TREK2 Lipid Binding Preferences Revealed by Native Mass Spectrometry.

TREK2, a two-pore domain potassium channel, is recognized for its regulation by various stimuli, including lipids. While previous members of the TREK subfamily, TREK1 and TRAAK, have been investigated to elucidate their lipid affinity and selectivity, TREK2 has not been similarly studied in this regard. Our findings indicate that while TRAAK and TREK2 exhibit similarities in terms of electrostatics and share an overall structural resemblance, there are notable distinctions in their interaction with lipids. Specifically, SAPI(4,5)P2,1-stearoyl-2-arachidonoyl-sn-glycero-3-phospho-(1'-myo-inositol-4',5'-bisphosphate) exhibits a strong affinity for TREK2, surpassing that of dOPI(4,5)P2,1,2-dioleoyl-sn-glycero-3-phospho-(1'-myo-inositol-4',5'-bisphosphate), which differs in its acyl chains. TREK2 displays lipid binding preferences not only for the headgroup of lipids but also toward the acyl chains. Functional studies draw a correlation for lipid binding affinity and activity of the channel. These findings provide important insight into elucidating the molecular prerequisites for specific lipid binding to TREK2 important for function.

Nonlocal structural effects of water on DNA homology recognition.

The mechanism behind mutual recognition of homologous DNA sequences prior to genetic recombination is one of the remaining puzzles in molecular biology. Leading models of homology recognition, based on classical electrostatics, neglect the short-range nonlocal screening effects arising from structured water around DNA, and hence may only provide insight for relatively large separations between interacting DNAs. We elucidate the role of the effects of the nonlocal dielectric response of water on DNA-DNA interaction and show that these can dramatically enhance the driving force for recognition.

Molecular interactions of the Omicron, Kappa, and Delta SARS-CoV-2 spike proteins with quantum dots of graphene oxide.

CONTEXT: The Omicron, Kappa, and Delta variants are different strains of the SARS-CoV-2 virus. Graphene oxide quantum dots (GOQDs) represent a burgeoning class of oxygen-enriched, zero-dimensional materials characterized by their sub-20-nm dimensions. Exhibiting pronounced quantum confinement and edge effects, GOQDs manifest exceptional physical-chemical attributes. This study delves into the potential of graphene oxide quantum dots, elucidating their inherent properties pertinent to the surface structures of SARS-CoV-2, employing an integrated computational approach for the repositioning of inhibitory agents. METHODS: Following rigorous adjustment tests, a spectrum of divergent bonding conformations emerged, with particular emphasis placed on identifying the conformation exhibiting optimal adjustment scores and interactions. The investigation employed molecular docking simulations integrating affinity energy evaluations, electrostatic potential clouds, molecular dynamics encompassing average square root calculations, and the computation of Gibbs-free energy. These values quantify the strength of interaction between GOQDs and SARS-CoV-2 spike protein variants. The receptor structures were optimized using the CHARM-GUI server employing force field AMBERFF14SB. The algorithm embedded in CHARMM offers an efficient interpolation scheme and automatic step size selection, enhancing the efficiency of the optimization process. The 3D structures of the ligands are constructed and optimized with density functional theory (DFT) method based on the most stable conformer of each binder. Autodock Vina Software (ADV) was utilized, where essential parameters were specified. Electrostatic potential maps (MEPs) provide a visual depiction of molecules' charge distributions and related properties. After this, molecular dynamics simulations employing the CHARM36 force field in Gromacs 2022.2 were conducted to investigate GOs' interactions with surface macromolecules of SARS-CoV-2 in an explicit aqueous environment. Furthermore, our investigation suggests that lower values indicate stronger binding. Notably, GO-E consistently showed the most negative values across interactions with different variants, suggesting a higher affinity compared to other GOQDs (GO-A to GO-D).

Layer-over-Layer Electrostatic Self-Assembly of Bioresourced Compounds in Thermoreversible Polylactide Gels as an Effective Approach to Enhance the Flame Retardancy of Aerogels.

