Search

Enhancers have critical functions in the precise, spatiotemporal control of transcription during development. It is thought that enhancer grammar, or the characteristics and arrangements of transcription factor binding sites, underlie the specific functions of developmental enhancers. In this study, we sought to identify grammatical constraints that direct enhancer activity in the naïve state of pluripotency, focusing on the enhancers for the naïve-state specific gene, Klf4. Using a combination of biochemical tests, reporter assays, and endogenous mutations in mouse embryonic stem cells, we have studied the binding sites for the transcription factors OCT4 and SOX2. We have found that the three Klf4 enhancers contain suboptimal OCT4-SOX2 composite binding sites. Substitution with a high-affinity OCT4-SOX2 binding site in Klf4 enhancer E2 rescued enhancer function and Klf4 expression upon loss of the ESRRB and STAT3 binding sites. We also observed that the low-affinity of the OCT4-SOX2 binding site is crucial to drive the naïve-state specific activities of Klf4 enhancer E2. Altogether, our work suggests that the affinity of OCT4-SOX2 binding sites could facilitate enhancer functions in specific states of pluripotency. [ABSTRACT FROM AUTHOR]

[Display omitted] Ion channel activation upon ligand gating triggers a myriad of biological events and, therefore, evolution of ligand gating mechanism is of fundamental importance. TRPM2, a typical ancient ion channel, is activated by adenosine diphosphate ribose (ADPR) and calcium and its activation has evolved from a simple mode in invertebrates to a more complex one in vertebrates, but the evolutionary process is still unknown. Molecular evolutionary analysis of TRPM2s from more than 280 different animal species has revealed that, the C-terminal NUDT9-H domain has evolved from an enzyme to a ligand binding site for activation, while the N-terminal MHR domain maintains a conserved ligand binding site. Calcium gating pattern has also evolved, from one Ca2+-binding site as in sea anemones to three sites as in human. Importantly, we identified a new group represented by olTRPM2, which has a novel gating mode and fills the missing link of the channel gating evolution. We conclude that the TRPM2 ligand binding or activation mode evolved through at least three identifiable stages in the past billion years from simple to complicated and coordinated. Such findings benefit the evolutionary investigations of other channels and proteins. [ABSTRACT FROM AUTHOR]

Cyclo (Phe-Pro) (cFP), a cyclic dipeptide with notable antifungal, antibacterial, and antiviral properties, shows great promise for biological control of plant diseases. Produced as a byproduct by non-ribosomal peptide synthetases (NRPS), the regulatory mechanism of cFP biosynthesis remains unclear. In a screening test of 997 Tn5 mutants of Burkholderia seminalis strain R456, we identified eight mutants with enhanced antagonistic effects against Fusarium graminearum (Fg). Among these, mutant 88's culture filtrate contained cFP, confirmed through HPLC and LC-MS, which actively inhibited Fg. The gene disrupted in mutant 88 is part of the Dct transport system (Dct-A, -B, -D), responsible for C4-dicarboxylate transport. Knockout mutants of Dct genes exhibited higher cFP levels than the wild type, whereas complementary strains showed no significant difference. Additionally, the presence of exogenous C4-dicarboxylates reduced cFP production in wild type R456, indicating that these substrates negatively regulate cFP synthesis. Given that cFP synthesis is related to NRPS, we previously identified an NRPS cluster in R456, horizontally transferred from algae. Specifically, knocking out gene 2061 within this NRPS cluster significantly reduced cFP production. A Fur box binding site was predicted upstream of gene 2061, and yeast one-hybrid assays confirmed Fur protein binding, which increased with additional C4-dicarboxylates. Knockout of the Fur gene led to up-regulation of gene 2061 and increased cFP production, suggesting that C4-dicarboxylates suppress cFP synthesis by enhancing Fur-mediated repression of gene 2061. [ABSTRACT FROM AUTHOR]

Excessive activity of the tyrosinase enzyme during melanogenesis results in hyperpigmentation in the skin. To address this issue, there is a need to develop effective tyrosinase inhibitors as a treatment for hyperpigmentation. In this study, we synthesized some novel 4H-chromene-3-carbonitrile compounds (6a-o) and assessed their inhibitory activities against tyrosinase, comparing them with kojic acid, which is known as a positive control. Compound 6f emerged as the most effective inhibitor, with an IC50 of 35.38 ± 2.12 µM. Kinetic studies of 6f exhibited competitive inhibition, with Ki = 16.15 µM. Molecular docking studies highlighted the importance of π-π stacking and hydrogen bonding interactions within the binding site. Molecular dynamics simulations showed that the R-enantiomer 6f exhibited superior binding stability compared to the S-enantiomer, with a lower standard deviation of RMSD and more persistent interactions with the key active site residues. These findings underscore the potential of the R-enantiomer of compound 6f as a potent tyrosinase inhibitor and provide insights for developing effective treatments for hyperpigmentation and related skin conditions. [ABSTRACT FROM AUTHOR]

Cyclopamine, a natural alkaloid, can act as an agonist when it binds to the Cysteine-Rich Domain (CRD) of Smoothened receptor and as an antagonist when it binds to the Transmembrane Domain (TMD). To study the effect of cyclopamine binding to each site experimentally, mutations in the other site are required. Hence, simulations are critical for understanding the WT activity due to binding at different sites. Using multi-milliseconds long aggregate MD simulations combined with Markov state models and machine learning, we explore the dynamic behavior of cyclopamine's interactions with different domains of WT SMO. A higher population of the active state at equilibrium, a lower free energy barrier of ~2 kcal/mol, and expansion of hydrophobic tunnel to facilitate cholesterol transport agrees with cyclopamine's agonistic behavior when bound to CRD. A higher population of the inactive state at equilibrium, a higher free energy barrier of ~4 kcal/mol and restricted hydrophobic tunnel shows cyclopamine's antagonistic behavior when bound to TMD. With cyclopamine bound to both sites, there is a slightly larger inactive population at equilibrium and an increased free energy barrier (~3.5 kcal/mol) exhibiting an overall weak antagonistic effect. These findings show cyclopamine's domain-specific modulation of SMO regulates Hedgehog signaling and cholesterol transport. Millisecond scale MD simulations explain how cyclopamine modulates human Smoothened receptor activity based on different binding positions. [ABSTRACT FROM AUTHOR]

A previous study using Thermostable Group II Intron Reverse Transcriptase sequencing (TGIRT-seq) found human plasma contains short (≤300 nt) structured full-length excised linear intron (FLEXI) RNAs with potential to serve as blood-based biomarkers. Here, TGIRT-seq identified >9,000 different FLEXI RNAs in human cell lines, including relatively abundant FLEXIs with cell-type-specific expression patterns. Analysis of public CLIP-seq datasets identified 126 RNA-binding proteins (RBPs) that have binding sites within the region corresponding to the FLEXI or overlapping FLEXI splice sites in pre-mRNAs, including 53 RBPs with binding sites for ≥30 different FLEXIs. These included splicing factors, transcription factors, a chromatin remodeling protein, cellular growth regulators, and proteins with cytoplasmic functions. Analysis of ENCODE datasets identified subsets of these RBPs whose knockdown impacted FLEXI host gene mRNA levels or proximate alternative splicing, indicating functional interactions. Hierarchical clustering identified six subsets of RBPs whose FLEXI binding sites were co-enriched in six subsets of functionally related host genes: AGO1-4 and DICER, including but not limited to agotrons or mirtron pre-miRNAs; DKC1, NOLC1, SMNDC1, and AATF (Apoptosis Antagonizing Transcription Factor), including but not limited to snoRNA-encoding FLEXIs; two subsets of alternative splicing factors; and two subsets that included RBPs with cytoplasmic functions (e.g., LARP4, PABPC4, METAP2, and ZNF622) together with regulatory proteins. Cell fractionation experiments showed cytoplasmic enrichment of FLEXI RNAs with binding sites for RBPs with cytoplasmic functions. The subsets of host genes encoding FLEXIs with binding sites for different subsets of RBPs were co-enriched with non-FLEXI other short and long introns with binding sites for the same RBPs, suggesting overarching mechanisms for coordinately regulating expression of functionally related genes. Our findings identify FLEXIs as a previously unrecognized large class of cellular RNAs and provide a comprehensive roadmap for further analyzing their biological functions and the relationship of their RBPs to cellular regulatory mechanisms. Author summary: We characterized a previously unrecognized, large class of full-length excised liner intron (FLEXI) RNAs that are ≤300 nucleotides in length and relatively stable in human cells and plasma. These included subsets of FLEXIs with binding sites for different subsets of RNA-binding proteins (RBPs) that have different cellular functions and are co-enriched in subsets of functionally related genes with other short and long introns with binding sites for the same RBPs, potentially enabling coordinate regulation of different gene sets. Many of the proteins that have binding sites in different subsets of FLEXIs were also identified as interacting with each other by STRING protein-network analysis, potentially enabling co-localization of subsets of proteins to different intracellular locations, including the cytoplasm. Our findings provide a comprehensive road map for further analysis of the functions of FLEXIs and their associated RBPs and for the identification of FLEXIs that can serve as biomarkers in human cells and plasma. [ABSTRACT FROM AUTHOR]

