Molecular dynamics simulations of lung surfactant lipid monolayers

Pulmonary Surfactant: A Mighty Thin Film

Pulmonary surfactant is a critical component of lung function in healthy individuals. It functions in part by lowering surface tension in the alveoli, thereby allowing for breathing with minimal effort. The prevailing thinking is that low surface tension is attained by a compression-driven squeeze-out of unsaturated phospholipids during exhalation, forming a film enriched in saturated phospholipids that achieves surface tensions close to zero. A thorough review of past and recent literature suggests that the compression-driven squeeze-out mechanism may be erroneous. Here, we posit that a surfactant film enriched in saturated lipids is formed shortly after birth by an adsorption-driven sorting process and that its composition does not change during normal breathing. We provide biophysical evidence for the rapid formation of an enriched film at high surfactant concentrations, facilitated by adsorption structures containing hydrophobic surfactant proteins. We examine biophysical evidence for and against the compression-driven squeeze-out mechanism and propose a new model for surfactant function. The proposed model is tested against existing physiological and pathophysiological evidence in neonatal and adult lungs, leading to ideas for biophysical research, that should be addressed to establish the physiological relevance of this new perspective on the function of the mighty thin film that surfactant provides.

Theoretical and Experimental Study of Molecular Interactions of Fluralaner with Lipid Membranes

Fluralaner is a relatively new insecticide belonging to the isoxazoline group, whose action mechanism involves the blocking of GABA_A-receptors in the insect nervous system. Because of its high hydrophobicity, fluralaner could bioaccumulate and reach toxic local concentrations. Since there are no data available about the penetration and persistence of isoxazolines in biological membranes, we intend to evaluate fluralaner permanence as a pollutant by using model membranes. We used experimental and in silico models to characterize the incorporation of fluralaner into the lipid phase at different packing states. We determined its impact in the membrane structure and organization. Our results confirm that fluralaner is capable of penetrating, holding, and accumulating in the lipid membrane and provide details on its precise location and orientation. These properties would allow fluralaner to reach high local concentrations in different membranes and organs, which could be dangerous for vertebrate organisms if its handling is not properly controlled.

Fluid Films as Models for Understanding the Impact of Inhaled Particles in Lung Surfactant Layers

Pollution is currently a public health problem associated with different cardiovascular and respiratory diseases. These are commonly originated as a result of the pollutant transport to the alveolar cavity after their inhalation. Once pollutants enter the alveolar cavity, they are deposited on the lung surfactant (LS) film, altering their mechanical performance which increases the respiratory work and can induce a premature alveolar collapse. Furthermore, the interactions of pollutants with LS can induce the formation of an LS corona decorating the pollutant surface, favoring their penetration into the bloodstream and distribution along different organs. Therefore, it is necessary to understand the most fundamental aspects of the interaction of particulate pollutants with LS to mitigate their effects, and design therapeutic strategies. However, the use of animal models is often invasive, and requires a careful examination of different bioethics aspects. This makes it necessary to design in vitro models mimicking some physico-chemical aspects with relevance for LS performance, which can be done by exploiting the tools provided by the science and technology of interfaces to shed light on the most fundamental physico-chemical bases governing the interaction between LS and particulate matter. This review provides an updated perspective of the use of fluid films of LS models for shedding light on the potential impact of particulate matter in the performance of LS film. It should be noted that even though the used model systems cannot account for some physiological aspects, it is expected that the information contained in this review can contribute on the understanding of the potential toxicological effects of air pollution.

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.

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.

Modulation of membrane physical properties by natural insecticidal ketones

The insecticidal activity of Mentha oil and its main components has been tested and established for various insects/pests. Several mint ketones have demonstrated to act on GABA_A receptors (GABA_A-R), a transmembrane channel target of several important insecticides whose activity can be modulated by surface-active compounds and by changes in the physical properties of the lipid membrane. In the present work, we analyze the capacity of monoterpenic ketones most commonly found in Mentha species, pulegone and menthone, to interact with DPPC membranes by molecular dynamics (MD) simulations and Langmuir monolayers. The experimental results indicate that the presence of menthone and pulegone in the subphase modify the interfacial characteristics of DPPC isotherms. The changes were reflected as expansion of the isotherms and disappearance or bringing forward of DPPC phase transition. MD simulation corroborate these results and indicate that both ketones are located at the region of the carbonyl group, at the interface with the acyl chains. Ketone intercalation between lipid molecules would induce an increasing intermolecular interaction, diminishing the film elasticity and causing an ordering effect. Our results suggest that the insecticidal activity of both ketones could involve their interaction with lipid molecules causing disturbance of the cell membrane as postulated for several larvicide compounds, or at least modulating the receptor surrounding.