Polylactide is a high potential polymer that can satisfy the growing demand for sustainable and lightweight materials in construction, packaging, and structural applications. However, their high flammability poses a serious concern. Herein, with the aid of solvent exchange and noncovalent interactions, poly(l-lactide) (PLLA) thermoreversible gel was modified with sodium alginate (SA), chitosan (CS), and phytic acid (PA) via a layer-over-layer approach. Freeze-drying of the modified hydrogel furnished a highly flame retardant aerogel with shape stability and no shrinkage. The modified PLLA aerogel (PLLA@SA@CS@PA) exhibited self-extinguishment of flame, the highest limiting oxygen index of any porous polylactide (∼32%), and a tremendous reduction in flammability parameters such as the heat release rate, heat release capacity, total heat release, etc. A comprehensive mechanism of flame retardancy was proposed. This work provides a sustainable strategy for the flame retardant modification of semicrystalline polymer-based aerogels and is expected to expand their practical applications in various industrial sectors.

Exploring changes in aggregation and gel network morphology of soybean protein isolate induced by pH, NaCl, and temperature in view of interactions.

The texture of soybean protein-based products is primarily influenced by the aggregation and gel morphology of the protein, which is modulated by manufacturing factors. Interactions involved in protein morphology changes include disulfide bonds, hydrophobic interactions, electrostatic interactions, and hydrogen bonds. Notably, an interaction perspective probably provides a new way to explaining the aggregation and gel morphology, which could help overcome the hurdle of developing a textured product. Based on the interaction perspective, this review provides detailed information and evidence on aggregation, conformational stability, and gel network morphology of soybean protein and its components induced by pH, NaCl, and temperature. pH-induced electrostatic interactions and hydrogen bonds, NaCl-induced electrostatic interactions, and temperature-induced hydrophobic interactions and disulfide linkages are the main motivations responsible for changes in soybean aggregation and gel morphology. By reducing the proportion of strong-interactions, such as disulfide linkages and hydrophobic interactions, and increasing the proportion of weak-interactions, such as electrostatic interactions and hydrogen bonds, the protein total surface area expands, indicating increased conformational stretching and decreased cohesion. This possibly results in reduced hardness and increased toughness of textured proteins. The opposite effect can be observed when the proportion of strong interactions is increased and that of weak interactions is decreased.

Polyelectrolyte complex formation of alginate and chito oligosaccharide is influenced by their proportion and alginate molecular weight.

Sodium alginate (SA) and chito oligosaccharide (COS) are widely used food additives in the food industry, and exploring their interaction to form polyelectrolyte complexes (PECs) may provide insights into food development. In the present study, the effects of viscosity-average molecular weight (Mv) and relative amounts of SA on the formation of sodium alginate/chito oligosaccharide polyelectrolyte (SCP) complexes were investigated. The results showed that the electrostatic interaction between -COOH and -NH2 and the hydrogen bonding between OH, were attributed to the formation of the SCP complexes. Then the formation and properties of SCP complexes were greatly dependent on the Mv and the relative amount of SA. SA with Mv of ≥2.16 × 106 Da could form spherical SCP complexes, while the SA/COS ratio (w/w) ≥ 0.8 was not conducive to the formation of SCP complexes. Moreover, the SCP complexes were more stable in the gastric environment than in the intestinal condition. In addition, 1.73 × 107 Da was the optimal Mv of SA for SCP complexes formation. This study contributed to a comprehensive understanding of the interaction between SA and COS, and shed light on the potential application of SA and COS formulation to develop new food products.

A new strategy to improve the quality of frozen chicken wings: High voltage electrostatic field combined with phosphorus-free water retaining agent.

Freezing is a commonly used method for long-term storage of chicken wing products, of which disadvantages are mainly the product damage caused in the process. The aim of this study was to improve the freezing quality of chicken wings with a combination of phosphorus-free water retaining agent (WRA) and high-voltage electrostatic field (HVEF). The effect of WRA acting at different HVEF intensities (0, 1, 3, and 5 kV/cm) on the quality attributes of frozen chicken wings was investigated in 0, 7, 14, 21, 28 and 35 days of frozen storage. The results showed that WRA had functional properties of significantly improving the water holding capacity (WHC), color and texture properties, and fat stability of frozen chicken wing samples. The application of HVEF on this basis helped to promote the absorption of WRA and inhibit oxidative deterioration of chicken wing samples during frozen storage. Meanwhile, the combination of HVEF at 3 kV/cm was more prominent in terms of improvement in WHC, moisture content, color, protein secondary structure and microstructure integrity. This advantage had been consistently maintained with the extension of storage time. Overall, WRA combined with HVEF of 3 kV/cm can be used as an effective strategy to improve the freezing quality of chicken wing samples and has the potential to maintain the frozen chicken wing samples quality for a long time.

