Search

Reconfigurable chiral plasmonic complexes are fabricated by planar assembly of multiple individual gold nanorod dimers using DNA origami templates. Additionally, each chiral center can be controlled to switch among achiral, left-handed, and right-handed states. We demonstrate that their overall circular dichroism is determined by the coupling of individual chiral centers and is heavily influenced by the precise number and arrangement of these centers. Our study offers a novel self-assembly method for constructing intricate and dynamic chiral plasmonics as well as investigating the interactions among several plasmonic chiral centers. [ABSTRACT FROM AUTHOR]

Oligomerization presents a wide range of opportunities for transforming light olefins into liquid fuels. This study centers on a novel catalyst system – phosphotungstic acid (PW) loaded onto MCM-41 prepared via impregnation, aiming to tackle these challenges. The ordered mesoporous structure, high surface area, and facile recovery of MCM-41 make it an ideal support for PW. Under the mild reaction conditions of 70 °C, 1 MPa, and 5 h, the 20% PW/MCM-41 catalyst exhibited remarkable catalytic performance, achieving an isopentene conversion rate of 77.8%, a selectivity of 93.5% towards the C10 dimer product, and a yield of 72.7%. Encouragingly, the catalyst could be reused without special treatment, maintaining a selectivity above 93% for the C10 dimer product over five cycles, showcasing outstanding stability and regeneration capability. This research not only provides robust insights into catalyst design for isopentene dimerization but also paves the way for sustainable advancements in industrial catalysis. [ABSTRACT FROM AUTHOR]

The discovery of unspecific peroxygenases (UPOs) completely changed the paradigm of enzyme-based oxyfunctionalization reactions, as these enzymes can transform a wide variety of substrates with a relatively simple reaction mechanism. The fact that UPO can exert both peroxygenative and peroxidative activity in either aromatic or aliphatic carbons, represents a great potential in the production of high value-added products from natural antioxidants. In this work, the flavonoid rutin has been considered as possible substrate for UPO from Agrocybe aegerita , and its peroxygenation or its peroxidation and successive oligomerization have been studied. Different experiments were performed in order to reduce the range of process variables involved and gaining insight on the behavior of this enzyme, leading to a multivariable optimization of UPO-based rutin modification. While trying to preserve enzyme activity this optimization aimed for maximizing the production of more soluble antioxidants. Reusability of the enzyme was evaluated recovering UPO using an enzymatic membrane reactor, revealing challenges in enzyme stability due to inactivation during the filtration stages. The influence of the radical scavenger ascorbic acid on product formation was investigated, revealing its role in directing the reaction towards hydroxylated rutin derivatives, hence indicating a shift towards more soluble and bioactive products. [Display omitted] • UPO transforms rutin to more soluble products with enhanced antioxidant activity. • H 2 O 2 feeding rate, initial enzymatic activity and reaction time were optimized. • Peroxygenative and peroxidative activities are crucial to increase both bioactivity and solubility. • A poor stability of the enzyme limits its reuse in successive cycles. • Ascorbic acid concentration allows modulation of the characteristics of the products. [ABSTRACT FROM AUTHOR]

A lateral expansion of molecular spoked wheels (MSWs) based on an all‐phenylene backbone is described. The MSWs contain a central hub, six spokes, and a rim that is formed by a sixfold Yamamoto coupling of the respective non‐cyclized dodecabromo precursor yielding MSWs with up to 30 phenylene rings in the perimeter. Attempts to prepare compounds of such size without flexible side groups at the spokes were unsuccessful, most probably due to an aggregation and accompanying oligomerization of the precursors during the cyclization. To overcome these problems, fluorene units are inserted into the spokes. These contain additional alkyl chains and lead to a curvature of the wheels. Quantum chemical calculations on the mechanism of the Yamamoto coupling lead to geometry and strain‐related criteria for the successful rim closure to the respective MSW. Subsequently, MSWs are prepared with four and even six phenylene units at each edge of the hexagonal wheels. The resulting MSWs are characterized by spectroscopic methods, and additionally some of them are visualized via scanning tunneling microscopy (STM). [ABSTRACT FROM AUTHOR]

NRCs are essential helper NLR (nucleotide-binding domain and leucine-rich repeat) proteins that execute immune responses triggered by sensor NLRs. The resting state of NbNRC2 was recently shown to be a homodimer, but the sensor-activated state remains unclear. Using cryo-EM, we determined the structure of sensor-activated NbNRC2, which forms a hexameric inflammasome-like resistosome. Mutagenesis of the oligomerization interface abolished immune signaling, confirming the functional significance of the NbNRC2 resistosome. Comparative structural analyses between the resting state homodimer and sensor-activated homohexamer revealed substantial rearrangements, providing insights into NLR activation mechanisms. Furthermore, structural comparisons between NbNRC2 hexamer and previously reported CC-NLR pentameric assemblies revealed features allowing an additional protomer integration. Using the NbNRC2 hexamer structure, we assessed the recently released AlphaFold 3 for predicting activated CC-NLR oligomers, revealing high-confidence modeling of NbNRC2 and other CC-NLR amino-terminal a1 helices, a region proven difficult to resolve structurally. Overall, our work sheds light on NLR activation mechanisms and expands understanding of NLR structural diversity. [ABSTRACT FROM AUTHOR]

AlphaFold can accurately predict static protein structures but does not account for solvent conditions. Human leucine zipper EF-hand transmembrane protein-1 (LETM1) has one sequence-identifiable EF-hand but how calcium (Ca2+) affects structure and function remains enigmatic. Here, we used highly confident AlphaFold Cα predictions to guide nuclear Overhauser effect (NOE) assignments and structure calculation of the LETM1 EF-hand in the presence of Ca2+. The resultant NMR structure exposes pairing between a partial loop-helix and full helix-loop-helix, forming an unprecedented F-EF-hand with non-canonical Ca2+ coordination but enhanced hydrophobicity for protein interactions compared to calmodulin. The structure also reveals the basis for pH sensing at the link between canonical and partial EF-hands. Functionally, mutations that augmented or weakened Ca2+ binding increased or decreased matrix Ca2+, respectively, establishing F-EF as a two-way mitochondrial Ca2+ regulator. Thus, we show how to synergize AI prediction with NMR data, elucidating a solution-specific and extraordinary LETM1 F-EF-hand. [Display omitted] • An AI-informed NMR structure elucidation method reveals a unique LETM1 F-EF-hand • The Ca2+ bound LETM1 F-EF-hand adopts an open conformation with high hydrophobicity • High affinity LETM1 F-EF-hand Ca2+ binding increases mitochondrial matrix Ca2+ • Abrogated LETM1 F-EF-hand Ca2+ binding decreases mitochondrial matrix Ca2+ AI has revolutionized structural biology but must be applied responsibly. Lin et al. present a method for synergizing AlphaFold predictions with solution NMR data, using the approach to expose an unprecedented F-EF-hand domain in LETM1. This LETM1 F-EF-hand functions as a weak Ca2+ binding sensor that modulates mitochondrial matrix Ca2+. [ABSTRACT FROM AUTHOR]

Synthesis of BODIPY oligomers has attracted increasing attention due to their intriguing properties and promising applications. Significant progress has been made to synthesize BODIPY oligomers via post‐functionalization, either single‐bond linked or fully conjugated. This concept article highlights the recent developments of BODIPY oligomers, including the synthetic routes, their photophysical properties and applications in the areas of NIR light absorbing dye, photodynamic therapy, and bioimaging etc. [ABSTRACT FROM AUTHOR]

