Search Results (1,089)

Two metallacyclic tetranuclear Fe(III) complexes, [{Fe₂(μ-O)(μ-RCOO)₂(tpon)}₂](BPh₄)₄ [R = Me (1), Ph (2)], where the flexible ditopic ligand tpon (N,N,N′,N′-tetrakis(2-pyridylmethyl)octane-1,8-diamine) links two μ-oxo-bis(μ-carboxylato) triple-bridged dinuclear units, have been prepared. Single-crystal X-ray diffraction establishes that both complexes adopt a 26-membered macrocyclic framework featuring an internal cavity capable of guest inclusion. Notably, incorporation of a monoatomic μ-oxo bridge enforces an outward orientation of the ligand alkyl chains, thereby suppressing the “zipper effect” observed in the previously reported Mn(II) analogue and facilitating the encapsulation of an acetone molecule. UV–vis absorption and diffuse-reflectance spectra confirm that the tetranuclear scaffold remains intact in both the solid state and in solution. These results demonstrate that modulating local coordination directionality via μ-oxo bridging is an effective strategy for controlling the global conformation and host–guest properties of large metallasupramolecular architectures. Full article

Background: Amorphous drug formulations are commonly used to improve the solubility and bioavailability of poorly soluble molecular pharmaceuticals, yet less is known about their molecular conformations and local bonding interactions than their crystalline phases. Methods: High-energy X-ray diffraction structure factor measurements have been made on liquid and glassy nifedipine (NIF), felodipine (FEL), NIF 1:3 polyvinylpyrrolidone (PVP), and FEL 1:3 PVP wt.% mixtures. The corresponding X-ray pair distribution functions have been interpreted using empirical potential structure refinement using different models and density functional theory conformer calculations. Results: In both NIF and FEL, the NH···O inter-molecular hydrogen bonds between the pyridyl nitrogen and ester carbonyls are found to be considerably weaker than those observed in the crystalline polymorphs. For nifedipine, it is proposed that either inter-molecular NH…ON nitro bonds are present and/or a fraction (<20%) of conformational changes, with the aryl ring flipped, occur in the liquid state. For felodipine, the models indicate significant disorder associated with the methyl and ethyl side chains in the liquid state, with the main peak intensity at 3.0 Å arising from intra-molecular Cl-Cl atom pairs. When nifedipine molecules are incorporated into PVP, our models show they possess stronger NH···O bonds to the PVP polymer than felodipine molecules, which have stronger affinity for bonding to the polymer than to other felodipine molecules. Conclusions: The amorphous forms of both NIF and FEL show much weaker hydrogen bonding than found in their crystalline phases. Liquid NIF also exhibits configurations which are not observed in the crystal phases. Full article

Lophatherum gracile Brongn. (L. gracile) has been utilized as a food or medicinal plant for a long time. A series of chemical and spectroscopic methods was used to characterize the extracted and purified L. gracile polysaccharide (LGP). Its in vivo antitumor activity in the H22 tumor-bearing mice model was studied. LGP has a molecular weight of 1.42 × 10⁶ Da and is mainly composed of arabinose (Ara), galactose (Gal), xylose (Xyl), and other monosaccharides. NMR spectra suggest that LGP may be composed of 1,3-β-Galp and 1,3,6-β-Galp main chains, and a side chain formed by a 1,5-α-Araf short chain. The termini are composed of T-α-Araf, while [→4) -α-GalpA-(1→2)-α-Rhap-(1→] are attached to the backbone as short side chains, and the other monosaccharides are an arabinogalactan composed of the termini. SEM and AFM revealed that LGP presents a lamellar morphology with smooth surfaces and notable molecular aggregation. The Congo red assay, CD spectroscopy, and XRD collectively indicated the absence of a triple helix conformation and an overall amorphous structure in LGP. Compared with the model group, LGP treatment improved body responses, immune organs, and SOD and MDA levels. The tumor cell apoptosis rate in the high-dose LGP group was 50.0%. In the distribution of the tumor cell cycle, the proportions of the S phase were 29.1% and 41.1% in the low-dose LGP and high-dose LGP groups, respectively, compared with 12.2% in the model group. These results suggest that LGP exhibits preliminary antitumor activity, indicating its potential as a candidate for further cancer research. Full article

