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At least 1,801 records · Page 100

The Structure and Catalytic Mechanism of Sorghum bicolor Caffeoyl-CoA O-Methyltransferase

Caffeoyl-coenzyme A 3-O-methyltransferase (CCoAOMT) is an S-adenosyl methionine (SAM)-dependent O-methyltransferase responsible for methylation of the meta-hydroxyl group of caffeoyl-coenzyme A (CoA) on the pathway to monolignols, with their ring methoxylation status characteristic of guaiacyl or syringyl units in lignin. In order to better understand the unique class of type 2 O-methyltransferases from monocots, we have characterized CCoAOMT from sorghum (Sorghum bicolor; SbCCoAOMT), including the SAM binary complex crystal structure and steady-state enzyme kinetics. Key amino acid residues were validated with site-directed mutagenesis. Isothermal titration calorimetry data indicated a sequential binding mechanism for SbCCoAOMT, wherein SAM binds prior to caffeoyl-CoA, and the enzyme showed allosteric behavior with respect to it. 5-Hydroxyferuloyl-CoA was not a substrate for SbCCoAOMT. We propose a catalytic mechanism in which lysine-180 acts as a catalytic base and deprotonates the reactive hydroxyl group of caffeoyl-CoA. This deprotonation is facilitated by the coordination of the reactive hydroxyl group by Ca 2+ in the active site, lowering the pK a of the 3'-OH group. Collectively, these data give a new perspective on the catalytic mechanism of CCoAOMTs and provide a basis for the functional diversity exhibited by type 2 plant OMTs that contain a unique insertion loop (residues 208–231) conferring affinity for phenylpropanoid-CoA thioesters. The structural model of SbCCoAOMT can serve as the basis for protein engineering approaches to enhance the nutritional, agronomic, and industrially relevant properties of sorghum.

Walker, Alexander M.↗

Applications of Artificial Neural Networks in Structural Engineering with Emphasis on Continuum Models

The use of continuum models for the analysis of discrete built-up complex aerospace structures is an attractive idea especially at the conceptual and preliminary design stages. But the diversity of available continuum models and hard-to-use qualities of these models have prevented them from finding wide applications. In this regard, Artificial Neural Networks (ANN or NN) may have a great potential as these networks are universal approximators that can realize any continuous mapping, and can provide general mechanisms for building models from data whose input-output relationship can be highly nonlinear. The ultimate aim of the present work is to be able to build high fidelity continuum models for complex aerospace structures using the ANN. As a first step, the concepts and features of ANN are familiarized through the MATLAB NN Toolbox by simulating some representative mapping examples, including some problems in structural engineering. Then some further aspects and lessons learned about the NN training are discussed, including the performances of Feed-Forward and Radial Basis Function NN when dealing with noise-polluted data and the technique of cross-validation. Finally, as an example of using NN in continuum models, a lattice structure with repeating cells is represented by a continuum beam whose properties are provided by neural networks.

Kapania, Rakesh K.↗

Synthesis and structural characterization of new dithiocarbamate complexes from Sb(III) and Bi(III)

Twenty new antimony and bismuth dithiocarbamate complexes which employed ten different type of amines have been successfully synthesized. The synthesized complexes with metal to dithiocarbamate ratio at 1:3. Elemental analysis of the complexes gave the general formula of MCl[S{sub 2}CNR’R”]{sub 2} where M = Sb(III), Bi(III); R’ = methyl, ethyl, propyl, isopropyl, butyl, sec-butyl, benzyl; R” = ethanol, methyl, ethyl, propyl, isopropyl, cyclohexyl, benzyl. The complexes were analysed by IR and NMR spectroscopy. The crystal structure of five-coordinated antimony (III) complex have been determined by X-ray single crystal diffraction. Single crystal X-ray diffraction studies on SbCl[S{sub 2}CN(C{sub 4}H{sub 9})(C{sub 2}H{sub 5})]{sub 2} adopted a triclinic system with a space group P1 with a = 10.0141(8) Å, b = 10.1394(7) Å, c = 11.8665(9) Å, α = 67.960°, β =87.616°, γ = 80.172°.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-scale topology optimization of multi-material structures with controllable geometric complexity — Applications to heat transfer problems