2D covalent organic frameworks (COFs) are attractive for fluorescence sensing due to their lightweight, robust, and highly ordered porous structures. However, the highly conjugated structures between adjacent layers of covalent organic frameworks can often result in aggregation‐caused quenching (ACQ) properties. Here, the study designs two flexible hydrazone‐linked COFs to suppress ACQ effects, thereby enhancing their luminescent activities. Furthermore, the high density of nitrogen and oxygen atoms on these flexible walls serves as binding sites for hydrogen bonding interactions, indicating sensitivity and selectivity towards 2,4,6‐trinitrophenol detection. [ABSTRACT FROM AUTHOR]

Cross‐species prediction of TF binding remains a major challenge due to the rapid evolutionary turnover of individual TF binding sites, resulting in cross‐species predictive performance being consistently worse than within‐species performance. In this study, a novel Nucleotide‐Level Deep Neural Network (NLDNN) is first proposed to predict TF binding within or across species. NLDNN regards the task of TF binding prediction as a nucleotide‐level regression task, which takes DNA sequences as input and directly predicts experimental coverage values. Beyond predictive performance, it also assesses model performance by locating potential TF binding regions, discriminating TF‐specific single‐nucleotide polymorphisms (SNPs), and identifying causal disease‐associated SNPs. The experimental results show that NLDNN outperforms the competing methods in these tasks. Then, a dual‐path framework is designed for adversarial training of NLDNN to further improve the cross‐species prediction performance by pulling the domain space of human and mouse species closer. Through comparison and analysis, it finds that adversarial training not only can improve the cross‐species prediction performance between humans and mice but also enhance the ability to locate TF binding regions and discriminate TF‐specific SNPs. By visualizing the predictions, it is figured out that the framework corrects some mispredictions by amplifying the coverage values of incorrectly predicted peaks. [ABSTRACT FROM AUTHOR]

Pores containing molecular adapters provide internal selective binding sites, thereby allowing the stochastic sensing of analytes. Herein, we demonstrate that semiaza‐bambusuril (BU) acts as a non‐covalent molecular adapter when lodged within the lumen of the wild‐type α‐hemolysin (WT‐αHL) protein pore. Because the bambusurils are recognized as anion receptors, the anion binding site within the adapter‐nanopore complex allows the detection of chloride anions, thus converting a non‐selective pore into an anion sensor. [ABSTRACT FROM AUTHOR]

The postsynthetic metalation (PSM) of metal-organic frameworks (MOFs) with intrinsic metal binding sites is an intriguing strategy to introduce catalytic function into MOFs. The spatial distribution of the catalytic sites within the MOF crystal will affect the efficiency of the material, but the factors that govern depth distribution of the introduced metal sites are often not well understood. Herein, we employ Rutherford backscattering spectrometry (RBS) to investigate the metal distribution in a series of post-synthetically metalated mixed linker bpdc/BPY UiO-67 (UiO = Universitet i Oslo, bpdc = biphenyl-dicarboxylate, BPY = 2,2'-bipyridine-5,5'-dicarboxylate) single crystals as a function of linker ratio and metalation time. The RBS spectra reveal large differences in the depth distribution of inserted Ni2+ ions, and core/shell architectures are observed in high BPY materials at shorter incubation times. The incubation times to achieve uniform metal incorporation increases with increasing BPY ratios in the materials, suggesting that the presence of the BPY linkers slow down metal uptake. We propose a combination of ionic interactions and pore clogging, where coordinated ions reduce the available pore space for further ions to diffuse deeper into the framework as reasons for the observed trends. The observations are likely relevant for other mixed-linker MOF systems, and understanding the effect that linker ratios have on PSM and cation distribution will aid in future optimizations of catalytic MOFs. [ABSTRACT FROM AUTHOR]

Covalent organic frameworks (COFs) are a novel type of nanoporous and crystalline polymers with a precise and highly conjugated skeleton, making them promising candidates for constructing emissive materials. However, the strong high conjugation structures between adjacent layers easily lead to aggregation-caused quenching (ACQ) of emission properties. In this study, we have designed COFs with a flexible skeleton to suppress ACQ effects, enhancing their luminescence activity. In addition, the high density of nitrogen and oxygen atoms on these flexible walls serves as binding sites for hydrogen bonding interactions, indicating sensitivity and selectivity towards nitro-explosives. This strategy establishes a new approach for creating luminescent materials for chemical sensors. [ABSTRACT FROM AUTHOR]

Human serum albumin (HSA) is a multifunctional circulatory protein essential for many physiological processes including oncotic pressure maintenance, ligand/drug binding and transport, antioxidant activity, etc. Abnormal HSA levels in biological fluids have been reported in a variety of clinical disorders, making it a potential biomarker for early diagnosis. Low serum albumin levels have been linked to increased long- and short-term mortality rates in ICU patients. Therefore, quantifying HSA in biofluids such as serum and urine offers a convenient approach for the early identification of underlying clinical conditions and assessing the risk factors. Herein, we report a series of fluorescent 1,4-dihydropyridine (DHP) derivatives for the detection and quantification of HSA in biofluids. Their response towards HSA can be tuned by varying the substituents at the C-4 and the N-1 of the DHP ring. Depending on the nature of the substituents, they generated either a turn-on or ratiometric response with a LoD in low nanomolar or subnanomolar levels. A pair of enantiomers obtained by introducing a chiral center on the N-substituents highlighted the importance of stereochemistry in HSA-ligand interactions. Quantification of HSA in complex biofluids, such as blood serum and urine, was also accomplished using these probes. The high selectivity of some of the probes towards HSA over the homologous BSA allowed the discrimination of these two proteins. The preferred binding location of the probes was the hemin binding site and the detection mechanism was identified as the restriction of intramolecular rotation. Additionally, a prototype of a smartphone-integrated point-of-care device was also fabricated to demonstrate the feasibility of utilizing these probes in clinical settings. [ABSTRACT FROM AUTHOR]

Adaptation of the response to stimuli is a fundamental process for all organisms. Here, we show that the adaptation enzyme CheB methylesterase of Escherichia coli assembles to the ON state receptor array after exposure to the repellent l-isoleucine and dissociates from the array after adaptation is complete. The duration of increased CheB localization and the time of highly clockwise-biased flagellar rotation were similar and depended on the strength of the stimulus. The increase in CheB at the receptor array and the decrease in cytoplasmic CheB were both ~100 molecules, which represents 15 to 20% of the total cellular content of CheB. We confirmed that the main binding site for CheB in the ON state array is the P2 domain of phosphorylated CheA, with a second minor site being the carboxyl-terminal pentapeptide of the serine chemoreceptor. Thus, we have been able to quantify the regulation of the signal output of the receptor array by the intracellular dynamics of an adaptation enzyme. [ABSTRACT FROM AUTHOR]

