Structural Rearrangements Research Articles

Anion exchanger1 (AE1/SLC4A1) function is impaired in red blood cells from prediabetic subjects: Potential benefits of finger lime (Citrus australasica, Faustrime cultivar) juice extract.

Prediabetes is a risk state that defines a high chance of developing diabetes and cardiovascular disease. Oxidative stress mediated by hyperglycemia-induced production of reactive species could play a crucial role in this context. In the present study, we investigated whether the anion exchange capability mediated by AE1 (SLC4A1), which is sensitive to oxidative stress, was altered in human red blood cells (RBCs) obtained from prediabetic volunteers. In addition, we assessed the precise composition of bioactive compounds and the potential benefits of finger lime juice extract (Citrus australasica, Faustrime cultivar) in counteracting oxidative stress-related functional alterations. Human RBCs from normal and prediabetic volunteers were incubated with 50 µg/mL juice extract for 2 h at 25°C. Juice extract restored alterations of the anion exchange capability mediated by AE1 and prevented the structural rearrangements of AE1 and α/β-spectrin in prediabetic RBCs. AE1 functional and structural alterations were not associated with an increase in lipid peroxidation or protein oxidation at the level of the plasma membrane. An increased production of intracellular ROS, which provoked the oxidation of hemoglobin to methemoglobin, both reverted by juice extract, was instead observed. Importantly, juice extract also induced a reduction in glycated hemoglobin levels in prediabetic RBCs. Finally, juice extract blunted the overactivation of the endogenous antioxidant enzymes catalase and superoxide dismutase and prevented glutathione depletion in prediabetic RBCs. These findings contribute to clarifying cellular and molecular mechanisms related to oxidative stress and glycation events that may influence RBC and systemic homeostasis in prediabetes, identify AE1 as a sensitive biomarker of RBC structural and function alterations in prediabetes and propose finger lime juice extract as a natural antioxidant for the treatment and/or prevention of the complications associated with the prediabetic condition.

Derivative and non-derivative aneuploidy rates in PGT tested blastocysts from carriers of structural rearrangements

Derivative and non-derivative aneuploidy rates in PGT tested blastocysts from carriers of structural rearrangements

Comparative structure and evolution of the organellar genomes of Padina usoehtunii (Dictyotales) with the brown algal crown radiation clade

BackgroundOrganellar genomes have become increasingly essential for studying genetic diversity, phylogenetics, and evolutionary histories of seaweeds. The order Dictyotales (Dictyotophycidae), a highly diverse lineage within the Phaeophyceae, is long-term characterized by a scarcity of organellar genome datasets compared to orders of the brown algal crown radiation (Fucophycidae).ResultsWe sequenced the organellar genomes of Padina usoehtunii, a representative of the order Dictyotales, to investigate the structural and evolutionary differences by comparing to five other major brown algal orders. Our results confirmed previously reported findings that the rate of structural rearrangements in chloroplast genomes is higher than that in mitochondria, whereas mitochondrial sequences exhibited a higher substitution rate compared to chloroplasts. Such evolutionary patterns contrast with land plants and green algae. The expansion and contraction of the inverted repeat (IR) region in the chloroplast correlated with the changes in the number of boundary genes. Specifically, the size of the IR region influenced the position of the boundary gene rpl21, with complete rpl21 genes found within the IR region in Dictyotales, Sphacelariales and Ectocarpales, while the rpl21 genes in Desmarestiales, Fucales, and Laminariales span both the IR and short single copy (SSC) regions. The absence of the rbcR gene in the Dictyotales may indicate an endosymbiotic transfer from the chloroplast to the nuclear genome. Inversion of the SSC region occurred at least twice in brown algae. Once in a lineage only represented by the Ectocarpales in the present study and once in a lineage only represented by the Fucales. Photosystem genes in the chloroplasts experienced the strongest signature of purifying selection, while ribosomal protein genes in both chloroplasts and mitochondria underwent a potential weak purifying selection.ConclusionsVariations in chloroplast genome structure among different brown algal orders are evolutionarily linked to their phylogenetic positions in the Phaeophyceae tree. Chloroplast genomes harbor more structural rearrangements than the mitochondria, despite mitochondrial genes exhibiting faster mutation rates. The position and the change in the number of boundary genes likely shaped the IR regions in the chloroplast, and the produced structural variability is important mechanistically to create gene diversity in brown algal chloroplast.