Modeling Gas-Liquid Interfaces by Dissipative Particle Dynamics: Adsorption and Surface Tension of Cetyl Trimethyl Ammonium Bromide at the Air-Water Interface

Adsorption of surfactants at gas-liquid interfaces that causes reduction in the surface tension is a classical problem in colloid and interface science with multiple practical applications in oil and gas recovery, separations, cosmetics, personal care, and biomedicine. Here, we develop an original coarse-grained model of the liquid-gas interface within the conventional dissipative particle dynamics (DPD) framework with the goal of quantitatively predicting the surface tension in the presence of surfactants. As a practical case-study example, we explore the adsorption of the cationic surfactant cetyl trimethyl ammonium bromide (CTAB) on the air-water interface. The gas phase is modeled as a DPD fluid composed of fictitious hard-core "gas" beads with exponentially decaying repulsive potentials to prevent penetration of the liquid phase components. A rigorous parametrization scheme is proposed based on matching the bulk and interfacial properties of water and octane taken as the reference compounds. Quantitative agreement between the simulated and experimental surface tension of CTAB solutions is found for a wide range of bulk surfactant concentrations (∼10^-3 to ∼1 mmol/L) with the reduction of the surface tension from ∼72 mN/m (pure water) to the limiting value of ∼37.5 mN/m at the critical micelle concentration. The gas phase DPD model with the proposed parametrization scheme can be extended and applied to modeling various gas-liquid interfaces with surfactant and lipid monolayers, such as bubble suspensions, foams, froths, etc.

A coarse-grain force field based on quantum mechanics (CGq FF) for molecular dynamics simulation of poly(ethylene glycol)-block-poly(ε-caprolactone) (PEG-b-PCL) micelles

In order to provide the means to predict from molecular dynamics (MD) simulations the structures of copolymer-based micelles in solution, we developed coarse grain force field (CGq FF) parameters for poly(ethylene glycol) (PEG) and for poly(ε-caprolactone) (PCL). A key advance here is the use of quantum mechanics to train the parameters describing the non-bonded (NB) interactions between the CG beads. The functional forms are the same as the MARTINI CG FF so standard MD codes can be used. Our CGq FF describes well the experimentally observed properties for the polymer-air and polymer-water interfaces, indicating the accuracy of the NB interactions. The structural properties (density, radius of gyration (R_g), and end-to-end distance (h)) match both experiment and all atom (AA) simulations. We illustrate the application of this CGq FF by following the formation of a spherical micelle from 250 chains of PEG₂₃-b-PCL₉ diblock copolymer, each block with molecular weight of 1000 Daltons (10 500 beads, corresponding to 123 250 atoms), in a water box with 119 139 water beads (426 553 water molecules).

Interactions of particulate matter and pulmonary surfactant: Implications for human health

Particulate matter (PM), which is the primary contributor to air pollution, has become a pervasive global health threat. When PM enters into a respiratory tract, the first body tissues to be directly exposed are the cells of respiratory tissues and pulmonary surfactant. Pulmonary surfactant is a pivotal component to modulate surface tension of alveoli during respiration. Many studies have proved that PM would interact with pulmonary surfactant to affect the alveolar activity, and meanwhile, pulmonary surfactant would be adsorbed to the surface of PM to change the toxic effect of PM. This review focuses on recent studies of the interactions between micro/nanoparticles (synthesized and environmental particles) and pulmonary surfactant (natural surfactant and its models), as well as the health effects caused by PM through a few significant aspects, such as surface properties of PM, including size, surface charge, hydrophobicity, shape, chemical nature, etc. Moreover, in vitro and in vivo studies have shown that PM leads to oxidative stress, inflammatory response, fibrosis, and cancerization in living bodies. By providing a comprehensive picture of PM-surfactant interaction, this review will benefit both researchers for further studies and policy-makers for setting up more appropriate regulations to reduce the adverse effects of PM on public health.

