Search Results (162)

Caffeine (1,3,7-trimethylxanthine) is a widely consumed psychoactive drug and neurostimulant, yet its molecular organization and permeation behavior in lipid membranes are not fully understood. We employ microseconds-long, united-atom molecular dynamics simulations to investigate caffeine interactions with a solvated DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) bilayer at its fluid phase. Caffeine molecules initially aggregate in the aqueous phase to form ordered stackings, which successively permeate into the membrane. The stacked assemblies gradually dissolve, reaching a stable dispersed state where caffeine molecules preferentially reside near the headgroup–acyl chain interface and orient parallel to the lipid acyl chains, consistent with previous experimental and simulation studies. Simulations initiated with caffeine in the membrane hydrophobic phase converge to the same equilibrium state, indicating a preferred localization at the interface region. Present simulation findings are further supported by free-energy calculations that demonstrate caffeine’s high affinity at the headgroup–acyl chain interface. Caffeine partitioning transiently and slightly reduces bilayer thickness and increases the membrane surface area while enhancing acyl chain stiffness near the hydrophilic part of the membrane. These observed trends are reproducible over different system sizes and independent simulations. Overall, this study provides atomic-level insights into the caffeine permeation process, including its effect on the lipid bilayer structure. Full article

Cells contain an unexpectedly large diversity of lipid molecules. Modern lipidomics studies have revealed that even a single cell type can harbor hundreds to thousands of distinct lipid species that differ in headgroup structure, acyl chain length, and degree of unsaturation. While this remarkable diversity is now well established, its biological significance remains incompletely understood. Why do cells maintain such complex lipidomes? In this review, we examine several conceptual frameworks that may help explain the origin and functional significance of lipid diversity. First, the physical properties of biological membranes impose constraints on lipid composition, as variations in lipid structure influence membrane fluidity, curvature, thickness, and phase behavior. Second, lipids can regulate membrane protein function through specific interactions and through the physical environment of the lipid bilayer. Third, lipid metabolism generates signaling molecules that participate in diverse regulatory pathways. Fourth, lipid metabolic networks continuously remodel membrane composition, producing dynamic lipidomes that can adapt to physiological conditions. Finally, evolutionary processes have shaped membrane lipid composition across different domains of life, suggesting that lipid diversity may reflect long-term adaptation to functional and environmental constraints. Taken together, these perspectives suggest that lipid diversity is unlikely to be a simple byproduct of metabolism. Instead, the cellular lipidome may emerge from the interplay of membrane biophysics, metabolic network architecture, protein regulation, and evolutionary pressures. Understanding why cells contain thousands of lipid species therefore represents an important challenge for modern cell biology and may reveal fundamental principles governing the organization of biological membranes. Full article

Background: Phospholipids are essential components of bacterial membranes and play central roles in membrane integrity and adaptation to antibiotic stress. However, confident annotation of phospholipid molecular species remains challenging due to the complexity of the lipidome and the limited structural constraints in conventional lipidomics workflows. Methods: Here, we present a bacterial phospholipidomic framework that integrates orthogonal structural evidence to achieve high-confidence and traceable annotation. Thin-layer chromatography (TLC) provides phospholipid headgroup assignment, gas chromatography–mass spectrometry (GC–MS) defines the acyl-chain pool, and Paternò–Büchi derivatization enables C=C localization, collectively restricting the structural search space prior to liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis. A rule-based ion prediction library further standardizes diagnostic ion assignment and reduces annotation ambiguity. Results: Applying this platform, we found Escherichia coli in the stationary phase remodeled the membrane phospholipids, with cardiolipin (CL) increasing from ~5% to ~10% and cyclopropane-containing phospholipid species rising to ~75%. Similar remodeling patterns are observed under diverse antibiotic exposures at sub-inhibitory concentrations, consistent with convergence toward a tolerance-associated membrane state. Extension of the framework to Enterococcus faecium supports proof-of-concept application in an additional Gram-positive model, with vancomycin-resistant strains exhibiting pronounced phosphatidylglycerol (PG) enrichment and reduced CL. Conclusions: Our work provides a scalable and reproducible strategy for bacterial phospholipid annotation, enabling molecular-species-resolved investigation of membrane adaptation and offering a framework for future exploration of lipid homeostasis pathways as potential antimicrobial targets. Full article

