Investigation of Ion Channel Activities of Gramicidin A in the Presence of Ionic Liquids Using Model Cell Membranes

Ionic Liquid Gating Induces Anomalous Permeation through Membrane Channel Proteins

Membrane channel proteins (MCPs) play key roles in matter transport through cell membranes and act as major targets for vaccines and drugs. For emerging ionic liquid (IL) drugs, a rational understanding of how ILs affect the structure and transport function of MCP is crucial to their design. In this work, GPU-accelerated microsecond-long molecular dynamics simulations were employed to investigate the modulating mechanism of ILs on MCP. Interestingly, ILs prefer to insert into the lipid bilayer and channel of aquaporin-2 (AQP2) but adsorb on the entrance of voltage-gated sodium channels (Nav). Molecular trajectory and free energy analysis reflect that ILs have a minimal impact on the structure of MCPs but significantly influence MCP functions. It demonstrates that ILs can decrease the overall energy barrier for water through AQP2 by 1.88 kcal/mol, whereas that for Na+ through Nav is increased by 1.70 kcal/mol. Consequently, the permeation rates of water and Na+ can be enhanced and reduced by at least 1 order of magnitude, respectively. Furthermore, an abnormal IL gating mechanism was proposed by combining the hydrophobic nature of MCP and confined water/ion coordination effects. More importantly, we performed experiments to confirm the influence of ILs on AQP2 in human cells and found that treatment with ILs significantly accelerated the changes in cell volume in response to altered external osmotic pressure. Overall, these quantitative results will not only deepen the understanding of IL-cell interactions but may also shed light on the rational design of drugs and disease diagnosis.

Mechanisms of Biological Effects of Ionic Liquids: From Single Cells to Multicellular Organisms

The review presents a detailed discussion of the evolving field studying interactions between ionic liquids (ILs) and biological systems. Originating from molten salt electrolytes to present multiapplication substances, ILs have found usage across various fields due to their exceptional physicochemical properties, including excellent tunability. However, their interactions with biological systems and potential influence on living organisms remain largely unexplored. This review examines the cytotoxic effects of ILs on cell cultures, biomolecules, and vertebrate and invertebrate organisms. Our understanding of IL toxicity, while growing in recent years, is yet nascent. The established findings include correlations between harmful effects of ILs and their ability to disturb cellular membranes, their potential to trigger oxidative stress in cells, and their ability to cause cell death via apoptosis. Future research directions proposed in the review include studying the distribution of various ILs within cellular compartments and organelles, investigating metabolic transformations of ILs in cells and organisms, detailed analysis of IL effects on proteins involved in oxidative stress and apoptosis, correlation studies between IL doses, exposure times and resulting adverse effects, and examination of effects of subtoxic concentrations of ILs on various biological objects. This review aims to serve as a critical analysis of the current body of knowledge on IL-related toxicity mechanisms. Furthermore, it can guide researchers toward the design of less toxic ILs and the informed use of ILs in drug development and medicine.

Silicon Nitride-Based Micro-Apertures Coated with Parylene for the Investigation of Pore Proteins Fused in Free-Standing Lipid Bilayers

In this work, we present a microsystem setup for performing sensitive biological membrane translocation measurements. Thin free-standing synthetic bilayer lipid membranes (BLM) were constructed in microfabricated silicon nitride apertures (<100 µm in diameter), conformal coated with Parylene (Parylene-C or Parylene-AF4). Within these BLMs, electrophysiological measurements were conducted to monitor the behavior of different pore proteins. Two approaches to integrate pore-forming proteins into the membrane were applied: direct reconstitution and reconstitution via outer membrane vesicles (OMVs) released from Gram-negative bacteria. The advantage of utilizing OMVs is that the pore proteins remain in their native lipid and lipopolysaccharide (LPS) environment, representing a more natural state compared to the usage of fused purified pore proteins. Multiple aperture chips can be easily assembled in the 3d-printed holder to conduct parallel membrane transport investigations. Moreover, well defined microfabricated apertures are achievable with very high reproducibility. The presented microsystem allows the investigation of fast gating events (down to 1 ms), pore blocking by an antibiotic, and gating events of small pores (amplitude of approx. 3 pA).