Viral replication organelles: the highly complex and programmed replication machinery.

Viral infections usually induce the rearrangement of cellular cytoskeletal proteins and organelle membrane structures, thus creating independent compartments [termed replication organelles (ROs)] to facilitate viral genome replication. Within the ROs, viral replicases, including polymerases, helicases, and ligases, play functional roles during viral replication. These viral replicases are pivotal in the virus life cycle, and numerous studies have demonstrated that the viral replicases could be the potential targets for drugs development. Here, we summarize primarily the key replicases within viral ROs and emphasize the advancements of antiviral drugs targeting crucial viral replicases, providing novel insights into the future development of antiviral strategies.

Hydrogen Bonding Analysis of Structural Transition-Induced Symmetry Breaking and Spin Splitting in a Hybrid Perovskite Employing a Synergistic Diffraction-DFT Approach.

Two-dimensional (2D) hybrid organic-inorganic perovskites (HOIPs) offer an outstanding opportunity for spin-related technologies owing in part to their tunable structural symmetry breaking and distortions driven by organic-inorganic hydrogen (H) bonds. However, understanding how H-bonds tailor inorganic symmetry and distortions and therefore enhance spin splitting for more effective spin manipulation remains imprecise due to challenges in measuring H atom positions using X-ray diffraction. Here, we report a thermally induced structural transition (at ∼209 K) for a 2D HOIP, (2-BrPEA)2PbI4 [2-BrPEA = 2-(2-bromophenyl)ethylammonium], which induces inversion asymmetry and a strong spin splitting (ΔE > 30 meV). While X-ray diffraction generally establishes heavy atom coordinates, we utilize neutron diffraction for accurate H atom position determination, demonstrating that the structural transition-induced rearrangement of H-bonds with distinct bond strengths asymmetrically shifts associated iodine atom positions. Consequences of this shift include an increased structural asymmetry, an enhanced difference between adjacent interoctahedra distortions (i.e., Pb-I-Pb bond angles), and therefore significant spin splitting. We further show that H-only density-functional theory (DFT) relaxation of the X-ray structure shifts H atoms to positions that are consistent with the neutron experimental data, validating a convenient pathway to more generally improve upon HOIP H-bonding analyses derived from quicker/less-expensive X-ray data.

Predictive Guidelines for Electrocyclization of Dithienylethenes.

Molecular photoswitches undergo a structural transformation upon photoexcitation to interconvert between two or more stable forms. In some cases, the structural rearrangement involves the transition between ring-open and ring-closed forms. In this work, we develop simple guidelines for the design of organic molecules able to undergo photochemical electrocyclization, using electronic structure calculations on dithienylethene (DTE)-based compounds. We conclude that the ability to photocyclize can be predicted from the localization and symmetry of frontier molecular orbitals. These ideas are based on the Woodward-Hoffmann rules but go beyond them, allowing us to address a more general family of chromophores. Our methodology has been experimentally validated in a novel series of quinoline-based DTEs, where the ability for photocyclization depends on specific chemical modifications. We use the DTE scaffold as the workhorse model in our study; however, these simple yet powerful guidelines are expected to be generally valid to guide the design of other diarylethenes.

Structural insights into the assembly of type IIA topoisomerase DNA cleavage-religation center.

