Dimer Formation Research Articles

UV damage induces production of mitochondrial DNA fragments with specific length profiles.

UV light is a potent mutagen that induces bulky DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). Photodamage and other bulky lesions occurring in nuclear genomes can be repaired through nucleotide excision repair (NER), where incisions on both sides of a damaged site precede the removal of a single-stranded oligonucleotide containing the damage. Mitochondrial genomes (mtDNAs) are also susceptible to damage from UV light, but current evidence suggests that the only way to eliminate bulky mtDNA damage is through mtDNA degradation. Damage-containing oligonucleotides excised during NER can be captured with antidamage antibodies and sequenced (XR-seq) to produce high-resolution maps of active repair locations following UV exposure. We analyzed previously published datasets from Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster to identify reads originating from the mtDNA (and plastid genome in A. thaliana). In A. thaliana and S. cerevisiae, the mtDNA-mapping reads have unique length distributions compared to the nuclear-mapping reads. The dominant fragment size was 26 nt in S. cerevisiae and 28 nt in A. thaliana with distinct secondary peaks occurring in regular intervals. These reads also show a nonrandom distribution of di-pyrimidines (the substrate for CPD formation) with TT enrichment at positions 7-8 of the reads. Therefore, UV damage to mtDNA appears to result in production of DNA fragments of characteristic lengths and positions relative to the damaged location. The mechanisms producing these fragments are unclear, but we hypothesize that they result from a previously uncharacterized DNA degradation pathway or repair mechanism in mitochondria.

Enzymatic Production of Glycerol from Glycolaldehyde and Formaldehyde

Glycerol is a simple and important polyol in both biological and industrial field. To produce glycerol in an eco‐friendly manner, we established a one‐pot cascade reaction by fructose‐6‐phosphate aldolase (FSA) and aldehyde reductase (ALR) from formaldehyde (FALD) and its dimerized form glycolaldehyde (GALD) via L‐glyceraldehyde. For this, we characterized two FSAs at various conditions. Among them, FSA from Gilliamella apicola (GaFSA) has shown the higher L‐glyceraldehyde production activity in the phosphate buffer than the well‐known FSA from Escherichia coli (EcFSA) by more than 2 times. We also characterized two ALRs (xylose reductase from Candida tenuis; CtXR, the annotated DL‐glyceraldehyde reductase from Hypocrea jecorina; HjGLD) that specifically reduce L‐glyceraldehyde into glycerol. Bioproduction of glycerol from FALD and GALD was performed using GaFSA and CtXR, which produced ~8.8 mM glycerol from 25 mM of FALD and GALD (conversion yield of ~35%). This suggested that a simple process would help in designing a green production of glycerol from a wasteful one‐carbon chemicals.

ESM1 enhances fatty acid synthesis and vascular mimicry in ovarian cancer by utilizing the PKM2-dependent warburg effect within the hypoxic tumor microenvironment

BackgroundThe hypoxic tumor microenvironment is a key factor that promotes metabolic reprogramming and vascular mimicry (VM) in ovarian cancer (OC) patients. ESM1, a secreted protein, plays an important role in promoting proliferation and angiogenesis in OC. However, the role of ESM1 in metabolic reprogramming and VM in the hypoxic microenvironment in OC patients has not been determined.MethodsLiquid chromatography coupled with tandem MS was used to analyze CAOV3 and OV90 cells. Interactions between ESM1, PKM2, UBA2, and SUMO1 were detected by GST pull-down, Co-IP, and molecular docking. The effects of the ESM1-PKM2 axis on cell glucose metabolism were analyzed based on an ECAR experiment. The biological effects of the signaling axis on OC cells were detected by tubule formation, transwell assay, RT‒PCR, Western blot, immunofluorescence, and in vivo xenograft tumor experiments.ResultsOur findings demonstrated that hypoxia induces the upregulation of ESM1 expression through the transcription of HIF-1α. ESM1 serves as a crucial mediator of the interaction between PKM2 and UBA2, facilitating the SUMOylation of PKM2 and the subsequent formation of PKM2 dimers. This process promotes the Warburg effect and facilitates the nuclear translocation of PKM2, ultimately leading to the phosphorylation of STAT3. These molecular events contribute to the promotion of ovarian cancer glycolysis and vasculogenic mimicry. Furthermore, our study revealed that Shikonin effectively inhibits the molecular interaction between ESM1 and PKM2, consequently preventing the formation of PKM2 dimers and thereby inhibiting ovarian cancer glycolysis, fatty acid synthesis and vasculogenic mimicry.ConclusionOur findings demonstrated that hypoxia increases ESM1 expression through the transcriptional regulation of HIF-1α to induce dimerization via PKM2 SUMOylation, which promotes the OC Warburg effect and VM.