This study presents a topology optimization method to design assemblies of periodic cellular materials with controllable geometric complexity. The framework is based on a novel multi-scale and multi-material design model in which the structure, the layout of the material subdomains, and their micro-structures are optimized concurrently. To allow a tight control over its geometrical complexity, the layout at the macro-scale is described by level-set fields, parameterized by geometric primitives. The micro-scale geometry is represented through a density approach. A nonlinear programming algorithm drives the optimization process using design sensitivities computed by the discrete adjoint method. The proposed design framework is studied with heat transfer problems. Practical design problems, such as a heat sink and a thermal storage unit with phase change are discussed. The macro-scale analysis model relies on a generalized transient diffusion equation. At the micro-scale, homogenization is used to compute equivalent material properties. The numerical examples in this study show that the optimized multi-scale multi-material layouts outperform the corresponding mono-scale structures while maintaining geometric simplicity at the macro-scale level.

42 ENGINEERING↗

Direct Ink Write and Processing of Complex 3D Marine Compatible Structures with Calcium Carbonate Slurries

Ocean acidification heavily impacts marine ecosystems by reducing calcification. Many coral-algae symbiotic relationships are in jeopardy due to the destruction of coral reefs. Here, a ceramic ink compatible with the direct ink write additive manufacturing technique was formulated and used to print marine compatible structures that could grow algae and restore that relationship. A diacrylate polymer was mixed with calcium carbonate, a material that comprises a coral skeleton, to create a slurry with shear thinning properties. Rheology studies were conducted to confirm printing properties and characterize the slurry. Printed parts demonstrated strong control over print features, including size and infill design. Various infill patterns and percentages were attempted to optimize printability and potential algae growth. Thermogravimetric analysis helped determine a logical burnout and sintering procedure to avoid large cracking. This project developed a printable and sinter-able calcium carbonate ceramic slurry for complex marine-compatible structures and algae growth. This research was conducted in the support of the Eco Reef project.

36 MATERIALS SCIENCE↗

CryoEM Structures of the Nitrogenase Complex During Catalytic Turnover

The enzyme nitrogenase couples adenosine triphosphate (ATP) hydrolysis to the multi-electron reduction of atmospheric dinitrogen into ammonia. Despite extensive research, the mechanistic details of ATP-dependent energy transduction and dinitrogen reduction by nitrogenase are not well understood, requiring new strategies to monitor its structural dynamics during catalytic action. Here we report the cryogenic electron microscopic interrogation of the nitrogenase complex under enzymatic turnover conditions, which has enabled the structural characterization of the nitrogenase reaction intermediates at high resolution for the first time. Our structures show that asymmetry governs all aspects of nitrogenase mechanism including ATP hydrolysis, protein-protein interactions, and catalysis. Furthermore, they reveal several previously unobserved, mechanistically relevant conformational changes near the catalytic iron-molybdenum cofactor that are correlated with the nucleotide-hydrolysis state of the enzyme.

Hannah L. Rutledge↗

Cryogenic electron tomography reveals novel structures in the apical complex of Plasmodium falciparum

Intracellular infectious agents, like the malaria parasite, Plasmodium falciparum, face the daunting challenge of how to invade a host cell. This problem may be even harder when the host cell in question is the enucleated red blood cell, which lacks the host machinery co-opted by many pathogens for internalization. Evolution has provided P. falciparum and related single-celled parasites within the phylum Apicomplexa with a collection of organelles at their apical end that mediate invasion. This apical complex includes at least two sets of secretory organelles, micronemes and rhoptries, and several structural features like apical rings and a putative pore through which proteins may be introduced into the host cell during invasion. We perform cryogenic electron tomography (cryo-ET) equipped with Volta Phase Plate on isolated and vitrified merozoites to visualize the apical machinery. Through tomographic reconstruction of cellular compartments, we see new details of known structures like the rhoptry tip interacting directly with a rosette resembling the recently described rhoptry secretory apparatus (RSA), or with an apical vesicle docked beneath the RSA. Subtomogram averaging reveals that the apical rings have a fixed number of repeating units, each of which is similar in overall size and shape to the units in the apical rings of tachyzoites of Toxoplasma gondii. Comparison of these polar rings in Plasmodium and Toxoplasma parasites also reveals them to have a structurally conserved assembly pattern. These results provide new insight into the essential and structurally conserved features of this remarkable machinery used by apicomplexan parasites to invade their respective host cells.