Background: Locating small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many drug-discovery scenarios. Since it is not always easy to find such binding sites using conventional methods, different deep learning methods to predict binding sites out of protein structures have been developed in recent years. The existing deep learning based methods have several limitations, including (1) the inefficiency of the CNN-only architecture, (2) loss of information due to excessive post-processing, and (3) the under-utilization of available data sources. Methods: We present a new model architecture and training method that resolves the aforementioned problems. First, by layering geometric self-attention units on top of residue-level 3D CNN outputs, our model overcomes the problems of CNN-only architectures. Second, by configuring the fundamental units of computation as residues and pockets instead of voxels, our method reduced the information loss from post-processing. Lastly, by employing inter-resolution transfer learning and homology-based augmentation, our method maximizes the utilization of available data sources to a significant extent. Results: The proposed method significantly outperformed all state-of-the-art baselines regarding both resolutions—pocket and residue. An ablation study demonstrated the indispensability of our proposed architecture, as well as transfer learning and homology-based augmentation, for achieving optimal performance. We further scrutinized our model's performance through a case study involving human serum albumin, which demonstrated our model's superior capability in identifying multiple binding sites of the protein, outperforming the existing methods. Conclusions: We believe that our contribution to the literature is twofold. Firstly, we introduce a novel computational method for binding site prediction with practical applications, substantiated by its strong performance across diverse benchmarks and case studies. Secondly, the innovative aspects in our method— specifically, the design of the model architecture, inter-resolution transfer learning, and homology-based augmentation—would serve as useful components for future work. [ABSTRACT FROM AUTHOR]

Paraoxonase 1 (PON1) is an antioxidant enzyme that prevents lipid oxidation by hydrolysing lipid peroxides in the oxidised low‐density lipoprotein (LDL) structure, bound to high‐density lipoprotein (HDL) in serum, and exhibits esterase and lactonase activity. In this work, the hPON1 enzyme was purified from human serum using a hydrophobic gel with Sepharose 4B‐L‐tyrosine‐naphthylamine, and the affinity of some steroid derivatives previously isolated from fungal steroid biotransformations was examined on the pure hPON1 enzyme. The results indicate that all these derivaties activate the hPON1 enzyme to a different extent. Additionally, the binding potential of the most active five steroid derivatives to the PON1 enzyme to form a stable complex was explored through molecular docking and molecular dynamics (MD) simulation. The compounds with the highest potency in the enzymatic assay, S‐8 and S‐20, had the highest binding potential to the enzyme. The stability of the complexes formed by the two compounds was assessed and compared to the stability of the unbound enzyme structure. The enzyme‐compound complexes generally had similar stability to the unbound enzyme structure. Together with this, the MD simulation revealed that compound S‐8 would remain inside the enzyme's binding site during the simulation period, unlike compound S‐20. This situation varies according to the respective derivatives' functional groups and hydrophobic characteristics. [ABSTRACT FROM AUTHOR]

The interaction between linamarin (LIN), a cyanogenic glycoside, and human serum albumin (HSA) was studied by multiple spectroscopic techniques and molecular docking simulation. All measurements were performed under physiological conditions. The obtained results (including the binding constants, effective quenching constant and a number of binding sites) showed that the complex of HSA‐LIN is formed. The values of Stern‐Volmer constants (6.70×103, 5.53×103 and 1.95×103) indicate that fluorescence quenching of HSA was static. Results of site marker experiments showed that the binding site of LIN is mainly located in site I (subdomain IIA) of HSA. The thermodynamic parameters showed that binding process occurs spontaneously through hydrophobic interactions. Molecular docking results are in good agreement with experimental data. Furthermore, computational results revealed LIN binds in the cavity of TRP 214, that is, subdomain IIA (site I) of HSA. This comprehensive study provides a deeper insight into ligand binding in HSA which may be useful in drug design and pharmacology. [ABSTRACT FROM AUTHOR]

Heart failure (HF) is highly prevalent. Mechanisms underlying HF remain incompletely understood. Splicing factors (SF), which control pre‐mRNA alternative splicing, regulate cardiac structure and function. This study investigated regulation of the splicing factor heterogeneous nuclear ribonucleoprotein‐L (hnRNPL) in the failing heart. hnRNPL protein increased in left ventricular tissue from mice with transaortic constriction‐induced HF and from HF patients. In left ventricular tissue, hnRNPL was detected predominantly in nuclei. Knockdown of the hnRNPL homolog Smooth in Drosophila induced cardiomyopathy. Computational analysis of predicted mouse and human hnRNPL binding sites suggested hnRNPL‐mediated alternative splicing of tropomyosin, which was confirmed in C2C12 myoblasts. These findings identify hnRNPL as a sensor of cardiac dysfunction and suggest that disturbances of hnRNPL affect alternative splicing in HF. [ABSTRACT FROM AUTHOR]

Summary Covalent Bruton's tyrosine kinase‐inhibitors (cBTK‐i) are highly active in MYD88‐mutated (MYD88Mut) Waldenstrom's macroglobulinaemia and suppress nuclear factor kappa‐light‐chain‐enhancer of activated B cells and extracellular signal‐regulated kinases‐1/2 (ERK1/2)‐related signalling. BTKCys481 mutations are associated with cBTK‐i acquired resistance and are accompanied by reactivation of ERK1/2 that promotes inflammatory cytokine secretion and paracrine‐mediated resistance of BTK wild‐type (BTKWT) tumour cells. Pirtobrutinib is a non‐covalent BTK‐inhibitor that binds at non‐BTKCys481 sites. We show that pirtobrutinib blocked p‐ERK1/2, ERK1/2‐driven inflammatory cytokines, and overcame paracrine‐mediated resistance in MYD88Mut lymphoma cells expressing mutated BTKCys481. Our results provide important mechanistic insights for the activity of pirtobrutinib in MYD88Mut lymphomas carrying BTKCys481 mutations. [ABSTRACT FROM AUTHOR]

The signaling lipid phosphatidylinositol-4,5-bisphosphate (PIP2) regulates many ion channels. It inhibits eukaryotic cyclic nucleotide-gated (CNG) channels while activating their relatives, the hyperpolarization-activated and cyclic nucleotide-modulated (HCN) channels. The prokaryotic SthK channel from Spirochaeta thermophila shares features with CNG and HCN channels and is an established model for this channel family. Here, we show SthK activity is inhibited by PIP2. A cryo-EM structure of SthK in nanodiscs reveals a PIP2-fitting density coordinated by arginine and lysine residues from the S4 helix and the C-linker, located between voltage-sensing and pore domains of adjacent subunits. Mutation of two arginine residues weakens PIP2 inhibition with the double mutant displaying insensitivity to PIP2. We propose that PIP2 inhibits SthK by gluing S4 and S6 together, stabilizing a resting channel conformation. The PIP2 binding site is partially conserved in CNG channels suggesting the possibility of a similar inhibition mechanism in the eukaryotic homologs. Thon et al. showed that the signaling lipid PIP2 inhibits a bacterial homolog of cyclic nucleotide-gated ion channels by binding between the voltage-sensing and pore domains of adjacent subunits and stabilizing a resting channel state. [ABSTRACT FROM AUTHOR]

Enzymes are crucial in numerous biological processes, with the Enzyme Commission (EC) number being a commonly used method for defining enzyme function. However, current EC number prediction technologies have not fully recognized the importance of enzyme active sites and structural characteristics. Here, we propose GraphEC, a geometric graph learning-based EC number predictor using the ESMFold-predicted structures and a pre-trained protein language model. Specifically, we first construct a model to predict the enzyme active sites, which is utilized to predict the EC number. The prediction is further improved through a label diffusion algorithm by incorporating homology information. In parallel, the optimum pH of enzymes is predicted to reflect the enzyme-catalyzed reactions. Experiments demonstrate the superior performance of our model in predicting active sites, EC numbers, and optimum pH compared to other state-of-the-art methods. Additional analysis reveals that GraphEC is capable of extracting functional information from protein structures, emphasizing the effectiveness of geometric graph learning. This technology can be used to identify unannotated enzyme functions, as well as to predict their active sites and optimum pH, with the potential to advance research in synthetic biology, genomics, and other fields. The Enzyme Commission (EC) number is a commonly used method for defining enzyme function. Here, authors propose GraphEC, a geometric graph learning-based EC number predictor to identify unannotated enzyme functions, predict their active sites, and determine their optimal pH. [ABSTRACT FROM AUTHOR]

