Lipid Organization of the Plasma Membrane

Atomistic Simulations and Analysis of Peripheral Membrane Proteins with Model Lipid Bilayers

All-atom molecular dynamics (AAMD) is a computational technique that predicts the movement of particles based on the intermolecular forces acting on the system. It enables the study of biological systems at atomic detail, complements observations from experiments, and can help the selection of experimental targets. Here, we describe the applications of MD simulations to study the interaction between peripheral membrane proteins and lipid bilayers. Specifically, we provide step-by-step instructions to set up MD simulations to study the binding and interaction of ALPS, the amphipathic helix of the lipid transport protein Osh4, and Thanatin, an antimicrobial peptide with model membranes. We describe examples of systems built with fully atomistic lipid tails and those truncated with the highly-mobile-membrane-mimetic method to enhance conformational sampling. We also comment on the importance of lipid diversity, molecular resolution, and best practices for constructing, running, and analyzing protein-lipid simulation systems. In this second edition, we include a brief discussion on alternative approaches and software to construct protein-membrane coordinate systems, as well as analysis tools and practices that have become relevant to examining protein-lipid interactions since the first edition of this chapter.

Type I IFN induces long-chain acyl-CoA synthetase 1 to generate a phosphatidic acid reservoir for lipotoxic saturated fatty acids

Long-chain acyl-CoA synthetase 1 (ACSL1) catalyzes the conversion of long-chain fatty acids to acyl-CoAs. ACSL1 is required for β-oxidation in tissues that rely on fatty acids as fuel, but no consensus exists on why ACSL1 is induced by inflammatory mediators in immune cells. We used a comprehensive and unbiased approach to investigate the role of ACSL1 induction by interferon type I (IFN-I) in myeloid cells in vitro and in a mouse model of IFN-I overproduction. Our results show that IFN-I induces ACSL1 in macrophages via its interferon-α/β receptor, and consequently that expression of ACSL1 is increased in myeloid cells from individuals with systemic lupus erythematosus (SLE), an autoimmune condition characterized by increased IFN production. Taking advantage of a myeloid cell-targeted ACSL1-deficient mouse model and a series of lipidomics, proteomics, metabolomics and functional analyses, we show that IFN-I leverages induction of ACSL1 to increase accumulation of fully saturated phosphatidic acid species in macrophages. Conversely, ACSL1 induction is not needed for IFN-I's ability to induce the prototypical IFN-stimulated protein signature or to suppress proliferation or macrophage metabolism. Loss of ACSL1 in IFN-I stimulated myeloid cells enhances apoptosis and secondary necrosis in vitro, especially in the presence of increased saturated fatty acid load, and in a mouse model of atherosclerosis associated with IFN overproduction, resulting in larger lesion necrotic cores. We propose that ACSL1 induction is a mechanism used by IFN-I to increase phosphatidic acid saturation while protecting the cells from saturated fatty acid-induced cell death.

Effects of Ca2+ on the Structure and Dynamics of PIP3 in Model Membranes Containing PC and PS

Phosphatidylinositol phosphates (PIPs) are a family of seven different eukaryotic membrane lipids that have a large role in cell viability, despite their minor concentration in eukaryotic cellular membranes. PIPs tightly regulate cellular processes, such as cellular growth, metabolism, immunity, and development through direct interactions with partner proteins. Understanding the biophysical properties of PIPs in the complex membrane environment is important to understand how PIPs selectively regulate a partner protein. Here, we investigate the structure and dynamics of PIP3 in lipid bilayers that are simplified models of the natural membrane environment. We probe the effects of the anionic lipid phosphatidylserine (PS) and the divalent cation Ca2+ by using full-length lipids in well-formed bilayers. We used solution and solid-state NMR on naturally abundant 1H, 31P, and 13C atoms combined with molecular dynamics (MD) simulations to characterize the structure and dynamics of PIPs. 1H and 31P 1D spectra show good resolution at temperatures above the phase transition with isolated peaks in the headgroup, interfacial, and bilayer regions. Site-specific assignment of the chemical shifts of these reporters enables the measurement of the effects of Ca2+ and PS at the single atom level. In particular, the resolved 31P signals of the PIP3 headgroup allow for extremely well-localized information about PIP3 phosphate dynamics, which the MD simulations can further explain. A quantitative assessment of cross-polarization kinetics provides additional dynamics measurements for the PIP3 headgroups.

Delineating lipidomic landscapes in human and mouse ovaries: Spatial signatures and chemically-induced alterations via MALDI mass spectrometry imaging: Spatial ovarian lipidomics

This study addresses the critical gap in understanding the ovarian lipidome's abundance, distribution, and vulnerability to environmental disruptors, a largely unexplored field. Leveraging the capabilities of matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI), we embarked on a novel exploration of the ovarian lipidome in both mouse and human healthy tissues. Our findings revealed that the obesogenic chemical tributyltin (TBT), at environmentally relevant exposures, exerts a profound and region-specific impact on the mouse ovarian lipidome. TBT exposure predominantly affects lipid species in antral follicles and oocytes, suggesting a targeted disruption of lipid homeostasis in these biologically relevant regions. Our comprehensive approach, integrating advanced lipidomic techniques and bioinformatic analyses, documented the disruptive effects of TBT, an environmental chemical, on the ovarian lipid landscape. Similar to mice, our research also unveiled distinct spatial lipidomic signatures corresponding to specific ovarian compartments in a healthy human ovary that may also be vulnerable to disruption by chemical exposures. Findings from this study not only underscore the vulnerability of the ovarian lipidome to environmental factors but also lay the groundwork for unraveling the molecular pathways underlying ovarian toxicity mediated through lipid dysregulation.

Molecular dynamics simulations unveil the aggregation patterns and salting out of polyarginines at zwitterionic POPC bilayers in solutions of various ionic strengths

This study employs molecular dynamics (MD) simulations to investigate the adsorption and aggregation behavior of simple polyarginine cell-penetrating peptides (CPPs), specifically modeled as R9 peptides, at zwitterionic phosphocholine POPC membranes under varying ionic strengths of two peptide concentrations and two concentrations of NaCl and CaCl2. The results reveal an intriguing phenomenon of R9 aggregation at the membrane, which is dependent on the ionic strength, indicating a salting-out effect. As the peptide concentration and ionic strength increase, peptide aggregation also increases, with aggregate lifetimes and sizes showing a corresponding rise, accompanied by the total decrease of adsorbed peptides at the membrane surface. Notably, in high ionic strength environments, large R9 aggregates, such as octamers, are also observed occasionally. The salting-out, typically uncommon for short positively charged peptides, is attributed to the unique properties of arginine amino acid, specifically by its side chain containing amphiphilic guanidinium (Gdm+) ion which makes both intermolecular hydrophobic like-charge Gdm+ - Gdm+ and salt-bridge Gdm+ - C-terminus interactions, where the former are increased with the ionic strength, and the latter decreased due to electrostatic screening. The aggregation behavior of R9 peptides at membranes can also be linked to their CPP translocation properties, suggesting that aggregation may aid in translocation across cellular membranes.

Localization, aggregation, and interaction of glycyrrhizic acid with the plasma membrane

Glycyrrhizic acid (GLA) is the most important bioactive constituent of licorize root and exhibits antiviral, antimicrobial, anti-oxidant, anti-inflammatory, anti-allergic, and antitumor activities. GLA has an amphiphilic nature consisting of two hydrophilic and one hydrophobic part, and its mechanism of action could be mediated by its incorporation into the membrane. Furthermore, GLA presents two different forms, protonated (GLA) and deprotonated (GLAD), and has been suggested that their location inside the membrane could be different. Since GLA could be a source against many types of diseases, we have localized the GLA molecule in the presence of a complex membrane and established the detailed interactions of GLA with lipids using all-atom molecular dynamics. Our outcomes sustain that GLA/GLAD tend to locate amid the CHOL oxygen atom and the phospholipid phosphates, preferably perpendicular to the membrane surface, increasing membrane fluidity. Interestingly, GLA and GLAD tend to be surrounded by specific phospholipids, different for each type of molecule. Outstandingly, both GLA and GLAD tend to spontaneously associate in solution forming aggregates, precluding them from inserting into the membrane and, therefore, interacting with it. Consequently, some of the biological properties of GLA/GLAD could be credited to the alteration of the membrane biophysical properties by interacting with specific lipids. However, the formation of an aggregate in solution could hinder its bioactive properties and should be considered a suited vehicle when prepared to be used in biological or clinical assays.