The emergence of membrane boundaries represents a decisive transition in the origin of life, yet the molecular nature of the earliest abiotic membranes remains uncertain. Existing models based on simple fatty acids, while experimentally tractable, often lack the environmental robustness required under fluctuating prebiotic conditions. Furthermore, the absence of clear pathways linking primitive amphiphiles to later phospholipid systems highlights the need for chemically continuous intermediate frameworks. Here, we explore borate-bridged amphiphile–carbohydrate conjugates as plausible intermediates between simple prebiotic surfactants and modern lipid bilayers. These conjugates arise from low-molecular-weight polyols—including glycerol, butane-1,2,3,4-tetraol, pentane-1,2,3,4,5-pentaol, and hexane-1,2,3,4,5,6-hexitol—reacting with long-chain alkyl ethers and borate species under alkaline conditions, enabling reversible coupling to ribose and other vicinal diol-containing sugars. This chemistry integrates three essential properties for early compartmentalization: hydrolytically robust ether-linked hydrophobic domains, multivalent and highly hydrated headgroups, and environmentally responsive borate coordination. Comparative physicochemical analysis suggests that single-tail alkylglycerol derivatives preferentially form micelles and interfacial films, while di- and tri-tail tetritol and pentitol conjugates favor lamellar assemblies and vesicle formation across realistic prebiotic pH and salinity ranges. Hexitol-based systems, particularly those bearing three hydrophobic chains, may act as membrane-stabilizing components that enhance rigidity and reduce permeability under extreme conditions. We propose that heterogeneous mixtures dominated by two-tail polyol diethers, supplemented by tri-tail stabilizers and surface-active alkylglycerols, could provide mechanically robust, pH-tunable, and sugar-decorated abiotic membranes. Such borate-mediated amphiphiles offer a chemically coherent framework linking carbohydrate stabilization, ether lipid persistence, and dynamic self-assembly, potentially representing a transitional stage in the evolutionary pathway from primitive amphiphilic films to biologically encoded membranes. Full article

Background: The reliable co-loading of paclitaxel (PTX) and indocyanine green (ICG) into a single lipid nanoparticle (LNP) enables synergistic antitumor delivery but remains challenging due to their distinct physicochemical properties. Methods: This study integrated COSMO-RS calculations, molecular dynamics simulations, and in vitro assays to systematically investigate the effects of lipid composition, drug modification, particle size, and solvent environment on dual-drug loading. Results: This work indicate that DMPS lipid membranes featuring highly polar headgroups and ordered bilayer structures stably bind both ICG and PTX, achieving drug-loading efficiencies (DLEs) of 7.2% and 5.6%, respectively. Carboxylation of PTX enhanced hydrogen bonding with DMPS, while alkyl chain modifications improved membrane insertion, though excessive chain length (e.g., C12) reduced stability due to increased flexibility. Increasing the LNP size from 50 nm to 250 nm raised the DLE of PTX from 4.7% to 8.1%, while sizes beyond 500 nm led to membrane destabilization. The use of 20 vol% ethanol increased total drug loading by 51% by disrupting the hydration shell of ICG and suppressing PTX aggregation; however, ethanol concentrations exceeding 40 vol% intensified drug–solvent competition and weakened membrane binding. Conclusions: This study provides a comprehensive elucidation of the multifactorial regulatory mechanisms underlying dual-drug loading in LNPs, offering a theoretical basis for the rational design of efficient co-delivery systems. Full article