Microscopic Molecular Insights into Hydrate Formation and Growth in Pure and Saline Water Environments

The growth dynamics of natural gas hydrates in saline water has been studied using copious experiments and spectroscopic observations; however, the microscopic evidences to the structural and molecular transformations that they have provided are poorly understood. In this view, we perform extensive molecular dynamics simulations to gain physical insights into the formation and growth mechanism of naturally occurring gas hydrates with a wide variation in the amount of methane (1:5 to 1:18 methane/water ratio) in pure and salt (0-5 wt %) water environments at 50 MPa and 260 K. A couple of new findings analyzed from the number of cages and F_4φ order parameter are as follows: (a) 1:6 (methane/water ratio) is an optimum ratio for the rapid growth of a properly ordered hydrate in pure water at which the hydrate growth retards with increasing salt concentration, (b) there is an inconsequential difference between methane hydrate dynamics in pure water and 0.8 and 1.5 wt % salt water at a ratio of 1:12 (methane/water), and (c) lower methane (1:18) and salt (0.8 wt %) concentrations promote hydrate growth. Besides, this study observes the structural coexistence of S-I and S-II methane hydrates as the large 5¹²6⁴ cages appear along with the small 5¹² and large 5¹²6² cages, in which the low methane concentration favors the S-II structure.

Molecular Ordering in Lipid Monolayers: An Atomistic Simulation

We report on atomistic simulations of DPPC lipid monolayers using the CHARMM36 lipid force field (and also the Slipid force field as a control case), combined with a four-point OPC water model. The entire two-phase region where domains of the "liquid-condensed" (LC) phase coexist with domains of the "liquid-expanded" (LE) phase has been explored. The simulations are long enough that the complete phase-transition stage, with two domains coexisting in the monolayer, is reached in all cases. Also, system sizes used are larger than those in previous works. As expected, domains of the minority phase are elongated, emphasizing the importance of anisotropic van der Waals and/or electrostatic dipolar interactions in the monolayer plane. The molecular structure is quantified in terms of distribution functions for the hydrocarbon chains and the PN dipoles. In contrast to previous work, where average distributions are calculated, distributions are here extracted for each of the coexisting phases by first identifying lipid molecules that belong to either LC or LE regions. In the case of the CHARMM36 force field, the three-dimensional distributions show that the average tilt angle of the chains with respect to the normal outward direction is (39.0 ± 0.1)° in the LC phase and (48.1 ± 0.5)° in the LC phase. In the case of the PN dipoles, the distributions indicate a tilt angle of (110.8 ± 0.5)° in the LC phase and (112.5 ± 0.5)° in the LE phase. These results are quantitatively different from those in previous works, which indicated a smaller normal component of the PN dipole. Also, the distributions of the monolayer-projected chains and PN dipoles have been calculated. Chain distributions peak along a particular direction in the LC domains, while they are uniform in the LE phase. Long-range ordering associated with the projected PN dipoles is absent in both phases. These results strongly suggest that LC domains do not exhibit dipolar ordering in the plane of the monolayer, the effect of these components being averaged out at short distances. Therefore, the only relevant component of the molecular dipoles, with regard to both intra- and long-range interdomain interactions, is normal to the monolayer. Also, the local orientation of chain projections is almost constant in LC domains and points in the direction along which domains are elongated, suggesting that the line tension driving the phase transition might be anisotropic with respect to the interfacial domain boundary.

In Silico Prediction of the Thermodynamic Equilibrium of Solute Partition in Multiphase Complex Fluids: A Case Study of Oil-Water Microemulsion

Multiphase complex fluids such as micelles, microemulsions, and dispersions are ubiquitous in product formulations of foods, pharmaceuticals, cosmetics, and fine chemicals. Quantifying how active solutes partition in the microstructure of such multiphase fluids is necessary for designing formulations that can optimally deliver the benefits of functional actives. In this paper, we at first predict the structure of a heptane/butanol/sodium dodecyl sulfate droplet in water that self-assembled to form a microemulsion through the molecular dynamics (MD) simulation and subsequently investigate the thermodynamic equilibrium of solute partitioning using COSMOmic. To our knowledge, this is the first time that the MD/COSMOmic approach is used for predicting solute partitioning in a microemulsion. The predicted partition coefficients are compared to experimental values derived from retention measurements of the same microemulsion. We show that the experimental data of droplet-water partition coefficients (K_droplet/w) can be reliably predicted by the method that combines MD simulations with COSMOmic.

