Molecular dynamics simulation of phase transitions in model lung surfactant monolayers

Graph Theoretical Description of Phase Transitions in Complex Multiscale Phases with Supramolecular Assemblies

Phase transitions are typically quantified using order parameters, such as crystal lattice distances and radial distribution functions, which can identify subtle changes in crystalline materials or high-contrast phases with large structural differences. However, the identification of phases with high complexity, multiscale organization and of complex patterns during the structural fluctuations preceding phase transitions, which are essential for understanding the system pathways between phases, is challenging for those traditional analyses. Here, it is shown that for two model systems- thermotropic liquid crystals and a lyotropic water/surfactant mixtures-graph theoretical (GT) descriptors can successfully identify complex phases combining molecular and nanoscale levels of organization that are hard to characterize with traditional methodologies. Furthermore, the GT descriptors also reveal the pathways between the different phases. Specifically, centrality parameters and node-based fractal dimension quantify the system behavior preceding the transitions, capturing fluctuation-induced breakup of aggregates and their long-range cooperative interactions. GT parameterization can be generalized for a wide range of chemical systems and be instrumental for the growth mechanisms of complex nanostructures.

A Review on Investigating the Interactions between Nanoparticles and the Pulmonary Surfactant Monolayer with Coarse-Grained Molecular Dynamics Method

Pulmonary drug delivery has garnered significant attention due to its targeted local lung action, minimal toxic side effects, and high drug utilization. However, the physicochemical properties of inhaled nanoparticles (NPs) used as drug carriers can influence their interactions with the pulmonary surfactant (PS) monolayer, potentially altering the fate of the NPs and impairing the biophysical function of the PS monolayer. Thus, the objective of this review is to summarize how the physicochemical properties of NPs affect their interactions with the PS monolayer. Initially, the definition and properties of NPs, as well as the composition and characteristics of the PS monolayer, are introduced. Subsequently, the coarse-grained molecular dynamics (CGMD) simulation method for studying the interactions between NPs and the PS monolayer is presented. Finally, the implications of the hydrophobicity, size, shape, surface charge, surface modification, and aggregation of NPs on their interactions with the PS monolayer and on the composition of biomolecular corona are discussed. In conclusion, gaining a deeper understanding of the effects of the physicochemical properties of NPs on their interactions with the PS monolayer will contribute to the development of safer and more effective nanomedicines for pulmonary drug delivery.

The concentration-dependent effect of hydrocortisone on the structure of model lung surfactant monolayer by using an in silico approach

Understanding the adsorption mechanism of corticosteroids in the lung surfactant requires the knowledge of corticosteroid molecular interactions with lung surfactant monolayer (LSM). We employed coarse-grained molecular dynamics simulation to explore the action of hydrocortisone on an LSM comprised of a phospholipid, cholesterol and surfactant protein. The structural and dynamical morphology of the lung surfactant monolayer at different surface tensions were investigated to assess the monolayer compressibility. The simulations were also conducted at the two extreme ends of breathing cycles: exhalation (0 mN m-1 surface tension) and inhalation (20 mN m-1 surface tension). The impact of surface tension and hydrocortisone concentration on the monolayer compressibility and stability are significant, resulting the monolayer expansion at higher surface tension. However, at low surface tension, the highly compressed monolayer induces monolayer instability in the presence of the drug due to the accumulation of surfactant protein and drug. The constant area per lipid simulation results demonstrate that the surface pressure-area isotherms show a decrease in area-per-lipid with increased drug concentration. The drug-induced expansion causes considerable instability in the monolayer after a specific drug concentration is attained at inhalation breathing condition, whereas, for exhalation breathing, the monolayer gets more compressed, causing the LSM to collapse. The monolayer collapse occurs for inhalation due to the higher drug concentration, whereas for exhalation due to the accumulation of surfactant proteins and drugs. The findings from this study will aid in enhancing the knowledge of molecular interactions of corticosteroid drugs with lung surfactants to treat respiratory diseases.

Concentration-Dependent Effect of the Steroid Drug Prednisolone on a Lung Surfactant Monolayer

The lung surfactant monolayer (LSM) is the main barrier for particles entering the lung, including steroid drugs used to treat lung diseases. The present study combines Langmuir experiments and coarse-grained (CG) molecular dynamics simulations to investigate the concentration-dependent effect of steroid drug prednisolone on the structure and morphology of a model LSM. The surface pressure-area isotherms for the Langmuir monolayers reveal a concentration-dependent decrease in area per lipid (APL). Results from simulations at a fixed surface tension, representing inhalation and exhalation conditions, suggest that at high drug concentrations, prednisolone induces a collapse of the LSM, which is likely caused by the inability of the drug to diffuse into the bilayer. Overall, the monolayer is most susceptible to drug-induced collapse at surface tensions representing exhalation conditions. The presence of cholesterol also exacerbates the instability. The findings of this investigation might be helpful for better understanding the interaction between steroid drug prednisolone and lung surfactants in relation to off-target effects.