Cyclotides are exceptionally stable plant peptides whose biological activity is widely attributed to interactions with lipid membranes, yet the molecular mechanisms underlying these interactions remain incompletely resolved. Here, we employ microsecond-scale (1 μs) all-atom molecular dynamics simulations to investigate the membrane association of the cyclotide kalata B1 with phospholipid bilayers of distinct headgroup composition, including POPC, POPE, and POPG. This extended timescale enables full bilayer equilibration and allows observation of slower peptide-induced membrane responses that are not accessible in shorter simulations. Across all systems, kalata B1 rapidly adsorbs to the membrane surface and remains predominantly surface-associated throughout the simulations, while the cyclic cystine knot motif remains structurally intact, confirming the exceptional robustness of the cyclotide fold during membrane engagement. Lipid-dependent differences arise primarily from variations in peptide orientation, conformational flexibility, and interfacial dynamics rather than deep bilayer insertion or pore formation. Zwitterionic POPC membranes favor compact, upright peptide configurations, whereas POPE and POPG bilayers promote enhanced lateral spreading and dynamic reorganization driven by hydrogen bonding and electrostatic interactions, respectively. Leaflet-resolved analyses of lipid contacts, membrane thickness, and area per lipid reveal localized, asymmetric perturbations confined to the peptide-exposed leaflet, with no evidence of sustained bilayer thinning or global destabilization. Together, these results support an interfacial, headgroup-dependent mechanism of cyclotide membrane activity and reconcile previous experimental observations. This work provides molecular-level insight into lipid selectivity and early-stage cyclotide–membrane interactions that may inform future design of cyclotide-based bioactive agents. Full article

Biological membranes are dynamic, information-rich platforms whose structural and functional properties are dictated by lipid composition rather than acting as passive barriers. Recent advances in lipidomics have revealed that variations in lipid headgroups, acyl-chain length and saturation, sn-positional architecture, and oxidative modifications profoundly influence membrane mechanics, lateral organization, and protein–lipid interactions. These features collectively regulate fundamental cellular processes, including signaling, trafficking, curvature generation, and transbilayer asymmetry. In parallel, a wide range of pathological conditions—including cancer, metabolic disorders, neurodegeneration, and inflammatory diseases—are increasingly associated with coordinated lipid remodeling that reshapes membrane material properties and electrostatic landscapes. In this review, we integrate biophysical principles with lipidomics-based evidence to elucidate how lipid chemical diversity translates into membrane-level behavior. We discuss the roles of major membrane lipid classes, the functional consequences of acyl-chain and sn-positional remodeling, and the biological significance of lipid asymmetry and lateral heterogeneity. Particular attention is given to disease-associated lipid reprogramming and extracellular vesicle lipidomes as functional extensions of cellular membranes. Finally, we examine key analytical barriers in modern lipidomics and outline strategies required to connect lipid structural information with biological function. Together, this framework highlights membrane lipid architecture as a central determinant of cellular physiology and a promising axis for mechanistic insight and translational biomarker discovery. Full article

Background/Objectives: The high volatility of volatile drugs significantly restricts their clinical applicability. Although excipients capable of strong interactions can reduce volatilization, conventional screening methods rely on empirical trial-and-error, resulting in low efficiency and high resource consumption. To address this limitation, this study introduces an artificial intelligence (AI)-driven strategy for screening drug–excipient interactions. Using d-borneol as a model drug, this approach aims to efficiently identify strongly interacting excipients and develop stable nano-formulations. Methods: High-throughput simulations were performed using the Protenix structure prediction model to evaluate interactions between d-borneol and 472 FDA-approved excipients. The top 50 candidate excipients were selected based on these simu-lations. Molecular docking and stability experiments were conducted to validate the predictions. Results: Molecular docking and stability experiments confirmed the consistency between predicted and experimental results, validating the model’s reliability. Among the candidates, soybean phospholipid (PC) was identified as the optimal excipient. A lyophilized liposomal formulation prepared with PC significantly suppressed the volatilization of d-borneol and improved both thermal and storage stability. Mechanistic investigations indicated that d-borneol stably incorporates into the hydro-phobic region of phospholipids, enhancing membrane ordering via hydrophobic interactions without disturbing the polar headgroups. Conclusions: This study represents the first application of a structure prediction model to excipient screening for volatile drugs. It successfully addresses the stability challenges associated with d-borneol and offers a new paradigm for developing nano-formulations for volatile pharmaceuticals. Full article