Cocrystal Prediction of Nifedipine Based on the Graph Neural Network and Molecular Electrostatic Potential Surface.

Nifedipine (NIF) is a dihydropyridine calcium channel blocker primarily used to treat conditions such as hypertension and angina. However, its low solubility and low bioavailability limit its effectiveness in clinical practice. Here, we developed a cocrystal prediction model based on Graph Neural Networks (CocrystalGNN) for the screening of cocrystals with NIF. And scoring 50 coformers using CocrystalGNN. To validate the reliability of the model, we used another prediction method, Molecular Electrostatic Potential Surface (MEPS), to verify the prediction results. Subsequently, we performed a second validation using experiments. The results indicate that our model achieved high performance. Ultimately, cocrystals of NIF were successfully obtained and all cocrystals exhibited better solubility and dissolution characteristics compared to the parent drug. This study lays a solid foundation for combining virtual prediction with experimental screening to discover novel water-insoluble drug cocrystals.

Charge block-driven liquid-liquid phase separation - mechanism and biological roles.

Liquid-liquid phase separation (LLPS) has increasingly been found to play pivotal roles in a number of intracellular events and reactions, and has introduced a new paradigm in cell biology to explain protein-protein and enzyme-ligand interactions beyond conventional molecular and biochemical theories. LLPS is driven by the cumulative effects of weak and promiscuous interactions, including electrostatic, hydrophobic and cation-π interactions, among polypeptides containing intrinsically disordered regions (IDRs) and describes the macroscopic behaviours of IDR-containing proteins in an intracellular milieu. Recent studies have revealed that interactions between 'charge blocks' - clusters of like charges along the polypeptide chain - strongly induce LLPS and play fundamental roles in its spatiotemporal regulation. Introducing a new parameter, termed 'charge blockiness', into physicochemical models of disordered polypeptides has yielded a better understanding of how the intrinsic amino acid sequence of a polypeptide determines the spatiotemporal occurrence of LLPS within a cell. Charge blockiness might also explain why some post-translational modifications segregate within IDRs and how they regulate LLPS. In this Review, we summarise recent progress towards understanding the mechanism and biological roles of charge block-driven LLPS and discuss how this new characteristic parameter of polypeptides offers new possibilities in the fields of structural biology and cell biology.

Accelerating electrostatic particle-in-cell simulation: A novel FPGA-based approach for efficient plasma investigations.

Particle-in-cell (PIC) simulation serves as a widely employed method for investigating plasma, a prevalent state of matter in the universe. This simulation approach is instrumental in exploring characteristics such as particle acceleration by turbulence and fluid, as well as delving into the properties of plasma at both the kinetic scale and macroscopic processes. However, the simulation itself imposes a significant computational burden. This research proposes a novel implementation approach to address the computationally intensive phase of the electrostatic PIC simulation, specifically the Particle-to-Interpolation phase. This is achieved by utilizing a high-speed Field Programmable Gate Array (FPGA) computation platform. The suggested approach incorporates various optimization techniques and diminishes memory access latency by leveraging the flexibility and performance attributes of the Intel FPGA device. The results obtained from our study highlight the effectiveness of the proposed design, showcasing the capability to execute hundreds of functional operations in each clock cycle. This stands in contrast to the limited operations performed in a general-purpose single-core computation platform (CPU). The suggested hardware approach is also scalable and can be deployed on more advanced FPGAs with higher capabilities, resulting in a significant improvement in performance.

Heteroaggregation and deposition behaviors of carboxylated nanoplastics with different types of clay minerals in aquatic environments: Important role of calcium(II) ion-assisted bridging.