Scission energy and topology of micelles controlled by the molecular structure of additives

We employ coarse-grained (CG) molecular dynamics simulations (MD) to investigate the effects of the molecular structure of additives on the scission energy and morphology of charged micelles. Considering sodium dodecyl sulfate (SDS) as a representative charged surfactant and taking trimethylphenylammonium chloride (TMPAC) and octyltrimethylammonium bromide (OTAB) as oppositely charged additives, we show that the scission energy and topology of micelles vary significantly depending on the molecular structure of the hydrophobic part of the additives. The cyclic aromatic tail of the TMPAC disrupts the core structure of the SDS micelle and hence decreases the micelle scission energy, whereas the linear alkyl tail of the OTAB packs very well with the micelle core and increases the scission energy. Although both the additives have similar head structures, they lead to very different micelle morphologies because of the difference in the shape of their tail structures; ring-like or toroidal shaped micelles are formed in SDS/TMPAC solution whereas bicelle-like structures are formed in SDS/OTAB solution when the additive to surfactant ratio is higher than a certain value.

Lipid21: Complex Lipid Membrane Simulations with AMBER

We extend the modular AMBER lipid force field to include anionic lipids, polyunsaturated fatty acid (PUFA) lipids, and sphingomyelin, allowing the simulation of realistic cell membrane lipid compositions, including raft-like domains. Head group torsion parameters are revised, resulting in improved agreement with NMR order parameters, and hydrocarbon chain parameters are updated, providing a better match with phase transition temperature. Extensive validation runs (0.9 μs per lipid type) show good agreement with experimental measurements. Furthermore, the simulation of raft-like bilayers demonstrates the perturbing effect of increasing PUFA concentrations on cholesterol molecules. The force field derivation is consistent with the AMBER philosophy, meaning it can be easily mixed with protein, small molecule, nucleic acid, and carbohydrate force fields.

Drug Meets Monolayer: Understanding the Interactions of Sterol Drugs with Models of the Lung Surfactant Monolayer Using Molecular Dynamics Simulations

The lung surfactant monolayer (LSM) is a thin layer of lipids and proteins that forms the air/water interface of the alveoli. The primary function of the LSM is to reduce the surface tension at the air/water interface during breathing. The LSM also forms the main biological barrier for any inhaled particles, including drugs, to treat lung diseases. Elucidating the mechanism by which these drugs bind to and absorb into the LSM requires a molecular-level understanding of any drug-induced changes to the morphology, structure, and phase changes of the LSM.Molecular dynamics simulations have been used extensively to study the structure and dynamics of the LSM. The monolayer is usually simulated in at least two states: the compressed state, mimicking exhalation, and the expanded state, mimicking inhalation. In this chapter, we provide detailed instructions on how to set up, run, and analyze coarse-grained MD simulations to study the concentration-dependent effect of a sterol drug on the LSM, both in the expanded and compressed state.

The steroid mometasone alters protein containing lung surfactant monolayers in a concentration-dependent manner

Mometasone is an investigational anti-inflammatory steroidal drug to treat inflammation via pulmonary administration. For steroid drugs to be effective they need to be adsorbed by lung surfactants, a thin monolayer at the air-water interface in alveoli that reduces surface tension. Information on the molecular-level interactions of the drug with lung surfactants is useful to understand the mechanism of adsorption. In this study, we use coarse-grained molecular dynamics simulation to understand the concentration-dependent effect of mometasone on a lung surfactant monolayer (LSM) composed of lipids and surfactant proteins, under two different breathing conditions (exhalation, at surface tension 0 mNm^-1 and inhalation, surface tension 20-25 mNm^-1). A series of fixed-APL and fixed-surface tension simulations were used to demonstrate that in the absence of drugs, the model LSM reproduces the surface tensions for the compressed and expanded states, as well as compressibility at different surface tensions. In-depth analysis of simulations of a LSM in the presence of five different drug concentrations shows that mometasone alters the structure and dynamics of the LSM in a concentration-dependent manner. Mometasone induces a collapse in the monolayer that is affected by the surfactant protein and surface tension. Overall, these findings suggest that the surfactant proteins, surface tension and drug concentration are all critical components affecting monolayer stability and drug adsorption. The outcomes of this study may be beneficial for a more in-depth understanding of how mometasone is adsorbed by lung surfactants.

Interfacial behavior of phospholipid monolayers revealed by mesoscopic simulation

A mesoscopic model with molecular resolution is presented for dipalmitoyl phosphatidylcholine (DPPC) and palmitoyl oleoyl phosphatidylcholine (POPC) monolayer simulations at the air-water interface using many-body dissipative particle dynamics (MDPD). The parameterization scheme is rigorously based on reproducing the physical properties of water and alkane and the interfacial property of the phospholipid monolayer by comparison with experimental results. Using much less computing cost, these MDPD simulations yield a similar surface pressure-area isotherm as well as similar pressure-related morphologies as all-atom simulations and experiments. Moreover, the compressibility modulus, order parameter of lipid tails, and thickness of the phospholipid monolayer are quantitatively in line with the all-atom simulations and experiments. This model also captures the sensitive changes in the pressure-area isotherms of mixed DPPC/POPC monolayers with altered mixing ratios, indicating that the model is promising for applications with complex natural phospholipid monolayers. These results demonstrate a significant improvement of quantitative phospholipid monolayer simulations over previous coarse-grained models.