Interaction of imidazolium-based ionic liquids with supported phospholipid bilayers as model biomembranes

The cytotoxicity of ionic liquids (ILs) is receiving increasing attention due to their potential biological and environmental impact. We have used atomic force microscopy to investigate the interaction of ILs with supported phospholipid bilayers, as models of biomembranes.

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.

Selective ion transport across a lipid bilayer in a protic ionic liquid

Ionic liquids (ILs) have exhibited enormous potential as electrolytes, designer solvents and reaction media, as well as being surprisingly effective platforms for amphiphile self-assembly and for preserving structure of complex biomolecules. This has led to their exploration as media for long-term biopreservation and in biosensors, for which their viability depends on their ability to sustain both structure and function within complex, multicomponent nanoscale compartments and assemblies. Here we show that a tethered lipid bilayer can be assembled directly in a purely IL environment that retains its structure upon exchange between IL and aqueous buffer, and that the membrane transporter valinomycin can be incorporated so as to retain its functionality and cation selectivity. This paves the way for the development of long-lived, non-aqueous microreactors and sensor assemblies, and demonstrates the potential for complex proteins to retain functionality in non-aqueous, ionic liquid solvents.

Deciphering the Structure of the Gramicidin A Channel in the Presence of AOT Reverse Micelles in Pentane Using Molecular Dynamics Simulations

Structural studies of proteins and, in particular, integral membrane proteins (IMPs) using solution NMR spectroscopy approaches are challenging due to not only their inherent structural complexities but also the fact that they need to be solubilized in biomimetic environments (such as micelles), which enhances the slow molecular reorientation. To deal with these difficulties and increase the effective rate of molecular reorientation, the encapsulation of IMPs in the aqueous core of the reverse micelle (RM) dissolved in a low-viscosity solvent has been proven to be a viable approach. However, the effect of the reverse micelle (RM) environment on the IMP structure and function is little known. To gain insight into these aspects, this article presents a series of atomistic unconstrained molecular dynamics (MD) of a model ion channel (gramicidin A, gA) with RMs formed with anionic surfactant diacyl chain bis(2-ethylhexyl) sodium succinate (AOT) in pentane at a water-to-surfactant molar ratio (W₀) of 6. The simulations were carried out with different protocols and starting conditions for a total of 2.4 μs and were compared with other MDs used with the gA channel inserted in models of the SDS micelle or the DMPC membrane. We show here that in the presence of AOT RMs the gA dimer did not look like the "dumbbell-like" model anticipated by experiments, where the C-terminal parts of the gA are capped with two RMs and the rest of the dimer is protected from the oil solvent by the AOT acyl chains. In contrast, the MD simulations reveal that the AOT, Na⁺, and water formed two well-defined and elongated RMs attached to the C-terminal ends of the gA dimer, while the rest is in direct contact with the pentane. The initial β^6.3 secondary structure of the gA is well conserved and filled with 6-9 waters, as in SDS micelles or the DMPC membrane. Finally, the water movement inside the gA is strongly affected by the presence of RMs at each extremity, and no passage of water molecules through the gA channel is observed even after a long simulation period, whereas the opposite was found for gA in SDS and DMPC.