In this study, cationic surfactant cetyltrimethylammonium bromide (CTAB) and anionic surfactant sodium bis(2-ethylhexyl) sulfosuccinate (AOT) are employed to systematically investigate surface and wetting properties on hydrophobic surfaces, specifically in mixed solvents composed of ethylene glycol (EG) and water at 298.15 K. By varying the concentration of each surfactant within the EG–water mixture, both surface tension and contact angle measurements are performed to elucidate how surfactant type and solvent composition influence interfacial behavior and wettability. PTFE and wax surfaces were chosen as model hydrophobic surfaces. Surface tension measurements obtained in pure water and in water–EG mixtures containing 5, 10, and 20 volume percentage EG reveal a consistent decrease in the premicellar slope (${\displaystyle \frac{d\gamma }{d\mathit{log}C}}$) with increasing EG content. This reduction reflects weakened hydrophobic interactions and less effective surfactant adsorption at the air–solution interface. The corresponding decline in maximum surface excess (${\Gamma }_{max}$) and increase in minimum area per molecule ($A_{min}$) confirm looser interfacial packing due to EG participation in the solvation layer. Plots of adhesion tension (A_T) versus surface tension (γ) exhibit negative slopes, consistent with reduced solid–liquid interfacial tension (${\Gamma }_{LG}$) and greater redistribution of surfactant molecules toward the solid–liquid interface. AOT shows stronger sensitivity to EG compared to CTAB, reflecting structural headgroup-specific adsorption behavior. Work of adhesion (W_A) measurements demonstrate enhanced wettability at higher EG concentrations, highlighting the cooperative impact of co-solvent environment and surfactant type on wetting phenomena. Full article

Background/Objectives: Methicillin-resistant Staphylococcus aureus (MRSA) poses a significant global health threat due to its increasing resistance to conventional antibiotics. Antimicrobial peptides (AMPs) derived from natural sources represent a promising alternative. Fragments of spider membrane-active toxins can serve as AMPs with anti-MRSA activity. Methods: To demonstrate this, amino acid sequences of approximately 2000 linear spider venom peptides were fragmented into 9–22-residue-long moieties (75,235 in total) and pre-trained neural networks were used to predict their anti-MRSA activity. As many as 15 peptides with high predicted activity were synthesized, and three AMPs with high anti-MRSA and low hemolytic activities were selected. One of these peptides was studied using high-resolution ¹H-, ¹³C-, and ¹⁵N-NMR spectroscopy in an aqueous solution and lyso-palmitoylphosphatidylglycerol (LPPG) micelles. Wide-line ³¹P-NMR was applied to multilamellar phospholipid liposomes composed of phosphatidylcholine (PC) or phosphatidylglycerol (PG). Results: Low hemolytic activity is explained by non-specific interaction with PC whereas high antibacterial activity arises from specific interaction with PG accompanied with the formation of a tight complex between the N-terminal tripeptide fragment and PG headgroup. The structure of a such complex, stabilized by an ionic interaction between the N-terminal NH₃⁺ group and the lipid phosphate, was determined based on peptide–LPPG NOEs. The most favorable ratio between anti-MRSA and hemolytic activities, i.e., selectivity of the peptides, is attained when the tripeptide consists exclusively of phenylalanine and tryptophan residues. Confocal microscopy confirmed that the most selective peptide deteriorates the plasma membrane of S. aureus. Conclusions: This approach may enable the production of highly selective AMPs against Stapylococci, including MRSA. Full article