Covering: up to 2024 This review aims to draw a parallel between all known oligomers of monoterpene indole alkaloids (MIAs) by illustrating the chemical logic underlying their assembly. For this purpose, oligomeric MIAs were first comprehensively listed and organized according to the names of the backbones of their constitutive monomers and the binding sites. From this extensive list, an oligomer network was generated and unprecedented MIA statistics were mined and shared herein. Subsequently, oligomeric MIAs were categorized according to the number of connections instigated between their monomeric components (single, double, triple, and mixed tethering), then subdivided according to the uniqueness or combination of oligomerization assembly reactions. This effort outlined oligomerization trends in a scaffold-specific manner, and established binding reactivity patterns facilitating the comprehension of the associated biosynthetic processes. At last, this review illustrates a unique initiative in crafting a comprehensive repository of machine-readable metadata for MIA oligomers that could be leveraged for chemoinformatic purposes. [ABSTRACT FROM AUTHOR]

Serum amyloid A (SAA) is a small protein consisting of 104 residues and, under physiological conditions, exists mainly in hexameric form. It belongs to the positive acute-phase proteins, which means that its plasma concentration increases rapidly in response to injury, inflammation, and infection. The accumulation of SAA molecules promotes the formation of amyloid aggregates, which deposit extracellularly in many organs, causing their dysfunction. In our previous work, we successfully designed a peptidomimetic that inhibited the aggregation of amyloidogenic SAA fragments. In the present paper, we show how the same inhibitor, named saa3Dip, affects the oligomerization and aggregation processes of MetSAA1.1 protein. The thioflavin T assay showed that saa3Dip inhibited its fibrillization. The measurement of the internal fluorophore fluorescence (Trp) showed differences that occurred in the tertiary structure of MetSAA1.1 in the presence of the inhibitor, which was also confirmed by CD spectra in the aromatic range. FTIR results suggested that saa3Dip could stabilize some fragments of the native structure of MetSAA1.1, which was confirmed by determining the melting temperature (Tm) of the protein–inhibitor complex. AFM images demonstrated that the presence of saa3Dip prevented the formation of large SAA aggregates. Our results suggest that saa3Dip stabilizes the native conformation of MetSAA1.1. [ABSTRACT FROM AUTHOR]

During seed maturation, plants may experience severe desiccation, leading to the accumulation of late embryogenesis abundant (LEA) proteins. These intrinsically disordered proteins also accumulate in plant tissues under water deficit. Functional roles of LEA proteins have been proposed based on in vitro studies, where monomers are considered as the functional units. However, the potential formation of homo‐oligomers has been little explored. In this work, we investigated the potential self‐association of Arabidopsis thaliana group 4 LEA proteins (AtLEA4) using in vitro and in vivo approaches. LEA4 proteins represent a compelling case of study due to their high conservation throughout the plant kingdom. This protein family is characterized by a conserved N‐terminal region, with a high alpha‐helix propensity and invitro protective activity, as compared to the highly disordered and low‐conserved C‐terminal region. Our findings revealed that full‐length AtLEA4 proteins oligomerize and that both terminal regions are sufficient for self‐association in vitro. However, the ability of both amino and carboxy regions of AtLEA4‐5 to self‐associate invivo is significantly lower than that of the entire protein. Using high‐resolution and quantitative fluorescence microscopy, we were able to disclose the unreported ability of LEA proteins to form high‐order oligomers in planta. Additionally, we found that high‐order complexes require the simultaneous engagement of both terminal regions, indicating that the entire protein is needed to attain such structural organization. This research provides valuable insights into the self‐association of LEA proteins in plants and emphasizes the role of protein oligomer formation. [ABSTRACT FROM AUTHOR]

The inner membrane associated protein of 30 kDa (IM30), a member of the endosomal sorting complex required for transport (ESCRT‐III) superfamily, is crucially involved in the biogenesis and maintenance of thylakoid membranes in cyanobacteria and chloroplasts. In solution, IM30 assembles into various large oligomeric barrel‐ or tube‐like structures, whereas upon membrane binding it forms large, flat carpet structures. Dynamic localization of the protein in solution, to membranes and changes of the oligomeric states are crucial for its in vivo function. ESCRT‐III proteins are known to form oligomeric structures that are dynamically assembled from monomeric/smaller oligomeric proteins, and thus these smaller building blocks must be assembled sequentially in a highly orchestrated manner, a still poorly understood process. The impact of IM30 oligomerization on function remains difficult to study due to its high intrinsic tendency to homo‐oligomerize. Here, we used molecular dynamics simulations to investigate the stability of individual helices in IM30 and identified unstable regions that may provide structural flexibility. Urea‐mediated disassembly of the IM30 barrel structures was spectroscopically monitored, as well as changes in the protein's tertiary and secondary structure. The experimental data were finally compared to a three‐state model that describes oligomer disassembly and monomer unfolding. In this study, we identified a highly stable conserved structural core of ESCRT‐III proteins and discuss the advantages of having flexible intermediate structures and their putative relevance for ESCRT‐III proteins. [ABSTRACT FROM AUTHOR]

The intermitochondrial cement (IMC) is a prominent germ granule that locates among clustered mitochondria in mammalian germ cells. Serving as a key platform for Piwi-interacting RNA (piRNA) biogenesis; however, how the IMC assembles among mitochondria remains elusive. Here, we identify that Tudor domain-containing 1 (TDRD1) triggers IMC assembly via phase separation. TDRD1 phase separation is driven by the cooperation of its tetramerized coiled-coil domain and dimethylarginine-binding Tudor domains but is independent of its intrinsically disordered region. TDRD1 is recruited to mitochondria by MILI and sequentially enhances mitochondrial clustering and triggers IMC assembly via phase separation to promote piRNA processing. TDRD1 phase separation deficiency in mice disrupts IMC assembly and piRNA biogenesis, leading to transposon de-repression and spermatogenic arrest. Moreover, TDRD1 phase separation is conserved in vertebrates but not in invertebrates. Collectively, our findings demonstrate a role of phase separation in germ granule formation and establish a link between membrane-bound organelles and membrane-less organelles. [Display omitted] • TDRD1 undergoes phase separation via oligomerization of coiled-coil domain • Tudor domains facilitate TDRD1 phase separation by recognizing sDMA • TDRD1 phase separation deficiency disrupts IMC assembly and piRNA biogenesis in mice • TDRD1 phase separation is conserved in vertebrates but not in invertebrates Gao et al. address the mechanism governing the assembly of mitochondrial-associated germ granules (IMCs) in mammalian germ cells. The IMC component TDRD1 undergoes phase separation to trigger IMC assembly, which is essential for piRNA biogenesis, transposon silencing, and male fertility in mice. [ABSTRACT FROM AUTHOR]

The primary aim of this research was to identify the structural characteristics of three newly derived procyanidins from cold plasma-treated (–)-epicatechin, known for their anti-inflammatory properties. The newly generated compounds were isolated through column chromatography, and their chemical structures were elucidated through spectroscopic data analyses, including both one-dimensional and two-dimensional nuclear magnetic resonance (NMR) and mass spectrometry (MS) techniques. Furthermore, their absolute configurations were determined via circular dichroism (CD) spectroscopy. The inhibitory activity of the isolated compounds on nitric oxide (NO) production and expression levels of inducible NO synthase (iNOS) in lipopolysaccharide (LPS)-induced RAW 264.7 macrophages was evaluated. Three new procyanidins—methylenetrisepicatechin (2), isomethylenetrisepicatechin (3), and methylenebisepicatechin (4)—along with two reported dimeric flavan-3-ols (5 and 6), were identified from plasma-treated (–)-epicatechin (1). The unique oligomerized products 2 and 3 linked by methylene bridges significantly suppressed both NO production and iNOS expression, demonstrating higher anti-inflammatory activities in LPS-stimulated RAW 264.7 cells compared with the parent compound. The newly oligomerized procyanidins have potential applications in the treatment of inflammatory diseases owing to their significant anti-inflammatory properties. [ABSTRACT FROM AUTHOR]