Discovery of a New Polymorph of 5-Methoxy-1H-Indole-2-Carboxylic Acid: Characterization by X-ray Diffraction, Infrared Spectroscopy, and DFT Calculations.

This study presents a new 5-methoxy-1H-indole-2-carboxylic acid (MI2CA) polymorph investigated by single-crystal X-ray diffraction, infrared spectroscopy, and density functional theory (ωB97X-D) calculations employing two basis sets (6-31++G(d,p) and aug-cc-pVTZ). The compound crystallizes in the monoclinic system, space group P21/c (a = 4.0305(2) Å, b = 13.0346(6) Å, c = 17.2042(9) Å, β = 91.871(5)°, Z = 4). In the crystalline structure, the formation of cyclic dimers via double hydrogen bonds O-H⋯O between MI2CA molecules was observed. Interactions between the NH groups of the indole rings and the adjacent methoxy groups, as well as C-H⋯O contacts, significantly influence the spatial arrangement of molecules. The results from DFT calculations, including dimeric and trimeric structures, agree well with the experimental structural and spectroscopic data. Analysis of the infrared spectra confirms the conclusions drawn from X-ray diffraction studies and reveals differences between the IR spectra of the newly obtained polymorph and that reported earlier in the literature. This comprehensive study sheds some light on the MI2CA polymorphism and is important for a potential pharmacological applications of this compound.

Ultrafast planarization of photoexcited ligands in metal–organic frameworks gates charge transfer to promote photocatalysis

Metal–organic frameworks (MOFs) have emerged as a highly tunable class of porous materials with wide-ranging applications from gas capture to photocatalysis. Developing these exciting properties to their fullest extent requires a thorough mechanistic understanding of the structure–function relationships. We implement an ultrafast spectroscopic toolset, femtosecond transient absorption and femtosecond stimulated Raman spectroscopy (FSRS), to elucidate the correlated electronic and vibrational dynamics of two isostructural 1,3,6,8-tetrakis(p-benzoic acid)pyrene (TBAPy)-based MOFs, which manifest drastically different photocatalytic behaviors. Systematic comparisons between the M3+-TBAPy MOFs and bare ligands in various environments reveal the unproductive dimer formation in Al-TBAPy, whereas Sc-TBAPy is dominated by a catalytically active charge-transfer (CT) process. Two ground-state FSRS marker bands of the TBAPy ligand at ∼1267 and 1617 cm−1 probe the chromophore environment at thermal equilibrium. For comparison, the excited-state FSRS of Sc-TBAPy suspended in neutral water unveils a key ∼300 fs twisting motion of the TBAPy peripheral phenyl groups toward planarity, promoting an efficient generation of CT species. This motion also exhibits high sensitivity to solvent environment, which can be a useful probe; we also showed the CT variation for ultrafast dynamics of Sc-TBAPy in the glyphosate aqueous solution. These new insights showcase the power of table-top tunable FSRS methodology to delineate structural dynamics of functional molecular systems in action, including MOFs and other photosensitive “nanomachines.” We expect the uncovered ligand motions (ultrafast planarization) to enable the targeted design of new MOFs with improved CT state characteristics (formation and lifetime) to power applications, including photocatalysis and herbicide removal from waterways.

Reviewing the effect of aggregates in Rhodamine 6G aqueous solution on fluorescence quantum efficiency