59 BASIC BIOLOGICAL SCIENCES↗

Wildfire Segmentation From Remotely Sensed Data Using Quantum-Compatible Conditional Vector Quantized-Variational Autoencoders

Wildfires represent a critical environmental hazard with multifaceted implications for ecosystems, communities, and public health [1]. The escalating frequency and intensity of wildfires globally have intensified the urgency for robust segmentation methodologies to facilitate effective mitigation, response, and recovery strategies [2]. Accurate wildfire segmentation is pivotal for delineating fire boundaries, assessing progression patterns, and prioritizing resource allocation during emergency scenarios. Furthermore, precise segmentation enables stakeholders, including policymakers, environmental scientists, and emergency responders, to formulate evidence-based strategies, thereby minimizing socio-economic disruptions and ecological degradation. Consequently, advancing wildfire segmentation techniques through innovative technological interventions remains a paramount research imperative. Although foundational in wildfire segmentation, traditional deterministic models exhibit inherent limitations that compromise their efficacy in dynamic and uncertain environments. These models often operate on rigid algorithms prioritizing deterministic classifications, thereby overlooking the inherent complexities and uncertainties associated with wildfire behavior and satellite data variability. Such deterministic frameworks tend to produce oversimplified representations that fail to capture the intricate nuances of evolving fire dynamics, spatial heterogeneity, and environmental interactions [1]. Consequently, the deterministic approach’s propensity for uncertainty collapsing [1, 3] hampers the accuracy, reliability, and applicability of segmentation outcomes in real-world scenarios. Contrastingly, stochastic models offer a more nuanced and adaptable framework for wildfire segmentation. By integrating probabilistic elements into the modeling paradigm, stochastic approaches, particularly probabilistic approaches such as variational auto encoders (VAEs) [4], facilitate comprehensive uncertainty assessment, enabling researchers to quantify and incorporate uncertainties into segmentation outcomes effectively. This probabilistic nature empowers stochastic models to encapsulate variability, account for data inconsistencies, and adapt to evolving environmental conditions, enhancing segmentation accuracy, reliability, and robustness. Embracing stochastic methodologies thus catalyzes advancements in wildfire science by fostering a more holistic, adaptive, and resilient segmentation framework. Despite VAEs demonstrating significant promise in various applications, they come with inherent limitations that have garnered attention within the machine learning community. One of the primary drawbacks lies in their reliance on static priors, which essentially assume a fixed distribution for latent variables, thereby limiting the model’s flexibility to capture complex data structures effectively [5]. This static nature leads to suboptimal representations, especially when dealing with complex and high-dimensional data. Additionally, VAEs often struggle with generating sharp and realistic samples, a phenomenon commonly referred to as mode collapse [5, 7, 6]. Furthermore, the optimization process in VAEs, which involves balancing the reconstruction loss and the regularization term, can sometimes be challenging to fine-tune [7]. In recent efforts to address these shortcomings, alternative approaches like Vector Quantized Variational Auto encoders(VQ-VAEs) [7], address the challenges by incorporating discrete latent variables and leveraging techniques that enhance the quality and diversity of generated samples while maintaining efficient training dynamics. VQ-VAEs propose a dynamic prior distribution generation mechanism that diverges from the static priors commonly associated with traditional VAEs. This dynamic approach allows for more adaptive and context-aware latent variable representations, thereby potentially capturing complex data structures more effectively. Unlike autoregressive prior models such as PixelCNN, which, despite their ability to model dependencies across data dimensions, suffer from significant computational inefficiencies and lack flexibility in handling diverse datasets. In our work, we propose to use a generative quantum-compatible approach to help alleviate the shortcomings of autoregressive prior model in VQ-VAEs. Restricted Boltzmann Machines (RBMs) are a viable alternative prior model that can learn prior distributions in a faster and more flexible manner. In this research endeavor, we meticulously curate a state-of-the-art dataset leveraging satellite MODIS data in conjunction with VIIRS fire masks, derived from Fire Radiative Power (FRP), thereby encapsulating diverse wildfire scenarios and environmental contexts. We developed a conditional VQ-VAE architecture with the RBM prior model that is trained in a supervised manner for segmenting wildfire masks. This innovative approach synergistically harnesses deep learning capabilities, enabling the generation of segmentation maps characterized by heightened precision, granularity, and contextual relevance. Furthermore, replacing the autoregressive prior learning method proposed by the original VQ-VAE with a prior density approximation via quantum-compatible RBM facilitates expedited inference processes, augments flexibility in prior sampling, optimizes computational efficiency and establishes a groundbreaking benchmark in wildfire segmentation methodologies.