Simulated Breathing: Application of Molecular Dynamics Simulations to Pulmonary Lung Surfactant

In this review, we delve into the topic of the pulmonary surfactant (PS) system, which is present in the respiratory system. The total composition of the PS has been presented and explored, from the types of cells involved in its synthesis and secretion, down to the specific building blocks used, such as the various lipid and protein components. The lipid and protein composition varies across species and between individuals, but ultimately produces a PS monolayer with the same role. As such, the composition has been investigated for the ways in which it imposes function and confers peculiar biophysical characteristics to the system as a whole. Moreover, a couple of theories/models that are associated with the functions of PS have been addressed. Finally, molecular dynamic (MD) simulations of pulmonary surfactant have been emphasized to not only showcase various group’s findings, but also to demonstrate the validity and importance that MD simulations can have in future research exploring the PS monolayer system.

Computational Studies of Lipid-Wrapped Gold Nanoparticle Transport Through Model Lung Surfactant Monolayers

Colloidal nanoparticles, such as gold nanoparticles (AuNPs), are promising materials for the delivery of hydrophilic drugs via the pulmonary route. The inhaled nanoparticle drug carriers primarily deposit in lung alveoli and interact with the alveolar surface known as lung surfactants. Therefore, it is vital to understand the interactions of nanocarriers with the surfactant layer. To understand the interactions at the molecular level, here we simulated model lung surfactant monolayers with phospholipid (PL)-wrapped AuNPs at the vacuum-water interface using coarse-grained molecular dynamics simulations. The PL-wrapped AuNPs quickly adsorbed into the surfactant layer, altered the structural properties of the monolayer, and at high concentrations initiated the compressed monolayer to collapse/buckle. Among the surfactant monolayer lipid components, cholesterol adsorbed to the AuNPs preferentially over PL species. The position of the adsorbed PL-AuNPs within the monolayer, and subsequent monolayer perturbation, vary depending on the monolayer phase, monolayer composition, and species of PL used as a ligand. Information provided by these molecular dynamic simulations helps to rationalize why some colloidal nanoparticles work better as nanocarriers than others and aid the design of new ones, to avoid biological toxicity and improve efficacy for pulmonary drug delivery.

Effect of TMAO on the Structure and Phase Transition of Lipid Membranes: Potential Role of TMAO in Stabilizing Cell Membranes under Osmotic Stress

Extremophiles adopt strategies to deal with different environmental stresses, some of which are severely damaging to their cell membrane. To combat high osmotic stress, deep-sea organisms synthesize osmolytes, small polar organic molecules, like trimethylamine-N-oxide (TMAO), and incorporate them in the cell. TMAO is known to protect cells from high osmotic or hydrostatic pressure. Several experimental and simulation studies have revealed the roles of such osmolytes on stabilizing proteins. In contrast, the effect of osmolytes on the lipid membrane is poorly understood and broadly debated. A recent experiment has found strong evidence of the possible role of TMAO in stabilizing lipid membranes. Using the molecular dynamics (MD) simulation technique, we have demonstrated the effect of TMAO on two saturated fully hydrated lipid membranes in their fluid and gel phases. We have captured the impact of TMAO's concentration on the membrane's structural properties along with the fluid/gel phase transition temperatures. On increasing the concentration of TMAO, we see a substantial increase in the packing density of the membrane (estimated by area, thickness, and volume) and enhancement in the orientational order of lipid molecules. Having repulsive interaction with the lipid head group, the TMAO molecules are expelled away from the membrane surface, which induces dehydration of the lipid head groups, increasing the packing density. The addition of TMAO also increases the fluid/gel phase transition temperature of the membrane. All of these results are in close agreement with the experimental observations. This study, therefore, provides a molecular-level understanding of how TMAO can influence the cell membrane of deep-sea organisms and help in combating the osmotic stress condition.