The ability to catalyze reversible DNA cleavage and religation is central to topoisomerases' role in regulating DNA topology. In type IIA topoisomerases (Top2), the formation of its DNA cleavage-religation center is driven by DNA-binding-induced structural rearrangements. These changes optimally position key catalytic modules, such as the active site tyrosine of the WHD domain and metal ion(s) chelated by the TOPRIM domain, around the scissile phosphodiester bond to perform reversible transesterification. To understand this assembly process in detail, we report the catalytic core structures of human Top2α and Top2β in an on-pathway conformational state. This state features an in trans formation of an interface between the Tower and opposing TOPRIM domain, revealing a groove for accommodating incoming G-segment DNA. Structural superimposition further unveils how subsequent DNA-binding-induced disengagement of the TOPRIM and Tower domains allows a firm grasp of the bound DNA for cleavage/religation. Notably, we identified a previously undocumented protein-DNA interaction, formed between an arginine-capped C-terminus of an α-helix in the TOPRIM domain and the DNA backbone, significantly contributing to Top2 function. This work uncovers a previously unrecognized role of the Tower domain, highlighting its involvement in anchoring and releasing the TOPRIM domain, thus priming Top2 for DNA binding and cleavage.

Evident structural anisotropies arising from near-zero particle asphericity in granular spherocylinder packings.

With magnetic resonance imaging experiments, we study packings of granular spherocylinders with merely 2% asphericity. Evident structural anisotropies across all length scales are identified. Most interestingly, the global nematic order decreases with increasing packing fraction, while the local contact anisotropy shows an opposing trend. We attribute this counterintuitive phenomenon to a competition between gravity-driven ordering aided by frictional contacts and a geometric frustration effect at the marginally jammed state. It is also surprising to notice that such slight particle asphericity can trigger non-negligible correlations between contact-level and mesoscale structures, manifested in drastically different nonaffine structural rearrangements upon compaction from that of granular spheres. These observations can help improve statistical mechanical models for the orientational order transformation of nonspherical granular particle packings, which involves complex interplays between particle shape, frictional contacts, and external force field.

Synthesis of Keratin Nanoparticles Extracted from Human Hair through Hydrolysis with Concentrated Sulfuric Acid: Characterization and Cytotoxicity.

Human hair, composed primarily of keratin, represents a sustainable waste material suitable for various applications. Synthesizing keratin nanoparticles (KNPs) from human hair for biomedical uses is particularly attractive due to their biocompatibility. In this study, keratin was extracted from human hair using concentrated sulfuric acid as the hydrolysis agent for the first time. This process yielded KNPs in both the supernatant (KNPs-S) and precipitate (KNPs-P) phases. Characterization involved scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), Zeta potential analysis, X-ray diffraction (XRD), and thermogravimetric analysis (TG). KNPs-S and KNPs-P exhibited average diameters of 72 ± 5 nm and 27 ± 5 nm, respectively. The hydrolysis process induced a structural rearrangement favoring β-sheet structures over α-helices in the KNPs. These nanoparticles demonstrated negative Zeta potentials across the pH spectrum. KNPs-S showed higher cytotoxicity (CC50 = 176.67 µg/mL) and hemolytic activity, likely due to their smaller size compared to KNPs-P (CC50 = 246.21 µg/mL), particularly at concentrations of 500 and 1000 µg/mL. In contrast, KNPs-P did not exhibit hemolytic activity within the tested concentration range of 32.5 to 1000 µg/mL. Both KNPs demonstrated cytocompatibility with fibroblast cells in a dose-dependent manner. Compared to other methods reported in the literature and despite requiring careful washing and neutralization steps, sulfuric acid hydrolysis proved effective, rapid, and feasible for producing cytocompatible KNPs (biomaterials) in single-step synthesis.

Pyridyl-Substituted Nitronyl Nitroxides: Comprehensive Magnetochemical and Quantum Chemical Study.