quantum machine learning↗

Actinide arene-metalates: ion pairing effects on the electronic structure of unsupported uranium–arenide sandwich complexes

Addition of [UI 2 (THF) 3 (μ-OMe)] 2 ·THF (2·THF) to THF solutions containing 6 equiv. of K[C 14 H 10 ] generates the heteroleptic dimeric complexes [K(18-crown-6)(THF) 2 ] 2 [U(η 6 -C 14 H 10 )(η 4 -C 14 H 10 )(μ-OMe)] 2 ·4THF (1 18C6 ·4THF) and {[K(THF) 3 ][U(η 6 -C 14 H 10 )(η 4 -C 14 H 10 )(μ-OMe)]} 2 (1 THF ) upon crystallization of the products in THF in the presence or absence of 18-crown-6, respectively. Both 1 18C6 ·4THF and 1 THF are thermally stable in the solid-state at room temperature; however, after crystallization, they become insoluble in THF or DME solutions and instead gradually decompose upon standing. X-ray diffraction analysis reveals 1 18C6 ·4THF and 1 THF to be structurally similar, possessing uranium centres sandwiched between bent anthracenide ligands of mixed tetrahapto and hexahapto ligation modes. Yet, the two complexes are distinguished by the close contact potassium-arenide ion pairing that is seen in 1 THF but absent in 1 18C6 ·4THF, which is observed to have a significant effect on the electronic characteristics of the two complexes. Structural analysis, SQUID magnetometry data, XANES spectral characterization, and computational analyses are generally consistent with U(IV) formal assignments for the metal centres in both 1 18C6 ·4THF and 1 THF , though noticeable differences are detected between the two species. For instance, the effective magnetic moment of 1 THF (3.74 μ B ) is significantly lower than that of 1 18C6 ·4THF (4.40 μ B ) at 300 K. Furthermore, the XANES data shows the U L III -edge absorption energy for 1 THF to be 0.9 eV higher than that of 1 18C6 ·4THF, suggestive of more oxidized metal centres in the former. Of note, CASSCF calculations on the model complex {[U(η 6 -C 14 H 10 )(η 4 -C 14 H 10 )(μ-OMe)] 2 } 2– (1*) shows highly polarized uranium–arenide interactions defined by π-type bonds where the metal contributions are primarily comprised by the 6d-orbitals (7.3 ± 0.6%) with minor participation from the 5f-orbitals (1.5 ± 0.5%). These unique complexes provide new insights into actinide–arenide bonding interactions and show the sensitivity of the electronic structures of the uranium atoms to coordination sphere effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

EM structure of a helicase-loader complex depicting a 6:2 binding sub-stoichiometry from Geobacillus kaustophilus HTA426

During DNA replication, bacterial helicase is recruited as a complex in association with loader proteins to unwind the parental duplex. Previous structural studies have reported saturated 6:6 helicase-loader complexes with different conformations. However, structural information on the sub-stoichiometric conformations of these previously-documented helicase-loader complexes remains elusive. Here, with the aid of single particle electron-microscopy (EM) image reconstruction, we present the Geobacillus kaustophilus HTA426 helicase-loader (DnaC-DnaI) complex with a 6:2 binding stoichiometry in the presence of ATPγS. In the 19 Å resolution EM map, the undistorted and unopened helicase ring holds a robust loader density above the C-terminal RecA-like domain. Meanwhile, the path of the central DNA binding channel appears to be obstructed by the reconstructed loader density, implying its potential role as a checkpoint conformation to prevent the loading of immature complex onto DNA. Our data also reveals that the bound nucleotides and the consequently induced conformational changes in the helicase hexamer are essential for active association with loader proteins. These observations provide fundamental insights into the formation of the helicase-loader complex in bacteria that regulates the DNA replication process. - Highlights: • Helicase-loader complex structure with 6:2 sub-stoichiometry is resolved by EM. • Helicase hexamer in 6:2 sub-stoichiometry is constricted and un-opened. • 6:2 binding ratio of helicase-loader complex could act as a DNA loading checkpoint. • Nucleotides stabilize helicase-loader complex at low protein concentrations.