The Role of Protein-Lipid Interactions in Priming the Bacterial Translocon

Protein-lipid interactions demonstrate important regulatory roles in the function of membrane proteins. Nevertheless, due to the semi-liquid nature and heterogeneity of biological membranes, and dissecting the details of such interactions at high resolutions continues to pose a major challenge to experimental biophysical techniques. Computational techniques such as molecular dynamics (MD) offer an alternative approach with both temporally and spatially high resolutions. Here, we present an extensive series of MD simulations focused on the inner membrane protein YidC (PDB: 6AL2) from Escherichia coli, a key insertase responsible for the integration and folding of membrane proteins. Notably, we observed rare lipid fenestration events, where lipids fully penetrate the vestibule of YidC, providing new insights into the lipid-mediated regulation of protein insertion mechanisms. Our findings highlight the direct involvement of lipids in modulating the greasy slide of YidC and suggest that lipids enhance the local flexibility of the C1 domain, which is crucial for recruiting substrate peptides. These results contribute to a deeper understanding of how protein-lipid interactions facilitate the functional dynamics of membrane protein insertases, with implications for broader studies of membrane protein biology.

Hybrid neMD/MC lipid swapping algorithm to equilibrate membrane simulation with thermodynamic reservoir

Molecular dynamics (MD) simulations based on detailed all-atom models offer a powerful approach to study the structure and dynamics of biological membranes. However, the complexity of biological membranes in terms of chemical diversity presents an outstanding challenge. Particularly, difficulties are encountered when a given lipid type is present at very low abundance. While considering a very large simulation system with a small number of the low abundance lipid may offer a practical solution in some cases, resorting to increasingly large system rapidly becomes computationally costly and impractical. More fundamentally, an additional issue may be encountered if the low abundance lipid displays a high affinity for some protein in the simulation system. What is needed is to treat the simulation box as an open system in which the number of lipids can naturally fluctuate, as in the Grand Canonical Monte Carlo (MC) algorithm. However, this approach, in which a whole lipid molecule needs to be inserted or annihilated, is essentially impractical in the context of an all-atom simulation. To enforce equilibrium between a simulated system and an infinite surrounding bath, we propose a hybrid non-equilibrium (neMD)-MC algorithm, in which a randomly chosen lipid molecule in the simulated system is swapped with a lipid picked in a separate system standing as a thermodynamic "reservoir" with the desired mole fraction for all lipid components. The neMD/MC algorithm consists in driving the system via short non-equilibrium trajectories to generate a new state of the system that are subsequently accepted or rejected via a Metropolis MC step. The probability of exchanges in the context of an infinite reservoir with the desired mole fraction for all lipid components is derived and tested with a few illustrative systems for phosphatidylcholine and phosphatidylglycerol lipid mixtures.

Invagination of Giant Unilamellar Vesicles upon Membrane Mixing with Native Vesicles

We demonstrate rapid membrane mixing between GUVs of pure lipid compositions and membrane vesicles (MVs) isolated from the plasma membrane of Vero cells, resulting in the transfer of native lipids and proteins to the GUVs. The steps involved in the membrane mixing are docking followed by membrane fusion. We show that positively charged lipids of the GUVs are essential for the docking, and the native membrane components of MVs drive the fusion. The interleaflet and lateral asymmetry and a change in the membrane tension upon the membrane mixing trigger membrane invagination. We detected outward and inward invagination sites at the rim of the GUVs within 10-40 min of the membrane mixing. The extent of the invaginations depends on the cholesterol and sphingomyelin (SM) contents in the GUVs. Cholesterol content above a critical concentration disfavors membrane invaginations, and the SM lipid is an essential molecular factor for membrane invagination.

Self-Assembly at Curved Biointerfaces

Most of the biological interfaces are curved. Understanding the organizational structures and interaction patterns at such curved biointerfaces is therefore crucial not only for deepening our comprehension of the principles that govern life processes but also for designing and developing targeted drugs aimed at diseased cells and tissues. Despite the considerable efforts dedicated to this area of research, our understanding of curved biological interfaces is still limited. Many aspects of these interfaces remain elusive, presenting both challenges and opportunities for further exploration. In this review, we summarize the structural characteristics of biological interfaces found in nature, the current research status of materials associated with curved biointerfaces, and the theoretical advancements achieved to date. Finally, we outline future trends and challenges in the theoretical and technological development of curved biointerfaces. By addressing these challenges, people could bridge the knowledge gap and unlock the full potential of curved biointerfaces for scientific and technological advancements, ultimately benefiting various fields and improving human health and well-being.

KRas4b-Calmodulin Interaction with Membrane Surfaces: Role of Headgroup, Acyl Chain, and Electrostatics

KRas4b is a small plasma membrane-bound G-protein that regulates signal transduction pathways. The interaction of KRas4b with the plasma membrane is governed by both its basic C-terminus, which is farnesylated and methylated, and the lipid composition of the membrane itself. The signaling activity of KRas4b is intricately related to its interaction with various binding partners at the plasma membrane, underlining the critical role played by the lipid environment. The calcium-binding protein calmodulin binds farnesylated KRas4b and plays an important role in the dynamic spatial cycle of KRas4b trafficking in the cell. We utilize Biolayer Interferometry to assay the role of lipid headgroup, chain length, and electrostatics in the dissociation kinetics of fully post-translationally modified KRas4b from Nanodisc bilayers with defined lipid compositions. Our results suggest that calmodulin promotes the dissociation of KRas4b from an anionic membrane, with a comparatively slower displacement of KRas4b from PIP2 relative to PS containing bilayers. In addition to this headgroup dependence, KRas4b dissociation appears to be slower from Nanodiscs wherein the lipid composition contains mismatched, unsaturated acyl chains as compared to lipids with a matched acyl chain length. These findings contribute to understanding the role of the lipid composition in the binding of KRas4b and release from lipid bilayers, showing that the overall charge of the bilayer, the identity of the headgroups present, and the length and saturation of the acyl chains play key roles in KRas4b release from the membrane, potentially providing insights in targeting Ras-membrane interactions for therapeutic interventions.

Membrane-Nanoparticle Interactions: The Impact of Membrane Lipids

The growing field of nanotechnology presents opportunity for applications across many sectors. Nanostructures, such as nanoparticles, hold distinct properties based on their size, shape, and chemical modifications that allow them to be utilized in both highly specific as well as broad capacities. As the classification of nanoparticles becomes more well-defined and the list of applications grows, it is imperative that their toxicity be investigated. One such cellular system that is of importance are cellular membranes (biomembranes). Membranes present one of the first points of contact for nanoparticles at the cellular level. This review will address current studies aimed at defining the biomolecular interactions of nanoparticles at the level of the cell membrane, with a specific focus of the interactions of nanoparticles with prominent lipid systems.