The widespread utilization of plastic products ineluctably leads to the ubiquity of nanoplastics (NPs), causing potential risks for aquatic environments. Interactions of NPs with mineral surfaces may affect NPs transport, fate and ecotoxicity. This study aims to investigate systematically the deposition and aggregation behaviors of carboxylated polystyrene nanoplastics (COOH-PSNPs) by four types of clay minerals (illite, kaolinite, Na-montmorillonite, and Ca-montmorillonite) under various solution chemistry conditions (pH, temperature, ionic strength and type). Results demonstrate that the deposition process was dominated by electrostatic interactions. Divalent cations (i.e., Ca2+, Mg2+, Cd2+, or Pb2+) were more efficient for screening surface negative charges and compressing the electrical double layer (EDL). Hence, there were significant increases in deposition rates of COOH-PSNPs with clay minerals in suspension containing divalent cations, whereas only slight increases in deposition rates of COOH-PSNPs were observed in monovalent cations (Na+, K+). Negligible deposition occurred in the presence of anions (F-, Cl-, NO3-, CO32-, SO42-, or PO43-). Divalent Ca2+ could incrementally facilitate the deposition of COOH-PSNPs through Ca2+-assisted bridging with increasing CaCl2 concentrations (0-100 mM). The weakened deposition of COOH-PSNPs with increasing pH (2.0-10.0) was primarily attributed to the reduce in positive charge density at the edges of clay minerals. In suspensions containing 2 mM CaCl2, increased Na+ ionic strength (0-100 mM) and temperature (15-55 ◦C) also favored the deposition of COOH-PSNPs. The ability of COOH-PSNPs deposited by four types of clay minerals followed the sequence of kaolinite > Na-montmorillonite > Ca-montmorillonite > illite, which was related to their structural and surface charge properties. This study revealed the deposition behaviors and mechanisms between NPs and clay minerals under environmentally representative conditions, which provided novel insights into the transport and fate of NPs in natural aquatic environments.

Quantum Chemistry-Based Protein-Protein Docking without Empirical Parameters.

This study developed a novel protein-protein docking approach based on quantum chemistry. To judge the appropriateness of complex structures, we introduced two criterion values, EV1 and EV2, computed using the fragment molecular orbital method without any empirical parameters. These criterion values enable us to search complex structures in which patterns of the electrostatic potential of the two proteins are optimally aligned at their interface. The performance of our method was validated using 53 complexes in a benchmark set provided for protein-protein docking. When employing bound state structures, docking success rates reached 64% for EV1 and 76% for EV2. On the other hand, when employing unbound state structures, docking success rates reached 13% for EV1 and 17% for EV2.

Directed-evolution mutations enhance DNA-binding affinity and protein stability of the adenine base editor ABE8e.

Adenine base editors (ABEs), consisting of CRISPR Cas nickase and deaminase, can chemically convert the A:T base pair to G:C. ABE8e, an evolved variant of the base editor ABE7.10, contains eight directed evolution mutations in its deaminase TadA8e that significantly increase its base editing activity. However, the functional implications of these mutations remain unclear. Here, we combined molecular dynamics (MD) simulations and experimental measurements to investigate the role of the directed-evolution mutations in the base editing catalysis. MD simulations showed that the DNA-binding affinity of TadA8e is higher than that of the original deaminase TadA7.10 in ABE7.10 and is mainly driven by electrostatic interactions. The directed-evolution mutations increase the positive charge density in the DNA-binding region, thereby enhancing the electrostatic attraction of TadA8e to DNA. We identified R111, N119 and N167 as the key mutations for the enhanced DNA binding and confirmed them by microscale thermophoresis (MST) and in vivo reversion mutation experiments. Unexpectedly, we also found that the directed mutations improved the thermal stability of TadA8e by ~ 12 °C (Tm, melting temperature) and that of ABE8e by ~ 9 °C, respectively. Our results demonstrate that the directed-evolution mutations improve the substrate-binding ability and protein stability of ABE8e, thus providing a rational basis for further editing optimisation of the system.

Versatile Self-Assembly of Triblock Peptides into Stable Collagen Mimetic Heterotrimers.