Rhodamines constitute a class of dyes extensively investigated and applied in various contexts, primarily attributed to their high luminescence quantum yield. This study delves into the impact of aggregation on the thermal and optical properties of Rhodamine 6G (R-6G) solutions in distilled water. Examined properties encompass thermal diffusivity (D), temperature coefficient of the refractive index (dn/dT), fluorescence quantum efficiency (η), and energy transfer (ET). These parameters were assessed through thermal lens (TL) and conventional absorption and emission spectroscopic techniques. The dimerization of R-6G solutions was revisited, revealing that an increase in R-6G concentration alters the features of absorption and emission spectra due to dimer formation, resulting in unexpected behavior of η. Consequently, we introduce a novel model for the fraction of absorbed energy converted into heat (φ), which accounts for emissions from both monomers and dimers. Employing this model, we investigate and discuss the concentration-dependent behaviors of η for monomers (ηm) and dimers (ηd). Notably, our findings demonstrate that ηm values necessitate ηd = 0.2, a relatively substantial value that cannot be disregarded. Additionally, applying the Förster theory for dipole–dipole electric ET, we calculate microparameters for ET between monomers (CDD) and monomer–dimer (CDA). Critical ranges for ET in each case are quantified. Microparameter analysis indicates that ET between monomer–monomer and monomer–dimer species of R-6G dissolved in distilled water holds significance, particularly in determining ηm. These results bear significance, especially in scenarios involving high dye concentrations. While applicable to R-6G in water, similar assessments in other media featuring aggregates are encouraged.

4S-fluorination of ProB29 in insulin lispro slows fibril formation

Recombinant insulin is a life-saving therapeutic for millions of patients affected by diabetes mellitus. Standard mutagenesis has led to insulin variants with improved control of blood glucose; for instance, the fast-acting insulin lispro contains two point mutations that suppress dimer formation and expedite absorption. However, insulins undergo irreversible denaturation, a process accelerated for the insulin monomer. Here we replace ProB29 of insulin lispro with 4R-fluoroproline, 4S-fluoroproline, and 4,4-difluoroproline. All three fluorinated lispro variants reduce blood glucose in diabetic mice, exhibit similar secondary structure as measured by circular dichroism, and rapidly dissociate from the zinc- and resorcinol-bound hexamer upon dilution. Notably, however, we find that 4S-fluorination of ProB29 delays the formation of undesired insulin fibrils that can accumulate at the injection site in vivo, and can complicate insulin production and storage. These results demonstrate how subtle molecular changes achieved through non-canonical amino acid mutagenesis can improve the stability of protein therapeutics.

Abstract PO3-29-03: An Emerging Class of ER mutations Enhances ER Dimerization and Promotes ER Activity

Abstract Physiological activation of estrogen receptor alpha (ERα) requires the binding of estradiol (E2) to the ligand binding domain (LBD) of the receptor. This interaction triggers a repositioning of helix 12 (H12), facilitating the recruitment of coactivator proteins to the unoccupied coactivator binding groove. However, in the context of breast cancer, point mutations of ERα at H12 lead to its repositioning and self-activation in the absence of E2. Through MSK clinical sequencing breast cancer cohort (MSK-IMPACT), we assayed 8302 samples of ER+ breast cancer patients and identified 649 mutations within the LBD of ERα. 471 of these mutations (73%) were located at H11-H12 loops (D538, Y537, L536), while the remaining 27% were located near the dimer interface of ERα (V422, G442, F461, S463P, L469). Through in vitro biochemical and cell assays, we identified that these mutations promote dimer formation and hormone-independent transcriptional activity. Tumors expressing these mutations exhibited significantly accelerated growth compared to their wild-type controls. Unlike Y537S, cells harboring mutations at the dimer interface maintain their sensitivity to Selective Estrogen Receptor Degraders (SERDs), including Fulvestrant, recently FDA-approved Elacestrant, and Camizestrant, as well as Selective Estrogen Receptor Modulators (SERMs) including Tamoxifen and Raloxifene. By utilizing machine learning and computational structural analyses, we uncovered that these mutants, unlike Y537 repositions H12, act distinctly through conformational change across the ERα dimer interface. Further cell assays proved that the dimerization leads to increased stability of the receptor and facilitates its nuclear localization, which is required for ERα activation. Collectively, our finding unveiled a new class of ER mutations that enforce receptor dimerization and activation of the ER signaling pathway. The discovery opens up a new therapeutic interventional possibility, suggesting that targeting dimerization could emerge as a new strategy to combat these malignancies. Citation Format: Seema Irani, Wuwei Tan, Qing Li, Weiyi Toy, Catherine Jones, Mayur Gadiya, Antonio Marra, John Katzenellenbogen, Kathryn Carlson, Benita S. Katzenellenbogen, Yang Shen, Sarat Chandarlapaty. An Emerging Class of ER mutations Enhances ER Dimerization and Promotes ER Activity [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-29-03.

Structural and Magnetic Transitions Caused by Dimer Formation in the CrCl3–MoCl3 Solid Solution

Structural and Magnetic Transitions Caused by Dimer Formation in the CrCl₃–MoCl₃ Solid Solution

Search for Chirality in Hydrogenated Magnesium Nanosilicates: A DFT and TD-DFT Investigation.