Mechanisms of action of ionic liquids on living cells: the state of the art

Ionic liquids (ILs) are a relatively new class of organic electrolytes composed of an organic cation and either an organic or inorganic anion, whose melting temperature falls around room-temperature. In the last 20 years, the toxicity of ILs towards cells and micro-organisms has been heavily investigated with the main aim to assess the risks associated with their potential use in (industrial) applications, and to develop strategies to design greener ILs. Toxicity, however, is synonym with affinity, and this has stimulated, in turn, a series of biophysical and chemical-physical investigations as well as few biochemical studies focused on the mechanisms of action (MoAs) of ILs, key step in the development of applications in bio-nanomedicine and bio-nanotechnology. This review has the intent to present an overview of the state of the art of the MoAs of ILs, which have been the focus of a limited number of studies but still sufficient enough to provide a first glimpse on the subject. The overall picture that emerges is quite intriguing and shows that ILs interact with cells in a variety of different mechanisms, including alteration of lipid distribution and cell membrane viscoelasticity, disruption of cell and nuclear membranes, mitochondrial permeabilization and dysfunction, generation of reactive oxygen species, chloroplast damage (in plants), alteration of transmembrane and cytoplasmatic proteins/enzyme functions, alteration of signaling pathways, and DNA fragmentation. Together with our earlier review work on the biophysics and chemical-physics of IL-cell membrane interactions (Biophys. Rev. 9:309, 2017), we hope that the present review, focused instead on the biochemical aspects, will stimulate a series of new investigations and discoveries in the still new and interdisciplinary field of "ILs, biomolecules, and cells."

Ionic Liquids Chemical Stress Triggers Sphingoid Base Accumulation in Aspergillus nidulans

Understanding stress responses and signaling pathways in fungi became a fundamental need for the discovery of new specific antifungal targets for fighting emerging life-threatening pathogens and drug resistance. Ionic liquids constitute a unique class of chemicals, which structural diversity and tunable physical and chemical properties can provide a great diversity of stimuli. In this study, we propose the use of ionic liquids as tools to unravel signaling of stress responses in the filamentous fungus Aspergillus nidulans. We assessed how three ionic liquids with distinct effects over the cell wall and plasma membrane affect the biosynthesis of sphingolipids and accumulation of free sphingoid bases in this fungus. The stress imposed by each ionic liquid triggered the sphingolipid biosynthetic pathway and led to distinct profiles of sphingoid bases accumulation. Dodecyltributylphosphonium chloride and 1-decyl-3-methylimidazolium chloride induced the accumulation of sphingosine and of a yet unknown sphingoid base, respectively, while cholinium decanoate did not seem to accumulate any of these intermediates. This study brings further light to the roles of sphingoid bases in A. nidulans. In particular, sphingosine as a possible response mediator to cell wall damage induced by dodecyltributylphosphonium chloride, and involvement of an unknown sphingoid base in the response to plasma membrane permeabilization caused by 1-decyl-3-methylimidazolium chloride. In addition, we completed the genetic assignment of the glucosylceramide pathway in A. nidulans through the identification of the sphingolipid Δ4-desaturase gene (AN4405). The knowledge established reinforces the idea of targeting sphingolipids biosynthesis in the search of improved antifungal compounds.

Biomimetic Membranes with Transmembrane Proteins: State-of-the-Art in Transmembrane Protein Applications

In biological cells, membrane proteins are the most crucial component for the maintenance of cell physiology and processes, including ion transportation, cell signaling, cell adhesion, and recognition of signal molecules. Therefore, researchers have proposed a number of membrane platforms to mimic the biological cell environment for transmembrane protein incorporation. The performance and selectivity of these transmembrane proteins based biomimetic platforms are far superior to those of traditional material platforms, but their lack of stability and scalability rule out their commercial presence. This review highlights the development of transmembrane protein-based biomimetic platforms for four major applications, which are biosensors, molecular interaction studies, energy harvesting, and water purification. We summarize the fundamental principles and recent progress in transmembrane protein biomimetic platforms for each application, discuss their limitations, and present future outlooks for industrial implementation.

Imidazolium-Based Ionic Liquids Affect Morphology and Rigidity of Living Cells: An Atomic Force Microscopy Study