The construction of peptides to mimic heterogeneous proteins such as type I collagen plays a pivotal role in deciphering their function and pathogenesis. However, progress in the field has been severely hampered by the lack of capability to create stable heterotrimers with desired functional sequences and without the effect of homotrimers. We have herein developed a set of triblock peptides that can assemble into collagen mimetic heterotrimers with desired amino acids and are free from the interference of homotrimers. The triblock peptides comprise a central collagen-like block and two oppositely charged N-/C-terminal blocks, which display inherent incompetency of homotrimer formation. The favorable electrostatic attraction between two paired triblock peptides with complementary terminal charged sequences promptly leads to stable heterotrimers with controlled chain composition. The independence of the collagen-like block from the two terminal blocks endows this system with the adaptability to incorporate desired amino acid sequences while maintaining the heterotrimer structure. The triblock peptides provide a versatile and robust tool to mimic the composition and function of heterotrimer collagen and may have great potential in the design of innovative peptides mimicking heterogeneous proteins.

[Study on the mesoscopic dynamic effects of tumor treating fields on cell tubulin].

Tumor treatment fields (TTFields) can effectively inhibit the proliferation of tumor cells, but its mechanism remains exclusive. The destruction of cellular microtubule structure caused by TTFields through electric field force is considered to be the main reason for inhibiting tumor cell proliferation. However, the validity of this hypothesis still lacks exploration at the mesoscopic level. Therefore, in this study, we built force models for tubulins subjected to TTFields, based on the physical and electrical properties of tubulin molecules. We theoretically analyzed and simulated the dynamic effects of electric field force and torque on tubulin monomer polymerization, as well as the alignment and orientation of α/ß tubulin heterodimer, respectively. Research results indicate that the interference of electric field force induced by TTFields on tubulin monomer is notably weaker than the inherent electrostatic binding force among tubulin monomers. Additionally, the electric field torque generated by the TTFileds on α/ß tubulin dimers is also difficult to affect their random alignment. Therefore, at the mesoscale, our study affirms that TTFields are improbable to destabilize cellular microtubule structures via electric field dynamics effects. These results challenge the traditional view that TTFields destroy the microtubule structure of cells through TTFields electric field force, and proposes a new approach that should pay more attention to the "non-mechanical" effects of TTFields in the study of TTFields mechanism. This study can provide reliable theoretical basis and inspire new research directions for revealing the mesoscopic bioelectrical mechanism of TTFields.

Self-Assembly of Molecular Landers Equipped with Functional Moieties on the Surface: A Mini Review.

The bottom-up fabrication of supramolecular and self-assembly on various substrates has become an extremely relevant goal to achieve prospects in the development of nanodevices for electronic circuitry or sensors. One of the branches of this field is the self-assembly of functional molecular components driven through non-covalent interactions on the surfaces, such as van der Waals (vdW) interactions, hydrogen bonding (HB), electrostatic interactions, etc., allowing the controlled design of nanostructures that can satisfy the requirements of nanoengineering concepts. In this context, non-covalent interactions present opportunities that have been previously explored in several molecular systems adsorbed on surfaces, primarily due to their highly directional nature which facilitates the formation of well-ordered structures. Herein, we review a series of research works by combining STM (scanning tunneling microscopy) with theoretical calculations, to reveal the processes used in the area of self-assembly driven by molecule Landers equipped with functional groups on the metallic surfaces. Combining these processes is necessary for researchers to advance the self-assembly of supramolecular architectures driven by multiple non-covalent interactions on solid surfaces.

Structure-Activity Relationship Models to Predict Properties of the Dielectric Fluids for Transformer Insulation System.

Mineral oils and synthetic and natural esters are the predominant insulating liquids in electrical equipment. Structure-activity relationship models to predict the key properties of pure insulating liquids, including pulse breakdown strengths, AC breakdown voltages, dielectric constants, flash points, and kinematic viscosities, have been proposed for the first time. Dependence of the specific properties on the molecular structures has been illustrated quantitatively in terms of surface area, statistical total variance, and average deviation of positive and negative electrostatic potentials, as augmented by molecular weight, volume, and ovality. Moreover, the individual contribution of the functional groups to viscosity has been revealed by an additive approach. The predicted properties are in good agreement with the experimental data. The present theoretical work provides new insights on the development of novel dielectric fluids.