Targeted delivery of amphotericin B-loaded PLGA micelles displaying lipopeptides to drug-resistant Candida-infected skin

Amphotericin B (AmB) is an antifungal agent administered for the management of serious systemic fungal infections. However, its clinical application is limited because of its water insolubility and side effects. Herein, to apply the minimum dose of AmB that can be used to manage fungal infections, a targeted drug delivery system was designed using lipopeptides and poly(lactide-co-glycolide) (PLGA). Lipopeptides conjugated with PEGylated distearoyl phosphoethanolamine (DSPE) and short peptides via a maleimide-thiol reaction formed nanosized micelles with PLGA and AmB. The antifungal effects of AmB-loaded micelles containing lipopeptides were remarkably enhanced both in vitro and in vivo. Moreover, the intravenous injection of these micelles demonstrated their in vivo targeting capacity of short peptides in a mouse model infected with drug-resistant Candida albicans. Our findings suggest that short antifungal peptides displayed on the surfaces of micelles represent a promising therapeutic candidate for targeting drug-resistant fungal infections.

Changing Your Martini Can Still Give You a Hangover

The Martini 3.0 coarse-grained force field, which was parametrized to better capture transferability in top-down coarse-grained models, is analyzed to assess its accuracy in representing thermodynamic and structural properties with respect to the underlying atomistic representation of the system. These results are compared to those obtained following the principles of statistical mechanics that start from the same underlying atomistic system. To this end, the potentials of mean force for lateral association in Martini 3.0 binary lipid bilayers are decomposed into their entropic and enthalpic components and compared to those of corresponding atomistic bilayers that have been projected onto equivalent coarse-grained mappings but evolved under the fully atomistic forces. This is accomplished by applying the reversible work theorem to lateral pair correlation functions between coarse-grained lipid beads taken at a range of different temperatures. The entropy-enthalpy decompositions provide a metric by which the underlying statistical mechanical properties of Martini can be investigated. Overall, Martini 3.0 is found to fail to properly partition entropy and enthalpy for the PMFs compared to the mapped all-atom results, despite changes made to the force field from the Martini 2.0 version. This outcome points to the fact that the development of more accurate top-down coarse-grained models such as Martini will likely necessitate temperature-dependent terms in the corresponding CG force-field; although necessary, this may not be sufficient to improve Martini. In addition to the entropy-enthalpy decompositions, Martini 3.0 produces an incorrect undulation spectrum, in particular at intermediate length scales of biophysical pertinence.

Dispersion of Hydrophilic Nanoparticles in Natural Rubber with Phospholipids

Coarse-grained molecular dynamics (CGMD) simulations were employed to investigate the effects of phospholipids on the aggregation of hydrophilic, modified carbon-nanoparticle fillers in cis-polyisoprene (cis-PI) composites. The MARTINI force field was applied to model dipalmitoylphosphatidylcholine (DPPC) lipids and hydrophilic modified fullerenes (HMFs). The simulations of DPPC in cis-PI composites show that the DPPC lipids self-assemble to form a reverse micelle in a rubber matrix. Moreover, HMF molecules readily aggregate into a cluster, in agreement with the previous studies. Interestingly, the mixture of the DPPC and HMF in the rubber matrix shows a cluster of HMF is encapsulated inside the DPPC reverse micelle. The HMF encapsulated micelles disperse well in the rubber matrix, and their sizes are dependent on the lipid concentration. Mechanical and thermal properties of the composites were analyzed by calculating the diffusion coefficients (D), bulk modulus (κ), and glass transition temperatures (Tg). The results suggest that DPPC acts as a plasticizer and enhances the flexibility of the HMF-DPPC rubber composites. These findings provide valuable insights into the design and process of high-performance rubber composites, offering improved mechanical and thermal properties for various applications.

System size effects on the free energy landscapes from molecular dynamics of phase-separating bilayers

The "lipid raft" hypothesis proposes that cell membranes contain distinct domains of varying lipid compositions, where "rafts" of ordered lipids and cholesterol coexist with disordered lipid regions. Experimental and theoretical phase diagrams of model membranes have revealed multiple coexisting phases. Molecular dynamics (MD) simulations can also capture spontaneous phase separation of bilayers. However, these methods merely determine the sign of the free energy change upon phase separation-whether or not it is favorable-but not the amplitude. Recently, we developed a workflow to compute the free energy of phase separation from MD simulations using the weighted ensemble method. However, while theoretical treatments generally focus on infinite systems and experimental measurements on mesoscopic to macroscopic systems, MD simulations are comparatively small. Therefore, if we are to put the results of these calculations into the appropriate context, we need to understand the effects the finite size of the simulation has on the computed free energy landscapes. In this study, we investigate this phenomenon by computing free energy profiles for a model phase-separating system as a function of system size, ranging from 324 to 10 110 lipids. The results suggest that, within the limits of statistical uncertainty, bulk-like behavior emerges once the systems contain roughly 4000 lipids.

Topological Heterogeneity of Protein Kinase C Modulators in Human T-Cells Resolved with In-Cell Dynamic Nuclear Polarization NMR Spectroscopy

Phorbol ester analogs are a promising class of anticancer therapeutics and HIV latency reversing agents that interact with cellular membranes to recruit and activate protein kinase C (PKC) isoforms. However, it is unclear how these esters interact with membranes and how this might correlate with the biological activity of different phorbol ester analogs. Here, we have employed dynamic nuclear polarization (DNP) NMR to characterize phorbol esters in a native cellular context. The enhanced NMR sensitivity afforded by DNP and cryogenic operation reveals topological heterogeneity of 13C-21,22-phorbol-myristate-acetate (PMA) within T cells utilizing 13C-13C correlation and double quantum filtered NMR spectroscopy. We demonstrate the detection of therapeutically relevant amounts of PMA in T cells down to an upper limit of ∼60.0 pmol per million cells and identify PMA to be primarily localized in cellular membranes. Furthermore, we observe distinct 13C-21,22-PMA chemical shifts under DNP conditions in cells compared to model membrane samples and homogenized cell membranes, that cannot be accounted for by differences in conformation. We provide evidence for distinct membrane topologies of 13C-21,22-PMA in cell membranes that are consistent with shallow binding modes. This is the first of its kind in-cell DNP characterization of small molecules dissolved in the membranes of living cells, establishing in-cell DNP-NMR as an important method for the characterization of drug-membrane interactions within the context of the complex heterogeneous environment of intact cellular membranes. This work sets the stage for the identification of the in-cell structural interactions that govern the biological activity of phorbol esters.

Lipid remodeling in acrosome exocytosis: unraveling key players in the human sperm

It has long been thought that exocytosis was driven exclusively by well-studied fusion proteins. Some decades ago, the role of lipids became evident and escalated interest in the field. Our laboratory chose a particular cell to face this issue: the human sperm. What makes this cell special? Sperm, as terminal cells, are characterized by their scarcity of organelles and the complete absence of transcriptional and translational activities. They are specialized for a singular membrane fusion occurrence: the exocytosis of the acrosome. This unique trait makes them invaluable for the study of exocytosis in isolation. We will discuss the lipids' role in human sperm acrosome exocytosis from various perspectives, with a primary emphasis on our contributions to the field. Sperm cells have a unique lipid composition, very rare and not observed in many cell types, comprising a high content of plasmalogens, long-chain, and very-long-chain polyunsaturated fatty acids that are particular constituents of some sphingolipids. This review endeavors to unravel the impact of membrane lipid composition on the proper functioning of the exocytic pathway in human sperm and how this lipid dynamic influences its fertilizing capability. Evidence from our and other laboratories allowed unveiling the role and importance of multiple lipids that drive exocytosis. This review highlights the role of cholesterol, diacylglycerol, and particular phospholipids like phosphatidic acid, phosphatidylinositol 4,5-bisphosphate, and sphingolipids in driving sperm acrosome exocytosis. Furthermore, we provide a comprehensive overview of the factors and enzymes that regulate lipid turnover during the exocytic course. A more thorough grasp of the role played by lipids transferred from sperm can provide insights into certain causes of male infertility. It may lead to enhancements in diagnosing infertility and techniques like assisted reproductive technology (ART).

