Search Results (412)

The bulb of Fritillaria species called “Bei Mu” is a well-known traditional Chinese medicine. We have reported some potential off-target effects of “Bei Mu” due to peimine’s blockade of hERG (human Ether-a-go-go-Related Gene) channels. This research investigated the modulatory effects of three major alkaloid analogs of “Bei Mu” and their cooperative effects on hERG channels using manual whole-cell patch-clamp techniques. Results showed that peiminine and sipeimine blocked hERG currents with IC₅₀s of 36.8 ± 2.5 μM and 47.6 ± 9.8 μM, which were close to that of peimine (26.1 ± 3.5 μM). Peiminine-induced blockade increased with increasing depolarizing strengths, durations, and frequencies, which suggested a preferential binding to open or inactivated states. The reduced blockade by the less inactivating S631A mutation supported peiminine‘s inactivation preference. Molecular docking and dynamics simulations confirmed the hERG-blocking activities of the three alkaloids and provided further insight into potential mechanisms. We also discovered antagonistic effects of the three alkaloids at nearly all concentrations tested, which might help reduce potential cardiotoxicities. To our knowledge, this is the first study to investigate combination effects of chemicals from one herb on hERG channels. In conclusion, peiminine and sipeimine can block hERG channels in a way similar to peimine, but antagonistic effects exist among them. Full article

Sophorolipids (SLs) constitute a group of unique biosurfactants in light of their unique properties, among which their physicochemical characteristics and antimicrobial activity stand out. SLs can exist mainly in acidic and lactonic forms, both of which display inhibitory activity. This study explores the interaction of non-acetylated acidic SL with bovine serum albumin (BSA). SL significantly enhances BSA’s thermal stability, increasing its midpoint unfolding temperature from 61.9 °C to approximately 76.0 °C and ΔH from 727 to 1054 kJ mol⁻¹ at high concentrations, indicating cooperative binding. Fourier-Transform Infrared Spectroscopy (FTIR) analysis confirms SL’s protective effect against thermal unfolding, enabling BSA to maintain its helical structure at 70 °C, distinguishing it from other surfactants that cause denaturation. Furthermore, SL fundamentally alters the sequence of thermal unfolding events; β-aggregation precedes helical domain unfolding, suggesting protective binding to BSA’s helical regions. Computational docking reveals high-affinity binding (Kd = 14.5 μM). Uniquely, SL binds between BSA domains IB and IIIA, establishing hydrophobic interactions, salt bridges, and hydrogen bonds, thus stabilizing the protein’s 3D structure. This distinct binding site is attributed to SL’s amphipathic character. This work deepens the understanding of the molecular characteristics of SL–protein interactions and contributes to improving the general knowledge of this outstanding biosurfactant. Full article

Human methyltransferase-like protein 16 (METTL16) installs N⁶-methyladenosine on U6 small nuclear RNA (snRNA) and other RNAs. Multiple X-ray crystal structures of METTL16 have been published; however, we do not yet fully understand the structure–function relationships of specific residues. We designed 38 mutants, including seven cancer-associated mutants, and used electrophoretic mobility shift assays and single-turnover kinetic assays to better understand the functional roles of specific domains and amino acid residues in binding to U6 snRNA, formation of the METTL16•U6 snRNA•S-adenosylmethionine (SAM) complex, and the rate of methylation. While point mutations in the methyltransferase domain mildly weaken the binding of METTL16 to U6 snRNA, the C-terminal vertebrate conserved regions (VCRs), particularly the arginine-rich region (R382 to R388), mediate cooperative binding and contribute more to RNA binding. All METTL16 K-loop mutants displayed tighter SAM binding, suggesting that the K-loop blocks SAM binding. In addition, residues E133 and F227 are critical for stabilizing SAM binding. Mutations in the ₁₈₄NPPF₁₈₇ catalytic core and R282A abolished methyltransferase activity. Two METTL16 somatic cancer-associated mutants (G110C and R241Dfs*2) displayed reduced methylation activity. This mutational analysis expands our understanding of how specific domains and residues contribute to substrate-binding activity and methylation of U6 snRNA catalyzed by METTL16. Full article