Lipophosphoglycans (LPGs) are found on the surface of Leishmania, a protozoan parasite, and are immunologically important. Herein, disaccharide 1‐phosphate repeating units of LPGs were successfully synthesized on a solid support with high anomeric purity using a disaccharide α‐1‐phosphoramidite building block. To enhance solubility in the reaction solvent, hydroxy‐protecting groups in the form of para‐t‐butylbenzoyl were introduced to the building block. The saccharide chain was elongated via stable glycosyl boranophosphate linkages, followed by the conversion of inter‐sugar linkages to phosphodiester counterparts using an oxaziridine derivative. The addition of a silylating reagent post‐reaction with the oxaziridine derivative efficiently facilitated the conversion of boranophosohodiesters to phosphodiesters. This method enabled the α‐selective synthesis of up to 15 repeating units, marking the longest homogeneous repeating units of LPGs synthesized chemically. Given the chain length equivalence to native LPGs, the method developed herein holds promise for advancing anti‐Leishmanial pharmaceuticals and vaccines. [ABSTRACT FROM AUTHOR]

Synaptotagmin-1 (Syt1) is a calcium sensor that regulates synaptic vesicle fusion in synchronous neurotransmitter release. Syt1 interacts with negatively charged lipids and the SNARE complex to control the fusion event. However, it remains incompletely understood how Syt1 mediates Ca2+-trigged synaptic vesicle fusion. Here, we discovered that Syt1 undergoes liquid–liquid phase separation (LLPS) to form condensates both in vitro and in living cells. Syt1 condensates play a role in vesicle attachment to the PM and efficiently recruit SNAREs and complexin, which may facilitate the downstream synaptic vesicle fusion. We observed that Syt1 condensates undergo a liquid-to-gel-like phase transition, reflecting the formation of Syt1 oligomers. The phase transition can be blocked or reversed by Ca2+, confirming the essential role of Ca2+ in Syt1 oligomer disassembly. Finally, we showed that the Syt1 mutations causing Syt1-associated neurodevelopmental disorder impair the Ca2+- driven phase transition. These findings reveal that Syt1 undergoes LLPS and a Ca2+-sensitive phase transition, providing new insights into Syt1-mediated vesicle fusion. [ABSTRACT FROM AUTHOR]

Retroviral assembly is a highly coordinated step in the replication cycle. The process is initiated when the newly synthesized Gag and Gag-Pol polyproteins are directed to the inner leaflet of the plasma membrane (PM), where they facilitate the budding and release of immature viral particles. Extensive research over the years has provided crucial insights into the molecular determinants of this assembly step. It is established that Gag targeting and binding to the PM is mediated by interactions of the matrix (MA) domain and acidic phospholipids such as phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). This binding event, along with binding to viral RNA, initiates oligomerization of Gag on the PM, a process mediated by the capsid (CA) domain. Much of the previous studies have focused on human immunodeficiency virus type 1 (HIV-1). Although the general steps of retroviral replication are consistent across different retroviruses, comparative studies revealed notable differences in the structure and function of viral components. In this review, we present recent findings on the assembly mechanisms of Human T-cell leukemia virus type 1 and highlight key differences from HIV-1, focusing particularly on the molecular determinants of Gag–PM interactions and CA assembly. [ABSTRACT FROM AUTHOR]

Cellular processes are controlled by the thermodynamics of the underlying biomolecular interactions. Frequently, structural investigations use one monomeric binding partner, while ensemble measurements of binding affinities generally yield one affinity representative of a 1:1 interaction, despite the majority of the proteome consisting of oligomeric proteins. For example, viral entry and inhibition in SARS-CoV-2 involve a trimeric spike surface protein, a dimeric angiotensin-converting enzyme 2 (ACE2) cell-surface receptor and dimeric antibodies. Here, we reveal that cooperativity correlates with infectivity and inhibition as opposed to 1:1 binding strength. We show that ACE2 oligomerizes spike more strongly for more infectious variants, while exhibiting weaker 1:1 affinity. Furthermore, we find that antibodies use induced oligomerization both as a primary inhibition mechanism and to enhance the effects of receptor-site blocking. Our results suggest that naive affinity measurements are poor predictors of potency, and introduce an antibody-based inhibition mechanism for oligomeric targets. More generally, they point toward a much broader role of induced oligomerization in controlling biomolecular interactions. [ABSTRACT FROM AUTHOR]

Gasdermin D (GSDMD) executes the cell death program of pyroptosis by assembling into oligomers that permeabilize the plasma membrane. Here, by single-molecule imaging, we elucidate the yet unclear mechanism of Gasdermin D pore assembly and the role of cysteine residues in GSDMD oligomerization. We show that GSDMD preassembles at the membrane into dimeric and trimeric building blocks that can either be inserted into the membrane, or further assemble into higher-order oligomers prior to insertion into the membrane. The GSDMD residues Cys39, Cys57, and Cys192 are the only relevant cysteines involved in GSDMD oligomerization. S-palmitoylation of Cys192, combined with the presence of negatively-charged lipids, controls GSDMD membrane targeting. Simultaneous Cys39/57/192-to-alanine (Ala) mutations, but not Ala mutations of Cys192 or the Cys39/57 pair individually, completely abolish GSDMD insertion into artificial membranes as well as into the plasma membrane. Finally, either Cys192 or the Cys39/Cys57 pair are sufficient to enable formation of GSDMD dimers/trimers, but they are all required for functional higher-order oligomer formation. Overall, our study unveils a cooperative role of Cys192 palmitoylation-mediated membrane binding and Cys39/57/192-mediated oligomerization in GSDMD pore assembly. This study supports a model in which Gasdermin D oligomerization relies on a two-step mechanism mediated by specific cysteine residues. Synopsis: Gasdermin D (GSDMD) permeabilizes the plasma membrane during pyroptosis. This work reveals a complex process of GSDMD pore assembly involving specific cysteine residues mediating its membrane targeting and oligomerization. GSDMD membrane targeting is promoted by the synergistic action of Cys192 S-palmitoylation and the presence of negatively-charged lipids. At the membrane, GSDMD preassembles into dimeric and trimeric building units from which higher-order oligomers are generated. Dimer and trimer formation is redundantly mediated by either Cys192 or the Cys39/Cys57 pair. Higher-order oligomerization requires the cooperative action of Cys39/Cys57 and Cys192. The cysteine residue pair Cys39/Cys57 and palmitoylation of Cys192 mediate Gasdermin D membrane targeting and oligomer formation. [ABSTRACT FROM AUTHOR]

Cholesterol-dependent cytolysins (CDCs) are the distinct class of β-barrel pore-forming toxins (β-PFTs) that attack eukaryotic cell membranes, and form large, oligomeric, transmembrane β-barrel pores. Listeriolysin O (LLO) is a prominent member in the CDC family. As documented for the other CDCs, membrane cholesterol is essential for the poreforming functionality of LLO. However, it remains obscure how exactly cholesterol facilitates its pore formation. Here, we show that cholesterol promotes both membranebinding and oligomerization of LLO. We demonstrate cholesterol not only facilitates membrane-binding, it also enhances the saturation threshold of LLO-membrane association, and alteration of the cholesterol-recognition motif in the LLO mutant (LLOT515G-L516G) compromises its pore-forming efficacy. Interestingly, such defect of LLOT515G-L516G could be rescued in the presence of higher membrane cholesterol levels, suggesting cholesterol can augment the pore-forming efficacy of LLO even in the absence of a direct toxin-cholesterol interaction. Furthermore, we find the membrane-binding and pore-forming abilities of LLOT515G-L516G, but not those of LLO, correlate with the cholesterol-dependent rigidity/ ordering of the membrane lipid bilayer. Our data further suggest that the line tension derived from the lipid phase heterogeneity of the cholesterol-containing membranes could play a pivotal role in LLO function, particularly in the absence of cholesterol binding. Therefore, in addition to its receptor-like role, we conclude cholesterol can further facilitate the pore-forming, membrane-damaging functionality of LLO by asserting the optimal physicochemical environment in membranes. To the best of our knowledge, this aspect of the cholesterol-mediated regulation of the CDC mode of action has not been appreciated thus far. [ABSTRACT FROM AUTHOR]

