Detecting Interactions between Nanomaterials and Cell Membranes by Synthetic Nanopores

Discovery of novel Thymol-TPP antibiotics that eradicate MRSA persisters

The high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) strains and the formation of non-growing, dormant "persisters" subsets help bacteria evade antibiotic treatment and enhance bacterial resistance, which poses a serious threat to human life and health. It is urgent to discover novel antibacterial therapies effective against MRSA persisters. Thymol is a common nutraceutical with weak antibacterial and antitumor activities. A series of Thymol triphenylphosphine (TPP) conjugates (TPP-Thy3) was designed and synthesized. These compounds showed significantly improved inhibitory activity against Gram-positive bacteria compared with Thymol. Among them, Thy3d displayed a low probability of resistance selection and showed excellent biocompatibility. Interestingly, Thy3d elicited a rapid killing effect of MRSA persisters (99.999%) at high concentration. Fluorescence experiments, electron microscopy, molecular dynamics simulation and bilayer experiment confirmed that Thy3d conjugates exerted potent antimicrobial activity by disrupting the integrity of the membrane of bacterial even the persister. Furthermore, Thy3d exhibited considerable efficacy in a mouse model of subcutaneous murine MRSA infection. In summary, TPP-Thy3 conjugates are a series of novel antibacterial agents and could serve as a new therapeutic strategy for combating antibiotic resistance.

Toxicity of hexagonal boron nitride nanosheets to freshwater algae: Phospholipid membrane damage and carbon assimilation inhibition

Hexagonal boron nitride (h-BN) nanomaterials have attracted numerous attentions for application in various fields, including environmental governance. Understanding the environmental implications of h-BN is a prerequisite for its safe and sustainable use; nevertheless, information on the negative effect of h-BN on aquatic organisms and the underlying toxicity mechanisms is scarce. The present study found that low exposure doses (0.1-1 μg/mL) of micron-sized h-BN lamella apparently suppressed (maximally 45.3%) the growth of Chlorella vulgaris (a freshwater alga) via membrane damages and metabolic reprogramming. Experimental and simulation results verified that h-BN can penetrate into and then extract phospholipids from the cell membrane of algae due to the strong hydrophobic interactions between h-BN nanosheets and lipids, resulting in membrane permeabilization and integrity reduction. Oxidative stress-triggered lipid peroxidation also contributes to membrane destruction of algae. Metabolomics assay demonstrated that h-BN down-regulated the CO2-fixation associated Calvin cycle and glycolysis/gluconeogenesis pathways in algae, thereby inhibiting energy synthesis and antioxidation process. Despite releasing soluble B inside cells, the B species exhibited negligible toxicity. These findings highlight the phenomena and mechanisms of h-BN toxicity in photosynthetic algae, which have great implications for guiding their safe use under the scenarios of global carbon neutrality.

Mesoporous nanoperforators as membranolytic agents via nano- and molecular-scale multi-patterning

Plasma membrane lysis is an effective anticancer strategy, which mostly relying on soluble molecular membranolytic agents. However, nanomaterial-based membranolytic agents has been largely unexplored. Herein, we introduce a mesoporous membranolytic nanoperforators (MLNPs) via a nano- and molecular-scale multi-patterning strategy, featuring a spiky surface topography (nanoscale patterning) and molecular-level periodicity in the spikes with a benzene-bridged organosilica composition (molecular-scale patterning), which cooperatively endow an intrinsic membranolytic activity. Computational modelling reveals a nanospike-mediated multivalent perforation behaviour, i.e., multiple spikes induce nonlinearly enlarged membrane pores compared to a single spike, and that benzene groups aligned parallelly to a phospholipid molecule show considerably higher binding energy than other alignments, underpinning the importance of molecular ordering in phospholipid extraction for membranolysis. Finally, the antitumour activity of MLNPs is demonstrated in female Balb/c mouse models. This work demonstrates assembly of organosilica based bioactive nanostructures, enabling new understandings on nano-/molecular patterns co-governed nano-bio interaction.