A series of pyridyl-substituted nitronyl nitroxides was synthesized and structurally characterized. A comprehensive magnetochemical and quantum chemical study of extended raw of the nitroxides with different substituents R in the pyridine fragment was performed. It was shown, that temperature-dependent magnetic properties are determined by the short contacts between nitroxide groups of adjacent molecules as well as between nitroxide group and methyl substituents in the pseudo axial positions of imidazoline fragments. Quantum chemistry allows to select the appropriate model of exchange cluster for analysis of experimental magnetic data and evaluation of the exchange interaction parameters. For NN-PyCl the "order-disorder" transition was detected by means of low temperature XRD. The difference in the experimental and calculated exchange interaction energies may serve as an indicator of temperature-induced structural rearrangements. For instance, for methyl substituted nitronyl nitroxide NN-PyMe structural transformations and significant changes in exchange interaction energies were observed.

Structure and fragmentation of doubly ionized HNCS.

Double ionization spectra of isothiocyanic acid (HNCS) have been measured using multi-electron and multi-ion coincidence techniques combined with high-level theoretical calculations. The adiabatic double ionization energy of HNCS is found at 27.1 ± 0.1eV and is associated with the formation of the X 3A″ ground state of HNCS2+. The characteristics of different dissociation channels are examined and compared to the results of electronic structure calculations obtained by systematically elongating the three bonds H-NCS, HN-CS, and HNC-S. For instance, the adiabatic double ionization energy of the NCS fragment is deduced to be 30.95 ± 0.5eV. In addition, the C+ and NS+ dissociation channels are of particular interest, possibly indicating the involvement of a structural rearrangement process upon doubly ionizing HNCS.

Molecular basis for the activation of human spliceosome

The spliceosome executes pre-mRNA splicing through four sequential stages: assembly, activation, catalysis, and disassembly. Activation of the spliceosome, namely remodeling of the pre-catalytic spliceosome (B complex) into the activated spliceosome (Bact complex) and the catalytically activated spliceosome (B* complex), involves major flux of protein components and structural rearrangements. Relying on a splicing inhibitor, we have captured six intermediate states between the B and B* complexes: pre-Bact, Bact-I, Bact-II, Bact-III, Bact-IV, and post-Bact. Their cryo-EM structures, together with an improved structure of the catalytic step I spliceosome (C complex), reveal how the catalytic center matures around the internal stem loop of U6 snRNA, how the branch site approaches 5′-splice site, how the RNA helicase PRP2 rearranges to bind pre-mRNA, and how U2 snRNP undergoes remarkable movement to facilitate activation. We identify a previously unrecognized key role of PRP2 in spliceosome activation. Our study recapitulates a molecular choreography of the human spliceosome during its catalytic activation.

Plastome Evolution of Asyneuma japonicum: Insights into Structural Variation, Genomic Divergence, and Phylogenetic Tree

Asyneuma japonicum is an ornamental flowering plant in East Asia. The genus Asyneuma is difficult to distinguish taxonomically because of its morphological similarities with the genus Campanula. We constructed the first complete plastome of A. japonicum (NCBI accession number: OR805474) using the Illumina platform. This plastome is a circular ring structure with a length of 185,875 base pairs. It is organized into four parts: a pair of inverted repeats (33,084 bp each) as well as large (83,795 bp) and small (35,912 bp) single-copy regions. One hundred nine unique genes were encoded in the assembled plastome. Using structural variations, junction boundaries, rearrangements, divergent hotspots, and phylogenetic analysis, we revealed that A. japonicum was in the closest evolutionary position to Hanabusaya asiatica and it had a large evolutionary divergence from the Campanulaceae family due to gene rearrangements.

Extensive structural rearrangement of intraflagellar transport trains underpins bidirectional cargo transport

Bidirectional transport in cilia is carried out by polymers of the IFTA and IFTB protein complexes, called anterograde and retrograde intraflagellar transport (IFT) trains. Anterograde trains deliver cargoes from the cell tothe cilium tip, then convert into retrograde trains for cargo export. We set out to understand how the IFT complexes can perform these two directly opposing roles before and after conversion. We use cryoelectron tomography and in situ cross-linking mass spectrometry to determine the structure of retrograde IFT trains and compare it with the known structure of anterograde trains. The retrograde train is a 2-fold symmetric polymer organized around a central thread of IFTA complexes. We conclude that anterograde-to-retrograde remodeling involves global rearrangements of the IFTA/B complexes and requires complete disassembly of the anterograde train. Finally, we describe how conformational changes to cargo-binding sites facilitate unidirectional cargo transport in a bidirectional system.

