Effects of Low-level Lipid Peroxidation on the Permeability of Nitroaromatic Molecules across a Membrane: A Computational Study

Redox signaling and oxidative stress in systemic acquired resistance

Plants fully depend on their immune systems to defend against pathogens. Upon pathogen attack, plants not only activate immune responses at the infection site but also trigger a defense mechanism known as systemic acquired resistance (SAR) in distal systemic tissues to prevent subsequent infections by a broad-spectrum of pathogens. SAR is induced by mobile signals produced at the infection site. Accumulating evidence suggests that reactive oxygen species (ROS) play a central role in SAR signaling. ROS burst at the infection site is one of the earliest cellular responses following pathogen infection and can spread to systemic tissues through membrane-associated NADPH oxidase-dependent relay production of ROS. It is well known that ROS ignite redox signaling and, when in excess, cause oxidative stress, damaging cellular components. In this review, we summarize current knowledge on redox regulation of several SAR signaling components. We discuss the ROS amplification loop in systemic tissues involving multiple SAR mobile signals. Moreover, we highlight the essential role of oxidative stress in generating SAR signals including azelaic acid and extracellular NAD(P) [eNAD(P)]. Finally, we propose that eNAD(P) is a damage-associated molecular pattern serving as a converging point of SAR mobile signals in systemic tissues.

Effects of Nitro-Oxidative Stress on Biomolecules: Part 1-Non-Reactive Molecular Dynamics Simulations

Plasma medicine, or the biomedical application of cold atmospheric plasma (CAP), is an expanding field within plasma research. CAP has demonstrated remarkable versatility in diverse biological applications, including cancer treatment, wound healing, microorganism inactivation, and skin disease therapy. However, the precise mechanisms underlying the effects of CAP remain incompletely understood. The therapeutic effects of CAP are largely attributed to the generation of reactive oxygen and nitrogen species (RONS), which play a crucial role in the biological responses induced by CAP. Specifically, RONS produced during CAP treatment have the ability to chemically modify cell membranes and membrane proteins, causing nitro-oxidative stress, thereby leading to changes in membrane permeability and disruption of cellular processes. To gain atomic-level insights into these interactions, non-reactive molecular dynamics (MD) simulations have emerged as a valuable tool. These simulations facilitate the examination of larger-scale system dynamics, including protein-protein and protein-membrane interactions. In this comprehensive review, we focus on the applications of non-reactive MD simulations in studying the effects of CAP on cellular components and interactions at the atomic level, providing a detailed overview of the potential of CAP in medicine. We also review the results of other MD studies that are not related to plasma medicine but explore the effects of nitro-oxidative stress on cellular components and are therefore important for a broader understanding of the underlying processes.

Lipid Corona Formation on Micro- and Nanoplastic Particles Modulates Uptake and Toxicity in A549 Cells

Plastic waste is a global issue leaving no continents unaffected. In the environment, ultraviolet radiation and shear forces in water and land contribute to generating micro- and nanoplastic particles (MNPP), which organisms can easily take up. Plastic particles enter the human food chain, and the accumulation of particles within the human body is expected. Crossing epithelial barriers and cellular uptake of MNPP involves the interaction of plastic particles with lipids. To this end, we generated unilamellar vesicles from POPC (1-palmitoyl-2-oleoyl-glycero-3-phosphocholine) and POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine) and incubated them with pristine, carboxylated, or aminated polystyrene spheres (about 1 µm in diameter) to generate lipid coronas around the particles. Lipid coronas enhanced the average particle sizes and partially changed the MNPP zeta potential and polydispersity. In addition, lipid coronas led to significantly enhanced uptake of MNPP particles but not their cytotoxicity, as determined by flow cytometry. Finally, adding proteins to lipid corona nanoparticles further modified MNPP uptake by reducing the uptake kinetics, especially in pristine and carboxylated plastic samples. In conclusion, our study demonstrates for the first time the impact of different types of lipids on differently charged MNPP particles and the biological consequences of such modifications to better understand the potential hazards of plastic exposure.

Leveraging Plasma Membrane Repair Therapeutics for Treating Neurodegenerative Diseases

Plasma membrane repair is an essential cellular mechanism that reseals membrane disruptions after a variety of insults, and compromised repair capacity can contribute to the progression of many diseases. Neurodegenerative diseases are marked by membrane damage from many sources, reduced membrane integrity, elevated intracellular calcium concentrations, enhanced reactive oxygen species production, mitochondrial dysfunction, and widespread neuronal death. While the toxic intracellular effects of these changes in cellular physiology have been defined, the specific mechanism of neuronal death in certain neurodegenerative diseases remains unclear. An abundance of recent evidence indicates that neuronal membrane damage and pore formation in the membrane are key contributors to neurodegenerative disease pathogenesis. In this review, we have outlined evidence supporting the hypothesis that membrane damage is a contributor to neurodegenerative diseases and that therapeutically enhancing membrane repair can potentially combat neuronal death.