The formation of silicate grains in the interstellar medium (ISM), especially those containing chiral surfaces such as clinopyroxenes, is poorly understood. Moreover, silicate interactions with various forms of hydrogen-proton (H+), neutral H (HI), and molecular hydrogen (H2) are of high importance as hydrogen comprises >90% of the ISM gas budget, and these species play important roles in the formation of new molecules in space. Furthermore, silicate surfaces catalyze the formation of H2 in the interstellar medium formed on dust grain surfaces by H-H association. The technical difficulty of in situ laboratory investigations of nanosilicate nucleation using astrophysically relevant environmental conditions makes computational chemistry a useful tool for studying potential nanosilicate structures. Furthermore, chiral surfaces interacting with chiral organic molecules could serve as templates that lead to the enantiomeric excess of l-amino acids and d-polyols detected in carbonaceous meteorites. However, in order for this effect to take place, an excess of one chiral form of a mineral is required to break the symmetry. This symmetry-breaking event could have been due to the asymmetric absorption of circularly polarized light by the nanosilicate as it traverses star-forming regions. We investigate this possibility using a metastable chiral form of an enstatite dimer as an input for density functional theory (DFT) and time-dependent (TD)-DFT calculations to obtain various properties and circular dichroism spectra. All in all, twenty-six magnesium nanosilicate structures were studied using varying degrees of hydrogenation: none, with HI, with H+, and with H2. The HSE06/aug-cc-pVQZ level of theory was used for the DFT calculations. TD-DFT calculations utilized the CAM-B3LYP/cc-pVQZ and ωB97X-D3/cc-pVQZ functional and basic set pairings. Results show that (1) all twenty-six structures have absorption bands that fall within the 0.6-28.3 μm range available with the newly launched James Webb Space Telescope and (2) there is a small enantioselective effect by UV-CPL on the eight chiral enstatite dimers (predicted g-values of up to 0.007). While the observed effect is small, it opens up the possibility that it is the inorganic material that becomes enantiomerically biased by UV-CPL, driving chiral enhancements in meteoric organic molecules.

Elucidating the Crystallization‐Caused Phosphorescence Quenching Mechanism to Achieve Efficient Photoactivated Persistent Luminescence for High‐Quality Light Printing

AbstractThe development of polymer‐based luminescent materials with efficient photoactivated ultralong organic phosphorescence (UOP) is of great importance but very challenging. Herein, a new class of organic phosphorescent luminogens is constructed by attaching phenyl rings and/or ethyl benzoates to the nitrogen atoms of a planar aromatic heterocycle pyrrolodiindole (PDI). The compounds show a significant elevation in phosphorescence emission capability after incorporating the ester group(s). However, they cannot produce room‐temperature phosphorescence in the crystalline state. These observations are identified to be associated with the formation of dimers and excimers and the motions of substituents within the molecules. In this context, the PDI derivatives are doped into epoxy polymers with compact and permanent 3D covalent networks. The resulting polymer films show reversible photoactivated UOP under ambient conditions, with quantum yields and lifetimes of up to 24.4% and 2.03 s, respectively, thereby enabling high‐quality and erasable light printing and multi‐level anti‐counterfeiting applications. In addition, they also exhibit excellent water and chemical resistance. This work is conducive to understanding the generation and decay mechanisms of the triplet excitons of organic luminophores with planar aromatic heterocycles in the crystalline state and provides a direction for the development of high‐performance photoactivated UOP materials.

Therapeutic efficacy of a novel self-assembled immunostimulatory siRNA combining apoptosis promotion with RIG-I activation in gliomas