Polymers are widely used in applications ranging from flexible electronics and thermal interface materials to structural composites and textile fabrics. Their inherently low $\kappa$, strongly governed by molecular structure and morphology, makes polymers a challenging yet scientifically rich class of materials for thermal transport studies. Over the past two decades, modeling and simulation have played a central role in elucidating heat transport mechanisms in polymers and in guiding the rational design of polymer systems with enhanced or tunable thermal properties. This review provides a comprehensive overview of the theoretical frameworks and computational approaches used to model thermal transport in polymers. We discuss atomistic methods including density functional theory, molecular dynamics, and first-principles Boltzmann transport equation approaches, as well as emerging data-driven and machine learning-based techniques. Special attention is devoted to the effects of chain conformation, crystallinity, orientation, interchain coupling, interfaces, and nanocomposite architectures. Current challenges and future research directions are highlighted, with particular emphasis on multiscale modeling, method integration, and predictive materials design. Full article

Peptide binders, serving as a critical drug modality bridging small-molecule compounds and protein macromolecules, can effectively mimic the secondary structural elements of natural proteins. Peptides exhibit unique physicochemical advantages when targeting protein protein interaction (PPI) interfaces, which are typically characterized by flat surfaces and extensive contact areas. Recently, diffusion models represented by RFdiffusion have established a new computational paradigm for protein backbone generation by defining a denoising process over the rigid-body transformation group. However, in the de novo design of binders targeting “undruggable” PPI targets, this general paradigm encounters significant adaptability bottlenecks. First, its underlying rigid-body assumption struggles to accurately describe the dynamic induced-fit process of peptides at the binding interface. Second, it lacks sufficient robustness to the experimental resolution heterogeneity inherent in training data. Furthermore, the decoupled two-stage generation of sequence and structure severs the synergy of physicochemical properties, leading to backbones with idealized, singular secondary structures that lack authentic spatial binding capacity and reasonable side-chain physicochemical features. To address these challenges, this study proposes PPI-Diff, a novel generative framework. While preserving the generative capability of diffusion models, PPI-Diff introduces three core mechanisms: (1) a resolution-aware constraint mechanism that maps the measurement precision of experimental data into explicit contextual constraints to dynamically suppress geometric noise from low-resolution samples; (2) an internal-coordinate-driven manifold diffusion model that performs conformational evolution on a Riemannian manifold constructed by dihedral angles, balancing local stereochemical validity with the precise capture of flexible peptide conformations; and (3) a geometry-semantic synergistic modeling mechanism that leverages the evolutionary embeddings of a pre-trained protein language model (ESM-2) as latent variables to align structure generation with biophysical functions. Systematic benchmarking demonstrates that, on a strictly non-homologous test set, the binders generated by PPI-Diff significantly outperform existing baseline models in terms of interface contact density, stereochemical validity, and sequence novelty. Full article

Mitochondria regulate nuclear genomes and their own genetic material, primarily to provide energy in eukaryotes. Currently, high-throughput sequencing technologies are being used to resolve the mitochondrial genomes of various edible fungi. However, the application of pan-genomes for the analysis of edible mushroom mitochondrial genomes remains unexplored. In this study, we conducted a comparative mitochondrial genome analysis of 31 Hypsizygus marmoreus strains (four newly sequenced monotypes and 27 public datasets), ranging from 98,284 to 111,087 bp. This variation was determined to be primarily driven by dynamic changes in non-coding regions, particularly intronic polymorphisms in the cox1 gene. Further, transfer RNA (tRNA) secondary structures exhibited atypical globular and elongated conformations alongside copy number variations. Additionally, codon usage showed a pronounced A/T bias, whereas core respiratory chain genes demonstrated an evolutionary pattern of strong purifying selection. Furthermore, the 31 mitochondrial genomes of H. marmoreus were found to harbor eight gene rearrangement patterns and five genetic clusters, and the pan-genome analysis (220,364 bp, 217 nodes) captured abundant single-nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and structural variations. This study provides breeding-relevant genetic markers and a genomic framework for H. marmoreus germplasm classification, genetic improvements, and the molecular breeding of stress-resilient varieties. Full article

