Structure and Mechanisms of F-Type ATP Synthases.

F1Fo ATP synthases produce most of the ATP in the cell. F-type ATP synthases have been investigated for more than 50 years, but a full understanding of their molecular mechanisms has become possible only with the recent structures of complete, functionally competent complexes determined by electron cryo-microscopy (cryo-EM). High-resolution cryo-EM structures offer a wealth of unexpected new insights. The catalytic F1 head rotates with the central γ-subunit for the first part of each ATP-generating power stroke. Joint rotation is enabled by subunit δ/OSCP acting as a flexible hinge between F1 and the peripheral stalk. Subunit a conducts protons to and from the c-ring rotor through two conserved aqueous channels. The channels are separated by ∼6 Šin the hydrophobic core of Fo, resulting in a strong local field that generates torque to drive rotary catalysis in F1. The structure of the chloroplast F1Fo complex explains how ATPase activity is turned off at night by a redox switch. Structures of mitochondrial ATP synthase dimers indicate how they shape the inner membrane cristae. The new cryo-EM structures complete our picture of the ATP synthases and reveal the unique mechanism by which they transform an electrochemical membrane potential into biologically useful chemical energy.

Structure of detergent-activated BAK dimers derived from the inert monomer.

A body of data supports the existence of core (α2-α5) dimers of BAK and BAX in the oligomeric, membrane-perturbing conformation of these essential apoptotic effector molecules. Molecular structures for these dimers have only been captured for truncated constructs encompassing the core domain alone. Here, we report a crystal structure of BAK α2-α8 dimers (i.e., minus its flexible N-terminal helix and membrane-anchoring C-terminal segment) that has been obtained through the activation of monomeric BAK with the detergent C12E8. Core dimers are evident, linked through the crystal by contacts via latch (α6-α8) domains. This crystal structure shows activated BAK dimers with the extended latch domain present. Our data provide direct evidence for the conformational change converting BAK from inert monomer to the functional dimer that destroys mitochondrial integrity. This dimer is the smallest functional unit for recombinant BAK or BAX described so far.

Ribosome Hibernation.

Protein synthesis consumes a large fraction of available resources in the cell. When bacteria encounter unfavorable conditions and cease to grow, specialized mechanisms are in place to ensure the overall reduction of costly protein synthesis while maintaining a basal level of translation. A number of ribosome-associated factors are involved in this regulation; some confer an inactive, hibernating state of the ribosome in the form of 70S monomers (RaiA; this and the following are based on Escherichia coli nomenclature) or 100S dimers (RMF and HPF homologs), and others inhibit translation at different stages in the translation cycle (RsfS, YqjD and paralogs, SRA, and EttA). Stationary phase cells therefore exhibit a complex array of different ribosome subpopulations that adjusts the translational capacity of the cell to the encountered conditions and ensures efficient reactivation of translation when conditions improve. Here, we review the current state of research regarding stationary phase-specific translation factors, in particular ribosome hibernation factors and other forms of translational regulation in response to stress conditions.

Antielectric Potential Synthesis of Plasmonic Au-Ag Multidimensional Dimers Array for High-Resolution Encrypted Information.

Plasmonic superstructures hold great potential in encrypted information chips but are still unsatisfactory in terms of resolution and maneuverability because of the limited fabrication strategies. Here, we develop an antielectric potential method in which the interfacial energy from the modification of 5-amino-2-mercapto benzimidazole (AMBI) ligand is used to overcome the electric resistance between the Au nanospheres (NSs) and substrate, thereby realizing the in situ growth of a Au-Ag heterodimers array in large scale. The morphology, number, and size of Ag domains on Au units can be controlled well by modulating the reaction kinetics and thermodynamics. Experiments and theoretical simulations reveal that patterned 3D Au-2D Ag and 3D Au-3D Ag dimer arrays with line widths of 400 nm exhibit cerulean and cyan colors, respectively, and achieve fine color modulation and ultrahigh information resolution. This work not only develops a facile strategy for fabricating patterned plasmonic superstructures but also pushes the plasmon-based high-resolution encrypted information chip into more complex applications.

Ultraviolet Radiation Biological and Medical Implications.