Effect of Fe3O4 Nanoparticles on Mixed POPC/DPPC Monolayers at Air-Water Interface

Fe₃O₄ nanoparticles (NPs) as a commonly used carrier in targeted drug delivery are widely used to carry drugs for the treatment of diseases. However, the mechanism of action of between Fe₃O₄ NPs and biological membranes is still unclear. Therefore, this article reports the influence of hydrophilic and hydrophobic Fe₃O₄ NPs on mixed 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) that were studied using the Langmuir-Blodgett (LB) film technique and an atomic force microscope (AFM). From surface pressure-area (π-A) isotherms, we have calculated the compression modulus. The results showed that hydrophobic Fe₃O₄ NPs enlarged the liquid-expanded (LE) and liquid-condensed (LC) phase of the mixed POPC/DPPC monolayers. The compressibility modulus of the mixed POPC/DPPC monolayer increases for hydrophilic Fe₃O₄ NPs, but the opposite happens for the hydrophobic Fe₃O₄ NPs. The adsorption of hydrophobic Fe₃O₄ NPs in mixed POPC/DPPC monolayers was much more than the hydrophilic Fe₃O₄ NPs. The interaction of hydrophilic Fe₃O₄ NPs with the head polar group of the mixed lipids increased the attraction force among the molecules, while the interaction of hydrophobic Fe₃O₄ NPs with the tail chain of the mixed lipids enhanced the repulsive force. The morphology of the monolayers was observed by AFM for validating the inferred results. This study is of great help for the application of Fe₃O₄ NPs in biological systems.

Cholesterol provides nonsacrificial protection of membrane lipids from chemical damage at air-water interface

The role of cholesterol in bilayer and monolayer lipid membranes has been of great interest. On the biophysical front, cholesterol significantly increases the order of the lipid packing, lowers the membrane permeability, and maintains membrane fluidity by forming liquid-ordered-phase lipid rafts. However, direct observation of any influence on membrane chemistry related to these cholesterol-induced physical properties has been absent. Here we report that the addition of 30 mol % cholesterol to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) or 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG) monolayers at the air-water interface greatly reduces the oxidation and ester linkage cleavage chemistries initiated by potent chemicals such as OH radicals and HCl vapor, respectively. These results shed light on the indispensable chemoprotective function of cholesterol in lipid membranes. Another significant finding is that OH oxidation of unsaturated lipids generates Criegee intermediate, which is an important radical involved in many atmospheric processes.

Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers

Lung surfactant and a tear film lipid layer are examples of biologically relevant macromolecular structures found at the air-water interface. Because of their complexity, they are often studied in terms of simplified lipid layers, the simplest example being a Langmuir monolayer. Given the profound biological significance of these lipid assemblies, there is a need to understand their structure and dynamics on the nanoscale, yet there are not many techniques able to provide this information. Atomistic molecular dynamics simulations would be a tool fit for this purpose; however, the simulation models suggested until now have been qualitative instead of quantitative. This limitation has mainly stemmed from the challenge to correctly describe the surface tension of water with simulation parameters compatible with other biomolecules. In this work, we show that this limitation can be overcome by using the recently introduced four-point OPC water model, whose surface tension for water is demonstrated to be quantitatively consistent with experimental data and which is also shown to be compatible with the commonly employed lipid models. We further establish that the approach of combining the OPC four-point water model with the CHARMM36 lipid force field provides nearly quantitative agreement with experiments for the surface pressure-area isotherm for POPC and DPPC monolayers, also including the experimentally observed phase coexistence in a DPPC monolayer. The simulation models reported in this work pave the way for nearly quantitative atomistic studies of lipid-rich biological structures at air-water interfaces.