The study of the toxicity, biocompatibility, and environmental sustainability of room-temperature ionic liquids (ILs) is still in its infancy. Understanding the impact of ILs on living organisms, especially from the aquatic ecosystem, is urgent, since large amounts of these substances are starting to be employed as solvents in industrial chemical processes, and on the other side, evidence of toxic effects of ILs on microorganisms and single cells have been observed. To date, the toxicity of ILs has been investigated by means of macroscopic assays aimed at characterizing the effective concentrations (like the EC₅₀) that cause the death of a significant fraction of the population of microorganisms and cells. These studies allow us to identify the cell membrane as the first target of the IL interaction, whose effectiveness was correlated to the lipophilicity of the cation, i.e., to the length of the lateral alkyl chain. Our study aimed at investigating the molecular mechanisms underpinning the interaction of ILs with living cells. To this purpose, we carried out a combined topographic and mechanical analysis by atomic force microscopy of living breast metastatic cancer cells (MDA-MB-231) upon interaction with imidazolium-based ILs. We showed that ILs are able to induce modifications of the overall rigidity (effective Young's modulus) and morphology of the cells. Our results demonstrate that ILs act on the physical properties of the outer cell layer (the membrane linked to the actin cytoskeleton), already at concentrations below the EC₅₀. These potentially toxic effects are stronger at higher IL concentrations, as well as with longer lateral chains in the cation.

[omim][BF4]-mediated toxicity in mussel hemocytes includes its interaction with cellular membrane proteins

The current study is based on the increasing demand for the assessment of ionic liquid (IL)-mediated aquatic toxicity. Specifically, although a lot of studies have been performed so far, investigating IL-mediated adverse effects on numerous aquatic organisms, little is known about their mode of action. Given that the use of in vitro models is considered as a reliable tool for determining the mediated biological effects, the modulation of specific biochemical pathways and the onset of various forms of damage with great precision and reproducibility, mixed primary cultures of mussel Mytilus galloprovincialis hemocytes were used for investigating whether 1-octyl-3-methylimidazolium tetrafluoroborate ([omim][BF₄]) mediated toxicity is related to its interaction with cellular membrane proteins. Specifically, [omim][BF₄]-mediated cytotoxic, oxidative and genotoxic effects were investigated in mussel hemocytes before and after pre-treatment of cells with non-toxic concentration of guanidine hydrochloride (1 mM GndHCl). The results showed that [omim][BF₄] at concentrations ranging from 0.7 to 1.75 μM can induce cytotoxic (almost <50% reduction of cell viability), oxidative (increased levels of O₂^•- production and lipid peroxidation by-products) and genotoxic (increased levels of DNA damage) effects, while cells pre-treated with 1 mM GndHCl showed a significant attenuation of IL's toxic potency in all cases. According to the latter, the current study showed that [omim][BF₄]-mediated toxicity could be related not only to its well-known interaction with membrane lipid bilayers, but also to its interference with membrane proteins. Using GndHCl, a chaotropic agent that disrupts the hydrogen bonding network and the stability of membrane proteins via its interference with the intramolecular interactions mediated by non-covalent forces on cellular membranes, it was firstly shown that altering the membrane integrity as well as the native state of cellular membrane proteins, by weakening the hydrophobic effect, could attenuate the possible interaction of [omim][BF₄] with cellular membranes and the concomitant induction of protein-based intracellular processes, commonly linked with the induction of severe cellular damage.

Room-Temperature Ionic Liquids and Biomembranes: Setting the Stage for Applications in Pharmacology, Biomedicine, and Bionanotechnology

Empirical evidence and conceptual elaboration reveal and rationalize the remarkable affinity of organic ionic liquids for biomembranes. Cations of the so-called room-temperature ionic liquids (RTILs), in particular, are readily absorbed into the lipid fraction of biomembranes, causing a variety of observable biological effects, including generic cytotoxicity, broad antibacterial potential, and anticancer activity. Chemical physics analysis of model systems made of phospholipid bilayers, RTIL ions, and water confirm and partially explain this evidence, quantifying the mild destabilizing effect of RTILs on the structural, dynamic, and thermodynamic properties of lipids in biomembranes. Our Feature Article presents a brief introduction to these systems and to their roles in biophysics and biotechnology, summarizing recent experimental and computational results on their properties. More importantly, it highlights the many developments in pharmacology, biomedicine, and bionanotechnology expected from the current research effort on this topic. To anticipate future developments, we speculate on (i) potential applications of (magnetic) RTILs to affect and control the rheology of cells and biological tissues, of great relevance for diagnostics and (ii) the use of RTILs to improve the durability, reliability, and output of biomimetic photovoltaic devices.