Ultraviolet (UV) radiation plays a crucial role in the development of melanoma and non-melanoma skin cancers. The types of UV radiation are differentiated by wavelength: UVA (315 to 400 nm), UVB (280 to 320 nm), and UVC (100 to 280 nm). UV radiation can cause direct DNA damage in the forms of cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs). In addition, UV radiation can also cause DNA damage indirectly through photosensitization reactions caused by reactive oxygen species (ROS), which manifest as 8-hydroxy-2'-deoxyguanine (8-OHdG). Both direct and indirect DNA damage can lead to mutations in genes that promote the development of skin cancers. The development of melanoma is largely influenced by the signaling of the melanocortin one receptor (MC1R), which plays an essential role in the synthesis of melanin in the skin. UV-induced mutations in the BRAF and NRAS genes are also significant risk factors in melanoma development. UV radiation plays a significant role in basal cell carcinoma (BCC) development by causing mutations in the Hedgehog (Hh) pathway, which dysregulates cell proliferation and survival. UV radiation can also induce the development of squamous cell carcinoma via mutations in the TP53 gene and upregulation of MMPs in the stroma layer of the skin.

Carbamic acid and its dimer: A computational study.

A recent work by Marks et al. on the formation of carbamic acid in NH 3 $$ {}_3 $$ -CO 2 $$ {}_2 $$ interstellar ices pointed out its stability in the gas phase and the concomitant production of its dimer. Prompted by these results and the lack of information on these species, we have performed an accurate structural, energetic and spectroscopic investigation of carbamic acid and its dimer. For the former, the structural and spectroscopic characterization employed composite schemes based on coupled cluster (CC) calculations that account for the extrapolation to the complete basis set limit and core correlation effects. A first important outcome is the definitive confirmation of the nonplanarity of carbamic acid, then followed by an accurate estimate of its rotational and vibrational spectroscopy parameters. As far as the carbamic acid dimer is concerned, the investigation started from the identification of its most stable forms. For them, structure and vibrational properties have been evaluated using density functional theory, while a composite scheme rooted in CC theory has been employed for the energetic characterization. Our results allowed us to provide a better interpretation of the feature observed in the recent experiment mentioned above.

Simulating the full spin manifold of triplet-pair states in a series of covalently linked TIPS-pentacenes.

Combined density functional theory and multireference configuration interaction methods have been used to elucidate singlet fission (SF) pathways and mechanisms in three regioisomers of side-on linked pentacene dimers. In addition to the optically bright singlets (S 1 $$ {}_1 $$ and S 2 $$ {}_2 $$ ) and singly excited triplets (T 1 $$ {}_1 $$ and T 2 $$ {}_2 $$ ), the full spin manifold of multiexcitonic triplet-pair states ( 1 $$ {}^1 $$ ME, 3 $$ {}^3 $$ ME, 5 $$ {}^5 $$ ME) has been considered. In the ortho- and para-regioisomers, the 1 $$ {}^1 $$ ME and S 1 $$ {}_1 $$ potentials intersect upon geometry relaxation of the S 1 $$ {}_1 $$ excitation. In the meta-regioisomer, the crossing occurs upon delocalization of the optically bright excitation. The energetic accessibility of these conical intersections and the absence of low-lying charge-transfer states suggests a direct SF mechanism, assisted by charge-resonance effects in the 1 $$ {}^1 $$ ME state. While the 5 $$ {}^5 $$ ME state does not appear to play a role in the SF mechanism of the ortho- and para-regioisomers, its participation in the disentanglement of the triplet pair is conceivable in the meta-regioisomer.

Deciphering the Mechanisms of Photo-Enhanced Catalytic Activities in Plasmonic Pd-Au Heteromeric Nanozymes for Colorimetric Analysis.