Unlocking the NIR-II AIEgen for High Brightness through Intramolecular Electrostatic Locking.

Fluorescent imaging and biosensing in the near-infrared-II (NIR-II) window holds great promise for non-invasive, radiation-free, and rapid-response clinical diagnosis. However, it's still challenging to develop bright NIR-II fluorophores. In this study, we report a new strategy to enhance the brightness of NIR-II aggregation-induced emission (AIE) fluorophores through intramolecular electrostatic locking. By introducing sulfur atoms into the side chains of the thiophene bridge in TSEH molecule, the molecular motion of the conjugated backbone can be locked through intramolecular interactions between the sulfur and nitrogen atoms. This leads to enhanced NIR-II fluorescent emission of TSEH in both solution and aggregation states. Notably, the encapsulated nanoparticles (NPs) of TSEH show enhanced brightness, which is 2.6-fold higher than TEH NPs with alkyl side chains. The in vivo experiments reveal the feasibility of TSEH NPs in vascular and tumor imaging with a high signal-to-background ratio and precise resection for tiny tumors. In addition, polystyrene nanospheres encapsulated with TSEH are utilized for antigen detection in lateral flow assays, showing a signal-to-noise ratio 1.9-fold higher than the TEH counterpart in detecting low-concentration antigens. This work highlights the potential for developing bright NIR-II fluorophores through intramolecular electrostatic locking and their potential applications in clinical diagnosis and biomedical research.

The interaction between formylphenoxyacetic acid derivatives (chalcone and flavones) and ionic surfactants: Insights into binding constants, solubilisation and physiochemical properties.

In this study, UV-vis spectroscopy was employed to investigate the interaction between formylphenoxyacetic acid (FPAA) and its derivatives (chalcone and flavones) with ionic surfactants (SDS, CTAB, and DTAB) in different physiological environments. Changes in the physiochemical properties of FPAA chalcone and flavones including binding constants, partitioning constants, and Gibbs free energy were observed which were influenced by the presence of ionic surfactants computed using mathematical models. The solubilization of the targeted compounds in the ionic surfactants was determined through the binding constant (Kb). The results of the present study indicated that electrostatic interactions played a significant role in the solubilization of the targeted compounds in SDS, CTAB, and DTAB. At pH 4.1, FPAA chalcone exhibited stronger binding affinity with SDS compared to CTAB and DTAB. However, at pH 7.4, chalcone showed stronger binding with DTAB compared to SDS, while negligible interaction with CTAB was observed at pH 7.4. The flavones demonstrated stronger binding with DTAB at pH 7.4 compared to SDS and CTAB and it exhibited strong bonding with CTAB at pH 4.1. The negative values of the Gibbs free energy for binding (ΔGb˚) and partitioning (ΔGp˚) constants displayed the spontaneity of the process. However, FPAA chalcone with SDS and FPAA flavones with DTAB furnished positive ΔGb˚, indicating a non-spontaneous process.

Effects of lactic acid and ascorbic acid electrostatic spraying on the physicochemical attributes and microbial diversity of beef aged at mild temperature (10 °C).

This study aimed to clarify the effect of electrostatic spraying of lactic acid (LE) and ascorbic acid (AE) on vacuum-packaged beef aged at 10 °C. The physicochemical attributes, flavor profiles, and microbial diversities were evaluated. Beef steaks were electrostatically sprayed twice with 4% LE, 0.5% AE, or a mixture of them (LAE). Afterward, the beef was vacuum-packaged and aged. All treated beef exhibited a decrease in quality and sensory scores over time. At the end of the study period, the total viable count (TVC) and the total volatile basic nitrogen values in the control group (7.34 log CFU/g and 15.52 mg/100 g, respectively) were higher than those in the acid-treated groups. The LAE group exhibited the best color stability and the lowest TVC and Enterobacteriaceae counts after aging. High-throughput sequencing analysis revealed that acid types and electrostatic spray could change the microbiota structure. Leuconostoc was the dominant bacteria in the AE and LAE groups, while Enterococcus became the predominant bacteria in the NLE and LE groups with aging. This indicates that electrostatic spray combined with acid treatment can ensure beef quality and microbiological safety at mild temperatures.