BackgroundCurrent cancer therapies often fall short in addressing the complexities of malignancies, underscoring the urgent need for innovative treatment strategies. RNA interference technology, which specifically suppresses gene expression, offers a promising new approach in the fight against tumors. Recent studies have identified a novel immunostimulatory small-interfering RNA (siRNA) with a unique sequence (sense strand, 5’-C; antisense strand, 3’-GGG) capable of activating the RIG-I/IRF3 signaling pathway. This activation induces the release of type I and III interferons, leading to an effective antiviral immune response. However, this class of immunostimulatory siRNA has not yet been explored in cancer therapy.MethodsIsiBCL-2, an innovative immunostimulatory siRNA designed to suppress the levels of B-cell lymphoma 2 (BCL-2), contains a distinctive motif (sense strand, 5’-C; antisense strand, 3’-GGG). Glioblastoma cells were subjected to 100 nM isiBCL-2 treatment in vitro for 48 h. Morphological changes, cell viability (CCK-8 assay), proliferation (colony formation assay), migration/invasion (scratch test and Transwell assay), apoptosis rate, reactive oxygen species (ROS), and mitochondrial membrane potential (MMP) were evaluated. Western blotting and immunofluorescence analyses were performed to assess RIG-I and MHC-I molecule levels, and ELISA was utilized to measure the levels of cytokines (IFN-β and CXCL10). In vivo heterogeneous tumor models were established, and the anti-tumor effect of isiBCL-2 was confirmed through intratumoral injection.ResultsIsiBCL-2 exhibited significant inhibitory effects on glioblastoma cell growth and induced apoptosis. BCL-2 mRNA levels were significantly decreased by 67.52%. IsiBCL-2 treatment resulted in an apoptotic rate of approximately 51.96%, accompanied by a 71.76% reduction in MMP and a 41.87% increase in ROS accumulation. Western blotting and immunofluorescence analyses demonstrated increased levels of RIG-I, MAVS, and MHC-I following isiBCL-2 treatment. ELISA tests indicated a significant increase in IFN-β and CXCL10 levels. In vivo studies using nude mice confirmed that isiBCL-2 effectively impeded the growth and progression of glioblastoma tumors.ConclusionsThis study introduces an innovative method to induce innate signaling by incorporating an immunostimulatory sequence (sense strand, 5’-C; antisense strand, 3’-GGG) into siRNA, resulting in the formation of RNA dimers through Hoogsteen base-pairing. This activation triggers the RIG-I signaling pathway in tumor cells, causing further damage and inducing a potent immune response. This inventive design and application of immunostimulatory siRNA offer a novel perspective on tumor immunotherapy, holding significant implications for the field.

Study of individual domains contributing to MALT1 dimerization in BCL10-independent and dependent assembly

The CARMA-BCL10-MALT1 (CBM) signalosome functions as a pivotal supramolecular module, integrating diverse receptor-induced signaling pathways to regulate BCL10-dependent NF-kB activation in innate and adaptive immunity. Conversely, the API2-MALT1 fusion protein in t(11; 18)(q21; q21) MALT lymphoma constitutively induces BCL10-independent NF-kB activation. MALT1 dimer formation is indispensable for the requisite proteolytic activity and is critical for NF-kB activation regulation in both scenarios. However, the molecular assembly of MALT1 individual domains in CBM activation remains elusive. Here we report the crystal structure of the MALT1 death domain (DD) at a resolution of 2.1 Å, incorporating reconstructed residues in previously disordered loops 1 and 2. Additionally, we observe a conformational regulation element (CRE) regulating stem-helix formation in NLRPs pyrin (PYD) within the MALT1 DD structure. The structure reveals a stem-helix-mediated dimer further corroborated in solution. To elucidate how the BCL10 filament facilitates MALT1 dimerization, we reconstitute a BCL10-CARD-MALT1-DD-IG1-IG2 complex model. We propose a N+7 rule for BCL10-dependent MALT1 dimerization via the IG1-IG2 domain and for MALT1-dependent cleavage in trans. Biochemical data further indicates concentration-dependent dimerization of the MALT1 IG1-IG2 domain, facilitating MALT1 dimerization in BCL10-independent manner. Our findings provide a structural and biochemical foundation for understanding MALT1 dimeric mechanisms, shedding light on potential BCL10-independent MALT1 dimer formation and high-order BCL10-MALT1 assembly.

Alternative splicing controls teneurin-3 compact dimer formation for neuronal recognition

Neuronal network formation is facilitated by recognition between synaptic cell adhesion molecules at the cell surface. Alternative splicing of cell adhesion molecules provides additional specificity in forming neuronal connections. For the teneurin family of cell adhesion molecules, alternative splicing of the EGF-repeats and NHL domain controls synaptic protein-protein interactions. Here we present cryo-EM structures of the compact dimeric ectodomain of two teneurin-3 isoforms that harbour the splice insert in the EGF-repeats. This dimer is stabilised by an EGF8-ABD contact between subunits. Cryo-EM reconstructions of all four splice variants, together with SAXS and negative stain EM, reveal compacted dimers for each, with variant-specific dimeric arrangements. This results in specific trans-cellular interactions, as tested in cell clustering and stripe assays. The compact conformations provide a structural basis for teneurin homo- and heterophilic interactions. Altogether, our findings demonstrate how alternative splicing results in rearrangements of the dimeric subunits, influencing neuronal recognition and likely circuit wiring.