The growing demand for highly active nanozymes in various fields has led to the development of several strategies to enhance their activity. Plasmonic enhancement, a strategy used in heterogenous catalysis, represents a promising strategy to boost the activity of nanozymes. Herein, Pd-Au heteromeric nanoparticles (Pd-Au dimers) with well-defined heterointerfaces have been explored as plasmonic nanozymes. As a model system, the Pd-Au dimers with integrated peroxidase (POD)-like activity and plasmonic activity are used to investigate the effect of plasmons on enhancing the activity of nanozymes under visible light irradiation. Mechanistic studies revealed that the generation of hot electron-hole pairs plays a dominant role in plasmonic effect, and it greatly enhances the decomposition of H2 O2 to the reactive oxygen species (ROS) intermediates (•OH, •O2 - and 1 O2 ), leading to elevated POD-like activity of the Pd-Au dimers. Finally, the Pd-Au dimers are applied in the plasmon-enhanced colorimetric method for the detection of alkaline phosphatase, exhibiting broad linear range and low detection limit. This study not only provides a straightforward approach for regulating nanozyme activity through plasmonic heterostructures but also sheds light on the mechanism of plasmon-enhanced catalysis of nanozymes.

Studies of Local DNA Backbone Conformation and Conformational Disorder Using Site-Specific Exciton-Coupled Dimer Probe Spectroscopy.

The processes of genome expression, regulation, and repair require direct interactions between proteins and DNA at specific sites located at and near single-stranded-double-stranded DNA (ssDNA-dsDNA) junctions. Here, we review the application of recently developed spectroscopic methods and analyses that combine linear absorbance and circular dichroism spectroscopy with nonlinear 2D fluorescence spectroscopy to study the local conformations and conformational disorder of the sugar-phosphate backbones of ssDNA-dsDNA fork constructs that have been internally labeled with exciton-coupled cyanine (iCy3)2 dimer probes. With the application of these methods, the (iCy3)2 dimer can serve as a reliable probe of the mean local conformations and conformational distributions of the sugar-phosphate backbones of dsDNA at various critical positions. The results of our studies suggest a possible structural framework for understanding the roles of DNA breathing in driving the processes of protein-DNA complex assembly and function.

The Interplay of Spacer Chirality and Parity in Mesogenic Dimers.

Introducing chirality into soft materials, including liquid crystals (LCs), profoundly impacts their self-organization and physical properties. In this study, we synthesized a novel series of LC dimers with a chiral center as part of their flexible spacer. The dimers were prepared in racemic and enantiomerically pure forms. Their spacer length and parity were varied to investigate the effect of spacer chirality and parity on mesomorphic behavior and on chiral induction in the nematic phase of achiral mesogens. Our results show that the even-membered chiral dimers only have chiral nematic phases. In contrast, the odd-membered dimers display rich mesomorphism, including the intriguing blue phase (BP) and chiral form of the twist-bend nematic phase (N*TB). The observed significant difference in the 3D surface morphology between the racemic and chiral forms of the N*TB phase suggests that the chiral moiety in the spacer promotes a chiral hierarchy. Furthermore, the chiral dimers show a prominent odd-even effect in the helical twisting power in nematic hosts. These findings highlight the importance of the position of the chiral group within the dimeric molecule and provide new insights into how intrinsic chirality in the spacer affects the overall structural chirality.

Ultraviolet C intensity dependence of decontamination efficiency for pathogens as function of repacked metamaterials with screw channels.

A new method for repackaging optical metamaterials formed from quartz spheres (fibers) of various diameters is proposed for ultraviolet C disinfection of infected liquids by pathogens (viruses and bacteria). The main idea of the new equipment is connected with the rotation of a contaminated fluid by screw channels within a metamaterial matrix prepared from UVC fibers/spherical optics, to improve the decontamination efficiency. In demonstration of the viability of this approach, dynamic and static inactivation of Baker's yeast via Ultraviolet C radiation regimes are used in this paper to show the efficacy of decontamination within the screw channels.

Urinary thymidine dimer excretion reflects personal ultraviolet radiation exposure levels.

