins, lack the melted portion seen in other bacterial T4P and share the packing arrangement of the archaeal T4P. We further show that a bacterial T4P, the Vibrio cholerae toxin coregulated pilus, which lacks Pro22 but is not in the tad family, has a continuous N-terminal α-helix, yet its α1 s are arranged similar to those in other bacterial T4P. Our results highlight the role of Pro22 in helix melting and support an evolutionary relationship between tad and archaeal T4P.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

2024 roadmap on 2D topological insulators

Abstract 2D topological insulators promise novel approaches towards electronic, spintronic, and quantum device applications. This is owing to unique features of their electronic band structure, in which bulk-boundary correspondences enforces the existence of 1D spin–momentum locked metallic edge states—both helical and chiral—surrounding an electrically insulating bulk. Forty years since the first discoveries of topological phases in condensed matter, the abstract concept of band topology has sprung into realization with several materials now available in which sizable bulk energy gaps—up to a few hundred meV—promise to enable topology for applications even at room-temperature. Further, the possibility of combining 2D TIs in heterostructures with functional materials such as multiferroics, ferromagnets, and superconductors, vastly extends the range of applicability beyond their intrinsic properties. While 2D TIs remain a unique testbed for questions of fundamental condensed matter physics, proposals seek to control the topologically protected bulk or boundary states electrically, or even induce topological phase transitions to engender switching functionality. Induction of superconducting pairing in 2D TIs strives to realize non-Abelian quasiparticles, promising avenues towards fault-tolerant topological quantum computing. This roadmap aims to present a status update of the field, reviewing recent advances and remaining challenges in theoretical understanding, materials synthesis, physical characterization and, ultimately, device perspectives.

Weber, Bent (ORCID:000000018586127X)↗

DOE OSTI2023

Gluon helicity in the nucleon from lattice QCD and machine learning

We present the first lattice QCD determination of the light cone gluon helicity correlation parton distribution function (PDF) with numerical evidence toward disfavoring negative gluon polarization in the nucleon. We present a solution for eliminating an inevitable contamination term that dominates the Euclidean correlations and makes determining gluon helicity PDF unfeasible. The proposed synergy between lattice QCD and artificial intelligence offers a superior platform to alleviate the defining challenge of extracting quark and gluon PDFs from the lattice data that are available in a limited domain due to a finite range of accessible hadron momenta. We suggest a systematically improvable method to extract PDFs from the lattice data, independent of inadequate parametrizations. The result of the gluon helicity will improve our understanding of the role of spin in the strong interaction and the nucleon-spin structure.

Lattice QCD↗

DOE OSTI2022

Cbp1, a fungal virulence factor under positive selection, forms an effector complex that drives macrophage lysis

Intracellular pathogens secrete effectors to manipulate their host cells. Histoplasma capsulatum (Hc) is a fungal intracellular pathogen of humans that grows in a yeast form in the host. Hc yeasts are phagocytosed by macrophages, where fungal intracellular replication precedes macrophage lysis. The most abundant virulence factor secreted by Hc yeast cells is Calcium Binding Protein 1 (Cbp1), which is absolutely required for macrophage lysis. Here we take an evolutionary, structural, and cell biological approach to understand Cbp1 function. We find that Cbp1 is present only in the genomes of closely related dimorphic fungal species of the Ajellomycetaceae family that lead primarily intracellular lifestyles in their mammalian hosts (Histoplasma, Paracoccidioides, and Emergomyces), but not conserved in the extracellular fungal pathogen Blastomyces dermatitidis. We observe a high rate of fixation of non-synonymous substitutions in the Cbp1 coding sequences, indicating that Cbp1 is under positive selection. We determine the de novo structures of Hc H88 Cbp1 and the Paracoccidioides americana (Pb03) Cbp1, revealing a novel “binocular” fold consisting of a helical dimer arrangement wherein two helices from each monomer contribute to a four-helix bundle. In contrast to Pb03 Cbp1, we show that Emergomyces Cbp1 orthologs are unable to stimulate macrophage lysis when expressed in the Hc cbp1 mutant. Consistent with this result, we find that wild-type Emergomyces africanus yeast are able to grow within primary macrophages but are incapable of lysing them. Finally, we use subcellular fractionation of infected macrophages and indirect immunofluorescence to show that Cbp1 localizes to the macrophage cytosol during Hc infection, making this the first instance of a phagosomal human fungal pathogen directing an effector into the cytosol of the host cell. We additionally show that Cbp1 forms a complex with Yps-3, another known Hc virulence factor that accesses the cytosol. Taken together, these data imply that Cbp1 is a fungal virulence factor under positive selection that localizes to the cytosol to trigger host cell lysis.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1981