Developing semi-empirical water model for efficiently simulating temperature-dependent chemisorption of CO2 in amine solvents

Classical molecular dynamics (MD) simulations without bond forming/breaking cannot be used to model chemical reactions (CRs) among small molecules. Although the first-principle MD simulation can adequately describe CRs with explicit water molecules, such simulation is normally too costly for most researchers to afford. Generally, water molecules in a solvent can exert hydrophobic forces on reacting molecules, which yields a so-called caging effect that cannot be ignored when constructing a free energy landscape for reacting molecules. Many recently developed semi-empirical methods (such as DFTB, PM6 and xTB) are highly efficient for modeling CRs, however none of them can be directly used to model bulk water properly. Here, we developed a modified xTB approach that enables the simulation of CRs in explicit water. Using the chemisorption of CO2 by amines in water as an example application, we demonstrate that our approach yielded results comparable with the first-principle ones, while only using a limited computing resource. Potentially, our proposed semi-empirical water model can be utilized for the computational study of any CR in water.

Impact of Plastic Particles on the Horizontal Transfer of Antibiotic Resistance Genes to Bacterium: Dependent on Particle Sizes and Antibiotic Resistance Gene Vector Replication Capacities

Plastic particles impact the propagation of antibiotic resistance genes (ARGs) in environmental media, and their perturbation on the horizontal gene transfer (HGT) of ARGs is recognized as a critical influencing mechanism. However, studies concerning the influence and influencing mechanisms of plastic particles on the HGT of ARGs were limited, particularly for the effect of particle sizes and ARG vector-associated mechanisms. This study explored the impact of polystyrene (PS) particles with sizes of 75, 90, 100, 1000, and 10000 nm on the HGT (via transformation) of ARGs mediated by pUC19, pSTV29, and pBR322 plasmids into Escherichia coli cells. PS particles with sizes ≤100 nm impacted the transformation of ARGs, but large particles (1000 and 10000 nm) showed no obvious effects. Effects of PS particles on the transfer of three plasmids were vastly distinct. For pUC19 with high replication capacities, the transfer was monotonously promoted. However, for pSTV29 and pBR322 with low replication capacities, suppressing effects were observed. This was attributed to two competing mechanisms. The enhancing mechanism was that the direct interaction of PS particles with membrane lipids and the indirect effect associated with bacterial oxidative stress response induced pore formation on the cell membrane and increased membrane permeability, thus enhancing plasmid entrance. The inhibiting mechanism was that PS particles interfered with plasmid replication inside E. coli, thus decreasing the bacterial tranformation. This study deepened our understanding of the environmental dissemination of ARGs in plastic contamination.

Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes

Two-dimensional (2D) nanomaterials such as graphene are increasingly used in research and industry for various biomedical applications. Extensive experimental and theoretical studies have revealed that 2D nanomaterials are promising drug delivery vehicles, yet certain materials exhibit toxicity under biological conditions. So far, it is known that 2D nanomaterials possess strong adsorption propensities for biomolecules. To mitigate potential toxicity and retain favorable physical and chemical properties of 2D nanomaterials, it is necessary to explore the underlying mechanisms of interactions between biomolecules and nanomaterials for the subsequent design of biocompatible 2D nanomaterials for nanomedicine. The purpose of this review is to integrate experimental findings with theoretical observations and facilitate the study of 2D nanomaterial interaction with biomolecules at the molecular level. We discuss the current understanding and progress of 2D nanomaterial interaction with proteins, lipid membranes, and DNA based on molecular dynamics (MD) simulation. In this review, we focus on the 2D graphene nanosheet and briefly discuss other 2D nanomaterials. With the ever-growing computing power, we can image nanoscale processes using MD simulation that are otherwise not observable in experiment. We expect that molecular characterization of the complex behavior between 2D nanomaterials and biomolecules will help fulfill the goal of designing effective 2D nanomaterials as drug delivery platforms.