Exposure to ultraviolet radiation (UVR) leads to skin DNA damage, specifically in the form of cyclobutane pyrimidine dimers, with thymidine dimers being the most common. Quantifying these dimers can indicate the extent of DNA damage resulting from UVR exposure. Here, a new liquid chromatography-mass spectrometry (LC-MS) method was used to quantify thymidine dimers in the urine after a temporary increase in real-life UVR exposure. Healthy Danish volunteers (n = 27) experienced increased UVR exposure during a winter vacation. Individual exposure, assessed via personally worn electronic UVR dosimeters, revealed a mean exposure level of 32.9 standard erythema doses (SEDs) during the last week of vacation. Morning urine thymidine dimer concentrations were markedly elevated both 1 and 2 days post-vacation, and individual thymidine dimer levels correlated with UVR exposure during the last week of the vacation. The strongest correlation with erythema-weighted personal UVR exposure (Power model, r2 = 0.64, p < 0.001) was observed when both morning urine samples were combined to measure 48-h thymidine dimer excretion, whereas 24-h excretion based on a single sample provided a weaker correlation (Power model, r2 = 0.55, p < 0.001). Sex, age, and skin phototype had no significant effect on these correlations. For the first time, urinary thymidine dimer excretion was quantified by LC-MS to evaluate the effect of a temporary increase in personal UVR exposure in a real-life setting. The high sensitivity to elevated UVR exposure and correlation between urinary excretion and measured SED suggest that this approach may be used to quantify DNA damage and repair and to evaluate photoprevention strategies.

Synthesis and antihepatoma activity of guaianolide dimers derived from lavandiolide I.

Guaianolide dimers represent a unique class of natural products with anticancer activities, but their low content in plants has limited in-depth pharmacological studies. Lavandiolide I is a guaianolide dimer isolated from Artemisia species, and had been synthesized on a ten-gram scale in four steps with 60 % overall yield, which showed potent antihepatoma activity on the HepG2, Huh7, and SK-Hep-1 cell lines with IC50 values of 12.1, 18.4, and 17.6 µM, respectively. To explore more active dimers, 33 lavandiolide I derivatives were designed, synthesized, and evaluated for their inhibitory activity on human hepatoma cell lines. Among them, 10 derivatives were more active than lavandiolide I and sorafenib on the three cell lines. The primary structure-activity relationship concluded that the introduction of aldehyde, ester, azide, amide, carbamate and urea functional groups at C-14' of the guaianolide dimer significantly enhanced the antihepatoma activity. Among these compounds, derivatives 25, 27, and 33 enhanced antihepatoma activity more than 1.2-5.8 folds than that of lavandiolide I, and demonstrated low toxicity to the human liver cell lines (THLE-2) and good safety profiles with selective index ranging from 1.3 to 3.4, while lavandiolide I was more toxic to THLE-2 cells. This work provides new insights into enhancing the antihepatoma efficacy and reducing the toxicity of sesquiterpenoid dimers.

Amino acid sequence homology of monoclonal serum free light chain dimers and tissue deposited light chains in AL amyloidosis: a pilot study.

OBJECTIVES: Diagnosis of light chain amyloidosis (AL) requires demonstration of amyloid deposits in a tissue biopsy followed by appropriate typing. Previous studies demonstrated increased dimerization of monoclonal serum free light chains (FLCs) as a pathological feature of AL. To further examine the pathogenicity of FLC, we aimed at testing amino acid sequence homology between circulating and deposited light chains (LCs). METHODS: Matched tissue biopsy and serum of 10 AL patients were subjected to tissue proteomic amyloid typing and nephelometric FLC assay, respectively. Serum FLC monomers (M) and dimers (D) were analyzed by Western blotting (WB) and mass spectrometry (MS). RESULTS: WB of serum FLCs showed predominance of either κ or λ type, in agreement with the nephelometric assay data. Abnormal FLC M-D patterns typical of AL amyloidosis were demonstrated in 8 AL-λ patients and in one of two AL-κ patients: increased levels of monoclonal FLC dimers, high D/M ratio values of involved FLCs, and high ratios of involved to uninvolved dimeric FLCs. MS of serum FLC dimers showed predominant constant domain sequences, in concordance with the tissue proteomic amyloid typing. Most importantly, variable domain sequence homology between circulating and deposited LC species was demonstrated, mainly in AL-λ cases. CONCLUSIONS: This is the first study to demonstrate homology between circulating FLCs and tissue-deposited LCs in AL-λ amyloidosis. The applied methodology can facilitate studying the pathogenicity of circulating FLC dimers in AL amyloidosis. The study also highlights the potential of FLC monomer and dimer analysis as a non-invasive screening tool for this disease.

Lindenane sesquiterpenoid dimers from Chloranthus japonicus improve LDL uptake by regulating PCSK9 and LDLR.