Surfactant Interactions and Organization at the Gas-Water Interface (CTAB with Added Salt)

We have studied adsorbed layers of cetyltrimethylammonium bromide (CTAB) at air-water interfaces in the presence of added electrolyte. Fast bubble compression/expansion measurements were used to obtain the surface equation of state, i.e., the surface tension vs CTAB surface concentration dependence. We show that while a simple model where the surfactant molecules are assumed to be noninteracting is insufficient to describe the measured response of the surfactant layer, a modified Frumkin equation where the local interactions between the molecular components depend on their surface concentration captures the response. The variation of the effective interactions in the surfactant layer in the model shows that the interactions in the surfactant layer change from effectively repulsive to attractive with increasing surface concentration. Molecular dynamics simulations are performed to probe the origins of the change in the interactions. The simulations indicate that already at low surface concentrations the surfactants aggregate as highly dynamic rafts with surfactant orientation parallel to the interface. Increasing the concentration leads to a change in the assembly morphology at the interface: the surfactant layer thickens and the surfactants sample a range of tilted orientations with respect to the interfacial plane. The change from transient raftlike assemblies to dynamical aggregates at the interface involves a clear increase in the degree of counterion binding: we speculate that the flip of the effective interaction parameter in the model used to interpret the experimental results could result from this. The work here presents basic steps toward a proper understanding of the molecular organization and interactions of surfactants at an air-water interface. This is crucially important in understanding macroscopic properties of surfactant-stabilized systems such as foams, emulsions, and colloidal dispersions.

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.

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.

The selective interactions of cationic tetra-p-guanidinoethylcalix[4]arene with lipid membranes: theoretical and experimental model studies

Behavior of cationic tetra-p-guanidinoethylcalix[4]arene (CX1) and its building block, p-guanidinoethylphenol (mCX1) in model monolayer lipid membranes was investigated using all atom molecular dynamics simulations and surface pressure measurements. Members of two classes of lipids were taken into account: zwitterionic 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and anionic 1,2-dimyristoyl-sn-glycero-3-phospho-l-serine sodium salt (DMPS) as models of eukaryotic and bacterial cell membranes, respectively. It was demonstrated that CX1 and mCX1 accumulate near the negatively charged DMPS monolayers. The adsorption to neutral monolayers was negligible. In contrast to mCX1, CX1 penetrated into the hydrophobic part of the monolayer. The latter effect, which is possible due to a flip-flop inversion of the CX1 orientation in the lipid layer compared to the aqueous phase, may be responsible for its antibacterial activity.

Three Dimensional Nano "Langmuir Trough" for Lipid Studies

A three-dimensional-phospholipid monolayer with tunable molecular structure was created on the surface of oil nanodroplets from a mixture of phospholipids, oil, and water. This simple nanoemulsion preparation technique generates an in situ prepared membrane model system with controllable molecular surface properties that resembles a lipid droplet. The molecular interfacial structure of such a nanoscopic system composed of hexadecane, 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC), and water was determined using vibrational sum frequency scattering and second harmonic scattering techniques. The droplet surface structure of DPPC can be tuned from a tightly packed liquid condensed phase like monolayer to a more dilute one that resembles the liquid condensed/liquid expanded coexistence phase by varying the DPPC/oil/water ratio. The tunability of the chemical structure, the high surface-to-volume ratio, and the small sample volume make this system an ideal model membrane for biochemical research.

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.

Protein modeling and molecular dynamics simulation of the two novel surfactant proteins SP-G and SP-H

Surfactant proteins are well known from the human lung where they are responsible for the stability and flexibility of the pulmonary surfactant system. They are able to influence the surface tension of the gas–liquid interface specifically by directly interacting with single lipids. This work describes the generation of reliable protein structure models to support the experimental characterization of two novel putative surfactant proteins called SP-G and SP-H. The obtained protein models were complemented by predicted posttranslational modifications and placed in a lipid model system mimicking the pulmonary surface. Molecular dynamics simulations of these protein-lipid systems showed the stability of the protein models and the formation of interactions between protein surface and lipid head groups on an atomic scale. Thereby, interaction interface and strength seem to be dependent on orientation and posttranslational modification of the protein. The here presented modeling was fundamental for experimental localization studies and the simulations showed that SP-G and SP-H are theoretically able to interact with lipid systems and thus are members of the surfactant protein family.