FOXP2 is a transcription factor associated with speech and language. Like other FOX transcription factors, it has a DNA binding region called the forkhead domain (FHD). This domain can exist as a monomer or a domain swapped dimer. In addition to the FHD, the leucine zipper region (LZ) of FOXP2 is also believed to be associated with both DNA binding and oligomerization. To better understand the relationship between DNA binding and oligomerization of FOXP2, we investigated its structure, stability and dynamics, focusing specifically on the FHD and the LZ. We did this by using two constructs: one containing the isolated FHD and one containing both the LZ and the FHD (LZ‐END). We demonstrate in this work, that while the FHD maintains a monomeric form that is capable of binding DNA, the LZ‐END undergoes a dynamic transition between oligomeric states in the presence of DNA. Our findings suggest that FOXP2's LZ domain influences DNA binding affinity through a change in oligomeric state. We show through hydrogen exchange mass spectroscopy that certain parts of the FHD and interlinking region become less dynamic when in the presence of DNA, confirming DNA binding and oligomerization in these regions. Moreover, the detection of a stable equilibrium intermediate state during LZ‐END unfolding supports the idea of cooperation between these two domains. Overall, our study sheds light on the interplay between two FOXP2 domains, providing insight into the protein's ability to respond dynamically to DNA, and enriching our understanding of FOXP2's role in gene regulation. [ABSTRACT FROM AUTHOR]

Intracellular accumulation of misfolded proteins causes serious human proteinopathies. The transmembrane emp24 domain 9 (TMED9) cargo receptor promotes a general mechanism of cytotoxicity by entrapping misfolded protein cargos in the early secretory pathway. However, the molecular basis for this TMED9-mediated cargo retention remains elusive. Here, we report cryo-electron microscopy structures of TMED9, which reveal its unexpected self-oligomerization into octamers, dodecamers, and, by extension, even higher-order oligomers. The TMED9 oligomerization is driven by an intrinsic symmetry mismatch between the trimeric coiled coil domain and the tetrameric transmembrane domain. Using frameshifted Mucin 1 as an example of aggregated disease-related protein cargo, we implicate a mode of direct interaction with the TMED9 luminal Golgi-dynamics domain. The structures suggest and we confirm that TMED9 oligomerization favors the recruitment of coat protein I (COPI), but not COPII coatomers, facilitating retrograde transport and explaining the observed cargo entrapment. Our work thus reveals a molecular basis for TMED9-mediated misfolded protein retention in the early secretory pathway. [ABSTRACT FROM AUTHOR]

5,18‐Dimesitylorangarin and its BF2 complex were synthesized by double SNAr reaction of 3,5‐dibromo‐BODIPY with 2‐pyrrolydipyrrin as the first examples of meso‐aryl‐substituted orangarin. These orangarins, delineated as [20]pentaphyrin(1.0.1.0.0), are strongly antiaromatic but rather stable. The free base orangarin was coupled by oxidation with MnO2 to give a 11,11′‐linked dimer, a cyclooctatetraene(COT)‐centered trimer, and a spiro‐trimer. Fused COT‐centered 3H‐orangarin dimer was oxidized to the corresponding 2H‐orangarin dimer, which was further coupled to give a triply COT‐centered 2H‐orangarin tetramer. 3H‐Orangarin oligomers are all antiaromatic as evinced by extremely low‐field‐shifted 1H NMR signals of the inner NH and ill‐defined absorption spectra with broad tails. In contrast, COT‐centered 2H‐orangarin dimer and tetramer show moderately low‐field‐shifted NH signals and intense NIR absorbance over 900 nm, suggesting effective π‐conjugation through the COT bridge and almost non‐antiaromatic character. These orangarin oligomers exhibit many reversible redox potentials owing to the intramolecular electronic interactions. Regardless of the different aromatic characters, all the orangarin monomers and oligomers exhibit very rapid excited‐state decays. [ABSTRACT FROM AUTHOR]

The stimulator of interferon genes (STING) pathway is a potent therapeutic target for innate immunity. Despite the efforts to develop pocket‐dependent small‐molecule STING agonists that mimic the endogenous STING ligand, cyclic guanosine monophosphate–adenosine monophosphate (cGAMP), most of these agonists showed disappointing results in clinical trials owing to the limitations of the STING pocket. In this study, we developed novel pocket‐independent STING‐activating agonists (piSTINGs), which act through multivalency‐driven oligomerization to activate STING. Additionally, a piSTING‐adjuvanted vaccine elicited a significant antibody response and inhibited tumour growth in therapeutic models. Moreover, a piSTING‐based vaccine combination with aPD‐1 showed remarkable potential to enhance the effectiveness of immune checkpoint blockade (ICB) immunotherapy. In particular, piSTING can strengthen the impact of STING pathway in immunotherapy and accelerate the clinical translation of STING agonists. [ABSTRACT FROM AUTHOR]

A series of novel diphosphinoamine (PNP) ligands bearing a P-alkenyl group were synthesized and applied in chromium-catalyzed selective ethylene tri-/tetramerization by in situ combination of Cr(acac)3 and modified methylalumoxane (MMAO-3A). The ligand substitution and oligomerization conditions have a remarkable influence on the catalytic activity and controllable selectivity. Most of these PNP ligands are highly active for ethylene tri-/tetramerization with considerable selectivity. An asymmetric diisopropenylphosphanyl ligand with an N-cyclohexyl group achieved the highest activity of 2036 kg (g Cr h−1)−1 with a high total selectivity of 81.1 wt% toward valuable 1-hexene (43.0 wt%) and 1-octene (38.1 wt%) at 40 bar ethylene and 60 °C. An asymmetric mixed isopropenyl/ethylphosphanyl ligand with an N-isopropyl group exhibited a high 1-octene selectivity of 65.5 wt% and a high total 1-hexene/1-octene selectivity (91.5 wt%) with a high activity of 1256 kg (g Cr h−1)−1. [ABSTRACT FROM AUTHOR]

A series of new thermosetting diimides containing terminal propargyl groups was synthesized via one-step high-temperature catalytic condensation of dianhydrides of a tetracarboxylic acid with N-Boc-(4-propargyloxy)aniline (APR) in the so-called "active medium", viz. molten benzoic acid. Structures of the obtained compounds were confirmed by 1H NMR and IR spectroscopy. The effect of symmetrical and unsymmetrical structures of the middle bis-imide moiety obtained from dianhydrides of isomeric diphenyltetracarboxylic acid on physicochemical characteristics of the diimides was evaluated. A similar comparison of properties was also carried out for a pair of new propargyl-containing diimides synthesized from dianhydrides of symmetric and asymmetric structure: 4,4-biphenylenedioxydiphthalic and 3,4-biphenylenedioxydiphthalic dianhydrides, respectively. Thermal properties of thermosetting oligoimides were estimated using DSC and TMA methods. It was found that their thermal properties and solubility in organic solvents depend significantly on the structure of central bis-imide moiety. [ABSTRACT FROM AUTHOR]