UPLC-TOF-MS/MDF directed phytochemical research of Chloranthus japonicus led to the isolation of 46 lindenane sesquiterpenoid dimers, which included 13 new analogs. Their structures with absolute configurations were elucidated by analysis of spectroscopic data. Fourteen compounds with ester chains significantly decreased PCSK9 protein level in medium of HepG2 cells, especially for compounds 14 and 29 (5 µM) with inhibition rates of 69.0% and 72.8%, respectively. Compound 14 in HepG2 cells was evaluated via DiI-LDL uptake assays and found to increase LDL uptake by upregulating LDLR mRNA and protein level. Meanwhile, 14 decreased the secretion of PCSK9 protein in medium and downregulated intracellular PCSK9 protein and mRNA level. The discovery of these natural small molecule compounds provides a novel structure basis for design PCSK9 regulators, making them a promising lead for development of new lipid-lowering agents.

Identification of diverse sesquiterpenoids with anti-fibrotic potential from Inula japonica Thunb.

In the chemical investigation of Inula japonica, a total of 29 sesquiterpenoids (1-29) were obtained, including pseudoguaine-, xanthane-, eudesmane-, and 1,10-secoeudesmane-type compounds, as well as their dimers. Among them, six new dimeric sesquiterpenoids, bisinulains A-F (1-5, 7), characterized by a [4 + 2] biogenetic pathway between different sesquiterpenoid monomers were identified. Additionally, three new monomers named inulaterins A-C (13, 18 and 21) were discovered. The structures of these compounds were determined through analysis of spectroscopic data, X-ray crystallographic data, and ECD experiments. To assess their potential anti-inflammatory activities, the sesquiterpenoid dimers were tested for their ability to inhibit NO production in LPS-stimulated RAW 264.7 cells. Furthermore, the compounds that exhibited anti-inflammatory effects underwent evaluation for their anti-fibrotic potential using a TGF-ß-induced epithelial-mesenchymal transition model in A549 cells. As a result, bisinulain B (2) was screened out to significantly inhibit the production of cytokines involved in pulmonary fibrosis such as NO, α-SMA, collagen I and fibronectin.

Abbott D-dimer assay: analytical performance and diagnostic accuracy in management of venous thromboembolism.

This study aimed to assess analytical characteristics and diagnostic accuracy in management of venous thromboembolism (VTE) in the Emergency Department (ED) of the Abbott D-dimer assay applied on the Alinity c clinical chemistry analyzer (Abbott Laboratories, Chicago, IL) compared to the INNOVANCE D-dimer assay (Siemens Healthineers, Marburg, Germany). Precision was determined at three concentration levels following the CLSI EP15-A3 protocol. Method comparison and diagnostic accuracy were assessed using samples obtained from 85 patients who were referred for diagnostic imaging and D-dimer testing due to clinically suspected VTE. Within-run coefficients of variation (CVs) were 3.0%, 0.5% and 0.5% at D-dimer concentrations of 0.54, 1.42 and 2.68 mg/L FEU, while respective between-run CVs were 2.0%, 3.4% and 2.7%, hence fulfilling the desirable biological variation criteria for imprecision (<12.6%). Passing-Bablok regression analysis yielded a small proportional difference between the two compared assays (y = 1.09 (95% confidence interval (CI): 1.01-1.18) x + 0.09 (95%CI: -0.09 to 0.16)), while Bland-Altman analysis showed significant negative absolute (-0.6 mg/L FEU, 95%CI: -0.9 to -0.3) and relative mean bias (-14.1%, 95%CI: -20.3 to -7.9). Spearman's ρ was 0.979 (95%CI: 0.967-0.986). Inter-assay agreement relative to the cut-off was 92% (kappa coefficient = 0.547 (95%CI: 0.255-0.839)). Diagnostic sensitivity, specificity, positive and negative predictive values of the Abbott assay were 100%, 9.2%, 25.3% and 100%, respectively, compared to the following data for the INNOVANCE assay: 95.0%, 15.4%, 25.7% and 90.9%. Abbott D-dimer assay has shown excellent analytical precision, high comparability with the INNOVANCE D-dimer and high NPV at manufacturer's cut-off.