Interaction of full-length Tau with negatively charged lipid membranes leads to polymorphic aggregates

The Tau protein is implicated in various diseases collectively known as tauopathies, including Alzheimer's disease and frontotemporal dementia. The precise mechanism underlying Tau pathogenicity remains elusive. Recently, the role of lipids has garnered interest due to their implications in Tau aggregation, secretion, uptake, and pathogenic dysregulation. Previous investigations have highlighted critical aspects: (i) Tau's tendency to aggregate into fibers when interacting with negatively charged lipids, (ii) its ability to form structured species upon contact with anionic membranes, and (iii) the potential disruption of the membrane upon Tau binding. In this study, we examine the disease-associated P301L mutation of the 2N4R isoform of Tau and its effects on membranes composed on phosphatidylserine (PS) lipids. Aggregation studies and liposome leakage assays demonstrate Tau's ability to bind to anionic lipid vesicles, leading to membrane disruption. Attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) reveals the accumulation of Tau on the membrane surface without protein insertion, structuration, or lipid removal. Plasmon waveguide resonance (PWR) demonstrates a strong binding of Tau on PS bilayers with an apparent Kd in the micromolar range, indicating the deposition of a thick protein layer. Atomic force microscopy (AFM) real-time imaging allows the observation of partial lipid solubilization and the deposition of polymorphic aggregates in the form of thick patches and fibrillary structures resembling amyloid fibers, which could grow from a combination of extracted anionic phospholipids from the membrane and Tau protein. This study deepens our understanding of full-length Tau's multifaceted interactions with lipids, shedding light on potential mechanisms leading to the formation of pathogenic Tau assemblies.

Computer-aided nanodrug discovery: recent progress and future prospects

Nanodrugs, which utilise nanomaterials in disease prevention and therapy, have attracted considerable interest since their initial conceptualisation in the 1990s. Substantial efforts have been made to develop nanodrugs for overcoming the limitations of conventional drugs, such as low targeting efficacy, high dosage and toxicity, and potential drug resistance. Despite the significant progress that has been made in nanodrug discovery, the precise design or screening of nanomaterials with desired biomedical functions prior to experimentation remains a significant challenge. This is particularly the case with regard to personalised precision nanodrugs, which require the simultaneous optimisation of the structures, compositions, and surface functionalities of nanodrugs. The development of powerful computer clusters and algorithms has made it possible to overcome this challenge through in silico methods, which provide a comprehensive understanding of the medical functions of nanodrugs in relation to their physicochemical properties. In addition, machine learning techniques have been widely employed in nanodrug research, significantly accelerating the understanding of bio-nano interactions and the development of nanodrugs. This review will present a summary of the computational advances in nanodrug discovery, focusing on the understanding of how the key interfacial interactions, namely, surface adsorption, supramolecular recognition, surface catalysis, and chemical conversion, affect the therapeutic efficacy of nanodrugs. Furthermore, this review will discuss the challenges and opportunities in computer-aided nanodrug discovery, with particular emphasis on the integrated "computation + machine learning + experimentation" strategy that can potentially accelerate the discovery of precision nanodrugs.

Self-diffusion is temperature independent on active membranes

Molecular transport maintains cellular structures and functions. For example, lipid and protein diffusion sculpts the dynamic shapes and structures on the cell membrane that perform essential cellular functions, such as cell signaling. Temperature variations in thermal equilibrium rapidly change molecular transport properties. The coefficient of lipid self-diffusion increases exponentially with temperature in thermal equilibrium, for example. Hence, maintaining cellular homeostasis through molecular transport is hard in thermal equilibrium in the noisy cellular environment, where temperatures can fluctuate widely due to local heat generation. In this paper, using both molecular and lattice-based modeling of membrane transport, we show that the presence of active transport originating from the cell's cytoskeleton can make the self-diffusion of the molecules on the membrane robust to temperature fluctuations. The resultant temperature-independence of self-diffusion keeps the precision of cellular signaling invariant over a broad range of ambient temperatures, allowing cells to make robust decisions. We have also found that the Kawasaki algorithm, the widely used model of lipid transport on lattices, predicts incorrect temperature dependence of lipid self-diffusion in equilibrium. We propose a new algorithm that correctly captures the equilibrium properties of lipid self-diffusion and reproduces experimental observations.

All-Atom Membrane Builder via Multiscale Simulation

I present an automated and flexible tool designed for constructing bilayer membranes at all-atom (AA) resolution. The builder initiates the construction and equilibration of bilayer membranes at Martini coarse-grained (CG) resolution, followed by resolution enhancement to the atomic level using the accompanying backmapping tool. Notably, this tool enables users to create bilayer membranes with user-defined lipid compositions and protein structures, while also offering the flexibility to accommodate new lipid types. To assess the simplicity and robustness of the tool, I demonstrate the construction of several membranes incorporating protein structures. The tool is freely available at github.com/ksy141/mstool.

Bisphenol F and Bisphenol S in a Complex Biomembrane: Comparison with Bisphenol A

Bisphenols are a group of endocrine-disrupting chemicals used worldwide for the production of plastics and resins. Bisphenol A (BPA), the main bisphenol, exhibits many unwanted effects. BPA has, currently, been replaced with bisphenol F (BPF) and bisphenol S (BPS) in many applications in the hope that these molecules have a lesser effect on metabolism than BPA. Since bisphenols tend to partition into the lipid phase, their place of choice would be the cellular membrane. In this paper, I carried out molecular dynamics simulations to compare the localization and interactions of BPA, BPF, and BPS in a complex membrane. This study suggests that bisphenols tend to be placed at the membrane interface, they have no preferred orientation inside the membrane, they can be in the monomer or aggregated state, and they affect the biophysical properties of the membrane lipids. The properties of bisphenols can be attributed, at least in part, to their membranotropic effects and to the modulation of the biophysical membrane properties. The data support that both BPF and BPS, behaving in the same way in the membrane as BPA and with the same capacity to accumulate in the biological membrane, are not safe alternatives to BPA.

Super-resolution microscopy to study membrane nanodomains and transport mechanisms in the plasma membrane

Biological membranes are complex, heterogeneous, and dynamic systems that play roles in the compartmentalization and protection of cells from the environment. It is still a challenge to elucidate kinetics and real-time transport routes for molecules through biological membranes in live cells. Currently, by developing and employing super-resolution microscopy; increasing evidence indicates channels and transporter nano-organization and dynamics within membranes play an important role in these regulatory mechanisms. Here we review recent advances and discuss the major advantages and disadvantages of using super-resolution microscopy to investigate protein organization and transport within plasma membranes.

Evaluation of Pregabalin bioadhesive multilayered microemulsion IOP-lowering eye drops

In spite of available treatment options, glaucoma continues to be a leading cause of irreversible blindness in the world. Current glaucoma medications have multiple limitations including: lack of sustained action; requirement for multiple dosing per day, ocular irritation and limited options for drugs with different mechanisms of action. Previously, we demonstrated that pregabalin, a drug with high affinity and selectivity for CACNA2D1, lowered IOP in a dose-dependent manner. The current study was designed to evaluate pregabalin microemulsion eye drops and to estimate its efficacy in humans using in silico methods. Molecular docking studies of pregabalin against CACNA2D1 of mouse, rabbit, and human were performed. Pregabalin microemulsion eye drops were characterized using multiple in vivo studies and its stability was evaluated over one year at different storage conditions. Molecular docking analyses and QSPR of pregabalin confirmed its suitability as a new IOP-lowering medication that functions using a new mechanism of action by binding to CACNA2D1 in all species evaluated. Because of its prolonged corneal residence time and corneal penetration enhancement, a single topical application of pregabalin ME can provide an extended IOP reduction of more than day in different animal models. Repeated daily dosing for 2 months confirms the lack of any tachyphylactic effect, which is a common drawback among marketed IOP-lowering medications. In addition, pregabalin microemulsion demonstrated good physical stability for one year, and chemical stability for 3-6 months if stored below 25 °C. Collectively, these outcomes greatly support the use of pregabalin eye drops as once daily IOP-lowering therapy for glaucoma management.