60 APPLIED LIFE SCIENCES↗

The crystal structure of DR6 in complex with the amyloid precursor protein provides insight into death receptor activation

The amyloid precursor protein (APP) has garnered considerable attention due to its genetic links to Alzheimer's disease. Death receptor 6 (DR6) was recently shown to bind APP via the protein extracellular regions, stimulate axonal pruning, and inhibit synapse formation. Here, we report the crystal structure of the DR6 ectodomain in complex with the E2 domain of APP and show that it supports a model for APP-induced dimerization and activation of cell surface DR6.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal Structure of a Nickel(II) Complex with the Macrocyclic Azadibenzo-14-crown-4 Ether Ligand Containing the Embedded Di(α-pyridyl)bispidone Moiety

The crystal structure of the nickel(II) complex with substituted azadibenzo-14-crown-4 ether containing the embedded di(α-pyridyl)bispidone moiety having the formula [L(H{sub 2}O)Ni(NO{sub 3}) Ni(H{sub 2}O)L](ClO{sub 4}){sub 3} · 0.7EtOH was studied by X-ray diffraction (T = 150(2) K, R = 0.0628). In the complex cation two five-coordinate nickel complexes are bridged by the nitrate anion to form a dimer. The distorted octahedral environment of Ni atoms is formed by four nitrogen atoms of the molecule L and the oxygen atoms of the water molecule and the NO{sub 3}{sup -} anion. In the nickel complex, like in the cobalt and copper complexes studied previously, the bispidine moiety of the molecule L adopts a chair-chair conformation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Method for Flow Simulation About Complex Geometries Using Both Structured and Unstructured Grids

A computational fluid dynamics code which utilizes both structured and unstructured grids was developed. The objective of this study was to develop and demonstrate the ability of such a code to achieve solutions about complex geometries in two dimensions. An unstructured grid generator and flow solver were incorporated into the PARC2D structured flow solver. This new unstructured grid generator capability allows for easier generation and manipulation of complex grids. Several examples of the grid generation capabilities are provided. The coupling of different grid topologies and the manipulation of individual grids is shown. Also, grids for realistic geometries, a NACA 0012 airfoil and a wing/nacelle installation, were created. The flow over a NACA 0012 airfoil was used as a test case for the flow solver. Eight separate cases were run. They were both the inviscid and viscous solutions for two freestream Mach numbers and airfoil angle of attacks of 0 to 3.86 degrees. The Mach numbers chosen were for a subsonic case, Mach 0.6, and a case where supersonic regions and a shock wave exists, Mach 0.8. These test case conditions were selected to match experimentally obtained data for code comparison. The results show that the code accurately predicts the flow field for all cases.

Debonis, James R.↗

An asymmetric heterodomain interface stabilizes a response regulator-DNA complex

Two-component signal transduction systems consist of pairs of histidine kinases and response regulators, which mediate adaptive responses to environmental cues. Most activated response regulators regulate transcription by binding tightly to promoter DNA via a phosphorylation-triggered inactive-to-active transition. The molecular basis for formation of stable response regulator–DNA complexes that precede the assembly of RNA polymerases is unclear. Here, we present structures of DNA complexed with the response regulator KdpE, a member of the OmpR/PhoB family. The distinctively asymmetric complex in an active-like conformation reveals a unique intramolecular interface between the receiver domain (RD) and the DNA-binding domain (DBD) of only one of the two response regulators in the complex. Structure–function studies show that this RD–DBD interface is necessary to form stable complexes that support gene expression. The conservation of sequence and structure suggests that these findings extend to a large group of response regulators that act as transcription factors.

Narayanan, Anoop↗

Studying light-harvesting models with superconducting circuits

The process of photosynthesis, the main source of energy in the living world, converts sunlight into chemical energy. The high efficiency of this process is believed to be enabled by an interplay between the quantum nature of molecular structures in photosynthetic complexes and their interaction with the environment. Investigating these effects in biological samples is challenging due to their complex and disordered structure. Here we experimentally demonstrate a technique for studying photosynthetic models based on superconducting quantum circuits, which complements existing experimental, theoretical, and computational approaches. We demonstrate a high degree of freedom in design and experimental control of our approach based on a simplified three-site model of a pigment protein complex with realistic parameters scaled down in energy by a factor of 10 5 . We show that the excitation transport between quantum-coherent sites disordered in energy can be enabled through the interaction with environmental noise. We also show that the efficiency of the process is maximized for structured noise resembling intramolecular phononic environments found in photosynthetic complexes.

42 ENGINEERING↗

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