Atomic force microscopy (AFM) imaging enables the visualization of protein molecules with high resolution, providing insights into their shape, size, and surface topography. Here, we use AFM to study the aggregation process of protein S100A9 in physiological conditions, in the presence of calcium at a molar ratio 4Ca2+:S100A9. We find that S100A9 readily assembles into a worm-like fibril, with a period dimension along the fibril axis of 11.5 nm. The fibril's chain length extends up to 136 periods after an incubation time of 144 h. At room temperature, the fibril's bending stiffness was found to be 2.95 × 10 − 28 Nm2, indicating that the fibrils are relatively flexible. Additionally, the values obtained for the Young's modulus ( E x = 6.96 × 10 5 Pa and E y = 3.37 × 10 5 Pa) are four orders of magnitude lower than those typically reported for canonical amyloid fibrils. Our findings suggest that, under the investigated conditions, a distinct aggregation mechanism may be in place in the presence of calcium. Therefore, the findings reported here could have implications for the field of biomedicine, particularly with regard to Alzheimer's disease. [ABSTRACT FROM AUTHOR]

Rotaviruses (RVs) are classified into nine species, A–D and F–J, with species A being the most studied. In rotavirus of species A (RVA), replication occurs in viroplasms, which are cytosolic globular inclusions composed of main building block proteins NSP5, NSP2, and VP2. The co-expression of NSP5 with either NSP2 or VP2 in uninfected cells leads to the formation of viroplasm-like structures (VLSs). Although morphologically identical to viroplasms, VLSs do not produce viral progeny but serve as excellent tools for studying complex viroplasms. A knowledge gap exists regarding non-RVA viroplasms due to the lack of specific antibodies and suitable cell culture systems. In this study, we explored the ability of NSP5 and NSP2 from non-RVA species to form VLSs. The co-expression of these two proteins led to globular VLSs in RV species A, B, D, F, G, and I, while RVC formed filamentous VLSs. The co-expression of NSP5 and NSP2 of RV species H and J did not result in VLS formation. Interestingly, NSP5 of all RV species self-oligomerizes, with the ordered C-terminal region, termed the tail, being necessary for self-oligomerization of RV species A–C and G–J. Except for NSP5 from RVJ, all NSP5 interacted with their cognate NSP2. We also found that interspecies VLS are formed between closely related RV species B with G and D with F. Additionally, VLS from RVH and RVJ formed when the tail of NSP5 RVH and RVJ was replaced by the tail of NSP5 from RVA and co-expressed with their respective NSP2. IMPORTANCE Rotaviruses (RVs) are classified into nine species, A–D and F–J, infecting mammals and birds. Due to the lack of research tools, all cumulative knowledge on RV replication is based on RV species A (RVA). The RV replication compartments are globular cytosolic structures named viroplasms, which have only been identified in RV species A. In this study, we examined the formation of viroplasm-like structures (VLSs) by the co-expression of NSP5 with NSP2 across RV species A to J. Globular VLSs formed for RV species A, B, D, F, G, and I, while RV species C formed filamentous structures. The RV species H and J did not form VLS with their cognates NSP5 and NSP2. Similar to RVA, NSP5 self-oligomerizes in all RV species, which is required for VLS formation. This study provides basic knowledge of the non-RVA replication mechanisms, which could help develop strategies to halt virus infection across RV species. [ABSTRACT FROM AUTHOR]

The use of heterogeneous catalysts to increase the development of green chemistry is a rapidly growing area of research to save industry money. In this paper, mesoporous SiO2-Al2O3 mixed oxide supports with various Si/Al ratios were prepared using two different sol–gel routes: hydrolytic sol–gel (HSG) and non-hydrolytic sol–gel (NHSG). The HSG route was investigated in both acidic and basic media, while the NHSG was explored in the presence of ethanol and diisopropyl ether as oxygen donors. The resulting SiO2-Al2O3 mixed oxide supports were characterized using EDX, N2 physisorption, powder XRD, 29Si, 27Al MAS-NMR and NH3-TPD. The mesoporous SiO2-Al2O3 supports prepared by NHSG seemed to be more regularly distributed and also more acidic. Consequently, a simple one-step NHSG (ether and alcohol routes) was selected to prepare mesoporous and acidic SiO2-Al2O3-NiO mixed oxide catalysts, which were then evaluated in ethylene oligomerization. The samples prepared by the NHSG ether route showed better activity than those prepared by the NHSG alcohol route in the oligomerization of ethylene at 150 °C. [ABSTRACT FROM AUTHOR]

This study systematically evaluates fluorine‐containing materials with varying compositions of K, Al, Co, Cu, Mg, and Zn as catalysts for glycerol oligomerization. Comprehensive analyses were conducted for all of the catalysts, considering their structural, compositional, morphological characteristics, and basicity, to understand them in greater depth. Among these analyses, gas chromatography was employed to examine the composition of the reaction products. The investigation extended to a recycling study under optimized conditions. Thermogravimetric analysis and X‐ray photoelectron spectroscopy were used to characterize the spent catalysts. Catalytic activity was found to be influenced strongly by the fluorine content, demonstrating remarkable performance for the materials containing fluoroperovskites such as KMgF3 in the catalyst KMgAFC, and K2ZnF6 in KZAFC. Remarkably, KZAFC with 20% fluorine exhibited superior glycerol conversion (68%) and selectivity for diglycerol (27%). Comparative analysis with ZnAl‐layered double hydroxide highlighted the positive impact of fluorine on catalytic activity. Introducing a calcination step in the catalyst recovery process also demonstrated improved activity during recycling. Interestingly, KZAFC exhibited stability over four reaction cycles, presenting an economic advantage over homogeneous catalysts. The study also shed light on the potential fluorine loss at the surface and potassium leaching into reaction products, correlating these phenomena with the observed decline in activity. These comprehensive findings contribute significantly to advancing sustainable glycerol valorization through heterogeneous catalysis. [ABSTRACT FROM AUTHOR]

Chemical modifications of proteins induced by ambient ozone (O 3) and nitrogen oxides (NO x) are of public health concerns due to their potential to trigger respiratory diseases. The laboratory and environmental exposure systems have been widely used to investigate their relevant mechanism in the atmosphere. Using bovine serum albumin (BSA) as a model protein, we evaluated the two systems and aimed to reduce the uncertainties of both the reactants and products in the corresponding kinetic study. In the laboratory simulation system, the generated gaseous pollutants showed negligible losses. Ten layers of BSA were coated on the flow tube with protein extraction recovery of 87.4%. For environmental exposure experiment, quartz fiber filter was selected as the upper filter with low gaseous O 3 (8.0%) and NO 2 (1.7%) losses, and cellulose acetate filter was appropriate for the lower filter with protein extraction efficiency of 95.2%. The protein degradation process was observed without the exposure to atmospheric oxidants and contributed to the loss of protein monomer mass fractions, while environmental factors (e.g., molecular oxygen and ultraviolet) may cause greater protein monomer losses. Based on the evaluation, the study exemplarily applied the two systems to protein modification and both showed that O 3 promotes the protein oligomerization and nitration, while increased temperature can accelerate the oligomerization and increased relative humidity can inhibit the nitration in the environmental exposure samples. The developed laboratory and environmental systems are suitable for studying protein modifications formed under different atmospheric conditions. A combination of the two will further reveal the actual mechanism of protein modifications. [Display omitted] [ABSTRACT FROM AUTHOR]

As a model of self-assembly from disordered monomers to fibrils, the amyloid-β fragment Aβ16-22 was subject to past numerous experimental and computational studies. Because dynamics information between milliseconds and seconds cannot be assessed by both studies, we lack a full understanding of its oligomerization. Lattice simulations are particularly well suited to capture pathways to fibrils. In this study, we explored the aggregation of 10 Aβ16–22 peptides using 65 lattice Monte Carlo simulations, each simulation consisting of 3 × 109 steps. Based on a total of 24 and 41 simulations that converge and do not converge to the fibril state, respectively, we are able to reveal the diversity of the pathways leading to fibril structure and the conformational traps slowing down the fibril formation. [ABSTRACT FROM AUTHOR]