Photochromic molecules, capable of reversible isomerization under specific light irradiation, are pivotal for developing advanced photo-responsive materials. Azobenzene derivatives, in particular, are renowned for their significant conformational change, excellent reversibility, and high photostability. This study presents a novel cyclic diazo compound (CDTA) comprising two azobenzene units connected via flexible glycol chains. The photo-responsive behavior of CDTA doped into the liquid crystal 4-cyano-4′-octylbiphenyl (8CB) was systematically investigated. The composite exhibits a pronounced photo-induced phase transition from a liquid crystalline to an isotropic state under 365 nm UV irradiation, accompanied by a reversible change in light transmittance. The response kinetics were found to be highly dependent on temperature and dopant concentration. At 35 °C, the UV response time was accelerated to 6.8 s, attributed to the transition of the host 8CB from a smectic to a nematic phase. Furthermore, the composite demonstrated dual responsiveness: optical switching under UV light and electrical switching under an applied field in its nematic state. This work elucidates the interaction between molecular structure and photo-response in a liquid crystalline matrix, offering insights for designing next-generation smart windows and adaptive optical devices. Full article

Charge transport underpins essential biological processes, including cellular respiration, photosynthesis, and enzymatic catalysis. Advances in molecular electronics have enabled single-molecule measurements that unequivocally establish redox-active proteins as efficient electron conductors, with their metal cofactors serving as intrinsic redox relays. By contrast, ubiquitous non-redox proteins lacking such redox centers have long been considered poor conductors. However, recent research has challenged this view, demonstrating that efficient charge transport in non-redox proteins can be mediated through polypeptide backbones, aromatic side-chain arrays, and hydrogen bond networks. This review surveys progress in understanding the single-molecule conductance of non-redox proteins. Firstly, we elucidate the fundamental transport mechanisms, highlighting the interplay between coherent tunneling and thermally activated hopping. We then provide an overview of state-of-the-art experimental techniques for single-molecule characterization. Through analysis of diverse systems spanning short peptides to large enzymes, we illustrate how aromatic amino acid networks and dynamic conformational fluctuations govern conductance, enabling emerging applications in label-free biosensing and single-molecule protein/DNA sequencing. Finally, we discuss persistent challenges and outline future opportunities for integrating protein-based conductors into bioelectronic devices. This review aims to stimulate further research and pave the way for novel applications harnessing protein conductance. Full article

Accumulation of microplastics (MPs) in aqueous environments poses a serious ecological problem nowadays. MP particles are able to adsorb pollutants of different kinds and to transport them to living organisms, leading to biotoxicity. Hence, investigation of the adsorption of pollutants of different molecular weights onto MP particles is an important task. We employed the numerical Scheutjens–Fleer self-consistent field method to study (i) the formation of MP particles consisting of homopolymer macromolecules and (ii) the adsorption of pollutant homopolymer chains onto the MP particles. Under poor solvent conditions, the polymer macromolecules were shown to form MPs with a constant density inside the particle and with an interfacial layer at its periphery. The size of the MP particles and the thickness of the interfacial layer were controlled by the solvent quality. MP particles were shown to adsorb pollutant polymer chains from the surrounding liquid due to higher compatibility of the MP particle with the pollutant polymer chains as compared to the solvent. The amount of adsorbed polymer pollutant increased with the increase of its concentration in solution. Softer MP particles were shown to adsorb larger amounts of pollutants due to a broader interfacial layer. The conformational characteristics of the adsorbed polymer chains (trains, loops, and tails) were studied in detail. Full article