The Caf1/CNOT7 nuclease is a catalytic component of the Ccr4-Not deadenylase complex, which is a key regulator of post-transcriptional gene regulation. In addition to providing catalytic activity, Caf1/CNOT7 and its paralogue Caf1/CNOT8 also contribute a structural function by mediating interactions between the large, non-catalytic subunit CNOT1, which forms the backbone of the Ccr4-Not complex and the second nuclease subunit Ccr4 (CNOT6/CNOT6L). To facilitate investigations into the role of Caf1/CNOT7 in gene regulation, we aimed to discover and develop non-nucleoside inhibitors of the enzyme. Here, we disclose that the tri-substituted 2-pyridone compound 5-(5-bromo-2-hydroxy-benzoyl)-1-(4-chloro-2-methoxy-5-methyl-phenyl)-2-oxo-pyridine-3-carbonitrile is an inhibitor of the Caf1/CNOT7 nuclease. Using a fluorescence-based nuclease assay, the activity of 16 structural analogues was determined, which predominantly explored substituents on the 1-phenyl group. While no compound with higher potency was identified among this set of structural analogues, the lowest potency was observed with the analogue lacking substituents on the 1-phenyl group. This indicates that substituents on the 1-phenyl group contribute significantly to binding. To identify possible binding modes of the inhibitors, molecular docking was carried out. This analysis suggested that the binding modes of the five most potent inhibitors may display similar conformations upon binding active site residues. Possible interactions include π-π interactions with His225, hydrogen bonding with the backbone of Phe43 and Van der Waals interactions with His225, Leu209, Leu112 and Leu115. [ABSTRACT FROM AUTHOR]

Dynamic range is a crucial aspect in the development of fluorescent chemosensors. We aimed to address this issue using molecular logic gates. By creating an AND logic gate with two binding sites for the same type of ion, we increased the dynamic range of a sodium chemosensor while still using the same ionophore. Naphthalimide derivatives 1 and 2 were synthesized to test the plausibility of this application. Being an AND logic gate, the second molecule requires two Na+ ions, while molecule 1 requires a single ion for sensing. The application of this molecular logic gate is a useful method of altering the chemosensor range. [ABSTRACT FROM AUTHOR]

Type-A γ-aminobutyric acid (GABAA) receptors are channel proteins crucial to mediating neuronal balance in the central nervous system (CNS). The structure of GABAA receptors allows for multiple binding sites and is key to drug development. Yet the formation mechanism of the receptor's distinctive pentameric structure is still unknown. This study aims to investigate the role of three predominant subunits of the human GABAA receptor in the formation of protein pentamers. Through purifying and refolding the protein fragments of the GABAA receptor α1, β2, and γ2 subunits, the particle structures were visualised with negative staining electron microscopy (EM). To aid the analysis, AlphaFold2 was used to compare the structures. Results show that α1 and β2 subunit fragments successfully formed homo-oligomers, particularly homopentameric structures, while the predominant heteropentameric GABAA receptor was also replicated through the combination of the three subunits. However, homopentameric structures were not observed with the γ2 subunit proteins. A comparison of the AlphaFold2 predictions and the previously obtained cryo-EM structures presents new insights into the subunits' modular structure and polymerization status. By performing experimental and computational studies, a deeper understanding of the complex structure of GABAA receptors is provided. Hopefully, this study can pave the way to developing novel therapeutics for neuropsychiatric diseases. [ABSTRACT FROM AUTHOR]

Steroidogenic factor 1 (SF-1) is a nuclear receptor that regulates steroidogenesis and reproductive development. NR5A1/SF-1 variants are associated with a broad spectrum of phenotypes across individuals with disorders of sex development (DSDs). Oligogenic inheritance has been suggested as an explanation. SF-1 interacts with numerous partners. Here, we investigated a constellation of gene variants identified in a 46,XY severely undervirilized individual carrying an ACMG-categorized 'pathogenic' NR5A1/SF-1 variant in comparison to the healthy carrier father. Candidate genes were revealed by whole exome sequencing, and pathogenicity was predicted by different in silico tools. We found variants in NR1H2 and INHA associated with steroidogenesis, sex development, and reproduction. The identified variants were tested in cell models. Novel SF-1 and NR1H2 binding sites in the AR and INHA gene promoters were found. Transactivation studies showed that wild-type NR5A1/SF-1 regulates INHA and AR gene expression, while the NR5A1/SF-1 variant had decreased transcriptional activity. NR1H2 was found to regulate AR gene transcription; however, the NR1H2 variant showed normal activity. This study expands the NR5A1/SF-1 network of interacting partners, while not solving the exact interplay of different variants that might be involved in revealing the observed DSD phenotype. It also illustrates that understanding complex genetics in DSDs is challenging. [ABSTRACT FROM AUTHOR]

Gene expression is orchestrated by a complex array of gene regulatory elements that govern transcription in a cell-type-specific manner. Though previously studied, the ability to utilize regulatory elements to identify disrupting variants remains largely elusive. To identify important factors within these regions, we generated enhancer–promoter interaction (EPI) networks and investigated the presence of disease-associated variants that fall within these regions. Our study analyzed six neuronal cell types across neural differentiation, allowing us to examine closely related cell types and across differentiation stages. Our results expand upon previous findings of cell-type specificity of enhancer, promoter, and transcription factor binding sites. Notably, we find that regulatory regions within EPI networks can identify the enrichment of variants associated with neuropsychiatric disorders within specific cell types and network sub-structures. This enrichment within sub-structures can allow for a better understanding of potential mechanisms by which variants may disrupt transcription. Together, our findings suggest that EPIs can be leveraged to better understand cell-type-specific regulatory architecture and used as a selection method for disease-associated variants to be tested in future functional assays. Combined with these future functional characterization assays, EPIs can be used to better identify and characterize regulatory variants' effects on such networks and model their mechanisms of gene regulation disruption across different disorders. Such findings can be applied in practical settings, such as diagnostic tools and drug development. [ABSTRACT FROM AUTHOR]

Endometritis is an inflammatory disease that negatively influences fertility and is common in milk-producing cows. An in vitro model for bovine endometrial inflammation was used to identify enrichment of cis-acting regulatory elements in differentially methylated regions (DMRs) in the genome of in vitro-cultured primary bovine endometrial epithelial cells (bEECs) before and after treatment with lipopolysaccharide (LPS) from E. coli, a key player in the development of endometritis. The enriched regulatory elements contain binding sites for transcription factors with established roles in inflammation and hypoxia including NFKB and Hif-1α. We further showed co-localization of certain enriched cis-acting regulatory motifs including ARNT, Hif-1α, and NRF1. Our results show an intriguing interplay between increased mRNA levels in LPS-treated bEECs of the mRNAs encoding the key transcription factors such as AHR, EGR2, and STAT1, whose binding sites were enriched in the DMRs. Our results demonstrate an extraordinary cis-regulatory complexity in these DMRs having binding sites for both inflammatory and hypoxia-dependent transcription factors. Obtained data using this in vitro model for bacterial-induced endometrial inflammation have provided valuable information regarding key transcription factors relevant for clinical endometritis in both cattle and humans. [ABSTRACT FROM AUTHOR]

Nucleoside diphosphate kinases (NDPKs) are encoded by nme genes and exist in various isoforms. Based on interactions with other proteins, they are involved in signal transduction, development and pathological processes such as tumorigenesis, metastasis and heart failure. In this study, we report a 1.25 Å resolution structure of human homohexameric NDPK-C bound to ADP and describe the yet unknown complexes formed with GDP, UDP and cAMP, all obtained at a high resolution via X-ray crystallography. Each nucleotide represents a distinct group of mono- or diphosphate purine or pyrimidine bases. We analyzed different NDPK-C nucleotide complexes in the presence and absence of Mg2+ and explain how this ion plays an essential role in NDPKs' phosphotransferase activity. By analyzing a nucleotide-depleted NDPK-C structure, we detected conformational changes upon substrate binding and identify flexible regions in the substrate binding site. A comparison of NDPK-C with other human isoforms revealed a strong similarity in the overall composition with regard to the 3D structure, but significant differences in the charge and hydrophobicity of the isoforms' surfaces. This may play a role in isoform-specific NDPK interactions with ligands and/or important complex partners like other NDPK isoforms, as well as monomeric and heterotrimeric G proteins. Considering the recently discovered role of NDPK-C in different pathologies, these high-resolution structures thus might provide a basis for interaction studies with other proteins or small ligands, like activators or inhibitors. [ABSTRACT FROM AUTHOR]