Mutations in the TP53 tumor suppressor gene are the most abundant genetic occurrences in cancer. Some of these mutations lead to loss of function of p53 protein, some are gain of function, and some variants are hypomorphic (partially functional). Currently, there is no clinical distinction between different p53 mutations and cancer therapy or prognosis. Mutations in the oligomerization domain of p53 appear to be quite distinct in function, compared to mutations in the DNA binding domain. Here we show that, like other p53 oligomerization domain mutants, the Ashkenazi-specific G334R mutant accumulates to very high levels in cells and is significantly impaired for the transactivation of canonical p53 target genes. Surprisingly, we find that this mutant retains the ability to bind to consensus p53 target sites. A mouse model reveals that mice containing the G334R variant show increased predisposition to cancer, but only a fraction of these mice develop late-onset cancer. We show that the G334R variant retains the ability to interact with the SP1 transcription factor and contributes to the transactivation of joint SP1-p53 target genes. The combined evidence indicates that G334R is a unique oligomerization domain mutant that retains some tumor suppressor function. [ABSTRACT FROM AUTHOR]

A series of novel asymmetric alkyl P‐substituted bis(phosphanyl)amine (PNP) Ph2PN (cyclopentyl) PR1R2‐type L1–L5 ligands and these corresponding Ni(II) precatalysts C1–C5 were synthesized and characterized. The structures of these complexes were confirmed by using 1H‐, 31P‐, 13C‐NMR, FT‐IR, and elemental analysis. Using ethylaluminum dichloride (EADC) as a cocatalyst, nickel complexes exhibited high activity in elective ethylene oligomerization, with the main products being dimers and a small number of trimers. Under optimized conditions of 60°C and 1.0 MPa ethylene pressure, C4, bearing a diisopropylphosphoryl group, exhibited highest catalytic activity of 1342.9 kg·g Ni−1·h−1 with 85.2% C4 and 14.8% C6 products selectivity, while C2, bearing a diethylphosphonyl group, showed catalytic activity of 596.4 kg·g Ni−1·h−1 with 88.2% C4 and 11.8% C6 product selectivity. Single crystal analysis offered a more comprehensive insight into the subtle effects of alkyl P‐substituted in the scaffold of C2 and C4 ligands on catalytic activity. Density functional theory (DFT) calculations indicated that lower energy of the LUMO in the C4A intermediate enhances the activity of ethylene oligomerization. It provides a new method for purposefully designing ligands for ethylene oligomerization with high catalytic activity. [ABSTRACT FROM AUTHOR]

The Cossee–Arlman mechanism of nickel-catalyzed oligomerization and dimerization with various N∩N-type ligands was studied using the DFT method. For the L1 ligands (L1 = 2,9-disubstituted 1,10-phenanthroline), the dimerization energy barriers for R = Me and R = Ph are about 17.9 and 15.8 kcal mol−1, respectively. However, the presence of Ph substituents at positions 2 and 9 of the L1 ligand reduces the free energy barriers for the dimerization and trimerization processes by approximately 2.1 and 8.1 kcal mol−1, respectively. Therefore, the Ph substituents prevent the removal of β-H from 1-butene, thus promoting the formation of 1-hexene. This result is consistent with experimental observations. In the case of the L2 ligands (L2 = substituted 2-benzoxazole-pyridines) with R1 = H and R2 = H or Me, and R3 = H, the calculated dimerization energy barriers for the systems (H-H) and (H-Me) are about 12.8 and 20.5 kcal mol−1, respectively. The energy barrier for the system with R1 = H and R2 = R3 = Me (Me-Me) is about 20.9 kcal mol−1. Thus, the activity of these systems towards the formation of 1-butene can be arranged as (H-H) > (H-Me) > (Me-Me). As for L3 ligands (L3 = 2-benzimidazolylpyridine derivatives), six systems with R1 = H, Me, tBu; R2 = H, Me, were studied. The calculated dimerization energy barrier values indicate that the (H-H), (H-Me), and (H-tBu) systems (10.8, 11.1, and 10.9 kcal mol−1, respectively) are more active than the (Me-H), (Me-Me) and (Me-tBu) systems (18.8, 19.1 and 19.0 kcal mol−1, respectively). Finally, for the L4 ligand (L4 = 2-benzoimidazol-8-alkylquinoline derivatives), nine systems were studied, divided into three groups: A system (R1 = H and R2 = H or Me or Et), B system R1 = Me with identical R2 substituents, and C system (R1 = Et with identical R2 substituents). Based on the values of the calculated energy barriers for dimerization and trimerization, the B system shows higher activity than the other systems. [ABSTRACT FROM AUTHOR]

Clostridioides (formerly Clostridium) difficile is a leading cause of infectious diarrhea associated with antibiotic therapy. The ability of this anaerobic pathogen to acquire enough iron to proliferate under iron limitation conditions imposed by the host largely determines its pathogenicity. However, since high intracellular iron catalyzes formation of deleterious reactive hydroxyl radicals, iron uptake is tightly regulated at the transcriptional level by the ferric uptake regulator Fur. Several studies relate lacking a functional fur gene in C. difficile cells to higher oxidative stress sensitivity, colonization defect and less toxigenicity, although Fur does not appear to directly regulate either oxidative stress response genes or pathogenesis genes. In this work, we report the functional characterization of C. difficile Fur and describe an additional oxidation sensing Fur‐mediated mechanism independent of iron, which affects Fur DNA‐binding. Using electrophoretic mobility shift assays, we show that Fur binding to the promoters of fur, feoA and fldX genes, identified as iron and Fur‐regulated genes in vivo, is specific and does not require co‐regulator metal under reducing conditions. Fur treatment with H2O2 produces dose‐dependent soluble high molecular weight species unable to bind to target promoters. Moreover, Fur oligomers are dithiotreitol sensitive, highlighting the importance of some interchain disulfide bond(s) for Fur oligomerization, and hence for activity. Additionally, the physiological electron transport chain NADPH‐thioredoxin reductase/thioredoxin from Escherichia coli reduces inactive oligomerized C. difficile Fur that recovers activity. In conjunction with available transcriptomic data, these results suggest a previously underappreciated complexity in the control of some members of the Fur regulon that is based on Fur redox properties and might be fundamental for the adaptive response of C. difficile during infection. [ABSTRACT FROM AUTHOR]

Brønsted acid zeolites catalyze alkene oligomerization reactions, an important route to produce fuels and chemicals from light hydrocarbon feedstocks. Propene dimerization rates (per H+, 503 K) decrease monotonically with increasing crystallite size in MFI zeolites because heavy oligomer products remain occluded within microporous voids and restrict intrazeolite diffusion of reactants and products. Here, we show that the preferential zoning of framework Al centers and their associated H+ sites toward exterior surfaces of MFI crystallites in an "egg-shell" architecture minimizes the extent of diffusion-enhanced secondary reactions within a given crystallite, which increases both propene dimerization rates (per H+) and selectivity to true oligomer products. These results show that tailoring Al distributions to be spatially zoned toward external surfaces of medium-pore zeolite crystallites is efficacious at minimizing diffusion path lengths to increase alkene oligomerization rates and selectivity to true oligomer products. [ABSTRACT FROM AUTHOR]