The escalating crisis of multidrug resistance, together with the persistence of antibiotic residues in clinical and environmental matrices, demands integrated strategies that couple sensitive detection, efficient decontamination, and controlled delivery. However, current techniques for quantifying avibactam (AVI)—a broad-spectrum β-lactamase inhibitor—such as HPLC-UV lack the sensitivity and specificity required for both therapeutic drug monitoring and environmental surveillance. Encapsulation of AVI within cyclodextrins (CDs) may simultaneously enhance its stability, bioavailability, and detectability, while the high binding affinities of CDs position them as molecular traps capable of scavenging residual AVI. In this study, the inclusion complexation of AVI with various CDs was examined through molecular dynamics (MD) simulations, experimental isothermal titration calorimetry (ITC), and non-covalent interaction (NCI) analysis. Stable 1:1 inclusion complexes were observed between AVI and β-cyclodextrin (β-CD), 2,6-dimethyl-β-cyclodextrin (DM-β-CD), and 2-hydroxypropyl-β-cyclodextrin (HP-β-CD), with standard Gibbs free energies of binding (ΔG°) of –3.64, –3.24, and –3.11 kcal/mol, respectively. In contrast, γ-cyclodextrin (γ-CD) exhibited significantly weaker binding (ΔG° = –2.25 kcal/mol). DFT-based NCI analysis revealed that cooperative interaction topology and cavity complementarity, rather than the sheer number of localized contacts, govern complex stability. Combined computational and experimental data establish β-CD derivatives as effective supramolecular hosts for AVI, despite an entropic penalty in the DM-β-CD/AVI complex. These CD–AVI affinities support the development of improved analytical methodologies and pharmaceutical formulations, and they also open avenues for decontamination strategies based on molecular trapping of AVI. Full article

DprA (also known as Smf) is a conserved RecA mediator originally characterized by its role in natural chromosomal transformation, yet its widespread presence across bacteria hints at broader DNA metabolic functions. Here, we demonstrate that Bacillus subtilis DprA enhances the frequency of Escherichia coli Hfr conjugation in vivo. In vitro, RecA·ATP binds and cooperatively polymerizes in a 50-nucleotide (nt) polydeoxy T (dT)₅₀ ssDNA to form dynamic filaments that SSB inhibits, an effect fully reversed by Bacillus subtilis DprA. Escherichia coli RecA bound to (dT)₂₁ exhibits minimal dATPase activity, but the addition of B. subtilis DprA significantly stimulates RecA dATP hydrolysis. B. subtilis RecA·dATP readily assembles on (dT)₂₀ complexes, and DprA allosterically activates RecA on even shorter (dT)₁₅ substrates. Combining biochemical assays with a fully atomic model of the RecA–DprA–ssDNA complex, we proposed that only one DNA binding site of the DprA dimer engages the ssDNA during RecA loading, owing to steric constraints. This work refines the mechanism of DprA-mediated RecA nucleation and defines the minimal ssDNA footprint required for mediator activity. Full article

To address the challenge of developing the first squaramide-based ion pair receptor acting as an iniferter in the polymerization process, a well-known BDPA molecule with specific radical functions was incorporated into its structure. The developed ditopic receptor demonstrated the ability to cooperatively bind ion pairs. Moreover, it proved to be an effective iniferter in the polymerization reaction using methyl methacrylate. The polymerization process preserved the ion-binding properties of the receptor, enabling the formation of functional polymeric materials. It was shown that the resulting polymer with the embedded receptor can be used for salt extraction from both solid and liquid phases, whereas the reference receptor lacking the BDPA unit did not exhibit this capability. This opens new avenues for the design of intelligent and selective polymeric materials for applications in supramolecular chemistry and separation technologies. Full article

The presence of sulfate anions induces the self-assembly of anion-binding bis(cyclopeptides) in which two cyclopeptide rings are connected via a rigid linker. In this way, 2:2 complexes are formed in which two anions are sandwiched between two bis(cyclopeptide) moieties. Mixed species can be formed if two bis(cyclopeptides) containing different linkers are present and the structural mismatch between the linkers can be compensated for in the self-assembled product. Sulfate complexation seems to proceed with positive cooperativity, leading primarily to the fully formed complexes. As a consequence, these bis(cyclopeptides) represent useful building blocks for the anion-mediated formation of self-assembled products with controllable structural complexity. Full article

Non-cooperative games in normal form are specified by a player set, sets of player strategies, and payoff functions. Cooperative games, meanwhile, are specified by a player set and a worth function that maps coalitions of players to payoffs they can feasibly achieve. Although these games study distinct aspects of social behavior, this paper proposes a novel attempt at relating the two models. In particular, cooperative games may be represented by a non-cooperative game in which players can freely sign binding agreements to form coalitions. These coalitions inherit a joint strategy set and seek to maximize collective payoffs. When these coalitions play against one another, the equilibrium payoffs for each coalition coincide with what is predicted by the worth function. This paper proves sufficient conditions under which cooperative games can be represented by non-cooperative games. This paper finds that all strictly superadditive partition function form (PFF) games can be represented under Nash equilibrium (NE) and rationalizability; that all weakly superadditive characteristic function form (CFF) games can be represented under NE; and that all weakly superadditive PFF games can be represented under trembling hand perfect equilibrium (THPE). Full article