Rhizopus oryzae lipase (ROL) is a key enzyme involved in olive oil spoilage and acts as a virulence factor in fungal infections. Natural lipophilic lipase inhibitors are crucial for mitigating economic losses resulting from lipid degradation in stored or decaying olive fruits. This study evaluated a series of enzymatically synthesized piperate esters with varying alkyl chain lengths (butyryl, C4; octyl, C8; dodecyl, C12) for their inhibitory effects on ROL activity. Octyl piperate (C8) demonstrated the highest potency, with IC₅₀ values of 0.05 mg/mL using methods B and C or 0.25 mg/mL using method A. Molecular docking indicated that C8 achieved the most favorable predicted binding energy (Gscore: –11.134 kcal/mol), primarily through hydrophobic interactions (Val329, Ala212, Phe209) and hydrogen bonds with oxyanion hole residues (Ser268, Thr206, Gln241). Molecular dynamics simulations confirmed that C8 maintained stable binding and stabilized the catalytic residues. In comparison, C4 exhibited weaker interactions, and the longer C12 chain induced conformational instability and steric hindrance. These results establish a parabolic structure–activity relationship, identifying the octyl chain (C8) as optimal for ROL inhibition among the tested derivatives. The rational design of lipophilic, biodegradable lipase inhibitors thus positions octyl piperate as a promising candidate for extending olive storage and shelf life, and as a scaffold for developing natural antifungal agents targeting virulent R. oryzae strains. Full article

Dietary fiber (DF) has a profound influence on human health mainly by modulating the gut microbiota. This review provides an overview of DF derived from cereals, legumes, fruits, vegetables, fungi, and seaweeds, specifically addressing the relationship between microbial utilization and source-specific structural characteristics (such as linking patterns, conformation, solubility, and fermentability). Due to these structural properties, different DFs display selective microbial responses that favor fermentation and the production of short-chain fatty acids (SCFAs). These microbial responses and fermentation-derived metabolites associated with DF intake may contribute to reduced risk of obesity, diabetes, inflammatory bowel disease, and other chronic disorders. This review does not address the trial heterogeneity, dose response, safety, and conflicting evidence, and much of the available evidence is largely observational and heterogeneous. Future studies should focus on dose–response trials of defined DF structures with standardized microbiome and metabolomic endpoints, including validation in human interventions. This review summarizes the DF source and structure, selective changes in the microbiota across various study types, including in vitro, animal models, and human studies, and how these relate to overall health. Full article

Ultrafine hematite particles (<10 μm), commonly generated in beneficiation circuits, exhibit poor flocculation and slow settling, posing challenges for solid–liquid separation. This study investigates the influence of the anionic polyacrylamide (APAM) molecular weight on ultrafine hematite flocculation under controlled laboratory conditions, combining macroscopic experiments with molecular dynamics simulations (MDSs). Sedimentation tests show that the APAM molecular weight strongly affects settling kinetics, supernatant clarity, and floc structure, with the settling rate, flocculation-stage reaction time, supernatant turbidity, and underflow concentration exhibiting a non-monotonic trend and optimal performance at seven million. Under this condition, particles aggregate most efficiently, achieving a turbidity of 182 NTU, an underflow concentration of 51.5%, and the largest compact flocs, averaging 379.8 μm with a fractal dimension of 1.71. Higher molecular weights (≥9 million) induce chain coiling, reduce floc compactness, increase water retention, and impair settling. MDS indicates that polymer–surface interactions improve with an increasing polymerisation degree only up to an intermediate chain length; a polymerisation degree of 30 exhibits the most favourable extended–flexible conformation, maximal surface enrichment, strongest coordination between carboxyl groups and surface Fe atoms, lowest adsorption energy, and fastest adsorption kinetics. The functional-group distribution and hydrogen-bond analyses show that –NH₂ and –COO^– groups dominate interfacial interactions, with a polymerisation degree of 30 yielding the highest density of interfacial hydrogen bonds. By correlating macroscopic experiments with molecular-scale observations, this work provides mechanistic insight into how the APAM chain length governs ultrafine hematite flocculation, highlighting the role of polymer conformation and multipoint adsorption in controlling the settling performance. Full article