Interaction between hydroxymethanesulfonic acid and several organic compounds and its atmospheric significance

The interactions of the micro-mechanism of hydroxymethanesulfonic acid (HMSA) with the typical small organic molecule in atmospheric (X = methanol, formaldehyde, formic acid, methyl formate, dimethyl ether, acetone) has been investigated by density functional theory (DFT), quantum theory of atoms in molecules (QTAIM), Generalized Kohn-Sham Enery Decomposition Analysis (GKS−EDA) and the atmospheric clusters dynamic code (ACDC). The results of DFT show that the stable six− to eight−membered ring structures are easily formed in HMSA−X clusters. According to the topological analysis results of the AIM theory and the IRI method, a strong hydrogen bonding interaction is present in the complex. GKS−EDA results show that electrostatic energy is the main contributor to the interaction energy as it accounts for 51 %–55 % of the total attraction energy. The evaporation rates of HMSA−HMSA and HMSA−HCOOH clusters were much lower than those of the other HMSA complexes. In addition, the Gibbs energy of formation (ΔG) of HMSA−X dimers is investigated under atmosphere temperature T = 217–298 K and p = 0.19–1.0 atm, the ΔG decreased with decreasing of the atmosphere temperature and increased with the decrease of atmospheric pressure, indicating that the low temperature and high pressure may significantly facilitate to the formation of dimers.

Selective Formation of Homochiral Dimers by Intermolecular Charge Transfer on a hBN Nanomesh.

In this study, a comprehensive characterization was conducted on a chiral starburst molecule (C57H48N4, SBM) using scanning tunneling microscopy. When adsorbed onto the hBN/Rh(111) nanomesh, these molecules demonstrate homochiral recognition, leading to a selective formation of homochiral dimers. Further tip manipulation experiments reveal that the chiral dimers are stable and primarily controlled by strong intermolecular interactions. Density functional theory (DFT) calculations supported that the chiral recognition of SBM molecules is governed by the intermolecular charge transfer mechanism, different from the common steric hindrance effect. This study emphasizes the importance of intermolecular charge transfer interactions, offering valuable insights into the chiral recognition of a simple bimolecular system. These findings hold significance for the future advancement in chirality-based electronic sensors and pharmaceuticals, where the chirality of molecules can impact their properties.

Aviation fuel hydrocarbons from camphorwood and low-density polyethylene: Cascade catalytic approach with CaO and Zn/HBeta

In this study, the co-pyrolysis of camphorwood and low-density polyethylene employing a cascade catalyst system consisting of CaO and Zn-modified HBeta in a fixed-bed reactor was investigated for the production of aviation fuel hydrocarbons (C8–C16). The effect of Zn loading on HBeta, CaO to Zn/HBeta mass ratio, and the feedstock to catalyst mass ratio on both oil yield and composition was investigated. Results revealed that loading Zn onto HBeta led to ZnO cluster and oxygen-bridged Zn dimers ([ZnOZn]2+) formation, which affects HBeta's acid properties and aromatization capacity. The 10 wt%Zn/HBeta catalyst with more ZnO content exhibited weak acid sites, and moderate aromatization capacity, increasing oil yield from 32.06 to 44.25 wt% compared to 3 wt%Zn/HBeta and favoring presence of straight-chain components in oil products. CaO also enhanced straight-chain alkane formation. The highest oil yield, reaching 48.44 wt%, was obtained when CaO and 10 wt%Zn/HBeta cascade by a 1:1 mass ratio was adopted, producing oil with aviation fuel with a maximum yield of 18.45 wt%, and selectivity of 38.09 area%, of which 26.54 area% being aromatics and 11.55 area% being alkanes. Furthermore, the feedstock-to-catalyst ratio influenced the products significantly, with lower feedstock-to-catalyst ratio enhanced aromatization and the ratio of 2:1 recommended. Therefore, this cascade catalytic approach, which combines cost-effective CaO and 10 wt%Zn/HBeta catalysts shows significant potential for enhancing bio-aviation fuel production from solid wastes. Moreover, it provides a viable and promising solution for addressing concerns related to low oil yield and excessive aromatization.