Membrane Order Effect on the Photoresponse of an Organic Transducer

Non-genetic photostimulation, which allows for control over cellular activity via the use of cell-targeting phototransducers, is widely used nowadays to study and modulate/restore biological functions. This approach relies on non-covalent interactions between the phototransducer and the cell membrane, thus implying that cell conditions and membrane status can dictate the effectiveness of the method. For instance, although immortalized cell lines are traditionally used in photostimulation experiments, it has been demonstrated that the number of passages they undergo is correlated to the worsening of cell conditions. In principle, this could impact cell responsivity against exogenous stressors, including photostimulation. However, these aspects have usually been neglected in previous experiments. In this work, we investigated whether cell passages could affect membrane properties (such as polarity and fluidity). We applied optical spectroscopy and electrophysiological measurements in two different biological models: (i) an epithelial immortalized cell line (HEK-293T cells) and (ii) liposomes. Different numbers of cell passages were compared to a different morphology in the liposome membrane. We demonstrated that cell membranes show a significant decrease in ordered domains upon increasing the passage number. Furthermore, we observed that cell responsivity against external stressors is markedly different between aged and non-aged cells. Firstly, we noted that the thermal-disordering effect that is usually observed in membranes is more evident in aged cells than in non-aged ones. We then set up a photostimulation experiment by using a membrane-targeted azobenzene as a phototransducer (Ziapin2). As an example of a functional consequence of such a condition, we showed that the rate of isomerization of an intramembrane molecular transducer is significantly impaired in aged cells. The reduction in the photoisomerization rate translates in cells with a sustained reduction of the Ziapin2-related hyperpolarization of the membrane potential and an overall increase in the molecule fluorescence. Overall, our results suggest that membrane stimulation strongly depends on membrane order, highlighting the importance of cell passage during the characterization of the stimulation tools. This study can shine light on the correlation between aging and the development of diseases driven by membrane degradation as well as on the different cell responsivities against external stressors, such as temperature and photostimulation.

The effects of molecular weight and orientation on the membrane permeation and partitioning of polycyclic aromatic hydrocarbons: a computational study

Membrane permeation and the partitioning of polycyclic aromatic hydrocarbons (PAHs) are crucial aspects affecting their carcinogenicity and mutagenicity. However, a clear understanding of these processes is still rare due to the difficulty of determining the details experimentally. Here, the interactions between PAHs and lipid bilayers were studied by molecular simulations, mainly to check the influence of molecular weight and orientation. The liposome-water partition coefficient (K_LW), transmembrane time (τ), and permeability coefficient (P) of the PAHs were calculated by integrating free energy profiles from umbrella sampling. For selected PAHs, the membrane adsorption is a spontaneous process. The preferred location is near the CC bond and the orientation is related to the molecular structure. The P values of all the PAHs are basically the same order of magnitude, which means that the molecular weight contributes little to the process. As for K_LW and τ, they show obvious increases with different molecular weights. Unconstrained simulations showed that a flat orientation on the membrane surface would prevent PAHs from being transported through the membrane. Highly hydrophobic driving forces are not always good for the absorption of PAHs, especially the formation of aggregates. In addition, the orientations and energetic barriers of PAHs near the midplane of the lipid bilayer explain the different transitions of high- and low-weight PAHs. This work provides molecular level details relating to the interactions of PAHs with lipid membranes, with significance for understanding the health effects of PAHs.

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.

Sampling efficiency of the counting method for permeability calculations estimated with the inhomogeneous solubility-diffusion model

Permeability is a key property in various fields such as membrane technology for chemical separation and transport of substances through cell membranes. At the molecular scale, the counting method uses the number of membrane crossings in a conventional unbiased molecular dynamics simulation to predict the permeability. This contribution investigates under which conditions the counting method has insufficient statistics. An equation is derived for a compartmental model based on the inhomogeneous solubility-diffusion (Smoluchowski) model, giving insight into how the flux correlates with the solubility of permeants. This equation shows that a membrane crossing is a rare event not only when the membrane forms a large free energy barrier but also when the membrane forms a deep free energy well that traps permeants. Such a permeant trap has a high permeability; yet, the counting method suffers from poor statistics. To illustrate this, coarse-grained MD was run for 16 systems of dipalmitoylphosphatidylcholine bilayer membranes with different permeant types. The composition rule for permeability is shown to also hold for fluxes, and it is highlighted that the considered thickness of the membrane causes uncertainty in the permeability calculation of highly permeable membranes. In conclusion, a high permeability in itself is not an effective indicator of the sampling efficiency of the counting method, and caution should be taken for permeants whose solubility varies greatly over the simulation box. A practical consequence relevant in, e.g., drug design is that a drug with high membrane permeability might get trapped by membranes thus reducing its efficacy.

Oxidation degree of a cell membrane model and its response to structural changes, a coarse-grained molecular dynamics approach

Oxidative stress plays an essential role in the regulation of vital processes in living organisms. Reactive oxygen species can react chemically with the constituents of the cells leading to irreversible damage. The first structure of the cell in contact with the environment that surrounds it is the membrane, which protects it and allows the exchange of substances. Some signals manifest when the components of a bilayer are undergoing oxidation, like an increase in the lipid area, decrease in the thickness of the bilayer, and exchange of the oxidized groups toward the bilayer surface. In this investigation, a molecular dynamics simulation was done on a set of Dioleoylphosphatidylcholine membranes with different percentage of oxidized lipids, in order to observe the effect of the oxidation degree on the membrane structure. It was found that, as higher the concentration of oxidized lipids is, the larger the damage of the membrane. This is reflected in the increase in the lipid area and the decrease in the thickness and membrane packing. Also, it was observed that hydrophobicity inside the membrane decreases as the oxidation percentage increases.Communicated by Ramaswamy H. Sarma.