This study presents in a systematic manner the key modeling results corroborated by experimental biophysical data and obtained by the authors during long-term research on bitopic (single-pass) membrane proteins (BMPs), which are the crucial elements of cell signaling. The manuscript does not claim to be a comprehensive review of the subject of interest, whereby the authors did not aim to describe accurately the current state of the art, given the numerous reliable publications. Rather, this is an essay illustrating the authors' understanding of the basic principles of organization of protein transmembrane domains (TMDs) and of their contribution to the cell functioning. Among the key topics highlighted in the present study are the fine-tuned processes of TMD oligomerization and the direct contribution from the dynamic membrane environment to this process, as well as the key role of TMD in the functioning of cell receptors and mutual relations between all the components of proteinmembrane complexes during the signal transduction in normal and pathological conditions. [ABSTRACT FROM AUTHOR]

Pathogenic Bacillus and clostridial (i.e., Clostridium and Clostridioides) bacteria express a diverse repertoire of effector proteins to promote disease. This includes production of binary toxins, which enter host epithelial cells and seriously damage the intestinal tracts of insects, animals, and humans. In particular, binary toxins form an AB-type complex composed of a catalytic subunit that is toxic (A) and an oligomeric cell-binding and delivery subunit (B), where upon delivery of A into the cytoplasm of the host cell it catalytically ADP-ribosylates actin and rapidly induces host cell death. In this review, binary toxins expressed by Bacillus thuringiensis, Clostridioides difficile, and Clostridium perfringens will be discussed, with particular focus placed upon the structural elucidations of their respective B subunits and how these findings help to deconvolute how toxic enzyme delivery into target host cells is achieved by these deadly bacteria. [ABSTRACT FROM AUTHOR]

This paper investigates the use of loaded Co/BETA molecular sieve catalysts for the selective oligomerization of isobutylene. The physicochemical properties of Co/BETA molecular sieves were characterized using XRD, BET, NH3-TPD, FT-IR, XPS, and Py-FTIR. The effects of different active component loadings, reaction temperatures, and reaction air velocities on the selective oligomerization of isobutylene were investigated in a fixed-bed reactor. The results showed that the catalytic effect was optimal when the Co loading was 6%, the reaction temperature was 60 °C, the reaction pressure was 1 MPa, and the reaction air speed was 1 h−1. The isobutylene conversion was greater than 74%, the C8= selectivity was approximately 70%, and the C8= yield reached 51.69% with minimal loss of n-butene, providing good catalytic capacity and efficiency. [ABSTRACT FROM AUTHOR]

C-Glycosyl amino acids are a group of C-glycosides in which a carbohydrate molecule is attached to the side chain or backbone of the amino acid via a C–C bond. Despite the numerous methods that have been developed for their synthesis, the C-glycosyl α-amino acids and their oligomers are relatively unexplored. In this work, we presented a protocol for the synthesis of oligomers containing alternating C-glycosyl α-amino acids and proteinogenic α-amino acids. The methodology is based on the modification of α-acyloxyamides obtained from the Passerini reaction using α- D -galactopyranose- and α- L -sorbofuranose-derived aldehydes as C-glycosyl donors. The protocol enabled the synthesis of homo- and heterochiral tetramers, and homo- and heterovalent tetramers in very good yields. [ABSTRACT FROM AUTHOR]

Borane catalysis has emerged as a powerful technology in epoxide polymerization. Still, the structure‐activity correlations for these catalysts are not fully understood to date, especially regarding compounds with nonionic backbones. Thus, in this work, 13 different borane catalysts of this respective type are described and investigated for their epoxide oligomerization and polymerization performance, using propylene oxide (PO), 1‐butylene oxide (BO) and allyl glycidyl ether (AGE) as monomers. Structurally, special emphasis is put on catalysts with different linker lengths and linker flexibilities as well as the introduction of more than two borane functionalities. Importantly, this screening is conducted both under typical polymerization conditions as well as under the chain transfer agent (CTA)‐rich conditions relevant for large‐scale production. It is found that suitable preorganization of the borane groups, such as present in biphenyl derivatives, offers a simple route to high‐performing catalysts and quantitative monomer conversion of the investigated epoxides. Furthermore, it is demonstrated that a diborane‐catalyzed oligomerization can be kept active over weeks, whereby repeated addition of monomer batches (14 steps) constantly results in full conversion and well‐defined oligoethers, underlining the practical potential of this method. The absence of co‐initiating counter ions is suggested as an inherent advantage of nonionic catalysts. [ABSTRACT FROM AUTHOR]

The arginyl-transferase ATE1 is a tRNA-dependent enzyme that covalently attaches an arginine molecule to a protein substrate. Conserved from yeast to humans, ATE1 deficiency in mice correlates with defects in cardiovascular development and angiogenesis and results in embryonic lethality, while conditional knockouts exhibit reproductive, developmental, and neurological deficiencies. Despite the recent revelation of the tRNA binding mechanism and the catalytic cycle of yeast ATE1, the structure-function relationship of ATE1 in higher organisms is not well understood. In this study, we present the three-dimensional structure of human ATE1 in an apo-state and in complex with its tRNA cofactor and a peptide substrate. In contrast to its yeast counterpart, human ATE1 forms a symmetric homodimer, which dissociates upon binding of a substrate. Furthermore, human ATE1 includes a unique and extended loop that wraps around tRNAArg, creating extensive contacts with the T-arm of the tRNA cofactor. Substituting key residues identified in the substrate binding site of ATE1 abolishes enzymatic activity and results in the accumulation of ATE1 substrates in cells. ATE1 is an essential gene in mammals and is recognized as a master regulator of cells. Here, the authors describe structural insights into human ATE1, revealing mechanisms that regulate arginylation activity in cells. [ABSTRACT FROM AUTHOR]

Aminopeptidases with varied substrate specificities are involved in different crucial physiological processes of cellular homeostasis. They also have wide applications in food and pharma industries. Within the bacterial cell, broad specificity aminopeptidases primarily participate in the recycling of amino acids by degrading oligopeptides generated via primary proteolysis mediated by cellular ATP‐dependent proteases. However, in bacteria, a truly broad specificity enzyme, which can cleave off acidic, basic, Gly and hydrophobic amino acid residues, is extremely rare. Here, we report structure–function of a putative glycyl aminopeptidase (M61xc) from Xanthomonas campestris pv campestris (Xcc) belonging to the M61 peptidase family. The enzyme exhibits broad specificity and cleaves Ala, Leu, Asp, Glu, Met, Ser, Phe, Tyr, Gly, Arg, and Lys at the N terminus, optimally of peptides with a length of 3–7 amino acids. Further, we report the high‐resolution crystal structure of M61xc in the apo form (2.1 Å) and bestatin‐bound form (1.95 Å), detailing its catalytic and substrate preference mechanisms. Comparative analysis of enzyme activity in crude cell extracts from both wild‐type and m61xc‐knockout mutant strains of Xcc has elucidated the unique intracellular role of M61xc. This study suggests that M61xc is the exclusive enzyme in these bacteria that is responsible for liberating Asp/Glu residues from the N‐termini of peptides. Also, in view of its broad specificity and peptide degradation ability, it could be considered equivalent to M1 or other oligomeric peptidases from families like M17, M18, M42 or S9, who have an important auxiliary role in post‐proteasomal protein degradation in prokaryotes. [ABSTRACT FROM AUTHOR]

Silicoaluminophosphate molecular sieves SAPO‑11 were obtained from gels with different silica contents. Silicoaluminophosphates as cubic crystals with 0.5 mm diameter were obtained from gels with SiO2/Al2O3 ratio equal to 0.1, while samples with the ratio SiO2/Al2O3 = 0.5 were obtained as extended prisms with 1‑2 mm diameter. Increasing the SiO2/Al2O3 ratio from 0.1 to 0.4 leads a greater amount of acid sites and a decrease in the specific surface. The conversion of a‑methylstyrene as well as the yield of linear dimers and cyclic trimers both increase with an increasing amount of acid sites and greater external surface. [ABSTRACT FROM AUTHOR]