Location and interaction of idebenone and mitoquinone in a membrane similar to the inner mitochondrial membrane. Comparison with ubiquinone 10

Oxygen is essential for aerobic life on earth but it is also the origin of harmful reactive oxygen species (ROS). Ubiquinone is par excellence the endogenous cellular antioxidant, but a very hydrophobic one. Because of that, other molecules have been envisaged, such as idebenone (IDE) and mitoquinone (MTQ), molecules having the same redox active benzoquinone moiety but higher solubility. We have used molecular dynamics to determine the location and interaction of these molecules, both in their oxidized and reduced forms, with membrane lipids in a membrane similar to that of the mitochondria. Both IDE and reduced IDE (IDOL) are situated near the membrane interface, whereas both MTQ and reduced MTQ (MTQOL) locate in a position adjacent to the phospholipid hydrocarbon chains. The quinone moieties of both ubiquinone 10 (UQ10) and reduced UQ10 (UQOL10) in contraposition to the same moieties of IDE, IDOL, MTQ and MTQOL, located near the membrane interphase, whereas the isoprenoid chains remained at the middle of the hydrocarbon chains. These molecules do not aggregate and their functional quinone moieties are located in the membrane at different depths but near the hydrophobic phospholipid chains whereby protecting them from ROS harmful effects.

Influence of phospholipid head and tail molecular structures on cell membrane mechanical response under tension

Biological cell membranes are primarily comprised of a diverse lipid bilayer with multiple phospholipid (lipid) types, each of which is comprised of a hydrophilic headgroup and two hydrophobic hydrocarbon tails. The lipid type determines the molecular structure of head and tail groups, which can affect membrane mechanics at nanoscale and subsequently cell viability under mechanical loading. Hence, using molecular dynamics simulations, the current study investigated seven membrane phospholipids and the effect of their structural differences on physical deformation, mechanoporation damage, and mechanical failure of the membranes under tension. The inspected phospholipids showed similar yield stresses and strains, as well as pore evolution and damage, but significantly different failure strains. In general, failure occurred at a lower strain for lipids with a larger equilibrium area per lipid. The obtained results suggest that larger headgroup structure, greater degree of unsaturation, and tail-length asymmetry influenced the phospholipids' ability to pack against each other, increased the fluidity and equilibrium area per lipid of the membrane, and resulted in lower failure strain. Overall, this study provides insights on how different phospholipid structures affect membrane physical responses at the molecular level and serves as a reference for future studies of more complex membrane systems with intricate biophysical properties.

Localization and Aggregation of Honokiol in the Lipid Membrane

Honokiol, a biphenyl lignan extracted from bark extracts belonging to Magnolia plant species, is a pleiotropic compound which exhibits a widespread range of antioxidant, antibacterial, antidiabetic, anti-inflammatory, antiaggregant, analgesic, antitumor, antiviral and neuroprotective activities. Honokiol, being highly hydrophobic, is soluble in common organic solvents but insoluble in water. Therefore, its biological effects could depend on its bioactive mechanism. Although honokiol has many impressive bioactive properties, its effects are unknown at the level of the biological membrane. Understanding honokiol's bioactive mechanism could unlock innovative perspectives for its therapeutic development or for therapeutic development of molecules similar to it. I have studied the behaviour of the honokiol molecule in the presence of a plasma-like membrane and established the detailed relation of honokiol with membrane components using all-atom molecular dynamics. The results obtained in this work sustain that honokiol has a tendency to insert inside the membrane; locates near and below the cholesterol oxygen atom, amid the hydrocarbon membrane palisade; increases slightly hydrocarbon fluidity; does not interact specifically with any membrane lipid; and, significantly, forms aggregates. Significantly, aggregation does not impede honokiol from going inside the membrane. Some of the biological characteristics of honokiol could be accredited to its aptitude to alter membrane biophysical properties, but the establishment of aggregate forms in solution might hamper its clinical use.

Arginine-Rich Cell-Penetrating Peptides Induce Lipid Rearrangements for Their Active Translocation across Laterally Heterogeneous Membranes

Arginine-rich cell-penetrating peptides (CPPs) have emerged as valuable tools for the intracellular delivery of bioactive molecules, but their membrane perturbation during cell penetration is not fully understood. Here, nona-arginine (R9)-mediated membrane reorganization that facilitates the translocation of peptides across laterally heterogeneous membranes is directly visualized. The electrostatic binding of cationic R9 to anionic phosphatidylserine (PS)-enriched domains on a freestanding lipid bilayer induces lateral lipid rearrangements; in particular, in real-time it is observed that R9 fluidizes PS-rich liquid-ordered (Lo) domains into liquid-disordered (Ld) domains, resulting in the membrane permeabilization. The experiments with giant unilamellar vesicles (GUVs) confirm the preferential translocation of R9 through Ld domains without pore formation, even when Lo domains are more negatively charged. Indeed, whenever R9 comes into contact with negatively charged Lo domains, it dissolves the Lo domains first, promoting translocation across phase-separated membranes. Collectively, the findings imply that arginine-rich CPPs modulate lateral membrane heterogeneity, including membrane fluidization, as one of the fundamental processes for their effective cell penetration across densely packed lipid bilayers.

Deep learning structural insights into heterotrimeric alternatively spliced P2X7 receptors

P2X7 receptors (P2X7Rs) are membrane-bound ATP-gated ion channels that are composed of three subunits. Different subunit structures may be expressed due to alternative splicing of the P2RX7 gene, altering the receptor's function when combined with the wild-type P2X7A subunits. In this study, the application of the deep-learning method, AlphaFold2-Multimer (AF2M), for the generation of trimeric P2X7Rs was validated by comparing an AF2M-generated rat wild-type P2X7A receptor with a structure determined by cryogenic electron microscopy (cryo-EM) (Protein Data Bank Identification: 6U9V). The results suggested AF2M could firstly, accurately predict the structures of P2X7Rs and secondly, accurately identify the highest quality model through the ranking system. Subsequently, AF2M was used to generate models of heterotrimeric alternatively spliced P2X7Rs consisting of one or two wild-type P2X7A subunits in combination with one or two P2X7B, P2X7E, P2X7J, and P2X7L splice variant subunits. The top-ranking models were deemed valid based on AF2M's confidence measures, stability in molecular dynamics simulations, and consistent flexibility of the conserved regions between the models. The structure of the heterotrimeric receptors, which were missing key residues in the ATP binding sites and carboxyl terminal domains (CTDs) compared to the wild-type receptor, help to explain their observed functions. Overall, the models produced in this study (available as supplementary material) unlock the possibility of structure-based studies into the heterotrimeric P2X7Rs.

Differential effects of ganglioside lipids on the conformation and aggregation of islet amyloid polypeptide

Despite causing over 1 million deaths annually, Type 2 Diabetes (T2D) currently has no curative treatments. Aggregation of the islet amyloid polypeptide (hIAPP) into amyloid plaques plays an important role in the pathophysiology of T2D and thus presents a target for therapeutic intervention. The mechanism by which hIAPP aggregates contribute to the development of T2D is unclear, but it is proposed to involve disruption of cellular membranes. However, nearly all research on hIAPP-lipid interactions has focused on anionic phospholipids, which are primarily present in the cytosolic face of plasma membranes. We seek here to characterize the effects of three gangliosides, the dominant anionic lipids in the outer leaflet of the plasma membrane, on the aggregation, structure, and toxicity of hIAPP. Our results show a dual behavior that depends on the molar ratio between the gangliosides and hIAPP. For each ganglioside, a low-lipid:peptide ratio enhances hIAPP aggregation and alters the morphology of hIAPP fibrils, while a high ratio eliminates aggregation and stabilizes an α-helix-rich hIAPP conformation. A more negative lipid charge more efficiently promotes aggregation, and a larger lipid headgroup improves inhibition of aggregation. hIAPP also alters the phase transitions of the lipids, favoring spherical micelles over larger tubular micelles. We discuss our results in the context of the available lipid surface area for hIAPP binding and speculate on a role for gangliosides in facilitating toxic hIAPP aggregation.