Metabolomics-Guided Discovery of New Dimeric Xanthones from Co-Cultures of Mangrove Endophytic Fungi Phomopsis asparagi DHS-48 and Phomopsis sp. DHS-11.

The co-culture strategy, which mimics natural ecology by constructing an artificial microbial community, is a useful tool for the activation of biosynthetic gene clusters (BGCs) to generate new metabolites, as well as to increase the yield of respective target metabolites. As part of our project aiming at the discovery of structurally novel and biologically active natural products from mangrove endophytic fungi, we selected the co-culture of a strain of Phomopsis asparagi DHS-48 with another Phomopsis genus fungus DHS-11, both endophyted in mangrove Rhizophora mangle considering the impart of the taxonomic criteria and ecological data. The competition interaction of the two strains was investigated through morphology observation and scanning electron microscopy (SEM), and it was found that the mycelia of the DHS-48 and DHS-11 compacted and tangled with each other with an interwoven pattern in the co-culture system. A new approach that integrates HPLC chromatogram, 1HNMR spectroscopy, UPLC-MS-PCA, and molecular networking enabled the targeted isolation of the induced metabolites, including three new dimeric xanthones phomoxanthones L-N (1-3), along with six known analogs (4-9). Their planar structures were elucidated by an analysis of their HRMS, MS/MS, and NMR spectroscopic data and the absolute configurations based on ECD calculations. These metabolites showed broad cytotoxic activity against the cancer cells assessed, of which compounds 7-9 displayed significant cytotoxicity towards human liver cells HepG-2 with IC50 values ranging from 4.83 µM to 12.06 µM. Compounds 1-6 exhibited weak immunosuppressive activity against the proliferation of ConA-induced (T-cell) and LPS-induced (B-cell) murine splenic lymphocytes. Therefore, combining co-cultivation with a metabolomics-guided strategy as a discovery tool will be implemented as a systematic strategy for the quick discovery of target bioactive compounds.

The therapeutic potential of indole hybrids, dimers, and trimers against drug-resistant ESKAPE pathogens.

Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter (ESKAPE) species as causative agents are characterized by increased levels of resistance toward multiple classes of first-line as well as last-resort antibiotics and represent serious global health concerns, creating a critical need for the development of novel antibacterials with therapeutic potential against drug-resistant ESKAPE species. Indole derivatives with structural and mechanistic diversity demonstrated broad-spectrum antibacterial activity against various clinically important pathogens including drug-resistant ESKAPE. Moreover, several indole-based agents that are exemplified by creatmycin have already been used in clinics or under clinical trials for the treatment of bacterial infections, demonstrating that indole derivatives hold great promise for the development of novel antibacterials. This review is an endeavor to highlight the current scenario of indole hybrids, dimers, and trimers with therapeutic potential against drug-resistant ESKAPE pathogens, covering articles published from 2020 to the present, to open new avenues for the exploration of novel antidrug-resistant ESKAPE candidates.

Mono- and bis(steroids) containing a cyclooctane core: Synthesis, antiproliferative activity, and action on cell cytoskeleton microtubules.

Steroid dimers of natural and synthetic origin possess an unusual and complex molecular architecture that may lead to the realization of peculiar effects in biological systems, in particular in different cancer cell lines. In the present work, diastereoselective ring-opening of mono- and polyoxiranes, containing a cyclooctane core, by azide-anion was performed to yield a series of azidoalcohols with different types of symmetry. The products were involved in copper-catalyzed azyde-alkyne cycloaddition (CuAAC) reaction with ethinylestradiol and ethinyltestosterone, and the resulting steroids and steroid dimers with triazole linkers were screened for their antiproliferative activity via (3-(4,5-dimethylthiazol-2-yl)2,5-diphenyl tetrazolium bromide) assay. All the compounds revealed cytotoxicity toward several cancer cell lines. The effect of the most potent compound, containing two estradiol moieties, on the microtubules (MT) dynamics was investigated by immunofluorescent microscopy. The disruption of the majority of interphase cell cytoplasmic MT and mitotic event disturbances in the presence of the studied compound were observed. The latter effect caused the appearance of numerous multinucleated cells.