Biofilm formation by Staphylococcus aureus is a major challenge in clinical settings due to its role in persistent infections. The AgrA protein, a key regulator in biofilm development, is a promising target for therapeutic intervention. This study investigates the antibiofilm potential of halogenated phenazine compounds by targeting AgrA and explores their molecular interactions to provide insights for drug development. We employed molecular docking, molecular dynamics simulations, and computational mutagenesis to evaluate the binding of halogenated phenazine compounds (C1 to C7, HP, and HP‐14) to AgrA. Binding free energy analysis was performed to assess the affinity of these compounds for the AgrA‐DNA complex. Additionally, the impact of these compounds on AgrA's structural conformation and salt bridge interactions was examined. The binding‐free energy analysis revealed that all compounds enhance binding affinity compared to the Apo form of AgrA, which has a ΔGbind of −80.75 kcal/mol. The strongest binding affinities were observed with compounds C7 (−113.84 kcal/mol), HP‐14 (−115.23 kcal/mol), and HP (−112.28 kcal/mol), highlighting their effectiveness. Molecular dynamics simulations demonstrated that these compounds bind at the hydrophobic cleft of AgrA, disrupting essential salt bridge interactions between His174‐Glu163 and His174‐Glu226. This disruption led to structural conformational changes and reduced DNA binding affinity, aligning with experimental findings on biofilm inhibition. The halogenated phenazine compounds effectively inhibit biofilm formation by targeting AgrA, disrupting its DNA‐binding function. The study supports the potential of these compounds as antibiofilm agents and provides a foundation for rational drug design targeting the AgrA‐DNA interaction. Future research should focus on further optimizing these lead compounds and exploring additional active sites on AgrA to develop novel treatments for biofilm‐associated infections. [ABSTRACT FROM AUTHOR]

Invasive growth is a critical process in tumor progression, requiring the activation of various molecular processes in tumor cells at the invasive front. Intercellular communication between heterogeneous tumor cells enhances cellular activation and adaptation to specific microenvironments. One mechanism of intercellular communication is the delivery of miRNAs through tumor cell-derived extracellular vesicles (EVs). In this context we have observed that conditioned media from a highly invasive cell subpopulation (BLM-HI) enhances the invasive capacity of the parental cell line (BLM). Therefore, we hypothesized that this complex change of cellular behavior is influenced by EV-transported miRNAs. The treatment of BLM cells with EVs derived from BLM-HI cells resulted in a significantly enhanced invasive capacity, as observed in Matrigel-embedded spheroids and in 2D Boyden chamber assays, with a dose-dependent effect. Conversely, the invasive capacity of BLM cells was reduced when secretion of EVs was inhibited by a sphingomyelinase inhibitor. To investigate the molecular mechanisms behind this effect, we performed next-generation sequencing and identified an enrichment of miR-1246 in these EVs. In functional analyses we demonstrated that both the EV mediated delivery of miR-1246 as well as overexpression contributes to the enhanced invasiveness of BLM cells. We identified a binding site of miR-1246 in the 3'UTR of cyclin G2 (CCNG2) and demonstrated direct binding by a luciferase reporter assay. Increased expression of CCNG2 has been associated with cancer metastasis and poor patient outcomes in other malignancies. Our study demonstrates that intercellular communication contributes to the transfer of properties, such as increased invasive capacity, between heterogeneous melanoma cells via EV-transported miRNAs. [ABSTRACT FROM AUTHOR]

Supramolecular self‐assembly with well‐defined building blocks like lipids, deoxyribonucleic acid, or ligands relies on accessible molecular structures and predictable interactions. However, assembling heterogeneous, undefined blocks, such as disordered proteins, amorphous solids, and catecholic derivatives, remains challenging due to their unpredictable assembly, leading to irreversible aggregation, severe precipitation, and unreliable performance. Here, the first programmable, sustainable, and durable self‐assembly strategy of supramolecules with heterogenous is presented, derived blocks via harmonizing multiple molecular interactions. This approach achieves reversible assembly/disassembly, ≈73.7% reduced precipitation, and salt‐ and alkaline‐durability under freeze‐thaw cycles in model catecholic derivatives, functioning effectively as robust adhesive primers and hydrogel interfacial strengtheners. Moreover, through molecular force measurements and computational simulations, the first general criterion and benchmark for high precision supramolecular self‐assembly is proposed, applicable to complex derivatives and interactions: with blocks bearing multiple binding sites existing, the co‐assembling blocks should bear at least two binding sites with minimum binding strength (≈17 to ≈37 kJ mol−1) to prevent disassembly. This study paves the way and provides benchmarks for precision self‐assembly of diverse supramolecules using heterogeneous derivatives for adhesion technology, nanomaterial synthesis and bio‐inspired applications. [ABSTRACT FROM AUTHOR]

Tumour necrosis factor (TNF) superfamily member 11 (TNFSF11), also known as RANKL, plays a crucial role in regulating several physiological and pathological activities. Additionally, it is a vital factor in bone physiology, and the sex hormone progesterone regulates the expansion of stem cells and the proliferation of mammary epithelial cells. It is essential for animal growth and reproductive physiological processes. This study aimed to evaluate the tissue-specific expression characteristics and promoter activity of the TNFSF11 gene in pigs. As a result, the study examined the presence of TNFSF11 expression in the tissues of Xiangsu pigs at 0.6 and 12 months of age. Moreover, the core promoter region of TNFSF11 was also identified by utilizing a combination of bioinformatic prediction and dual-luciferase activity tests. Finally, the effect of transcription factors on the transcriptional activity of the core promoter region was determined using site-directed mutagenesis. TNFSF11 was uniformly expressed in all tissues; however, its expression in muscles was comparatively low. The core promoter region of TNFSF11 was located in the −555 to −1 region. The prediction of the transcription start site of TNFSF11 gene-2000 ∼ + 500bp showed that there was a CpG site in 17 ∼ + 487bp. Analysis of mutations in the transcription factor binding sites revealed that mutations in the Stat5b , Myog , Trl , and EN1 binding sites had significant effects on the transcriptional activity of the TNFSF11 gene, particularly following the EN1 binding site mutation (P < 0.001). This study provides insights into both the tissue-specific expression patterns of TNFSF11 in the tissues of Xiangsu pigs and the potential regulatory effects of transcription factors on its promoter activity. These results may be helpful for future research aimed at clarifying the expression and role of the porcine TNFSF11 gene. [ABSTRACT FROM AUTHOR]

Acetamiprid is mainly used to control pests. However, the residues of acetamiprid have resulted in significant negative effects on mammals. Many researchers are working on developing acetamiprid detection methods. In our study, four truncated aptamers were designed based on the secondary structure of the original aptamer. Molecular docking simulation of truncated aptamers confirmed that all of the truncated aptamers bind to acetamiprid, and their binding sites were identified. The affinity, sensitivity, and specificity of these truncated aptamers were measured by a spectrophotometric method with gold nanoparticles (AuNPs). Acetamiprid aptamers with 17-mer (Apt-J2) and 16-mer (Apt-J4) were successfully obtained, which show higher detection sensitivity and satisfactory specificity. Additionally, a spectrophotometric detection route superior to the original aptamer was explored, and the linear ranges were from 1 to 70 μM and 0.5 to 40 μM, respectively. The truncated aptamers were applied to the analysis of lake water, indicating that the aptamers have potential for practical analysis. [ABSTRACT FROM AUTHOR]