Polar Glycerolipids and Membrane Lipid Rafts

Current understanding of the structure and functioning of biomembranes is impossible without determining the mechanism of formation of membrane lipid rafts. The formation of liquid-ordered and disordered phases (Lo and Ld) and lipid rafts in membranes and their simplified models is discussed. A new consideration of the processes of formation of lipid phases Lo and Ld and lipid rafts is proposed, taking into account the division of each of the glycerophospholipids into several groups. Generally accepted three-component schemes for modeling the membrane structure are critically considered. A four-component scheme is proposed, which is designed to more accurately assume the composition of lipids in the resulting Lo and Ld phases. The role of the polar head groups of phospholipids and, in particular, phosphatidylethanolamine is considered. The structure of membrane rafts and the possible absence of a clear boundary between the Lo and Ld phases are discussed.

Lipid Trolling to Optimize A3 Adenosine Receptor-Positive Allosteric Modulators (PAMs)

A3 adenosine receptor (A3AR) positive allosteric modulators (PAMs) (2,4-disubstituted-1H-imidazo[4,5-c]quinolin-4-amines) allosterically increase the Emax of A3AR agonists, but not potency, due to concurrent orthosteric antagonism. Following mutagenesis/homology modeling of the proposed lipid-exposed allosteric binding site on the cytosolic side, we functionalized the scaffold, including heteroatom substitutions and exocyclic phenylamine extensions, to increase allosteric binding. Strategically appended linear alkyl-alkynyl chains with terminal amino/guanidino groups improved allosteric effects at both human and mouse A3ARs. The chain length, functionality, and attachment position were varied to modulate A3AR PAM activity. For example, 26 (MRS8247, p-alkyne-linked 8 methylenes) and homologues increased agonist Cl-IB-MECA's Emax and potency ([35S]GTPγS binding). The putative mechanism involves a flexible, terminally cationic chain penetrating the lipid environment for stable electrostatic anchoring to cytosolic phospholipid head groups, suggesting "lipid trolling", supported by molecular dynamic simulation of the active-state model. Thus, we have improved A3AR PAM activity through rational design based on an extrahelical, lipidic binding site.

Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050

In the last quarter-century, the field of molecular dynamics (MD) has undergone a remarkable transformation, propelled by substantial enhancements in software, hardware, and underlying methodologies. In this Perspective, we contemplate the future trajectory of MD simulations and their possible look at the year 2050. We spotlight the pivotal role of artificial intelligence (AI) in shaping the future of MD and the broader field of computational physical chemistry. We outline critical strategies and initiatives that are essential for the seamless integration of such technologies. Our discussion delves into topics like multiscale modeling, adept management of ever-increasing data deluge, the establishment of centralized simulation databases, and the autonomous refinement, cross-validation, and self-expansion of these repositories. The successful implementation of these advancements requires scientific transparency, a cautiously optimistic approach to interpreting AI-driven simulations and their analysis, and a mindset that prioritizes knowledge-motivated research alongside AI-enhanced big data exploration. While history reminds us that the trajectory of technological progress can be unpredictable, this Perspective offers guidance on preparedness and proactive measures, aiming to steer future advancements in the most beneficial and successful direction.

Control of G protein-coupled receptor function via membrane-interacting intrinsically disordered C-terminal domains

G protein-coupled receptors (GPCRs) control intracellular signaling cascades via agonist-dependent coupling to intracellular transducers including heterotrimeric G proteins, GPCR kinases (GRKs), and arrestins. In addition to their critical interactions with the transmembrane core of active GPCRs, all three classes of transducers have also been reported to interact with receptor C-terminal domains (CTDs). An underexplored aspect of GPCR CTDs is their possible role as lipid sensors given their proximity to the membrane. CTD-membrane interactions have the potential to control the accessibility of key regulatory CTD residues to downstream effectors and transducers. Here, we report that the CTDs of two closely related family C GPCRs, metabotropic glutamate receptor 2 (mGluR2) and mGluR3, bind to membranes and that this interaction can regulate receptor function. We first characterize CTD structure with NMR spectroscopy, revealing lipid composition-dependent modes of membrane binding. Using molecular dynamics simulations and structure-guided mutagenesis, we then identify key conserved residues and cancer-associated mutations that modulate CTD-membrane binding. Finally, we provide evidence that mGluR3 transducer coupling is controlled by CTD-membrane interactions in live cells, which may be subject to regulation by CTD phosphorylation and changes in membrane composition. This work reveals an additional mechanism of GPCR modulation, suggesting that CTD-membrane binding may be a general regulatory mode throughout the broad GPCR superfamily.

Fragment-based approach to study fungicide-biomimetic membrane interactions

In this study, the molecular interactions of the allylamine-type fungicide butenafine and a set of substructures ("fragments") with liposomes mimicking biological membranes were studied to gain a better understanding of the structural factors governing membrane affinity and perturbation. Specifically, drug/fragment-membrane interactions were investigated using an interdisciplinary approach involving micro differential scanning calorimetry, open-tubular capillary electrochromatography, nanoplasmonic sensing, and quartz crystal microbalance. By incubating the drug and the fragment compounds with liposomes with varying lipid composition or by externally adding the compounds to preformed liposomes, a detailed mechanistic picture on the underlying drug/fragment-membrane interactions was obtained. The nature and the degree of ionisation of polar head groups of the lipids had a major influence on the nature of drug-membrane interactions, and so had the presence and relative concentration of cholesterol within the membranes. The in-depth understanding of drug/fragment-membranes interactions established by the presented interdisciplinary fragment-based approach may be useful in guiding the design and early-stage evaluation of prospective antifungal drug candidates, and the discovery of agents with improved membrane penetrating characteristics in general.

Curvature Footprints of Transmembrane Proteins in Simulations with the Martini Force Field

Membranes play essential roles in biological systems and are tremendously diverse in the topologies and chemical and elastic properties that define their functions. In many cases, a given membrane may display considerable heterogeneity, with localized clusters of lipids and proteins exhibiting distinct characteristics compared to adjoining regions. These lipid-protein assemblies can span nanometers to micrometers and are associated with cellular processes such as transport and signaling. While lipid-protein assemblages are dynamic, they can be stabilized by coupling between local membrane composition and shape. Due to the inherent difficulty in resolving atomistic details of membrane proteins in their native lipid environments, these complexes are notoriously challenging to study experimentally; however, molecular dynamics (MD) simulations might be a viable alternative. Here, we aim to assess the utility of coarse-grained (CG) MD simulations with the Martini force field for studying membrane curvature induced by transmembrane (TM) proteins that are reported to generate local curvature. The direction and magnitude of curvature induced by five different TM proteins, as well as certain lipid-protein and protein-protein interactions, were found to be in good agreement with available reference data.

There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning

We describe a complete methodology to bridge the scales between nanoscale molecular dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species are furthermore embedded. To go from the molecular to the mesoscale, we notably appeal to physical renormalization arguments enabling us to rigorously infer the mesoscale interaction parameters from its molecular counterpart. We also explain how to deal with the physical timescales at stake at the mesoscale. Simulating the as-obtained mesoscale system enables us to equilibrate the long wavelengths of the vesicles of interest, up to the vesicle size. Conversely, we then backmap from the meso- to the nano-scale, which enables us to equilibrate in turn the short wavelengths down to the molecular length-scales. By applying our approach to the specific situation of patterning a vesicle membrane, we show that macroscopic membranes can thus be equilibrated at all length-scales in achievable computational time offering an original strategy to address the fundamental challenge of timescale in simulations of large bio-membrane systems.