Effects of Structural Constraints on Excited-State Properties in Dimeric Cu(I) Diimine Complexes.

Copper(I) bis-diimine complexes have played important roles in light-activated processes that can lead to their potential applications in photocatalysis and chemical sensing. Their metal-to-ligand charge-transfer (MLCT) excited-state properties are tunable by various structural factors. Dimeric Cu(I) complexes with connecting diimine derivative ligands offer another structural tuning platform for the excited-state properties. Here, we investigate excited-state properties in two covalently connected dimeric Cu(I)'s with varying structural constraints exerted by the number of carbons in the polyethylene bridge (C0 and C4) connecting the two copper(I) diimine moieties. An interesting feature of Cu(I) diimine complexes is their ability to flatten following a photoinduced structural change. Herein, we observe larger structural constraints and more structural rearrangement required upon excitation of the longer bridged complex C4 to achieve a conformation toward a more flattened tetrahedral coordination geometry compared to the shorter bridged C0. Vibrational wavepacket analysis of these complexes further supports the effect of these structural constraints where we observe a more rapid dephasing of the C0 complex, as opposed to the C4 complex, despite similar normal mode vibrations. The experimental results were supplemented by TDDFT calculations. The studies provide insight into using metal-metal interactions through constraints to tune excited-state dynamics and pathways.

From mundane to surprising nonadditivity: drivers and impact on ML models.

Nonadditivity (NA) in Structure-Activity and Structure-Property Relationship (SAR) data is a rare but very information rich phenomenon. It can indicate conformational flexibility, structural rearrangements, and errors in assay results and structural assignment. While purely ligand-based conformational causes of NA are rather well understood and mundane, other factors are less so and cause surprising NA that has a huge influence on SAR analysis and ML model performance. We here report a systematic analysis across a wide range of properties (20 on-target biological activities and 4 physicochemical ADME-related properties) to understand the frequency of various different phenomena that may lead to NA. A set of novel descriptors were developed to characterize double transformation cycles and identify trends in NA. Double transformation cycles were classified into "surprising" and "mundane" categories, with the majority being classed as mundane. We also examined commonalities among surprising cycles, finding LogP differences to have the most significant impact on NA. A distinct behavior of NA for on-target sets compared to ADME sets was observed. Finally, we show that machine learning models struggle with highly nonadditive data, indicating that a better understanding of NA is an important future research direction.

Thermal Remodeling of Human HDL Particles Reveals Diverse Subspecies.

High-density lipoproteins (HDL) are micelle-like particles consisting of a core of triglycerides and cholesteryl esters surrounded by a shell of phospholipid, cholesterol, and apolipoproteins. HDL is considered "good" cholesterol, and its concentration in plasma is used clinically in assessing cardiovascular health. However, these particles vary in structure, composition, and therefore function, and thus can be resolved into subpopulations, some of which have specific cardioprotective properties. Mass measurements of HDL by charge detection mass spectrometry (CD-MS) previously revealed seven distinct subpopulations which could be delineated by mass and charge [Lutomski, C. A. et al. Anal. Chem. 2018]. Here, we investigate the thermal stabilities of these subpopulations; upon heating, the particles within each subpopulation undergo structural rearrangements with distinct transition temperatures. In addition, we find evidence for many new families of structures within each subpopulation; at least 15 subspecies of HDL are resolved. These subspecies vary in size, charge, and thermal stability. While this suggests that these new subspecies have unique molecular compositions, we cannot rule out the possibility that we have found evidence for new structural forms within the known subpopulations. The ability to resolve new subspecies of HDL particles may be important in understanding and delineating the role of unique particles in cardiovascular health and disease.