The genus Ilex belongs to the sole family and is the single genus within the order Aquifoliales, exhibiting significant phenotypic diversity. However, the genetic differences underlying these phenotypic variations have rarely been studied. In this study, collinearity analyses of three Ilex genomes, Ilex latifolia Thunb., Ilex polyneura (Hand.-Mazz.) S. Y. Hu, and Ilex asprella Champ. ex Benth., indicated a recent fusion event contributing to the reduction of chromosomes in I. asprella. Comparative genome analyses showed slight differences in gene annotation among the three species, implying a minimal disruption of genes following chromosomal fusion in I. asprella. Comprehensive annotation of transposable elements (TEs) revealed that TEs constitute a significant portion of the Ilex genomes, with LTR transposons being predominant. TEs exhibited an inverse relationship with gene density, potentially influencing gene regulation and chromosomal architecture. TE insertions were shown to affect the conformation and binding sites of key genes such as 7-deoxyloganetin glucosyltransferase and transmembrane kinase (TMK) genes, highlighting potential functional impacts. The structural variations caused by TE insertions suggest significant roles in the evolutionary dynamics, leading to either loss or gain of gene function. This study underscores the importance of TEs in shaping the genomic landscape and evolutionary trajectories of Ilex species. [ABSTRACT FROM AUTHOR]

Sudan grass (Sorghum sudanense S.) is a warm-season annual grass with high yield, rich nutritional value, good regeneration, and tolerance to biotic and abiotic stresses. However, prolonged drought affects the yield and quality of Sudan grass. As one of the largest families of multifunctional transcription factors in plants, MYB is widely involved in regulating plant growth and development, hormonal signaling, and stress responses at the gene transcription level. However, the regulatory role of MYB genes has not been well characterized in Sudan grass under abiotic stress. In this study, 113 MYB genes were identified in the Sudan grass genome and categorized into three groups by phylogenetic analysis. The promoter regions of SsMYB genes contain different cis-regulatory elements, which are involved in developmental, hormonal, and stress responses, and may be closely related to their diverse regulatory functions. In addition, collinearity analysis showed that the expansion of the SsMYB gene family occurred mainly through segmental duplications. Under drought conditions, SsMYB genes showed diverse expression patterns, which varied at different time points. Interaction networks of 74 SsMYB genes were predicted based on motif binding sites, expression correlations, and protein interactions. Heterologous expression showed that SsMYB8, SsMYB15, and SsMYB64 all significantly enhanced the drought tolerance of yeast cells. Meanwhile, the subcellular localization of all three genes is in the nucleus. Overall, this study provides new insights into the evolution and function of MYB genes and provides valuable candidate genes for breeding efforts in Sudan grass. [ABSTRACT FROM AUTHOR]

The activation of a G protein-coupled receptor (GPCR) leads to the formation of a ternary complex between agonist, receptor, and G protein that is characterized by high-affinity binding. Allosteric modulators bind to a distinct binding site from the orthosteric agonist and can modulate both the affinity and the efficacy of orthosteric agonists. The influence allosteric modulators have on the high-affinity active state of the GPCR-G protein ternary complex is unknown due to limitations on attempting to characterize this interaction in recombinant whole cell or membrane-based assays. Here, we use the purified M2 muscarinic acetylcholine receptor reconstituted into nanodiscs to show that, once the agonist-bound high-affinity state is promoted by the G protein, positive allosteric modulators stabilize the ternary complex that, in the presence of nucleotides, leads to an enhanced initial rate of signaling. Our results enhance our understanding of how allosteric modulators influence orthosteric ligand signaling and will aid the design of allosteric therapeutics. [ABSTRACT FROM AUTHOR]

Background: Variations in untranslated regions (UTR) alter regulatory pathways impacting phenotype, disease onset, and course of disease. Protein kinase C Zeta (PRKCZ), a serine-threonine kinase, is implicated in cardiovascular, neurological and oncological disorders. Due to limited research on PRKCZ, this study aimed to investigate the impact of UTR genetic variants' on binding sites for transcription factors and miRNA. RNA secondary structure, eQTLs, and variation tolerance analysis were also part of the study. Methods: The data related to PRKCZ gene variants was downloaded from the Ensembl genome browser, COSMIC and gnomAD. The RegulomeDB database was used to assess the functional impact of 5' UTR and 3'UTR variants. The analysis of the transcription binding sites (TFBS) was done through the Alibaba tool, and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) was employed to identify pathways associated with PRKCZ. To predict the effect of variants on microRNA binding sites, PolymiRTS was utilized for 3' UTR variants, and the SNPinfo tool was used for 5' UTR variants. Results: The results obtained indicated that a total of 24 variants present in the 3' UTR and 25 variants present in the 5' UTR were most detrimental. TFBS analysis revealed that 5' UTR variants added YY1, repressor, and Oct1, whereas 3' UTR variants added AP-2alpha, AhR, Da, GR, and USF binding sites. The study predicted TFs that influenced PRKCZ expression. RNA secondary structure analysis showed that eight 5' UTR and six 3' UTR altered the RNA structure by either removal or addition of the stem-loop. The microRNA binding site analysis highlighted that seven 3' UTR and one 5' UTR variant altered the conserved site and also created new binding sites. eQTLs analysis showed that one variant was associated with PRKCZ expression in the lung and thyroid. The variation tolerance analysis revealed that PRKCZ was an intolerant gene. Conclusion: This study laid the groundwork for future studies aimed at targeting PRKCZ as a therapeutic target. [ABSTRACT FROM AUTHOR]

Summary The objective was to evaluate the in vitro inhibition of enzymes related to neurodegeneration (prolyl endopeptidase, PEP; acetylcholinesterase, AChE; butyrylcholinesterase, BChE; lipoxygenase, LOX) and the antioxidant activity from fermented milks (FM) with Lactococcus and Lactobacillus spp. All FM presented antioxidant activity (ABTS and ORAC); however, FM with Lactococcus NRRL B‐50571 (FM‐571) presented higher (P < 0.05) oxidative haemolysis inhibition. Additionally, FM‐571 presented the lowest IC₅₀ for LOX (1.78 mg/mL), PEP (3.16 mg/mL), AChE (3.22 mg/mL) and BChE (2.14 mg/mL). Thus, FM‐571 was selected for in silico analysis for the prediction of binding sites of peptides present in this FM with enzymes active sites. Altogether, thirty peptides showed (P < 0.01) high binding potential to AChE, seventeen to BChE and LOX and sixteen to PEP. Thus, FM‐571 shows potential for the development of dairy products with potential neuroprotective effects. [ABSTRACT FROM AUTHOR]

The tertiary and quaternary structures of many proteins are stabilized by strong covalent forces, of which disulfide bonds are the most well known. A new type of intramolecular and intermolecular covalent bond has been recently reported, consisting of the Lys and Cys side-chains linked by an oxygen atom (NOS). These post-translational modifications are widely distributed amongst proteins, and are formed under oxidative conditions. Similar linkages are observed during antibiotic biosynthesis, where hydroxylamine intermediates are tethered to the sulfur of enzyme active site Cys residues. These linkages open the way to understanding protein structure and function, give new insights into enzyme catalysis and natural product biosynthesis, and offer new strategies for drug design. [ABSTRACT FROM AUTHOR]

Proteostasis and genomic integrity are respectively regulated by the endoplasmic reticulum-associated protein degradation (ERAD) and DNA damage repair signaling pathways, with both pathways essential for carcinogenesis and drug resistance. How these signaling pathways coordinate with each other remains unexplored. We found that ER stress specifically induces the DNA-PKcs-regulated nonhomologous end joining (NHEJ) pathway to amend DNA damage and impede cell death. Intriguingly, sustained ER stress rapidly decreased the activity of DNA-PKcs and DNA damage accumulated, facilitating a switch from adaptation to cell death. This DNA-PKcs inactivation was caused by increased KU70/KU80 protein degradation. Unexpectedly, the ERAD ligase HRD1 was found to efficiently destabilize the classic nuclear protein HDAC1 in the cytoplasm, by catalyzing HDAC1's polyubiquitination at lysine 74, at a late stage of ER stress. By abolishing HDAC1-mediated KU70/KU80 deacetylation, HRD1 transmits ER signals to the nucleus. The resulting enhanced KU70/KU80 acetylation provides binding sites for the nuclear E3 ligase TRIM25, resulting in the promotion of polyubiquitination and the degradation of KU70/KU80 proteins. Both in vitro and in vivo cancer models showed that genetic or pharmacological inhibition of HADC1 or DNA-PKcs sensitizes colon cancer cells to ER stress inducers, including the Food and Drug Administration-approved drug celecoxib. The antitumor effects of the combined approach were also observed in patient-derived xenograft models. These findings identify a mechanistic link between ER stress (ERAD) in the cytoplasm and DNA damage (NHEJ) pathways in the nucleus, indicating that combined anticancer strategies may be developed that induce severe ER stress while simultaneously inhibiting KU70/KU80/DNA-PKcs-mediated NHEJ signaling. [ABSTRACT FROM AUTHOR]