Molecular mechanisms underlying the role of the puckered surface in the biocompatibility of black phosphorus

As a newly emerging two-dimensional material, black phosphorus (BP) has received broad attention in the field of biomedical applications. Prior to its clinical application, its cytotoxicity to cells should be carefully evaluated; however, this field is still in its infancy. Motivated by this, we performed molecular dynamics (MD) simulations to systematically investigate the potential mechanisms of the cytotoxicity of BP to the lipid membrane, including lipid extraction, penetration into the membrane, and the impacts of BP on the physical properties of the membrane. Surprisingly, we observed that BP could not extract lipid molecules from the membrane. The thermodynamic analyses suggested that the puckered surface structure could weaken the interactions between BP and lipid molecules, thus inhibiting the lipid extraction. Additionally, through simulating the spontaneous interaction modes between BP and the lipid membrane, we found that the "passivated" edges of BP prohibited it from penetrating into the membrane. As a result, BP could only spontaneously lie parallel on the surface of the membrane, in which manner BP exerted little influence on the properties of the lipid membrane. To comprehensively appraise the cytotoxicity, we even artificially inserted BP into the membrane and compared the effects of BP and graphene on the properties of the membrane. Simulation results showed that the influences of the inserted BP on the lipid properties were much milder than those of graphene. Overall, the present work suggests that BP possesses distinctive biocompatibility benefiting from its puckered surface structure. This work provides a better understanding of the interactions between BP and the membrane, which may offer some useful suggestions for exploring strategies to improve the biocompatibility of nanomaterials.

Graphene nanosheets damage the lysosomal and mitochondrial membranes and induce the apoptosis of RBL-2H3 cells

The induced membrane damage is a key mechanism for the cytotoxicity of graphene nanosheets (GNSs). In this research, the physical interaction of GNSs on model membranes was investigated using artificial membranes and plasma membrane vesicles. The effects of the GNSs on plasma membrane, lysosomal and mitochondrial membranes were investigated using rat basophilic leukemia (RBL2H3) cells via lactate dehydrogenase (LDH) assay, acridine orange staining and JC-1 probe, respectively. The physical interaction with model membranes was dominated by electrostatic forces, and the adhered GNSs disrupted the membrane. The degree of physical membrane disruption was quantified by the quartz crystal microbalance with dissipation (QCM-D), confirming the serious membrane disruption. The internalized GNSs were mainly distributed in the lysosomes. They caused plasma membrane leakage, increased the lysosomal membrane permeability (LMP), and depolarized the mitochondrial membrane potential (MMP). The increased cellular levels of reactive oxygen species (ROS) were also detected after GNS exposure. The combination of physical interaction and the excess ROS production damaged the plasma and organelle membranes in living RBL-2H3 cells. The lysosomal and mitochondrial dysfunction, and the oxidative stress further induced cell apoptosis. Specially, the exposure to 25 mg/L GNSs caused severest cell mortality, plasma membrane damage, ROS generation, MMP depolarization and apoptosis. The research findings provide more comprehensive information on the graphene-induced plasma and organelle membrane damage, which is important to understand and predict the cytotoxicity of carbon-based nanomaterials.

Potential interference with microtubule assembly by graphene: a tug-of-war

With the ever-increasing demand for graphene-based materials and their promising applications in numerous nanotechnologies, the biological effects of graphene on living systems have become crucial and ought to be well understood. Previously, both the cytotoxicity of graphene towards biological cells and its potential application as a nanomedicine have been revealed experimentally and theoretically. Besides many existing anticancer drugs that target microtubules, here we investigate the possibility of using graphene as a nanomedicine, which could alter the dynamic assembly and disassembly of a microtubule. We found that when a graphene nanosheet is at the hydrophilic interface of two neighboring heterodimers (containing α and β tubulins), it can pull one dimer away from the other through a "tug-of-war" mechanism, driven by the strong dispersive interaction exerted by the surface of the graphene nanosheet. This work demonstrates that based on the existing methods for mitigating graphene's cytotoxicity (already developed in this field), a graphene-based nanomedicine could be designed to target microtubules of cancer cells and induce cell apoptosis.