Novel 3-Methyl-2-alkylthio Benzothiazolyl-Based Ionic Liquids: Synthesis, Characterization, and Antibiotic Activity

Three series of novel 3-methyl-2-alkylthio benzothiazolyl ionic liquids (ILs) were synthesized for the first time. After structural identification, their melting point, solubility, and thermostability together with antibiotic activity were determined successively. As a result, 3-methyl-2-alkylthio benzothiazolyl p-toluene sulfonate was found to have the highest antibacterial activity among the three series of ILs. Meanwhile, it has a good solubility in water as well. On the basis of comprehensive comparison with similar compounds, the effect of cations and anions of these benzothiazolium ILs on typical physical properties together with antibiotic performance was explored and discussed, which is very beneficial to take the greatest advantage of their structural designability for various purposes. Furthermore, the experiment data preliminarily discovered the relationships of the structure-properties/activities of the above three kinds ILs to a certain extent, which can provide useful references for future research and for the potential application of these new ILs as surfactant antiseptics or agricultural chemicals.

The role of phosphatidylinositol-3-OH-kinase (PI3-kinase) and respiratory burst enzymes in the [omim][BF4]-mediated toxic mode of action in mussel hemocytes

The present study investigates the role of phosphatidylinositol-3-OH-kinase (PI3-kinase) and respiratory burst enzymes, NADPH oxidase and NO synthase, in the 1-methyl-3-octylimidazolium tetrafluoroborate ([omim][BF₄])-mediated toxic mode of action in mussel hemocytes. Specifically, cell viability (using the neutral red uptake assay) was primarily tested in hemocytes treated with different concentrations of [omim][BF₄] (0.1-10 mg L^-1) and thereafter [omim][BF₄]-mediated oxidative (in terms of superoxide anions/O₂^- and nitric oxide/NO generation, as well as the enhancement of lipid peroxidation by-products, in terms of malondialdehyde/MDA) and genotoxic (in terms of DNA damage) effects were determined in hemocytes treated with 1 mg L^-1 [omim][BF₄]. Moreover, in order to investigate, even indirectly and non-entirely specific, the role of PI3-kinase, NADPH oxidase and NO synthase, the [omim][BF₄]-mediated effects were also investigated in hemocytes pre-incubated with wortmannin (50 nM), diphenyleneiodonium chloride (DPI 10 μM) and N^G-nitro-_l-arginine methyl ester (l-NAME 10 μM), respectively. The results showed that [omim][BF₄] ability to enhance O₂^-, NO, MDA and DNA damage, via its interaction with cellular membranes, was significantly attenuated in the presence of each inhibitor in almost all cases. The current findings revealed for the first time that certain signaling molecules, such as PI3-kinase, as well as respiratory burst enzymes activation, such as NADPH oxidase and NO synthase, could merely attribute to the [omim][BF₄]-mediated mode of action, thus enriching our knowledge for the molecular mechanisms of ILs toxicity.

Room-temperature ionic liquids meet bio-membranes: the state-of-the-art

Room-temperature ionic liquids (RTIL) are a new class of organic salts whose melting temperature falls below the conventional limit of 100 °C. Their low vapor pressure, moreover, has made these ionic compounds the solvents of choice of the so-called green chemistry. For these and other peculiar characteristics, they are increasingly used in industrial applications. However, studies of their interaction with living organisms have highlighted mild to severe health hazards. Since their cytotoxicity shows a positive correlation with their lipophilicity, several chemical-physical studies of their interactions with biomembranes have been carried out in the last few years, aiming to identify the molecular mechanisms behind their toxicity. Cation chain length and anion nature of RTILs have seemed to affect lipophilicity and, in turn, their toxicity. However, the emerging picture raises new questions, points to the need to assess toxicity on a case-by-case basis, but also suggests a potential positive role of RTILs in pharmacology, bio-medicine and bio-nanotechnology. Here, we review this new subject of research, and comment on the future and the potential importance of this emerging field of study.