Development of a composite geodetic structure for space construction, phase 2

Primary physical and mechanical properties were defined for pultruded hybrid HMS/E-glass P1700 rod material used for the fabrication of geodetic beams. Key properties established were used in the analysis, design, fabrication, instrumentation, and testing of a geodetic parameter cylinder and a lattice cone closeout joined to a short cylindrical geodetic beam segment. Requirements of structural techniques were accomplished. Analytical procedures were refined and extended to include the effect of rod dimensions for the helical and longitudinal members on local buckling, and the effect of different flexural and extensional moduli on general instability buckling.

Source record↗

NASA NTRS2009

Prominence Structure and Dynamics

Nonerupting prominences are not dull, static objects. Rather, they are composed of fine-scale blobs and threads that are highly dynamic, often appearing to travel in opposite directions on adjacent tracks (denoted counterstreaming). Because the plasma is largely constrained to travel along the magnetic field, these cool, dense features can serve as tracers of the prominence magnetic structure, a valuable resource in view of the long-standing difficulty of observing the coronal field. Conversely, greater understanding of the fundamental magnetic geometry of filament channels can provide important constraints on the physical processes governing the accumulation, support, motion, and eruption of the cool plasma. Despite over a century of detailed observations, large gaps remain in our knowledge of filament channel/plasma formation and evolution. Resolving these issues will shed light on the physics of coronal heating, helicity transport throughout the solar cycle, and the origins of eruptive activity on the Sun. I will discuss the leading models for the magnetic and plasma structure, and outline how new observations and theory /modeling could solve long-standing uncertainties regarding this majestic solar phenomenon.

Karpen, Judy T.↗

DOE OSTI2023

Manipulation of Scattering Spectra with Topology of Light and Matter

Structured lights, including beams carrying spin and orbital angular momenta, radially and azimuthally polarized vector beams, as well as spatiotemporal optical vortices, have attracted significant interest due to their unique amplitude, phase front, polarization, and temporal structures, enabling a variety of applications in optical and quantum communications, micromanipulation, and super-resolution imaging. In parallel, structured optical materials, metamaterials, and metasurfaces consisting of engineered unit cells—meta-atoms, opened new avenues for manipulating the flow of light and optical sensing. While several studies explored structured light effects on the individual meta-atoms, their shapes are largely limited to simple spherical geometries. However, the synergy of the structured light and complex-shaped meta-atoms has not been fully explored. Here, in this paper, the role of the helical wavefront of Laguerre–Gaussian beams in the excitation and suppression of higher-order resonant modes inside all-dielectric meta-atoms of various shapes, aspect ratios, and orientations, is demonstrated and the excitation of various multipolar moments that are not accessible via unstructured light illumination is predicted. The presented study elucidates the role of the complex phase distribution of the incident light in shape-dependent resonant scattering, which is of utmost importance in a wide spectrum of applications ranging from remote sensing to spectroscopy.

42 ENGINEERING↗

DOE OSTI2020

Structure of the Diphtheria Toxin at Acidic pH: Implications for the Conformational Switching of the Translocation Domain

Diphtheria toxin, an exotoxin secreted by Corynebacterium that causes disease in humans by inhibiting protein synthesis, enters the cell via receptor-mediated endocytosis. The subsequent endosomal acidification triggers a series of conformational changes, resulting in the refolding and membrane insertion of the translocation (T-)domain and ultimately leading to the translocation of the catalytic domain into the cytoplasm. Here, we use X-ray crystallography along with circular dichroism and fluorescence spectroscopy to gain insight into the mechanism of the early stages of pH-dependent conformational transition. For the first time, we present the high-resolution structure of the diphtheria toxin at a mildly acidic pH (5–6) and compare it to the structure at neutral pH (7). We demonstrate that neither catalytic nor receptor-binding domains change their structure upon this acidification, while the T-domain undergoes a conformational change that results in the unfolding of the TH2–3 helices. Surprisingly, the TH1 helix maintains its conformation in the crystal of the full-length toxin even at pH 5. This contrasts with the evidence from the new and previously published data, obtained by spectroscopic measurements and molecular dynamics computer simulations, which indicate the refolding of TH1 upon the acidification of the isolated T-domain. The overall results imply that the membrane interactions of the T-domain are critical in ensuring the proper conformational changes required for the preparation of the diphtheria toxin for the cellular entry.

59 BASIC BIOLOGICAL SCIENCES↗