Liposomal systems are advanced carriers of active substances which, thanks to their ability to encapsulate these substances, significantly improve their pharmacokinetics, bioavailability, and selectivity. This article presents the results of spectroscopic studies for a selected compound from the 1,3,4-thiadiazole group, namely 4-[5-(naphthalen-1-ylmethyl)-1,3,4-thiadiazol-2-yl]benzene-1,3-diol (NTBD, see below in the text), in selected liposomal systems formed from the phospholipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). Detailed spectroscopic analyses were carried out using electronic absorption and fluorescence spectroscopy; resonance light scattering (RLS) spectra measurements; dynamic light scattering (DLS); as well as time-resolved methods—fluorescence lifetime measurements using the TCSPC technique. Subsequently, based on the interpretation of spectra obtained by FTIR infrared spectroscopy, the preliminary molecular organization of the above-mentioned compounds within lipid multilayers was determined. It was found that NTBD preferentially occupies the region of polar lipid headgroups in the lipid multilayer, although it also noticeably interacts with the hydrocarbon chains of the lipids. Furthermore, X-ray diffraction (XRD) techniques were used to study the effect of NTBD on the molecular organization of DPPC lipid multilayers. Monomeric structures and aggregated forms of the above-mentioned 1,3,4-thiadiazole analogue were characterized using X-ray crystallography. Interesting dual fluorescence effects observed in steady-state fluorescence measurements were linked to the excited-state intramolecular proton transfer (ESIPT) effect (based on our earlier studies), which, in the obtained biophysical systems—liposomal systems with strong hydrophobicity—is greatly enhanced by aggregation-induced emission (AIE) effects. In summary, the research presented in this study, concerning the novel 1,3,4-thiadiazole derivative NTBD, is highly relevant to drug delivery systems, such as various model liposomal systems, as it demonstrates that depending on the concentration of the selected fluorophore, different forms may be present, allowing for appropriate modulation of its biological activity. Full article

The impact of counterion structure, especially variations in constitutional and stereochemical isomers, on the properties and performance of AABSs remains under-explored. This study investigates how structural variations, particularly the stereochemistry of diammonium cyclohexane (DACH) counterions, influence the self-assembly behavior of AABSs. Four AABSs: undecanoyl-glycine, -L-alanine, -L-valine, and -L-leucine, were paired with six DACH counterions representing cis/trans isomers of 1,2-, 1,3-, and 1,4-DACH. Critical micelle concentrations (CMCs) were determined via conductimetry, and micellar sizes were measured using dynamic light scattering. The degree of counterion binding (β) was calculated to probe micelle stability, while geometry-optimized structures of the DACH isomers were obtained using density functional theory. Lastly, pH measurements were taken to probe the protonation of DACH counterions at their natural pH, where both the DACH counterion and AABS headgroups intrinsically behave as buffers. Results indicate that while surfactant hydrophobicity primarily dictates CMC in other AABS/DACH combinations, trans-1,3-DACH leads to consistently higher CMCs. This deviation likely arises from its structural conformation, which positions the amine groups an intermediate distance of ~4.4–4.5 Å apart, allowing a small fraction of divalently charged counterions to form strong electrostatic bridging pockets at the micelle interface. These interactions dominate over headgroup effects, leading to elevated and surfactant-independent CMC values. Regarding size and other unusual trends in the systems, cis- isomers formed slightly larger micelles, and trans-1,4-DACH induces abnormal aggregation in undecanoyl-glycine leading to temperature dependent gel formation. These findings highlight the significant influence of counterion structure on AABS behavior and support counterion design as a strategy for enhancing surfactant performance in sustainable applications. Full article

Mesoporous silica nanoparticles have been synthesized through sol–gel synthesis in basic conditions. Gemini surfactants having urea in the headgroups were used as pore-forming agents. The effect of the spacer length of the surfactant on the particle morphology was studied on the sub-micrometer and nanometer scales using nitrogen porosimetry, small-angle X-ray scattering (SAXS), ultra-small-angle neutron scattering, and scanning and transmission electron microscopy (SEM, TEM). Depending on the spacer, spherical and/or cylindrical nanoparticles formed in different proportions, as revealed by statistical analysis of SEM micrographs. All prepared materials showed the hexagonal pore structure characteristic of the MCM-41 molecular sieves, with the exception of the sample prepared using the gemini surfactant with the shortest spacer length. The influence of the spacer length on the lattice parameter of the pore network, as well as the average size of the ordered domains, has been assessed by SAXS and TEM. Detailed analysis of the TEM images revealed a spread of the lattice parameter in a range of 10–20%. The broadening of the diffraction peaks was shown to be due to the combination of the effects of the finite domain size and the variance of the lattice parameter across the crystalline domains. The structural differences between the silica gels synthesized with the different surfactants were related to the variation of the micelle morphologies, reported in previous light scattering and small-angle scattering experiments. No connection could be revealed between the micelle shape and size and the pore sizes, showing that surfactants with a broad range of spacer lengths can equally well be used for the preparation of MCM-41 materials. Full article