Dry Two-Step Self-Assembly of Stable Supported Lipid Bilayers on Silicon Substrates

Artificial membranes are models for biological systems and are important for applications. We introduce a dry two-step self-assembly method consisting of the high-vacuum evaporation of phospholipid molecules over silicon, followed by a subsequent annealing step in air. We evaporate dipalmitoylphosphatidylcholine (DPPC) molecules over bare silicon without the use of polymer cushions or solvents. High-resolution ellipsometry and AFM temperature-dependent measurements are performed in air to detect the characteristic phase transitions of DPPC bilayers. Complementary AFM force-spectroscopy breakthrough events are induced to detect single- and multi-bilayer formation. These combined experimental methods confirm the formation of stable non-hydrated supported lipid bilayers with phase transitions gel to ripple at 311.5 ± 0.9 K, ripple to liquid crystalline at 323.8 ± 2.5 K and liquid crystalline to fluid disordered at 330.4 ± 0.9 K, consistent with such structures reported in wet environments. We find that the AFM tip induces a restructuring or intercalation of the bilayer that is strongly related to the applied tip-force. These dry supported lipid bilayers show long-term stability. These findings are relevant for the development of functional biointerfaces, specifically for fabrication of biosensors and membrane protein platforms. The observed stability is relevant in the context of lifetimes of systems protected by bilayers in dry environments.

Study of nitrogen implantation in Ti surface using plasma immersion ion implantation & deposition technique as biocompatible substrate for artificial membranes

The present investigation reports the modification of Ti substrates by a plasma technique to enhance their physio-chemical properties as biocompatible substrates for the deposition of artificial membranes. For that purpose, nitrogen ions are implanted into Ti substrate using the plasma immersion ion implantation & deposition (PIII&D) technique in a capacitively coupled radio frequency plasma. The plasma was characterized using optical emission spectroscopy, together with radio frequency compensated Langmuir probe, while the ion current towards the substrate was measured during the implantation process using an opto-electronic device. X-ray photoelectron spectroscopy (XPS) was used for chemical analysis of the surface, confirming the presence of δ-TiN. The penetration depth of the nitrogen ions into the Ti substrate was measured using secondary ions mass spectroscopy (SIMS) while the morphological changes were observed using atomic force microscopy (AFM). A calorimetric assay was used to prove that the TiN samples maintain the biocompatibility of the untreated Ti surface with its native oxide layer. The ion implantation increases the load bearing ability of Ti surface by the formation of α-Ti(N) and δ-TiN phases on the sub-surface of Ti, and maintains the bio compatibility of Ti surface. After the plasma treatment a thin layer of chitosan (CH) was deposited in order to provide a moisturizing matrix for the artificial membrane of 1,2-dipalmitoyl-sn-3- phosphor glycerocholine (DPPC). The CH and subsequently the DPPC were deposited on the plasma deposited TiN substrate by using physical vapor deposition. The formation of artificial membranes was confirmed by AFM, measuring the topography at different temperatures and performing force curves.

Spontaneous Curvature, Differential Stress, and Bending Modulus of Asymmetric Lipid Membranes

Lipid bilayers can exhibit asymmetric states, in which the physical characteristics of one leaflet differ from those of the other. This most visibly manifests in a different lipid composition, but it can also involve opposing lateral stresses in each leaflet that combine to an overall vanishing membrane tension. Here, we use theoretical modeling and coarse-grained simulation to explore the interplay between a compositional asymmetry and a nonvanishing differential stress. Minimizing the total elastic energy leads to a preferred spontaneous curvature that balances torques due to both bending moments and differential stress, with sometimes unexpected consequences. For instance, asymmetric flat bilayers, whose specific areas in each leaflet are matched to those of corresponding tensionless symmetric flat membranes, still exhibit a residual differential stress because the conditions of vanishing area strain and vanishing bending moment differ. We also measure the curvature rigidity of asymmetric bilayers and find that a sufficiently strong differential stress, but not compositional asymmetry alone, can increase the bending modulus. The likely cause is a stiffening of the compressed leaflet, which appears to be related to its gel transition but not identical with it. We finally show that the impact of cholesterol on differential stress depends on the relative strength of elastic and thermodynamic driving forces: if cholesterol solvates equally well in both leaflets, it will redistribute to cancel both leaflet tensions almost completely, but if its partitioning free energy prefers one leaflet over the other, the resulting distribution bias may even create differential stress. Because cells keep most of their lipid bilayers in an asymmetric nonequilibrium steady state, our findings suggest that biomembranes are elastically more complex than previously thought: besides a spontaneous curvature, they might also exhibit significant differential stress, which could strongly affect their curvature energetics.

Comprehensive Study of the Liquid Expanded-Liquid Condensed Phase Transition in 1,2-Dimyristoyl-sn-glycero-3-phospho-l-serine Monolayers: Surface Pressure, Volta Potential, X-ray Reflectivity, and Molecular Dynamics Modeling