Structural insights into GABAA receptor potentiation by Quaalude

Methaqualone, a quinazolinone marketed commercially as Quaalude, is a central nervous system depressant that was used clinically as a sedative-hypnotic, then became a notorious recreational drug in the 1960s-80s. Due to its high abuse potential, medical use of methaqualone was eventually prohibited, yet it persists as a globally abused substance. Methaqualone principally targets GABAA receptors, which are the major inhibitory neurotransmitter-gated ion channels in the brain. The restricted status and limited accessibility of methaqualone have contributed to its pharmacology being understudied. Here, we use cryo-EM to localize the GABAA receptor binding sites of methaqualone and its more potent derivative, PPTQ, to the same intersubunit transmembrane sites targeted by the general anesthetics propofol and etomidate. Both methaqualone and PPTQ insert more deeply into subunit interfaces than the previously-characterized modulators. Binding of quinazolinones to this site results in widening of the extracellular half of the ion-conducting pore, following a trend among positive allosteric modulators in destabilizing the hydrophobic activation gate in the pore as a mechanism for receptor potentiation. These insights shed light on the underexplored pharmacology of quinazolinones and further elucidate the molecular mechanisms of allosteric GABAA receptor modulation through transmembrane binding sites.

Comparative study of the interactions between C60 fullerene and SARS-CoV-2, HIV, eukaryotic, and bacterial model membranes: Insights into antimicrobial strategies with C60-peptide hybrids

The neutrophil-derived peptide, indolicidin, and the sphere-shaped carbon nanoparticle, C60, are contemporary components capable of acting as bactericides and virucides, among others. Herein, the coarse-grained molecular dynamics simulation method was used to simulate the interactions of gram-negative bacteria, eukaryotes, human immunodeficiency virus (HIV), and SARS-COV-2 membrane models with indolicidin, C60s, and C60-indolicidin hybrids. Our results demonstrated that the carbon nanoparticle penetrated all membrane models, except the bacterial membrane, which remained impenetrable to both the peptide and C60. Additionally, the membrane thickness did not change significantly. The peptide floated above the membranes, with only the side chains of the tryptophan (Trp)-rich site slightly permeating the membranes. After achieving stable contact between the membrane models and nanoparticles, the infiltrated C60s interacted with the unsaturated tail of phospholipids. The density results showed that C60s stayed close to indolicidin and continued to interact with it even after penetration. Indolicidin, especially its Trp-rich site, exhibited more contact with the head and tail of neutral phospholipids compared to other phospholipids. Moreover, both particles interacted with different kinds of glycosphingolipids located in the eukaryote membrane. This investigation has the potential to advance our knowledge of novel approaches to combat antimicrobial resistance.

Effects induced by η6-p-cymene ruthenium(II) complexes on Langmuir monolayers mimicking cancer and healthy cell membranes do not correlate with their toxicity

The mechanism of chemotherapeutic action of Ru-based drugs involves plasma membrane disruption and valuable insights into this process may be gained using cell membrane models. The interactions of a series of cytotoxic η6-p-cymene ruthenium(II) complexes, [Ru(η6-p-cymene)P(3,5-C(CH3)3-C6H3)3Cl2] (1), [Ru(η6-p-cymene)P(3,5-CH3-C6H3)3Cl2] (2), [Ru(η6-p-cymene)P(4-CH3O-3,5-CH3-C6H2)3Cl2] (3), and [Ru(η6-p-cymene)P(4-CH3O-C6H4)3Cl2] (4), were examined using Langmuir monolayers as simplified healthy and cancerous outer leaflet plasma membrane models. The cancerous membrane (CM1 and CM2) models contained either 40 % 1,2- dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) or 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 30 % cholesterol (Chol), 20 % 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), and 10 % 1,2-dipalmitoyl-sn-glycero-3-phospho-l-serine (DPPS). Meanwhile, the healthy membrane (HM1 and HM2) models were composed of 60 % DPPC or DOPC, 30 % Chol and 10 % DPPE. The complexes affected surface pressure isotherms and decreased compressional moduli of cancerous and healthy membrane models, interacting with the monolayers headgroup and tails according to data from polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS). However, the effects did not correlate with the toxicity of the complexes to cancerous and healthy cells. Multidimensional projection technique showed that the complex (1) induced significant changes in the CM1 and HM1 monolayers, though it had the lowest cytotoxicity against cancer cells and is not toxic to healthy cells. Moreover, the most toxic complexes (2) and (4) were those that least affected CM2 and HM2 monolayers. The findings here support that the ruthenium complexes interact with lipids and cholesterol in cell membrane models, and their cytotoxic activities involve a multifaceted mode of action beyond membrane disruption.

Chimeric nanobody-decorated liposomes by self-assembly

Liposomes as drug vehicles have advantages, such as payload protection, tunable carrying capacity and improved biodistribution. However, due to the dysfunction of targeting moieties and payload loss during preparation, immunoliposomes have yet to be favoured in commercial manufacturing. Here we report a chemical modification-free biophysical approach for producing immunoliposomes in one step through the self-assembly of a chimeric nanobody (cNB) into liposome bilayers. cNB consists of a nanobody against human epidermal growth factor receptor 2 (HER2), a flexible peptide linker and a hydrophobic single transmembrane domain. We determined that 64% of therapeutic compounds can be encapsulated into 100-nm liposomes, and up to 2,500 cNBs can be anchored on liposomal membranes without steric hindrance under facile conditions. Subsequently, we demonstrate that drug-loaded immunoliposomes increase cytotoxicity on HER2-overexpressing cancer cell lines by 10- to 20-fold, inhibit the growth of xenograft tumours by 3.4-fold and improve survival by more than twofold.

Does the surface charge of the nanoparticles drive nanoparticle-cell membrane interactions?

Classical Coulombic interaction, characterized by electrostatic interactions mediated through surface charges, is often regarded as the primary determinant in nanoparticles' (NPs) cellular association and internalization. However, the intricate physicochemical properties of particle surfaces, biomolecular coronas, and cell surfaces defy this oversimplified perspective. Moreover, the nanometrological techniques employed to characterize NPs in complex physiological fluids often exhibit limited accuracy and reproducibility. A more comprehensive understanding of nanoparticle-cell membrane interactions, extending beyond attractive forces between oppositely charged surfaces, necessitates the establishment of databases through rigorous physical, chemical, and biological characterization supported by nanoscale analytics. Additionally, computational approaches, such as in silico modeling and machine learning, play a crucial role in unraveling the complexities of these interactions.

Effects of Ca 2+ on the Structure and Dynamics of PIP3 in Model Membranes Containing PC and PS

Phosphatidylinositol phosphates (PIPs) are a family of seven different eukaryotic membrane lipids that have a large role in cell viability, despite their minor concentration in eukaryotic cellular membranes. PIPs tightly regulate cellular processes such as cellular growth, metabolism, immunity, and development through direct interactions with partner proteins. Understanding the biophysical properties of PIPs in the complex membrane environment is important to understand how PIPs selectively regulate a partner protein. Here we investigate the structure and dynamics of PIP3 in lipid bilayers that are simplified models of the natural membrane environment. We probe the effects of the anionic lipid phosphatidylserine (PS) and the divalent cation Ca 2+ . We use solution and solid-state 1 H, 31 P, and 13 C NMR all at natural abundance combined with MD simulations to characterize the structure and dynamics of PIPs. 1 H and 31 P 1D spectra show good resolution at high temperatures with isolated peaks in the headgroup, interfacial, and bilayer regions. Site specific assignment of these 1D reporters were made and used to measure the effects of Ca 2+ and PS. In particular, the resolved 31 P signals of the PIP3 headgroup allowed for extremely well localized information about PIP3 phosphate dynamics, which the MD simulations were able to help explain. Cross polarization kinetics provided additional site-specific dynamics measurements for the PIP3 headgroups.