Curli fimbriae are a major component of biofilm formation in Escherichia coli, and their expression is regulated by numerous transcription factors and small regulatory RNAs (sRNAs). The RcsD-RcsC-RcsB phosphorelay system, which is involved in the envelope stress response, plays a role in this regulation. In this study, we report that DNase-I footprinting analysis revealed that the response regulator RcsB interacts with the −31 to +53 region of the promoter region of csgD, which encodes a major regulator of biofilm formation, and thus contributes to its transcriptional repression. Additionally, overexpression of RcsB or RcsB D56A that could not be phosphorylated by the histidine kinases RcsC and D both significantly reduced csgD expression and suppressed Curli formation. This indicates that the phosphorylation of RcsB has an insignificant impact on its affinity for its operator sites. Furthermore, we confirm that RcsB binds cooperatively to the csgD promoter region in the presence of the nucleoid-associated protein H-NS. Our study also confirms that RcsB positively regulates the expression of an sRNA, RprA, which is known to reduce mRNA csgD mRNA translation RprA via its binding to the 5′-untranslated region (UTR) of csgD. These findings indicate that, in E. coli, the RcsBCD system suppresses csgD expression through both direct transcriptional repression by the regulator RcsB and translational repression by the sRNA RprA. Full article

Nucleolin (NCL), an RNA-binding protein which regulates critical cellular processes, is frequently dysregulated in human cancers, including breast cancer, making it an attractive therapeutic target. However, molecular details of the RNA-NCL interaction have not been investigated yet. A tRNA fragment named tRF3E, displaying tumor suppressor roles in breast cancer, was found to bind NCL with high affinity displacing NCL-controlled transcripts. Here, we investigated the determinants and cooperativity of tRF3E-NCL interaction by Electrophoretic Mobility Shift Assays and in silico docking analysis, using wild-type or mutated tRF3E. We found that NCL, through its RNA-binding domains (RBD1–2 and RBD3–4), binds simultaneously two tRF3E molecules, giving rise to an energetically favored complex. Instead, a mutant form of tRF3E (M19–24), in which the NCL recognition element in position 19–24 has been disrupted, contacts NCL exclusively at RBD3–4, causing the loss of cooperativity among RBDs. Importantly, when expressed in MCF7 breast cancer cells, tRF3E significantly reduced cell proliferation and colony formation, confirming its role as tumor suppressor, but tRF3E functional properties were lost when the 19–24 motif was mutated, suggesting that cooperativity among multiple domains is required for the NCL-mediated tRF3E antitumor function. This study sheds light on the dynamic of RNA-NCL interaction and lays the foundations for using tRF3E as a promising NCL-targeted biodrug candidate. Full article

T-2 toxin, a type A trichothecene mycotoxin produced by Fusarium species, is widely present in cereals and their processed products, posing a significant contaminant in food safety. To address the food safety challenges caused by this toxin, we established a dual signal enhancement by magnetic separation and split aptamer for ultrasensitive T-2 toxin detection. In this method, the introduction of magnetic graphene oxide (MGO) enhanced signal and increased sensitivity by reducing background interference. The shortened split aptamer reduces non-specific binding to MGO via decreased steric hindrance, thereby facilitating rapid target-induced dissociation and signal generation. A FAM fluorophore-labeled split aptamer probe FAM-SpA1-1 was quenched by MGO. While the fluorescence intensity remained nearly unchanged when the unlabeled split aptamer probe SpA1-2 was introduced alone, a significant fluorescence recovery was observed upon simultaneous addition of SpA1-2 and T-2 toxin. This recovery resulted from the cooperative binding of SpA1-1 and SpA1-2 to T-2 toxin, which distanced the FAM-SpA1-1 probe from MGO. Therefore, the proposed biosensor demonstrated excellent stability, reproducibility, and specificity, with a linear response range of 10–500 pM and a limit of detection (LOD) of 0.83 pM. Satisfactory recovery rates were achieved in spiked wheat (86.0–114.2%) and beer (112.0–129.6%) samples, highlighting the biosensor’s potential for practical applications in real-sample detection. This study establishes the T-2 toxin split aptamer and demonstrates a novel dual-signal enhancement paradigm that pushes the sensitivity frontier of aptamer-based mycotoxin sensors. Full article