An integrated approach is applied to reveal fine changes in the surface-normal structure of 1,2-dimyristoyl-sn-glycero-3-phospho-l-serine (DMPS) monolayers at the air-lipid-water interface occurring in a liquid expanded (LE)-liquid condensed (LC) transition. The combination of the Langmuir monolayer technique, X-ray reflectometry, and molecular dynamics (MD) modeling provides new insight into the molecular nature of electrostatic phenomena in different stages of lipid compression. A homemade setup with a laboratory X-ray source (λ = 1.54 Å) offers a nondestructive way to reveal the structural difference between the LE and LC phases of the lipid. The electron density profile in the direction normal to the interface is recovered from the X-ray reflectivity data with the use of both model-independent and model-based approaches. MD simulations of the DMPS monolayer are performed for several areas per lipid using the all-atom force field. Using the conventional theory of capillary waves, a comparison is made between the electron density profiles reconstructed from the X-ray data and those calculated directly from MD modeling, which demonstrates remarkable agreement between the experiment and simulations for all selected lipid densities. This confirms the validity of the simulations and allows an analysis of the contributions of the hydrophobic tails and hydrated polar groups to the electron density profile and to the dipole component of the electric field at the interface. According to the MD data, the dependence of the Volta potential on the area per lipid in the monolayer has a different molecular nature below and above the phase transition. In the LE state of the monolayer, the potential is determined mostly by the oriented water molecules in the polar region of the lipid. In the LE-LC transition, these molecules are displaced to the bulk, and their effect on the Volta potential becomes insignificant compared with the contribution of the hydrophobic tails. The hydrophobic tails are highly ordered in the state of the liquid crystal so that their dipole moments entirely determine the growth of the potential upon compression up to the monolayer collapse.

Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture

The separation of lipid mixtures into thermodynamically stable phase-separated domains is dependent on lipid composition, temperature, and system size. Using molecular dynamics simulations, the line tension between thermodynamically stable lipid domains formed from ternary mixtures of di-C16:0 PC:di-C18:2 PC:cholesterol at 40:40:20 mol. % ratio was investigated via two theoretical approaches. The line tension was found to be 3.1 ± 0.2 pN by capillary wave theory and 4.7 ± 3.7 pN by pressure tensor anisotropy approaches for coarse-grained models based on the Martini force field. Using an all-atom model of the lipid membrane based on the CHARMM36 force field, the line tension was found to be 3.6 ± 0.9 pN using capillary wave theory and 1.8 ± 2.2 pN using pressure anisotropy approaches. The discrepancy between estimates of the line tension based on capillary wave theory and pressure tensor anisotropy methods is discussed. Inclusion of protein in Martini membrane lipid mixtures was found to reduce the line tension by 25%-35% as calculated by the capillary wave theory approach. To further understand and predict the behavior of proteins in phase-separated membranes, we have formulated an analytical Flory-Huggins model and parameterized it against the simulation results. Taken together these results suggest a general role for proteins in reducing the thermodynamic cost associated with domain formation in lipid mixtures and quantifies the thermodynamic driving force promoting the association of proteins to domain interfaces.

Search for the Source of an Apparent Interfacial Resistance To Mass Transfer of CnEm Surfactants To the Water/Oil Interface

Experiments have shown that relaxation of oil/water interfacial tension by adsorption of alkyl ethoxylate surfactants from water onto an oil droplet is delayed relative to diffusion-controlled adsorption. We examine possible causes of this delay, and we show that several are implausible. We find that redissolution of the surfactant in the oil droplet cannot explain the apparent interfacial resistance at short times because the interface will preferentially fill before any such redissolution occurs. We also perform umbrella sampling with molecular dynamics simulation and do not find any evidence of a free-energy barrier or low-diffusivity zone near the interface. Nor do we find evidence from the simulation that premicellar aggregation slows diffusion enough to cause the observed resistance to interfacial adsorption. We are therefore unable to pinpoint the cause of the resistance, but we suggest that "dead time" associated with the experimental method could be responsible-specifically a local depletion of surfactant by the ejected droplet when creating the fresh interface between the oil and water.

Stretch and Breakage of Wormlike Micelles under Uniaxial Strain: A Simulation Study and Comparison with Experimental Results

We use coarse-grained (CG) molecular dynamics simulations to determine the effect of uniaxial strain on the stress, scission stress, and scission energy of solutions of wormlike micelles of cetyltrimethylammonium chloride/sodium salicylate (NaSal). We find that the breaking stress, stretch modulus, and scission energy of the charged micelles are nonmonotonic functions of oppositely charged hydrotrope (NaSal) concentration. While the stretch modulus shows a peak at a value of surfactant-to-hydrotrope concentration ratio ( R) close to unity as expected due to neutralization of head-group charge at R = 1, the breaking stress and scission energy produce a peak at R < 1.0 because of thinning of the micelle diameter with increased R. The breaking stress from the simulations depends on the rate of deformation and roughly agrees with the experimental values of Rothstein ( J. Rheol. 2003 , 47 , 1227 ) after extrapolation to the much lower experimental rates. The method and results can be used to predict the effects of flow and mechanical stress on rates of micellar breakage, which is important in the rheology of wormlike micellar solutions.

Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation

Cholesterol is essential to the formation of phase-separated lipid domains in membranes. Lipid domains can exist in different thermodynamic phases depending on the molecular composition and play significant roles in determining structure and function of membrane proteins. We investigate the role of cholesterol in the structure and dynamics of ternary lipid mixtures displaying phase separation using molecular dynamics simulations, employing a physiologically relevant span of cholesterol concentration. We find that cholesterol can induce formation of three regimes of phase behavior: 1) miscible liquid-disordered bulk, 2) phase-separated, domain-registered coexistence of liquid-disordered and liquid-ordered domains, and 3) phase-separated, domain-antiregistered coexistence of liquid-disordered and newly identified nanoscopic gel domains composed of cholesterol threads we name "cholesterolic gel" domains. These findings are validated and discussed in the context of current experimental knowledge, models of cholesterol spatial distributions, and models of ternary lipid-mixture phase separation.

Domain size polydispersity effects on the structural and dynamical properties in lipid monolayers with phase coexistence

In lipid monolayers with phase coexistence, domains of the liquid-condensed phase always present size polydispersity. However, very few theoretical works consider size distribution effects on the monolayer properties. Because of the difference in surface densities, domains have excess dipolar density with respect to the surrounding liquid expanded phase, originating a dipolar inter-domain interaction. This interaction depends on the domain area, and hence the presence of a domain size distribution is associated with interaction polydispersity. Inter-domain interactions are fundamental to understanding the structure and dynamics of the monolayer. For this reason, it is expected that polydispersity significantly alters monolayer properties. By means of Brownian dynamics simulations, we study the radial distribution function (RDF), the average mean square displacement and the average time-dependent self-diffusion coefficient, D(t), of lipid monolayers with normally distributed size domains. For this purpose, we vary the relevant system parameters, polydispersity and interaction strength, within a range of experimental interest. We also analyze the consequences of using a monodisperse model to determine the interaction strength from an experimental RDF. We find that polydispersity strongly affects the value of the interaction strength, which is greatly underestimated if polydispersity is not considered. However, within a certain range of parameters, the RDF obtained from a polydisperse model can be well approximated by that of a monodisperse model, by suitably fitting the interaction strength, even for 40% polydispersities. For small interaction strengths or small polydispersities, the polydisperse systems obtained from fitting the experimental RDF have an average mean square displacement and D(t) in good agreement with that of the monodisperse system.

Critical size dependence of domain formation observed in coarse-grained simulations of bilayers composed of ternary lipid mixtures

Model cellular membranes are known to form micro- and macroscale lipid domains dependent on molecular composition. The formation of macroscopic lipid domains by lipid mixtures has been the subject of many simulation investigations. We present a critical study of system size impact on lipid domain phase separation into liquid-ordered and liquid-disordered macroscale domains in ternary lipid mixtures. In the popular di-C16:0 PC:di-C18:2 PC:cholesterol at 35:35:30 ratio mixture, we find systems with a minimum of 1480 lipids to be necessary for the formation of macroscopic phase separated domains and systems of 10 000 lipids to achieve structurally converged conformations similar to the thermodynamic limit. To understand these results and predict the behavior of any mixture forming two phases, we develop and investigate an analytical Flory-Huggins model which is recursively validated using simulation and experimental data. We find that micro- and macroscale domains can coexist in ternary mixtures. Additionally, we analyze the distributions of specific lipid-lipid interactions in each phase, characterizing domain structures proposed based on past experimental studies. These findings offer guidance in selecting appropriate system sizes for the study of phase separations and provide new insights into the nature of domain structure for a popular ternary lipid mixture.

Enhanced Sampling of Phase Transitions in Coarse-Grained Lipid Bilayers

Freezing and melting of dipalmitoylphosphatidylcholine (DPPC) bilayers are simulated in both the explicit (Wet) and implicit solvent (Dry) coarse-grained MARTINI force fields with enhanced sampling, via the isobaric, molecular dynamics version of the generalized replica exchange method (gREM). Phase transitions are described with the entropic viewpoint, based upon the statistical temperature as a function of enthalpy, T_S(H) = 1/(dS(H)/dH), where S is the configurational entropy. Bilayer thickness, area per lipid, and the second-rank order parameter (P2) are calculated vs temperature in the transition range. In a 32-lipid Wet MARTINI system, transitions in the lipid and water subsystems are strongly coupled, giving rise to considerable structure in T_S(H) and the need to specify the state of the water when reporting a lipid transition temperature. For gel lipid + liquid water → fluid lipid + liquid water, we find 292.4 K. The small system is influenced by finite-size effects, but it is argued that the entropic approach is well suited to revealing them, which will be particularly relevant for studies of finite nanosystems where there is no thermodynamic limit. In a 390-lipid Dry MARTINI system, two-dimensional analogues of the topographies of coexisting states ("subphases") seen in pure fluids are found. They are not seen in the 32-lipid Wet or Dry system, but the Dry lipids show a new type of state with gel in one leaflet and tilted gel in the other. Dry bilayer transition temperatures are 333.3 K (390 lipids) and 338 K (32 lipids), indicating that the 32-lipid system is not too small for a qualitative study of the transition. Physical arguments are given for Dry lipid system size dependence and for the difference between Wet and Dry systems.