How ordered and mutually independent are semiflexible ring polymers (RPs) confined to a spherical cavity of variable radius? By varying the cavity radius, we systematically investigate the effect of the confinement size on the conformations of RPs using the coarse-grained molecular dynamics simulations. The results reveal that as the bending energy increases, the RPs exhibit a transition from a purely flexible coil to an elongated oblate-shaped object and, eventually, to a disk-like conformation. Simultaneously, the stacked aggregates composed of adjacent, mutually nearly parallel, semiflexible RPs emerge for stiffer chains. We find that the structural modulation of the stacked aggregates is regulated by the confinement size. For the conditions of strong confinement ($R<2R_g$, where $R_g$ is the radius of gyration of an RP), the semiflexible RPs undergo peculiar deformations and twisting that lead to disruption of the stacked aggregates. At $R\approx 2R_g$, the average number of the RPs per stack reaches a maximum. Concurrently, the order of spatial alignment of all semiflexible RPs is maximized with the global orientational-order parameter reaching the value $S\approx 0.79$. As the cavity radius further increases, at $R>3R_g$, the semiflexible RPs gain greater mobility resulting in diverse orientations of the aggregates being formed, with the order parameter dropping to $S\approx 0.05$. These findings provide important quantitative insights for future applications of the RPs, i.e., in micro- and nanodevice assembly. Full article

Growing demand for low-sodium surimi products has driven the search for safe salt alternatives. Anionic peptides (APPs) and cationic peptides (CPPs) were isolated from sheepskin collagen via Diethylaminoethyl (DEAE) chromatography. CPPs contained higher arginine (46.11%) and lysine (4.64%) than APPs (40.57% and 3.99%, respectively), while APPs were enriched in acidic amino acids like glutamic acid (3.88%). Comprehensive evaluations of low-salt silver carp surimi gels showed both peptides significantly improved gel strength and water-holding capacity (WHC). The water-holding capacity increased from 60.68% in the blank control group to 74.31% in the CPP-treated group, while that in the APP-treated group was 66.86%. Cooking loss was significantly reduced, decreasing from 40.64% in the blank control group to 28.57% in the CPP-treated group and 34.52% in the APP-treated group. The samples achieved a quality comparable to that of the NaCl-supplemented group, with CPP outperforming APP in terms of hardness and gel network density. The LF-NMR confirmed enhanced water retention by reducing free water (T₂₂) and increasing bound water (T₂b). The FTIR indicated a conformational shift from α-helix to β-sheet, and the SEM revealed denser networks with fewer large voids. The SDS-PAGE demonstrated enhanced myosin heavy chain (MHC) cross-linking, more pronounced in the CPP-treated samples. CPPs exerted stronger electrostatic attraction with negatively charged surimi proteins (isoelectric point 5.5), while APPs chelated Ca²⁺ to activate transglutaminase. These findings validate APPs and CPPs as promising salt substitutes, enabling low-sodium surimi production and high-value utilization of sheepskin by-products. Full article

The TonB-dependent receptors (TBDRs) FepA and FhuA transport the siderophores ferric enterobactin (FeEnt) and ferrichrome (Fc), respectively, through the Gram-negative bacterial outer membrane. Their uptake mechanism involves conformational change in an ~150 residue N-terminal luminal domain (NTLD), located within their C-terminal β-barrel (CTβB) channels. We identified four internal sites (1–4) in TBDR that form a conserved network of ion pairs encircling the NTLD-CTβB interface. We tested the mechanistic importance of these electrostatic interactions by engineering systematic Ala substitutions in FepA and FhuA for the acidic or basic side chains that comprise them. Siderophore nutrition assays, colicin susceptibility tests and fluorescence spectroscopic uptake measurements of the mutants showed the importance of site-2, that adheres the base of NL1/Nβ3 and Nβ5 of the NTLD to β14 and β17 on the interior of the CTβB. Disruption of electrostatic bonds at site-2 reduced or eliminated ferric siderophore uptake and severely curtailed colicin susceptibility. Despite these reductions in ligand transport, fluorescent spectroscopic binding measurements showed that the site-2 mutations did not alter the affinity of FepA for FeEnt, nor FhuA for Fc. Elimination of ionic interactions at the three other locations in FepA (sites-1, -3, -4) did not reduce FeEnt uptake. Lastly, the disruption of ionic bonding at site-2 in FepA rendered it more susceptible to proteolysis, in part by OmpT, suggesting that ablation of ionic interactions in site-2 destabilized the NTLD within the CTβB. Overall, the experiments demonstrated that the ion pairs at site-2 in FepA and FhuA, that are evolutionarily conserved in the TBDR superfamily, are essential to the movement of ferric siderophores through the CTβB into the periplasm. Full article