The function of pleckstrin homology (PH) domains is to recognize and bind to specific phosphoinositides in the membranes as part of diverse cellular signaling processes. The structure of some PH domains has been solved by X-ray crystallography, but structures of many PH domains remain to be elucidated. In green alga Chlamydomonas reinhardtii, none of the PH domains have been crystallized or characterized. The goal of our study was to model and characterize in detail the structures of all eleven of the PH domains identified in C. reinhardtii. Our computational strategy of integrating the information available on sequence, structure, and function with modeling and biophysical characterization has uncovered new biological predictions for these proteins. These predictions can be validated by future rationally designed experimental studies as an extension of this work. Our results suggest that nine of the eleven C. reinhardtii PH domains show the classical electrostatic polarization of PH domains with a positively charged binding pocket and negatively charged opposing end. Our docking results predict only two PH domains bind specifically to a particular phosphoinositide, while all the other nine PH domains may be able to bind various inositol phospholipids. The lack of preference for a specific phosphoinositide headgroup implies that the positive charge in the binding pocket of the PH domains may be crucial in driving the interaction with the negatively charged phosphoinositides in a non-specific or promiscuous manner. We identified putative homologs of Dynamin GTPase, calcium/calmodulin-dependent kinase, Arf GAP, Rhythm of Chloroplast 23 (ROC23), and oxysterol binding proteins in C. reinhardtii that contain PH domains. In addition, we identified two PH domain-containing proteins that may play a role in the mating process and others that may be important for signaling under phosphate deficiency. Full article

To stimulate the progress of clean fracturing fluid systems, an innovative erucyl ultra-long-chain gemini surfactant (EUCGS) was devised and manufactured during the course of this study. The target product was successfully prepared via a two-step reaction involving erucyl primary amine, 3-bromopropionyl chloride, and 1,3-bis(dimethylamino)propanediol, with an overall yield of 78.6%. FT-IR and ¹H NMR characterization confirmed the presence of C₂₂ ultra-long chains, cis double bonds, amide bonds, and quaternary ammonium headgroups in the product structure. Performance tests showed that EUCGS exhibited an extremely low critical micelle concentration (CMC = 0.018 mmol/L) and excellent ability to reduce surface tension (γCMC = 30.0 mN/m). Rheological property studies indicated that EUCGS solutions gradually exhibited significant non-Newtonian fluid characteristics with increasing concentration, and wormlike micelles with a network structure could self-assemble at a concentration of 1.0 mmol/L. Dynamic rheological tests revealed that the solutions showed typical Maxwell fluid behavior and significant shear-thinning properties, which originated from the orientation and disruption of the wormlike micelle network structure under shear stress. In the presence of 225 mmol/L NaCl, the apparent viscosity of a 20 mmol/L EUCGS solution increased from 86 mPa·s to 256 mPa·s. A temperature resistance evaluation showed that EUCGS solutions had a good temperature resistance at high shear rates and 100 °C. The performance evaluation of fracturing fluids indicates that the proppant settling rate (0.25 cm/min) of the EUCGS-FFS system at 90 °C is significantly superior to that of the conventional system. It features the low dosage and high efficiency of the breaker, with the final core damage rate being only 0.9%. The results demonstrate that the EUCGS achieves a synergistic optimization of high-efficiency interfacial activity, controllable rheological properties, and excellent thermal–salt stability through precise molecular structure design, providing a new material choice for the development of intelligent responsive clean fracturing fluids. Full article