A combined lipidomic and proteomic profiling of Arabidopsis thaliana plasma membrane

The plant plasma membrane (PM) plays a key role in perception of environmental signals, and set-up of adaptive responses. An exhaustive and quantitative description of the whole set of lipids and proteins constituting the PM is necessary to understand how these components allow to fulfill such essential physiological functions. Here we provide by state-of-the-art approaches the first combined reference of the plant PM lipidome and proteome from Arabidopsis thaliana suspension cell culture. We identified and quantified a reproducible core set of 2165 proteins, which is by far the largest set of available data concerning this plant PM proteome. Using the same samples, combined lipidomic approaches, allowing the identification and quantification of an unprecedented repertoire of 414 molecular species of lipids showed that sterols, phospholipids, and sphingolipids are present in similar proportions in the plant PM. Within each lipid class, the precise amount of each lipid family and the relative proportion of each molecular species were further determined, allowing to establish the complete lipidome of Arabidopsis PM, and highlighting specific characteristics of the different molecular species of lipids. Results obtained point to a finely tuned adjustment of the molecular characteristics of lipids and proteins. More than a hundred proteins related to lipid metabolism, transport, or signaling have been identified and put in perspective of the lipids with which they are associated. This set of data represents an innovative resource to guide further research relative to the organization and functions of the plant PM.

Dishevelled localization and function are differentially regulated by structurally distinct sterols

The Dishevelled (DVL) family of proteins form supramolecular protein and lipid complexes at the cytoplasmic interface of the plasma membrane to regulate tissue patterning, proliferation, cell polarity, and oncogenic processes through DVL-dependent signaling, such as Wnt/β-catenin. While DVL binding to cholesterol is required for its membrane association, the specific structural requirements and cellular impacts of DVL-sterol association are unclear. We report that intracellular sterols which accumulate within normal and pathological conditions cause aberrant DVL activity. In silico and molecular analyses suggested orientation of the β- and α-sterol face within the DVL-PDZ domain regulates DVL-sterol binding. Intracellular accumulation of naturally occurring sterols impaired DVL2 plasma membrane association, inducing DVL2 nuclear localization via Foxk2. Changes to intracellular sterols also selectively impaired DVL2 protein-protein interactions This work identifies sterol specificity as a regulator of DVL signaling, suggests intracellular sterols cause distinct impacts on DVL activity, and supports a role for intracellular sterol homeostasis in cell signaling.

Lysophosphatidylcholine Acetyltransferase 2 (LPCAT2) Influences the Gene Expression of the Lipopolysaccharide Receptor Complex in Infected RAW264.7 Macrophages, Depending on the E. coli Lipopolysaccharide Serotype

Escherichia coli (E. coli) is a frequent gram-negative bacterium that causes nosocomial infections, affecting more than 100 million patients annually worldwide. Bacterial lipopolysaccharide (LPS) from E. coli binds to toll-like receptor 4 (TLR4) and its co-receptor's cluster of differentiation protein 14 (CD14) and myeloid differentiation factor 2 (MD2), collectively known as the LPS receptor complex. LPCAT2 participates in lipid-raft assembly by phospholipid remodelling. Previous research has proven that LPCAT2 co-localises in lipid rafts with TLR4 and regulates macrophage inflammatory response. However, no published evidence exists of the influence of LPCAT2 on the gene expression of the LPS receptor complex induced by smooth or rough bacterial serotypes. We used RAW264.7-a commonly used experimental murine macrophage model-to study the effects of LPCAT2 on the LPS receptor complex by transiently silencing the LPCAT2 gene, infecting the macrophages with either smooth or rough LPS, and quantifying gene expression. LPCAT2 only significantly affected the gene expression of the LPS receptor complex in macrophages infected with smooth LPS. This study provides novel evidence that the influence of LPCAT2 on macrophage inflammatory response to bacterial infection depends on the LPS serotype, and it supports previous evidence that LPCAT2 regulates inflammatory response by modulating protein translocation to lipid rafts.

Protein-Mediated Changes in Membrane Fluidity and Ordering: Insights into the Molecular Mechanism and Implications for Cellular Function

Probing protein-membrane interactions is vital for understanding biological functionality for various applications such as drug development, targeted drug delivery, and creation of functional biomaterials for medical and industrial purposes. In this study, we have investigated interaction of Human Serum Albumin (HSA) with two different lipids, dipalmitoylphosphatidylglycerol (dDPPG) and dipalmitoylphosphatidylcholine (dDPPC), using Vibrational Sum Frequency Generation spectroscopy at different membrane fluidity values. In the liquid-expanded (LE) state of the lipid, HSA (at pH 3.5) deeply intercalated lipid chains through a combination of electrostatic and hydrophobic interactions, which resulted in more ordering of the lipid chains. However, in the liquid-condensed (LC) state, protein intercalation is decreased due to tighter lipid packing. Moreover, our findings revealed distinct differences in HSA's interaction with dDPPG and dDPPC lipids. The interaction with dDPPC remained relatively weak compared to dDPPG. These results shed light on the significance of protein mediated changes in lipid characteristics, which hold considerable implications for understanding membrane protein behavior, lipid-mediated cellular processes, and lipid-based biomaterial design.

Effect of GM1 concentration change on plasma membrane: molecular dynamics simulation and analysis

Ganglioside GM1 is a class of glycolipids predominantly located in the nervous system. Comprising a ceramide anchor and an oligosaccharide chain containing sialic acid, GM1 plays a pivotal role in various cellular processes, including signal transduction, cell adhesion, and membrane organization. Moreover, GM1 has been implicated in the pathogenesis of several neurological disorders, such as Parkinson's disease, Alzheimer's disease, and stroke. In this study, by creating a neural cell model membrane simulation system and employing rigorous molecular models, we utilize a coarse-grained molecular dynamics approach to explore the structural and dynamic characteristics of multi-component neuronal plasma membranes at varying GM1 ganglioside concentrations. The simulation results reveal that as GM1 concentration increases, a greater number of hydrogen bonds form between GM1 molecules, resulting in the formation of larger clusters, which leads to reduced membrane fluidity, increased lipid ordering, decreased membrane thickness and surface area and higher levels of GM1 dissociation. Through a meticulous analysis, while considering GM1's structural attributes, we offer valuable insights into the structural and dynamic traits of the cell membrane. This study provides a robust methodology for exploring membrane characteristics and enhances our comprehension of GM1 molecules, serving as a resource for both experimental and computational researchers in this field.

Simulating asymmetric membranes using P21 periodic boundary conditions

Molecular dynamics (MD) simulations of symmetric lipid bilayers are now well established, while those of asymmetric ones are considerably less developed. This disjunction arises in part because the surface tensions of leaflets in asymmetric bilayers can differ (unlike those of symmetric ones), and there is no simple way to determine them without assumptions. This chapter describes the use of P21 periodic boundary conditions (PBC), which allow lipids to switch leaflets, to generate asymmetric bilayers under the assumption of equal chemical potentials of lipids in opposing leaflets. A series of examples, ranging from bilayers with one lipid type to those with peptides and proteins, provides a guide for the use of P21 PBC. Critical properties of asymmetric membranes, such as spontaneous curvature, are highly sensitive to differences in the leaflet surface tensions (or differential stress), and equilibration with P21 PBC substantially reduces differential stress of asymmetric bilayers assembled with surface area-based methods. Limitations of the method are discussed. Technically, the nonstandard unit cell is difficult to parallelize and to incorporate restraints. Inherently, the assumption of equal chemical potentials, and therefore the method itself, is not applicable to all target systems. Despite these limitations, it is argued that P21 simulations should be considered when designing equilibration protocols for MD studies of most asymmetric membranes.