Background: The late embryogenesis abundant (LEA) gene family plays a critical role in abiotic stress tolerance during plant growth and development. Myricaria laxiflora, as a key pioneer species in the extreme hydrological fluctuation zone of the Yangtze River, has evolved unique adaptation mechanisms potentially linked to gene family evolution. However, the molecular mechanisms underlying how the LEA gene family responds to alternating flooding–drought cycles remain unclear. Methods and Results: In this study, we identified 31 LEA genes through whole-genome and transcriptome analyses using bioinformatics approaches, and classified them into nine subfamilies based on protein sequence similarity. These genes were distributed across 12 chromosomes. Our analysis revealed that LEA promoters contain cis-acting elements associated with anaerobic induction, abscisic acid (ABA) response, and combined low-temperature/light stress, suggesting their role in a multi-tiered environmental signal integration network. Spatio-temporal expression profiling further indicated that root-specific LEA genes maintain cellular integrity via membrane lipid binding, while leaf-predominant members cooperate with the antioxidant system to mitigate photoinhibition damage. Conclusions: This study elucidates the dynamic regulatory mechanisms of the LEA gene family during flooding-drought adaptation in M. laxiflora, providing molecular targets for ecological restoration in the Yangtze River Basin. Full article

In symmetric games with externalities across coalitions, we investigate how three players form coalitions using two solutions: ${\mathbf{n}}^{\ast }$, which is a focal prediction of coalition structure in a class of noncooperative coalitional bargaining games, and equilibrium binding agreements, which represent the cooperative blocking approach. We find that the coarsest equilibrium coalition structure (based on the latter notion) is never finer than ${\mathbf{n}}^{\ast }$, and we provide a sufficient and necessary condition for these two solutions to generate the same coalition structure (i.e., the two solutions coincide if and only if the first coalition to form in ${\mathbf{n}}^{\ast }$ is not a two-player coalition or a particular condition about average coalitional worths is satisfied). In symmetric games with more than three players, we demonstrate through a series of examples that any relationship between these two solutions is possible. We also discuss symmetric games with positive externalities or equal division in which these two solutions coincide. Full article

Receptors capable of binding both positive and negative ions are an important domain of supramolecular chemistry with valuable application potential. A Complete thermodynamic description of the equilibria related to ion pair recognition is beneficial in developing the optimized receptor systems, although it represents a difficult task that is rarely resolved due to various coupled processes. Here, we present a comprehensive study of ion pair (NaCl, NaHSO₄, and NaH₂PO₄) binding by a ureido–amide calix[4]arene host in acetonitrile using a series of experimental techniques and molecular dynamics simulations. We devoted particular attention to characterizing the side processes (ion association and salt precipitation) and included them in the models describing ion pair complex formation. For this purpose, a multimethod approach (potentiometry, conductometry, ITC, flame AES) was employed, generating reliable data which provided insight into the thermodynamic effect of each included equilibrium. Positive cooperativity was observed in the context of NaCl and NaHSO₄ binding by the studied calixarene. Computational results related to the NaCl complex in acetonitrile revealed that favorable Coulombic interactions, changes in affinity for solvent molecule inclusion, and intramolecular hydrogen bonding contributed to cation-induced cooperativity. Full article

Obesity is a significant global health issue, profoundly affecting metabolic and cardiovascular health and other related chronic conditions. In Chile, the prevalence of obesity is among the highest within the Organisation for Economic Cooperation and Development (OECD) countries, highlighting a critical public health challenge. This narrative review examines current evidence on the independent and potential synergistic roles of omega-3 fatty acids and exercise in managing obesity-related metabolic dysfunction. Omega-3 fatty acids, particularly eicosapentaenoic acid (EPA), have been shown to lower triglyceride levels, enhance lipid metabolism, and modulate inflammation via pathways involving peroxisome proliferator-activated receptors (PPARs) and sterol regulatory element-binding protein-1c (SREBP-1c). Exercise interventions, such as moderate-intensity continuous training (MICT) and high-intensity interval training (HIIT), provide distinct yet complementary metabolic benefits. Specifically, MICT improves body fat distribution and mitochondrial efficiency, whereas HIIT has notable effects on metabolic adaptability and insulin signaling. Additionally, emerging evidence points toward a potential role of the kinin-kallikrein system, particularly kallikrein 7 (KLK7), in obesity-associated insulin resistance. Despite these promising findings, several knowledge gaps persist regarding optimal dosing, intervention timing, population-specific effects, and the exact mechanisms behind the potential synergistic interactions between omega-3 supplementation and structured exercise. This review emphasizes the importance of conducting further research, particularly controlled clinical trials, to clarify these combined interventions’ effectiveness and establish targeted therapeutic strategies tailored to individual metabolic profiles. Full article