Synergistic effects of polymyxin and ionic liquids on lipid vesicle membrane stability and aggregation

Ionic liquids (ILs) have been investigated for potential antibacterial and antibiotic applications due to their ability to destabilize and permeabilize the lipid bilayers in cell membranes. Bacterial assays have shown that combining ILs with antibiotics can provide a synergistic enhancement of their antibacterial activities. We have characterized the mechanism by which the conventional ILs 1-butyl-3-methylimidazolium chloride (BMICl) and 1-butyl-3-methylimidazolium tetrafluoroborate (BMIBF₄) enhance the lipid membrane permeabilization of the well-known antibiotic polymyxin B (PMB). We studied the sizes and membrane permeabilities of multilamellar and unilamellar lipid bilayer vesicles in the presence of ILs alone in aqueous solution, PMB alone, and ILs combined together with PMB. Light scattering-based experiments show that vesicle sizes dramatically increase when ILs are combined with PMB, which suggests that the materials combine to synergistically enhance lipid membrane disruption leading to vesicle aggregation. Lipid bilayer leakage experiments using tris (2,2'-bipyridyl) ruthenium (II) (Ru(bpy)₃²⁺) trapped in lipid vesicles, in which the trapped Ru(bpy)₃²⁺ fluorescence lifetime increases when it leaks out of the vesicle, show that combining BMIBF₄ and PMB together permeabilize the membrane significantly more than with PMB or the IL alone. This demonstrates that ILs can assist in antibiotic permeabilization of lipid bilayers which could explain the increased antibiotic activities in the presence of ILs in solution.

Biological Activity of Ionic Liquids and Their Application in Pharmaceutics and Medicine

Ionic liquids are remarkable chemical compounds, which find applications in many areas of modern science. Because of their highly tunable nature and exceptional properties, ionic liquids have become essential players in the fields of synthesis and catalysis, extraction, electrochemistry, analytics, biotechnology, etc. Apart from physical and chemical features of ionic liquids, their high biological activity has been attracting significant attention from biochemists, ecologists, and medical scientists. This Review is dedicated to biological activities of ionic liquids, with a special emphasis on their potential employment in pharmaceutics and medicine. The accumulated data on the biological activity of ionic liquids, including their antimicrobial and cytotoxic properties, are discussed in view of possible applications in drug synthesis and drug delivery systems. Dedicated attention is given to a novel active pharmaceutical ingredient-ionic liquid (API-IL) concept, which suggests using traditional drugs in the form of ionic liquid species. The main aim of this Review is to attract a broad audience of chemical, biological, and medical scientists to study advantages of ionic liquid pharmaceutics. Overall, the discussed data highlight the importance of the research direction defined as "Ioliomics", studies of ions in liquids in modern chemistry, biology, and medicine.

Investigation of membrane condensation induced by CaCO3 nanoparticles and its effect on membrane protein function

Investigation of membrane condensation induced by calcium ions released from nano-CaCO₃.

Automated Lipid Bilayer Membrane Formation Using a Polydimethylsiloxane Thin Film

An artificial lipid bilayer, or black lipid membrane (BLM), is a powerful tool for studying ion channels and protein interactions, as well as for biosensor applications. However, conventional BLM formation techniques have several drawbacks and they often require specific expertise and laborious processes. In particular, conventional BLMs suffer from low formation success rates and inconsistent membrane formation time. Here, we demonstrate a storable and transportable BLM formation system with controlled thinning-out time and enhanced BLM formation rate by replacing conventionally used films (polytetrafluoroethylene, polyoxymethylene, polystyrene) to polydimethylsiloxane (PDMS). In this experiment, a porous-structured polymer such as PDMS thin film is used. In addition, as opposed to conventionally used solvents with low viscosity, the use of squalene permitted a controlled thinning-out time via slow solvent absorption by PDMS, prolonging membrane lifetime. In addition, by using a mixture of squalene and hexadecane, the freezing point of the lipid solution was increased (~16 °C), in addition, membrane precursors were produced that can be indefinitely stored and readily transported. These membrane precursors have reduced BLM formation time of < 1 hr and achieved a BLM formation rate of ~80%. Moreover, ion channel experiments with gramicidin A demonstrated the feasibility of the membrane system.