Summary: Nucleotide‐binding domain and leucine‐rich repeat (NLR) proteins with pathogen sensor activities have evolved to initiate immune signaling by activating helper NLRs. However, the mechanisms underpinning helper NLR activation by sensor NLRs remain poorly understood. Although coiled coil (CC) type sensor NLRs such as the Potato virus X disease resistance protein Rx have been shown to activate the oligomerization of their downstream helpers NRC2, NRC3 and NRC4, the domains involved in sensor–helper signaling are not known.Here, we used Agrobacterium tumefaciens‐mediated transient expression in Nicotiana benthamiana to show that the nucleotide‐binding (NB) domain within the NB‐ARC of Rx is necessary and sufficient for oligomerization and immune signaling of downstream helper NLRs. In addition, the NB domains of the disease resistance proteins Gpa2 (cyst nematode resistance), Rpi‐amr1, Rpi‐amr3 (oomycete resistance) and Sw‐5b (virus resistance) are also sufficient to activate their respective downstream NRC helpers.Using transient expression in the lettuce (Lactuca sativa), we show that Rx (both as full length or as NB domain truncation) and its helper NRC2 form a minimal functional unit that can be transferred from solanaceous plants (lamiids) to Campanulid species.Our results challenge the prevailing paradigm that NLR proteins exclusively signal via their N‐terminal domains and reveal a signaling activity for the NB domain of NRC‐dependent sensor NLRs. We propose a model in which helper NLRs can perceive the status of the NB domain of their upstream sensors. [ABSTRACT FROM AUTHOR]

An approach towards incorporating varied degrees of steric profiles around the ligand's backbone, which were envisaged to alter the catalytic paths leading to targeted 1-C8/1-C6 olefin products, were explored. Cr-pre-catalysts designed with PNP ligands comprising a fused aryl moiety were delivered at a relatively higher C8 olefin selectivity (up to 74.6 wt% and C8/C6 of 3.4) when the N-connection to the aromatic unit was placed at the 2-position. A relatively higher C6 olefin selectivity (up to 33.7 wt% and C8/C6 of 1.9) was achieved with the PNP unit anchored at the 1- or 6-position. Based on detailed catalytic studies, we confirm the fact that by introducing a controlled degree of bulkiness on the N-site through a judicious selection of the N-aryl moiety of different sizes, the selectivity of the targeted olefin product could be tuned in a rational manner. [ABSTRACT FROM AUTHOR]

Multivalency in lectins plays a pivotal role in influencing glycan cross-linking, thereby affecting lectin functionality. This multivalency can be achieved through oligomerization, the presence of tandemly repeated carbohydrate recognition domains, or a combination of both. Unlike lectins that rely on multiple factors for the oligomerization of identical monomers, tandem-repeat lectins inherently possess multivalency, independent of this complex process. The repeat domains, although not identical, display slightly distinct specificities within a predetermined geometry, enhancing specificity, affinity, avidity and even oligomerization. Despite the recognition of this structural characteristic in recently discovered lectins by numerous studies, a unified criterion to define tandem-repeat lectins is still necessary. We suggest defining them multivalent lectins with intrachain tandem repeats corresponding to carbohydrate recognition domains, independent of oligomerization. This systematic review examines the folding and phyletic diversity of tandem-repeat lectins and refers to relevant literature. Our study categorizes all lectins with tandemly repeated carbohydrate recognition domains into nine distinct folding classes associated with specific biological functions. Our findings provide a comprehensive description and analysis of tandem-repeat lectins in terms of their functions and structural features. Our exploration of phyletic and functional diversity has revealed previously undocumented tandem-repeat lectins. We propose research directions aimed at enhancing our understanding of the origins of tandem-repeat lectin and fostering the development of medical and biotechnological applications, notably in the design of artificial sugars and neolectins. [ABSTRACT FROM AUTHOR]

3',5'-cyclic uridine monophosphate (cUMP) and 3',5'-cyclic cytidine monophosphate (cCMP) have been established as bacterial second messengers in the phage defense system, named pyrimidine cyclase system for anti-phage resistance (Pycsar). This system consists of a pyrimidine cyclase and a cyclic pyrimidine receptor protein. However, the molecular mechanism underlying cyclic pyrimidine synthesis and recognition remains unclear. Herein, we determine the crystal structures of a uridylate cyclase and a cytidylate cyclase, revealing the conserved residues for cUMP and cCMP production, respectively. In addition, a distinct zinc-finger motif of the uridylate cyclase is identified to confer substantial resistance against phage infections. Furthermore, structural characterization of cUMP receptor protein PycTIR provides clear picture of specific cUMP recognition and identifies a conserved N-terminal extension that mediates PycTIR oligomerization and activation. Overall, our results contribute to the understanding of cyclic pyrimidine-mediated bacterial defense. Here, the author present crystal structures of uridylate and cytidylate cyclases, uncovering the molecular basis for pyrimidine recognition, receptor oligomerization and activation contributing to our understanding of cUMP-mediated bacterial defence. [ABSTRACT FROM AUTHOR]

The pincer complexes [NiIIBr(CNC)]Br (4), [CrIIIBr3(CNC)] (5 a) and [CrIIIBr2.3Cl0.7(CNC)] (5 b), where CNC=3,3′‐(pyridine‐2,6‐diyl)bis(1‐mesityl‐3,4,5,6‐tetrahydropyrimidin‐2‐ylidene), were obtained from the novel ligand CNC, generated in situ from the precursor (CHNCH)Br2 and [NiIIBr2(PPh3)2] or from [CrII{N(SiMe3)2}2(THF)2] and (CHNCH)Br2 by aminolysis, respectively. The tetrahedrally distorted square planar (τ4≅0.30) geometry and the singlet ground state of Ni in 4 were attributed to steric constraints of the CNC backbone. Computational methods highlighted the dependence of the coordination geometry and the singlet‐triplet energy difference on the size of the N‐substituent of the tetrahydropyrimidine wingtips and contrasted it to the situation in 5‐membered imidazolin‐2‐ylidene pincer analogues. The octahedral CrIII metal center in 5 a and 5 b is presumably formed after one electron oxidation from CH2Cl2. 4/MAO and 5 a/MAO were catalysts of moderate activity for the oligomerization and polymerization of ethylene, respectively. The analogous (CH^N^CH)Br2 precursor, where (CH^N^CH)=3,3′‐(pyridine‐2,6‐diylbis(methylene))bis(1‐mesityl‐3,4,5,6‐tetrahydropyrimidin‐1‐ium), was also prepared, however its coordination chemistry was not studied due to the inherent instability of the resulting free C^N^C ligand. [ABSTRACT FROM AUTHOR]

Arc (also known as Arg3.1) is an activity-dependent immediate early gene product enriched in neuronal dendrites. Arc plays essential roles in long-term potentiation, long-term depression, and synaptic scaling. Although its mechanisms of action in these forms of synaptic plasticity are not completely well established, the activities of Arc include the remodeling of the actin cytoskeleton, the facilitation of AMPA receptor (AMPAR) endocytosis, and the regulation of the transcription of AMPAR subunits. In addition, Arc has sequence and structural similarity to retroviral Gag proteins and self-associates into virus-like particles that encapsulate mRNA and perhaps other cargo for intercellular transport. Each of these activities is likely to be influenced by Arc's reversible self-association into multiple oligomeric species. Here, we used mass photometry to show that Arc exists predominantly as monomers, dimers, and trimers at approximately 20 nM concentration in vitro. Fluorescence fluctuation spectroscopy revealed that Arc is almost exclusively present as low-order (monomer to tetramer) oligomers in the cytoplasm of living cells, over a 200 nM to 5 μM concentration range. We also confirmed that an α-helical segment in the N-terminal domain contains essential determinants of Arc's self-association. [ABSTRACT FROM AUTHOR]