GC–IMS facilitates identification of carbapenem-resistant Klebsiella pneumoniae in simulated blood cultures

This study aimed to identify carbapenem-resistant Klebsiella pneumoniae (CRKP) based on changes in levels of its volatile organic compounds (VOCs) in simulated blood cultures (BCs) using the gas chromatography–ion mobility spectrometry (GC–IMS) technique. A comprehensive analysis of volatile metabolites produced by Klebsiella pneumoniae (K. pneumoniae) in BC bottles was conducted using GC–IMS. Subsequently, the released VOCs were analyzed to examine differences in VOC release between CRKP and carbapenem-susceptible Klebsiella pneumoniae (CSKP). A total of 54 VOCs were detected, of which 18 (6 VOCs found in both monomer and dimer forms) were successfully identified. The VOCs produced by K. pneumoniae in BC bottles (BacT/ALERT® SA) were primarily composed of organic acids, alcohols, esters, and ketones. The content of certain VOCs was significantly different between CRKP and CSKP after the addition of imipenem (IPM). Moreover, the inclusion of carbapenemase inhibitors facilitated the identification of carbapenemase-producing K. pneumoniae based on the variations in VOCs. This study demonstrates the utility of GC–IMS technology in identifying CRKP, and reveals that changes in VOCs are closely related to the growth and metabolism of K. pneumoniae, indicating that they can be leveraged to promote early identification of CRKP bacteremia. However, further in-depth studies and experiments are needed to validate our findings.

Structures of human γδ T cell receptor–CD3 complex

Gamma delta (γδ) T cells, a unique T cell subgroup, are crucial in various immune responses and immunopathology1–3. The γδ T cell receptor (TCR), which is generated by γδ T cells, recognizes a diverse range of antigens independently of the major histocompatibility complex2. The γδ TCR associates with CD3 subunits, initiating T cell activation and holding great potential in immunotherapy4. Here we report the structures of two prototypical human Vγ9Vδ2 and Vγ5Vδ1 TCR–CD3 complexes5,6, revealing two distinct assembly mechanisms that depend on Vγ usage. The Vγ9Vδ2 TCR–CD3 complex is monomeric, with considerable conformational flexibility in the TCRγ–TCRδ extracellular domain and connecting peptides. The length of the connecting peptides regulates the ligand association and T cell activation. A cholesterol-like molecule wedges into the transmembrane region, exerting an inhibitory role in TCR signalling. The Vγ5Vδ1 TCR–CD3 complex displays a dimeric architecture, whereby two protomers nestle back to back through the Vγ5 domains of the TCR extracellular domains. Our biochemical and biophysical assays further corroborate the dimeric structure. Importantly, the dimeric form of the Vγ5Vδ1 TCR is essential for T cell activation. These findings reveal organizing principles of the γδ TCR–CD3 complex, providing insights into the unique properties of γδ TCR and facilitating immunotherapeutic interventions.

Rational design of monomeric IL37 variants guided by stability and dynamical analyses of IL37 dimers

IL37 plays important roles in the regulation of innate immunity and its oligomeric status is critical to these roles. In its monomeric state, IL37 can effectively inhibit the inflammatory response of IL18 by binding to IL18Rα, a capacity lost in its dimeric form, underlining the pivotal role of the oligomeric status of IL37 in its anti-inflammatory action. Until now, two IL37 dimer structures have been deposited in PDB, reflecting a substantial difference in their dimer interfaces. Given this discrepancy, we analyzed the PDB structures of the IL37 dimer (PDB IDs: 6ncu, 5hn1) along with a AF2-multimer prediction by molecular dynamics (MD) simulations. Results showed that the 5hn1 and AF2-predicted dimers have the same interface and stably maintained their conformations throughout simulations, while the recent IL37 dimer (PDB ID: 6ncu) with a different interface did not, proposing a possible issue with the recent IL37 dimer structure (6ncu). Next, focusing on the stable dimer structures, we have identified five critical positions of V71/Y85/I86/E89/S114, three new positions compared to the literature, that would reduce dimer stability without affecting the monomer structure. Two quintuple mutants were tested by MD simulations and showed partial or complete dissociation of the dimer. Overall, the insights gained from this study reinforce the validity of the 5hn1 and AF2 multimer structures, while also advancing our understanding of the IL37 dimer interface through the generation of monomer-locked IL37 variants.