Micelles, Rods, Liposomes, and Other Supramolecular Surfactant Aggregates: Computational Approaches

Surfactants are an interesting class of compounds characterized by the segregation of polar and apolar domains in the same molecule. This peculiarity makes possible a whole series of microscopic and macroscopic effects. Among their features, their ability to segregate particles (fluids or entire domains) and to reduce the surface/interfacial tension is the utmost important. The interest in the chemistry of surfactants never weakened; instead, waves of increasing interest have occurred every time a new field of application of these molecules has been discovered. All these special characteristics depend largely on the ability of surfactants to self-assemble and constitute supramolecular structures where their chemical properties are amplified. The possibility to obtain structural and energy information and, above all, the possibility of forecast the self-organizing mechanisms of surfactants have had a significant boost via computational chemistry. The molecular dynamics models, initially coarse-grained and subsequently (with the increasing computer power) using more accurate models, allowed, over the years, to better understand different aspects of the processes of dispersion, self-assembly, segregation of surfactant. Moreover, several other aspects have been investigated as the effect of the counterions of many ionic surfactants in defining the final supramolecular structures, the mobility of side chains, and the capacity of some surfactant to envelope entire proteins. This review constitutes a perspective/prospective view of these results. On the other hand, some comparison of in silico results with experimental information recently acquired through innovative analytical techniques such as ion mobility mass spectrometry which have been introduced.

Prednisolone adsorption on lung surfactant models: insights on the formation of nanoaggregates, monolayer collapse and prednisolone spreading

The adsorption of prednisolone on a lung surfactant model was successfully performed using coarse grained molecular dynamics.

Parameters for Martini sterols and hopanoids based on a virtual-site description

Sterols play an essential role in modulating bilayer structure and dynamics. Coarse-grained molecular dynamics parameters for cholesterol and related molecules are available for the Martini force field and have been successfully used in multiple lipid bilayer studies. In this work, we focus on the use of virtual sites as a means of increasing the stability of cholesterol and cholesterol-like structures. We improve and extend the Martini parameterization of sterols in four different ways: 1-the cholesterol parameters were adapted to make use of virtual interaction sites, which markedly improves numerical stability; 2-cholesterol parameters were also modified to address reported shortcomings in reproducing correct lipid phase behavior in mixed membranes; 3-parameters for ergosterol were created and adapted from cholesterols; and 4-parameters for the hopanoid class of bacterial polycyclic molecules were created, namely, for hopane, diploptene, bacteriohopanetetrol, and for their polycyclic base structure.

Computer simulations of lung surfactant

Lung surfactant lines the gas-exchange interface in the lungs and reduces the surface tension, which is necessary for breathing. Lung surfactant consists mainly of lipids with a small amount of proteins and forms a monolayer at the air-water interface connected to bilayer reservoirs. Lung surfactant function involves transfer of material between the monolayer and bilayers during the breathing cycle. Lipids and proteins are organized laterally in the monolayer; selected species are possibly preferentially transferred to bilayers. The complex 3D structure of lung surfactant and the exact roles of lipid organization and proteins remain important goals for research. We review recent simulation studies on the properties of lipid monolayers, monolayers with phase coexistence, monolayer-bilayer transformations, lipid-protein interactions, and effects of nanoparticles on lung surfactant. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Swing motion as a diffusion mechanism of lipid bilayers in a gel phase

Lipid bilayers are a model system for studying the properties of cell membranes. For lipid bilayers of a single lipid component, there is a phase transition from a fluid phase to a gel phase as the temperature is decreased. The dynamic behavior of lipids in the gel phase is interesting: some models show dynamic heterogeneity with a large disparity in timescales between fast and slow molecules, and a spatial segregation of the slow molecules. In this paper we study the dynamics of coarse-grained models of lipid bilayers using the dry Martini, Lennard-Jones Martini, polarizable Martini, and BMW models. All four models show similar dynamical behaviors in the gel phase although the transition temperature is model-dependent. We find that the primary mode of transport in the gel phase is a hopping of the lipid molecules. Hopping is seen in both the translational and rotational dynamics, which are correlated, i.e., the lipid molecules display a swing-like motion in the gel phase.

Reduced Condensing and Ordering Effects by 7-Ketocholesterol and 5β,6β-Epoxycholesterol on DPPC Monolayers