Autophagy of glycogen (glycophagy) is crucial for the maintenance of cellular glucose homeostasis and physiology in mammals. STBD1 can serve as an autophagy receptor to mediate glycophagy by specifically recognizing glycogen and relevant key autophagic factors, but with poorly understood mechanisms. Here, we systematically characterize the interactions of STBD1 with glycogen and related saccharides, and determine the crystal structure of the STBD1 CBM20 domain with maltotetraose, uncovering a unique binding mode involving two different oligosaccharide-binding sites adopted by STBD1 CBM20 for recognizing glycogen. In addition, we demonstrate that the LC3-interacting region (LIR) motif of STBD1 can selectively bind to six mammalian ATG8 family members. We elucidate the detailed molecular mechanism underlying the selective interactions of STBD1 with ATG8 family proteins by solving the STBD1 LIR/GABARAPL1 complex structure. Importantly, our cell-based assays reveal that both the STBD1 LIR/GABARAPL1 interaction and the intact two oligosaccharide binding sites of STBD1 CBM20 are essential for the effective association of STBD1, GABARAPL1, and glycogen in cells. Finally, through mass spectrometry, biochemical, and structural modeling analyses, we unveil that STBD1 can directly bind to the Claw domain of RB1CC1 through its LIR, thereby recruiting the key autophagy initiation factor RB1CC1. In all, our findings provide mechanistic insights into the recognitions of glycogen, ATG8 family proteins, and RB1CC1 by STBD1 and shed light on the potential working mechanism of STBD1-mediated glycophagy. [ABSTRACT FROM AUTHOR]

Background: Carbazole-based molecules containing thiosemicarbazide functional groups are recognized for their diverse biological activities, particularly in enhancing therapeutic anticancer effects through inhibiting crucial pathways. These derivatives also exhibit noteworthy antioxidant properties. Objectives: This study aims to synthesize, characterize, and evaluate the antioxidant and anticancer activities of 18 novel carbazole derivatives. Methods: The radical scavenging capabilities of the compounds were assessed using the 2,2-diphenyl-1-picrylhydrazyl assay. Antiproliferative activities were evaluated on MCF-7 cancer cell lines through viability assays. Additionally, the modulation of the PI3K/Akt/mTOR pathway, apoptosis/necrosis induction, and cell cycle analysis were conducted for the most promising anticancer agents. Results: nine compounds showed potent antioxidant activities with IC50 values lower than the positive control acarbose, with compounds 4 h and 4y exhibiting the highest potency (IC50 values of 0.73 and 0.38 µM, respectively). Furthermore, compounds 4o and 4r displayed significant anticancer effects, with IC50 values of 2.02 and 4.99 µM, respectively. Compound 4o, in particular, exhibited promising activity by targeting the PI3K/Akt/mTOR signaling pathway, inhibiting tumor survival, inducing apoptosis, and causing cell cycle arrest in MCF-7 cell lines. Furthermore, compound 4o was showed significant antimicrobial activities against S. aureus and E. coli, and antifungal effect against C. albicans. Its potential to overcome drug resistance through this pathway inhibition highlights its promise as an anticancer agent. Molecular docking simulations supported these findings, revealing favorable binding profiles and interactions within the active sites of the enzymes PI3K, AKT1, and mTOR. Moreover, assessing the druggability of the newly synthesized thiosemicarbazide derivatives demonstrated optimal physicochemical properties, further endorsing their potential as drug candidates. [ABSTRACT FROM AUTHOR]

Nucleostemin (NS) plays a role in liver regeneration, and aging reduces its expression in the baseline and regenerating livers following 70% partial hepatectomy (PHx). Here we interrogate the mechanism controlling NS expression during liver regeneration and aging. The NS promoter was analyzed by TRANSFAC. Functional studies were performed using cell-based luciferase assay, endogenous NS expression in Hep3B cells, mouse livers with a gain-of-function mutation of C/EBPα (S193D), and mouse livers with C/EBPα knockdown. We found a CAAT box with four C/EBPα binding sites (-1216 to -735) and a GC box with consensus binding sites for c-Myc, E2F1, and p300-associated protein complex (-633 to -1). Age-related changes in NS expression correlated positively with the expression of c-Myc, E2F1, and p300, and negatively with that of C/EBPα and C/EBPβ. PHx upregulated NS expression at 1d, coinciding with an increase in E2F1 and a decrease in C/EBPα. C/EBPα bound to the consensus sequences found in the NS promoter in vitro and in vivo, inhibited its transactivational activity in a binding site-dependent manner, and decreased the expression of endogenous NS in Hep3B cells. In vivo activation of C/EBPα by the S193D mutation resulted in a 4th-day post-PHx reduction of NS, a feature shared by 16-m/o livers. Finally, C/EBPα knockdown increased its expression in aged (24-m/o) livers under both baseline and regeneration conditions. This study reports the C/EBPα suppression of NS expression in aged livers, providing a new perspective on the mechanistic orchestration of tissue homeostasis in aging. [ABSTRACT FROM AUTHOR]

Respiratory complex I is a central metabolic enzyme coupling NADH oxidation and quinone reduction with proton translocation. Despite the knowledge of the structure of the complex, the coupling of both processes is not entirely understood. Here, we use a combination of site‐directed mutagenesis, biochemical assays, and redox‐induced FTIR spectroscopy to demonstrate that the quinone chemistry includes the protonation and deprotonation of a specific, conserved aspartic acid residue in the quinone binding site (D325 on subunit NuoCD in Escherichia coli). Our experimental data support a proposal derived from theoretical considerations that deprotonation of this residue is involved in triggering proton translocation in respiratory complex I. [ABSTRACT FROM AUTHOR]

Prostate cancer (PCa) is a high‐mortality cancer. Docetaxel (DCT) combined with second‐generation anti‐androgens is considered the golden standard therapy for PCa, whose application is limited for DCT resistance (DR). Therefore, exploring the mechanism of DR is of great importance. In this study, PCa cell lines of PC3 and DU145 were employed, and DR cells were constructed by treatment with graded DCT. CircSLC4A7, miR‐1205, and microtubule‐associated protein tau (MAPT) transfections were established. Cell counting kit‐8 assay was performed to evaluate the cell activity and IC50 of DCT. After being treated with DCT, DR was assessed by colony formation assay, flow cytometry analysis, and terminal transferase‐mediated UTP nick end‐labeling assay. Real‐time quantitative PCR and western blotting analysis evaluated the expression levels of genes. The dual‐luciferase reporter gene assay verified the miR‐1205 binding sites with circSLC4A7 and MAPT. An animal experiment was performed to assess the tumor growth influenced by circSLC4A7. After conducting DR cells and isolated exosomes, we found that not only co‐culture with DR cells but also treatment with DR cells' exosomes would promote the DR of normal cells. Moreover, circSLC4A7 was highly expressed in DR cells and their exosomes. CircSLC4A7 overexpression enhanced DR, represented as raised IC50 of DCT, increased colony formation, and decreased cell apoptosis after DCT treatment, while circSLC4A7 knockdown had the opposite effect. MiR‐1205 was confirmed as a circSLC4A7‐sponged miRNA and miR‐1205 inhibitor reversed the effect of sh‐circSLC4A7. MAPT was further identified as a target of miR‐1205 and had a similar effect with circSLC4A7. The effect of circSLC4A7 on DR was also confirmed by xenograft experiments. Collectively, circSLC4A7 in resistant‐cells‐derived exosomes promotes DCT resistance of PCa via miR‐1205/MAPT axis, which may provide a new treatment strategy for DR of PCa. [ABSTRACT FROM AUTHOR]