Configuration rearrangement of squalane induced by carbon dioxide dissolution: A molecular simulation study

Squalane has emerged as a desirable absorbent material for carbon capture, utilization, and storage solutions due to its tunable sorption properties, microscopic structures, and cost-effectiveness in response to the increasing demand. Moreover, a thorough understanding of the fundamental characteristics of hydrocarbons and dissolved gases involved in the Fischer–Tropsch industrial synthesis processes is also essential for researching industrial purification and separation. However, these macromolecules may experience varying degrees of induced alterations in their structural rearrangement when absorbing absorbates, which impacts the performance indicators of squalane. This study examined the solubility characteristics of absorbents made from squalane and their interaction with gaseous CO2 molecules. The perturbed chain statistical associated fluid theory (PC–SAFT) was employed to comprehensively evaluate the macroscopic thermodynamic experimental density and solubility data. Simultaneously, the Monte Carlo (MC) simulation approach was utilized to investigate the rearrangement and swelling features of the squalane chain induced by the presence of CO2 gas in a broad spectrum of temperature and pressure conditions. This work indicated that elevated temperatures increased flexibility in the molecular structure of squalane, leading to a more pronounced spatial dispersion, while higher pressures may lead to spatial homogeneity and enhanced capacity for carrying additional CO2 molecules. The examples and methodologies presented demonstrate the effectiveness of molecular simulations in comprehending absorption–based phenomena at an atomistic and molecular level and offer essential guidance in forecasting the potential for separation, storage, or catalytic.

Ultrasonication: An Efficient Alternative for the Physical Modification of Starches, Flours and Grains.

Ultrasonic (USC) treatments have been applied to starches, flours and grains to modify their physicochemical properties and improve their industrial applicability. The extent of the modification caused by USC treatment depends on the treatment conditions and the natural characteristics of the treated matter. Cavitation leads to structural damage and fragmentation and partial depolymerization of starch components. The amorphous regions are more susceptible to being disrupted by ultrasonication, while the crystalline regions require extended USC exposure to be affected. The increased surface area in USC-treated samples has a higher interaction with water, resulting in modification of the swelling power, solubility, apparent viscosity, pasting properties and gel rheological and textural properties. Starch digestibility has been reported to be modified by ultrasonication to different extents depending on the power applied. The most important treatment variables leading to more pronounced modifications in USC treatments are the botanical origin of the treated matter, USC power, time, concentration and temperature. The interaction between these factors also has a significant impact on the damage caused by the treatment. The molecular rearrangement and destruction of starch structures occur simultaneously during the USC treatment and the final properties of the modified matrix will depend on the array of treatment parameters. This review summarizes the known effects of ultrasonic treatments in modifying starches, flours and grains.

Cost‐Effective Conductive Paste for Radiofrequency Devices Using Carbon‐Based Materials

With the increasing demand for compact, lightweight, cost‐effective, and high‐performance radiofrequency (RF) devices, the development of low‐profile antennas becomes crucial. This article presents a study of a novel carbon–cellulose‐based paste intended for screen printing RF devices. The investigation specifically explores the application of high‐reactivity carbon mixture (HRCM) particles as conductive fillers. The results demonstrate that optimal electrical conductivity values and discrete electromagnetic dipole performances can be achieved at lower concentrations of solid conductive material compared to conventional pastes, for similar applications. This offers benefits in terms of total cost, material consumption, and environmental impact. The paste formulation showcases a complex non‐Newtonian behavior, where yielding flow and thixotropicity are found to be independent and dependent on preshear conditions, respectively. This behavior can be attributed to the network orientation and rearrangement of filler structures within the paste system, which in turn are responsible for filler pattern uniformity and overall printing quality. Compared to traditional conductive materials, HRCM pastes are proven to be a viable alternative for RF devices fabrication, including printed Wi‐Fi antennas.