Understanding the Synergic Mechanism of Weak Interactions between Graphene Oxide and Lipid Membrane Leading to the Extraction of Lipids

Revealing how weak forces interact synergistically to induce differences in nanobio effects is critical to understanding the nature of the nanobio interface. Herein, graphene oxide (GO) and a lipid membrane are selected as a nanobio model, and interaction forces at the GO-biomembrane interface are modulated by varying the amounts and species of oxygenated functional groups on the surface of GO. A synergic mechanism of interfacial interaction forces is investigated by a combination of surface-enhanced infrared absorption (SEIRA) spectroscopy, confocal laser scanning microscopy (CLSM), and electrochemical impedance spectroscopy (EIS). The results reveal that after balancing with electrostatic repulsion, the moderate attraction between GO and lipid headgroups (such as electrostatic and/or hydrophobic interactions) is most favorable for lipid extraction, whereas lipid extraction is inhibited under an attraction that is too strong or too weak. Under moderate attraction between GO and the headgroups of lipids, the appropriate degree of rotation freedom is maintained for GO, which is beneficial to the hydrogen-bonding interaction between the C═O group in the phosphatide hydrophobic region and GO, thus triggering the insertion of GO into the lipid alkyl chain region, resulting in the rapid and significant extraction of lipids. Our results have important guiding significance for how to reveal the synergistic mechanism of weak interactions at the nanobio interface.

Graphene-Based Nanomaterials: From Production to Integration With Modern Tools in Neuroscience

Graphene, a two-dimensional carbon crystal, has emerged as a promising material for sensing and modulating neuronal activity in vitro and in vivo. In this review, we provide a primer for how manufacturing processes to produce graphene and graphene oxide result in materials properties that may be tailored for a variety of applications. We further discuss how graphene may be composited with other bio-compatible materials of interest to make novel hybrid complexes with desired characteristics for bio-interfacing. We then highlight graphene's ever-widen utility and unique properties that may in the future be multiplexed for cross-modal modulation or interrogation of neuronal network. As the biological effects of graphene are still an area of active investigation, we discuss recent development, with special focus on how surface coatings and surface properties of graphene are relevant to its biological effects. We discuss studies conducted in both non-murine and murine systems, and emphasize the preclinical aspect of graphene's potential without undermining its tangible clinical implementation.

Few layer graphene does not affect the function and the autophagic activity of primary lymphocytes

Carbon-based nanomaterials represent a new tool in future medical applications. Thus, focusing on the evaluation of the degree of their safety has been growing in the last years. In this study we were particularly interested in understanding the impact of few layer graphene (FLG) on primary murine lymphocytes. These B and T cells, that are the second, but specialized, line of defense of the immune system, rely on various mechanisms to ensure their efficient function and maintenance. One of these mechanisms is autophagy that can be triggered by various nanomaterials in some types of cells. For these reasons, we were interested in evaluating the way FLG could affect this process in lymphocytes. Our results point out that FLG neither impacts the viability and activation of T and B cells nor their autophagic activity. Using confocal microscopy, we were also able to see that FLG does not appear to cause any membrane damage and does not penetrate inside of these cells. Overall, our data do not show any effect of this material on lymphocyte homeostasis, which is one more argument in favor of the continuation of studies investigating the potential of FLG for therapeutic applications.

Modeling Interactions between Liposomes and Hydrophobic Nanosheets

2D nanomaterials could cause structural disruption and cytotoxic effects to cells, which greatly challenges their promising biomedical applications including biosensing, bioimaging, and drug delivery. Here, the physical and mechanical interaction between lipid liposomes and hydrophobic nanosheets is studied utilizing coarse-grained (CG) molecular dynamics (MD) simulations. The simulations reveal a variety of characteristic interaction morphologies that depend on the size and the orientation of nanosheets. Dynamic and thermodynamic analyses on the morphologic evolution provide insights into molecular motions such as "nanosheet rotation," "lipid extraction," "lipid flip-flop," and "lipid spreading." Driven by these molecular motions, hydrophobic nanosheets cause morphologic changes of liposomes. The lipid bilayer structure can be corrugated, and the overall liposome sphere can be split or collapsed by large nanosheets. In addition, nanosheets embedded into lipid bilayers greatly weaken the fluidity of lipids, and this effect can be cumulatively enhanced as nanosheets continuously intrude. These results could facilitate molecular-level understanding on the cytotoxicity of nanomaterials, and help future nanotoxicology studies associating computational modeling with experiments.