The mitochondrial enzyme methylenetetrahydrofolate dehydrogenase (MTHFD2) is involved in purine and thymidine synthesis via 1C metabolism. MTHFD2 is exclusively overexpressed in cancer cells but absent in most healthy adult human tissues. However, the two close homologs of MTHFD2 known as MTHFD1 and MTHFD2L are expressed in healthy adult human tissues and share a great structural resemblance to MTHFD2 with 54% and 89% sequence similarity, respectively. It is therefore notably challenging to find selective inhibitors of MTHFD2 due to the structural similarity, in particular protein binding site similarity with MTHFD1 and MTHFD2L. Tricyclic coumarin-based compounds (substrate site binders) and xanthine derivatives (allosteric site binders) are the only selective inhibitors of MTHFD2 reported till date. Nanomolar potent diaminopyrimidine-based inhibitors of MTHFD2 have been reported recently, however, they also demonstrate significant inhibitory activities against MTHFD1 and MTHFD2L. In this study, we have employed extensive computational modeling involving molecular docking and molecular dynamics simulations in order to investigate the binding modes and key interactions of diaminopyrimidine-based inhibitors at the substrate binding sites of MTHFD1, MTHFD2 and MTHFD2L, and compare with the tricyclic coumarin-based selective MTHFD2 inhibitor. The outcomes of our study provide significant insights into desirable and undesirable structural elements for rational structure-based design of new and selective inhibitors of MTHFD2 against cancer. [ABSTRACT FROM AUTHOR]

α,ω-Dicarboxylic acids, ω-aminoalkanoic acids, and α,ω-diaminoalkanes are valuable building blocks for the production of biopolyesters and biopolyamides. One of the key steps in producing these chemicals is the oxidation of ω-hydroxycarboxylic acids using alcohol dehydrogenases (e.g., ChnD of Acinetobacter sp. NCIMB 9871). However, the reaction and structural features of these enzymes remain mostly undiscovered. Thereby, we have investigated characteristics of ChnD based on enzyme kinetics, substrate-docking simulations, and mutation studies. Kinetic analysis revealed a distinct preference of ChnD for medium chain ω-hydroxycarboxylic acids, with the highest catalytic efficiency of 18.0 mM−1s−1 for 12-hydroxydodecanoic acid among C6 to C12 ω-hydroxycarboxylic acids. The high catalytic efficiency was attributed to the positive interactions between the carboxyl group of the substrates and the guanidino group of two arginine residues (i.e., Arg62 and Arg266) in the substrate binding site. The ChnD_R62L variant showed the increased efficiency and affinity, particularly for fatty alcohols (i.e., C6–C10) and branched-chain fatty alcohols, such as 3-methyl-2-buten-1-ol. Overall, this study contributes to the deeper understanding of medium-chain primary aliphatic alcohol dehydrogenases and their applications for the production of industrially relevant chemicals such as α,ω-dicarboxylic acids, ω-aminoalkanoic acids, and α,ω-diaminoalkanes from renewable biomass. • ChnD prefers oxidizing longer ω-hydroxycarboxylic acids, particularly 12-hydroxydodecanoic acid. • Carboxyl groups in ω-hydroxycarboxylic acids significantly enhance efficiency by interacting with arginine residue. • The ChnD_R62L variant shows improved efficiency and affinity for fatty and branched-chain alcohols. [ABSTRACT FROM AUTHOR]

Phosphorus limitation occurs in many soils as a significant amount of soil P is retained in forms inaccessible to plants, such as bound to iron (Fe) minerals. Prior studies have shown that silicon (Si) can mobilize P from the binding sites of such minerals. Several P extraction methods have been developed to account for different P pools. Nevertheless, each of those methods uses different extractants and mechanisms to extract different P pools in soils. However, there is no study comparing different P extraction methods in the presence of Si fertilization. We tested the effect of Si on P mobility and determined the efficiency of water, Calcium acetate lactate (CAL), Mehlich-III, and Bray and Kurtz extraction methods for extracting P in the presence of amorphous silica (ASi) fertilization using two soils of contrasting characteristics. Significantly higher amounts of P were found at 3% ASi treatments (10 and 21 mg P kg-1) compared to the control (4 and 10 mg P kg-1) in the water extract in the high and low-yield soil, respectively just after 6 hours of extraction and increased with time. This may be explained by Si directly competing with P for sorption to Fe minerals. Using CAL extraction, Si addition showed no effect on P extractability. In contrast, the Mehlich-III and Bray extraction methods showed decreasing P extractability, especially at 3% ASi treatment (95 and 60 mg P kg-1) compared to the control (115 and 80 mg P kg-1) for the high-yield soil. The decreasing P contents in the presence of Si found in the Mehlich-III and Bray extracts may be attributed to the decrease in extraction effectiveness of the extractants to extract P while extracting Si and Fe. Our results showed that the Mehlich-III and Bray extraction methods may not be suitable for the determination of P availability in the presence of ASi fertilization since both extractants also extract Si and this may limit the completeness of P extraction. Therefore, in the presence of Si fertilizer, the water extraction method may be suitable to determine P availability and mobilization due to ASi. [ABSTRACT FROM AUTHOR]

Single-cell multi-omics sequencing is a powerful approach to analyze complex mechanisms underlying neuronal development and regeneration. However, current methods lack the ability to simultaneously profile RNA alternative splicing and chromatin accessibility at the single-cell level. We develop a technique, single-cell RNA isoform and chromatin accessibility sequencing (scRICA-seq), which demonstrates higher sensitivity and cost-effectiveness compared to existing methods. scRICA-seq can profile both isoforms and chromatin accessibility for up to 10,000 single cells in a single run. Applying this method to human retinal organoids, we construct a multi-omic cell atlas and reveal associations between chromatin accessibility, isoform expression of fate-determining factors, and alternative splicing events in their binding sites. This study provides insights into integrating epigenetics, transcription, and RNA splicing to elucidate the mechanisms underlying retinal neuronal development and fate determination. Here, the authors present scRICA-seq, which is capable of profiling isoforms and chromatin accessibility for up to 10,000 single cells in a single run. By applying this method to human retinal organoids, they construct a multi-omic cell atlas. [ABSTRACT FROM AUTHOR]

Glycan-mediated interactions play a crucial role in biology and medicine, influencing signalling, immune responses, and disease pathogenesis. However, the use of glycans in biosensing and diagnostics is limited by cross-reactivity, as certain glycan motifs can be recognised by multiple biologically distinct protein receptors. To address this specificity challenge, we report the enzymatic synthesis of a 150-member library of site-specifically fluorinated Lewisx analogues ('glycofluoroforms') using naturally occurring enzymes and fluorinated monosaccharides. Subsequent incorporation of a subset of these glycans into nanoparticles or a microarray revealed a striking spectrum of distinct binding intensities across different proteins that recognise Lewisx. Notably, we show that for two proteins with unique binding sites for Lewisx, glycofluoroforms exhibited enhanced binding to one protein, whilst reduced binding to the other, with selectivity governed by fluorination patterns. We finally showcase the potential diagnostic utility of this approach in glycofluoroform-mediated bacterial toxin detection by lateral flow. Distinguishing between different proteins that each bind to the same type of glycan is challenging. Here, the authors demonstrate that an enzymatically synthesised library of Lewisx 'glycofluoroforms' that feature site-specific fluorination can discriminate closely related proteins. [ABSTRACT FROM AUTHOR]

Druggable pockets are protein regions that have the ability to bind organic small molecules, and their characterization is essential in target-based drug discovery. However, deriving pocket descriptors is challenging and existing strategies are often limited in applicability. We introduce PocketVec, an approach to generate pocket descriptors via inverse virtual screening of lead-like molecules. PocketVec performs comparably to leading methodologies while addressing key limitations. Additionally, we systematically search for druggable pockets in the human proteome, using experimentally determined structures and AlphaFold2 models, identifying over 32,000 binding sites across 20,000 protein domains. We then generate PocketVec descriptors for each site and conduct an extensive similarity search, exploring over 1.2 billion pairwise comparisons. Our results reveal druggable pocket similarities not detected by structure- or sequence-based methods, uncovering clusters of similar pockets in proteins lacking crystallized inhibitors and opening the door to strategies for prioritizing chemical probe development to explore the druggable space. PocketVec is a computational strategy to generate protein binding site descriptors through inverse virtual screening, which the authors use to systematically explore the human proteome and to characterize over 32,000 druggable pockets. [ABSTRACT FROM AUTHOR]