The exposure of organic-coated marine aerosols containing cholesterol (Chol) to radiation and/or an oxidizing atmosphere results in the formation of oxidized derivatives or oxysterols and will likely change aerosol surface properties. However, the intermolecular interactions between oxysterols and other lipid components and their influence on the surface properties of marine aerosols are not well-known. To address this question, the interfacial behavior and domain morphology of model Langmuir monolayers of two ring-substituted oxysterols, 7-ketocholesterol (7-KChol) and 5β,6β-epoxycholesterol (5,6β-EChol), mixed with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) were investigated by means of compression isotherms and Brewster angle microscopy (BAM) over a broad range of surface pressures and sterol molar ratios. Mixed DPPC/cholesterol (Chol) monolayers were also measured for comparison. The results of compression experiments showed that the condensing effect induced on mixed DPPC/sterol monolayers at low surface pressures and for intermediate molar ratios (0.3 ≤ X(sterol) ≤ 0.7) was weaker for oxysterols than for Chol. Additionally, mixed DPPC/oxysterol monolayers exhibited markedly smaller (∼2-3-fold) interfacial rigidity. Examination of the excess free energy of mixing further revealed that DPPC monolayers containing 7-KChol and Chol were thermodynamically more stable at high surface pressures than those with 5,6β-EChol, indicating that the strength of interactions between DPPC and 5,6β-EChol was the smallest. Finally, BAM images in the LE-LC phase of DPPC revealed that in comparison to Chol the addition of small amounts of oxysterols results in larger and less numerous domains, showing that oxysterols are not as effective in fluidizing the condensed phase of DPPC. Taken together, these results suggest that the strength of van der Waals interactions of DPPC alkyl chains with sterols follows the sterol hydrophobicity, with Chol being the most hydrophobic and oxysterols more hydrophilic due to their ketone and epoxy moieties. The difference in the condensing ability and stability of 7-KChol and 5,6β-EChol on DPPC likely originates from the distinct molecular structure and position of oxidation on the steroid nucleus. As suggested by recent MD simulations, depending on the oxidation position, ring-substituted oxysterols have a broader angular distribution of orientation than Chol in bilayers, which could be responsible for the observed reduction in condensing ability.

The mechanism of collapse of heterogeneous lipid monolayers

Collapse of homogeneous lipid monolayers is known to proceed via wrinkling/buckling, followed by folding into bilayers in water. For heterogeneous monolayers with phase coexistence, the mechanism of collapse remains unclear. Here, we investigated collapse of lipid monolayers with coexisting liquid-liquid and liquid-solid domains using molecular dynamics simulations. The MARTINI coarse-grained model was employed to simulate monolayers of ∼80 nm in lateral dimension for 10-25 μs. The monolayer minimum surface tension decreased in the presence of solid domains, especially if they percolated. Liquid-ordered domains facilitated monolayer collapse due to the spontaneous curvature induced at a high cholesterol concentration. Upon collapse, bilayer folds formed in the liquid (disordered) phase; curved domains shifted the nucleation sites toward the phase boundary. The liquid (disordered) phase was preferentially transferred into bilayers, in agreement with the squeeze-out hypothesis. As a result, the composition and phase distribution were altered in the monolayer in equilibrium with bilayers compared to a flat monolayer at the same surface tension. The composition and phase behavior of the bilayers depended on the degree of monolayer compression. The monolayer-bilayer connection region was enriched in unsaturated lipids. Percolation of solid domains slowed down monolayer collapse by several orders of magnitude. These results are important for understanding the mechanism of two-to-three-dimensional transformations in heterogeneous thin films and the role of lateral organization in biological membranes. The study is directly relevant for the function of lung surfactant, and can explain the role of nanodomains in its surface activity and inhibition by an increased cholesterol concentration.

Computer simulations of phase separation in lipid bilayers and monolayers

Studying phase coexistence in lipid bilayers and monolayers is important for understanding lipid-lipid interactions underlying lateral organization in biological membranes. Computer simulations follow experimental approaches and use model lipid mixtures of simplified composition. Atomistic simulations give detailed information on the specificity of intermolecular interactions, while coarse-grained simulations achieve large time and length scales and provide a bridge towards state-of-the-art experimental techniques. Computer simulations allow characterizing the structure and composition of domains during phase transformations at Angstrom and picosecond resolution, and bring new insights into phase behavior of lipid membranes.

Molecular dynamics of dibenz[a,h]anthracene and its metabolite interacting with lung surfactant phospholipid bilayers

Dibenz[a,h]anthracene and its metabolite may form aggregates, which have implications in the clearance process of the lung surfactant phospholipid bilayers.

Shape affects the interactions of nanoparticles with pulmonary surfactant

The interactions with the pulmonary surfactant, the initial biological barrier of respiratory pathway, determine the potential therapeutic applications and toxicological effects of inhaled nanoparticles (NPs). Although much attention has been paid to optimize the physicochemical properties of NPs for improved delivery and targeting, shape effects of the inhaled NPs on their interactions with the pulmonary surfactant are still far from clear. Here, we studied the shape effects of NPs on their penetration abilities and structural disruptions to the dipalmitoyl-phosphatidylcholine (DPPC) monolayer (being model pulmonary surfactant film) using coarse-grained molecular dynamics simulations. It is found that during the inspiration process (i.e., surfactant film expansion), shape effects are negligible. However, during the expiration process (i.e., surfactant film compression), NPs of different shapes show various penetration abilities and degrees of structural disruptions to the DPPC monolayer. We found that rod-like NPs showed the highest degree of penetration and the smallest side-effects to the DPPC monolayer. Our results may provide a useful insight into the design of NPs for respiratory therapeutics.

Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes?

Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.