Label-Free Sensitive Detection of Microcystin-LR via Aptamer-Conjugated Gold Nanoparticles Based on Solid-State Nanopores

A versatile and highly sensitive strategy for nanopore detection of microcystin-LR (MC-LR) is proposed herein based on the aptamer and host-guest interactions by employing a gold nanoparticle (AuNP) probe. The aptamer of MC-LR and its complementary DNA (cDNA) are respectively immobilized on AuNPs with distinct sizes (5 nm AuNPs for the aptamer and 20 nm for the cDNA), and the constructed polymeric AuNP network via the hybridization of the aptamer and cDNA was disintegrated upon the addition of MC-LR. The specific interactions between the aptamer and MC-LR disrupt and release the cDNA-AuNPs that were then removed by centrifugation, leaving the MC-LR-aptamer-AuNP species in the supernatant for subsequent nanopore determination. By monitoring the current blockade of released MC-LR-aptamer-AuNPs using a specific tailored nanopore (10 and 20 nm in diameter, generated by current dielectric breakdown), we could deduce the presence of MC-LR, as the bulky NP network could not pass through a nanopore with a relatively smaller size. We realized the detection of MC-LR with a concentration as low as 0.1 nM; additionally, we have proved the specificity of the interaction between the aptamer and MC-LR by replacing MC-LR with other congener toxins (MC-RR and MC-YR), chlorophyll (a component abundantly coexists in water), and the mixture of the four.

Saccharomyces-derived carbon dots for biosensing pH and vitamin B 12

Photoluminescence(PL) nano-biosensors that can be used for accurately and reliably monitoring pH and vitamin hold a great promise in biology and medicine. Herein, a high quantum yield of 16% saccharomyces-derived N-doped carbon dots (s-N-CDs) was synthesized through a simple and one-pot microwave-assisted hydrothermal approach. The produced s-N-CDs are an excellent multi-functional biosensor for the applications of pH sensing and vitamin probing. Fluorescence intensity and fluorescence lifetime dramatically increases with pH decreasing from 14 to 2. Moreover, the fluorescence intensity presents highly reversible abilty from 13 to 2 without any profound attenuation after ten consecutive circles. More importantly, the CDs prepared herein are sound option for assaying cobalamin (VB 12) based fluorescence resonance energy transfer (FRET) with a superior low detection limit of 2.19 μM.

Molecular Mechanism of Conductance Enhancement in Narrow Cation-Selective Membrane Channels

Membrane proteins known as ryanodine receptors (RyRs) display large conductance of ∼1 nS and nearly ideal charge selectivity. Both properties are inversely correlated in other large-conductance but nonselective biological nanopores (i.e., α-hemolysin) used as industrial biosensors. Although recent cryo-electron microscopy structures of RyR2 show similarities to K⁺- and Na⁺-selective channels, it remains unclear whether similar ion conduction mechanisms occur in RyR2. Here, we combine microseconds of all-atom molecular dynamics (MD) simulations with mutagenesis and electrophysiology experiments to investigate large K⁺ conductance and charge selectivity (cation vs anion) in an open-state structure of RyR2. Our results show that a water-mediated knock-on mechanism enhances the cation permeation. The polar Q4863 ring may function as a confinement zone amplifying charge selectivity, while the cytoplasmic vestibule can contribute to the efficiency of the cation attraction. We also provide direct evidence that the rings of acidic residues at the channel vestibules are critical for both conductance and charge discrimination in RyRs.