Structural properties of POPC monolayers under lateral compression: computer simulations analysis

1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a lipid comprising a saturated and an unsaturated acyl chain, belongs to the class of glycerophosphatidylcholines, major lipids in eukaryotic cell membranes. To get insight into the structural properties of this lipid within monolayers as membrane models, we performed molecular dynamics (MD) simulations of POPC monolayers under compression at the air/water interface. MD simulations were carried out at 300 K and at different surface pressures using the all-atom general Amber force field (GAFF). A good agreement was found between the simulated data and experimental isotherms. At surface pressures greater than 15 mN/m, two orientations of the head groups clearly appear: one nearly parallel to the monolayer interface and another one pointing toward the water. On the basis of the analysis of headgroup dihedral angles, we propose that the conformational variations around the bonds connecting the phosphorus atom to the adjacent oxygens are involved in these two orientations of the headgroup. The glycerol group orientation is characterized by a large distribution centered around 50° with respect to the monolayer normal. The acyl chains are predominantly in trans configuration from 7.5 to 43 mN/m surface pressures. Moreover, the calculated order parameter profiles of both chains suggest an independent behavior of the saturated and unsaturated chains that could be correlated with the formation of chain-type clusters observed along the simulated trajectories.

Simulations of lipid monolayers

A lipid monolayer lining a boundary between two immiscible phases forms a complex interface with inhomogeneous distribution of forces. Unlike lipid bilayers, monolayers are formed in asymmetric environment and their properties depend strongly on lipid surface density. The monolayer properties are also affected significantly by the representation of the pure interface. Here we give a brief theoretical introduction and describe methods to simulate lipid monolayers starting from force-fields and system setup to reproducing state points on the surface tension (pressure)-area isotherms and transformations between them.

Structural modelling and dynamics of proteins for insights into drug interactions

Proteins are the workhorses of biomolecules and their function is affected by their structure and their structural rearrangements during ligand entry, ligand binding and protein-protein interactions. Hence, the knowledge of protein structure and, importantly, the dynamic behaviour of the structure are critical for understanding how the protein performs its function. The predictions of the structure and the dynamic behaviour can be performed by combinations of structure modelling and molecular dynamics simulations. The simulations also need to be sensitive to the constraints of the environment in which the protein resides. Standard computational methods now exist in this field to support the experimental effort of solving protein structures. This review presents a comprehensive overview of the basis of the calculations and the well-established computational methods used to generate and understand protein structure and function and the study of their dynamic behaviour with the reference to lung-related targets.

Lung surfactant protein SP-B promotes formation of bilayer reservoirs from monolayer and lipid transfer between the interface and subphase

We investigated the possible role of SP-B proteins in the function of lung surfactant. To this end, lipid monolayers at the air/water interface, bilayers in water, and transformations between them in the presence of SP-B were simulated. The proteins attached bilayers to monolayers, providing close proximity of the reservoirs with the interface. In the attached aggregates, SP-B mediated establishment of the lipid-lined connection similar to the hemifusion stalk. Via this connection, a lipid flow was initiated between the monolayer at the interface and the bilayer in water in a surface-tension-dependent manner. On interface expansion, the flow of lipids to the monolayer restored the surface tension to the equilibrium spreading value. SP-B induced formation of bilayer folds from the monolayer at positive surface tensions below the equilibrium. In the absence of proteins, lipid monolayers were stable at these conditions. Fold nucleation was initiated by SP-B from the liquid-expanded monolayer phase by local bending, and the proteins lined the curved perimeter of the growing fold. No effect on the liquid-condensed phase was observed. Covalently linked dimers resulted in faster kinetics for monolayer folding. The simulation results are in line with existing hypotheses on SP-B activity in lung surfactant and explain its molecular mechanism.

Modifications to surfactant protein B structure and lipid interactions under respiratory distress conditions: consequences of tryptophan oxidation

These studies detail the altered structure-function relationships caused by oxidation of surfactant protein B (SP-B), a mode of damage thought to be important in acute respiratory distress syndrome (ARDS), a common and frequently fatal condition. An 18-residue fragment comprising the N-terminal helix of SP-B was investigated in oxidized and unmodified forms by solution and solid-state nuclear magnetic resonance (NMR), circular dichroism (CD), and molecular dynamics (MD) simulation. Taken together, the results indicate that tryptophan oxidation causes substantial disruptions in helical structure and lipid interactions. The structural modifications induced by tryptophan oxidation were severe, with a reduction in helical extent from approximately three helical turns to, at most, one turn, and were observed in a variety of solvent environments, including sodium dodecyl sulfate (SDS) micelles, dodecyl phosphocholine (DPC) micelles, and a 40% hexafluoro-2-propanol (HFIP) aqueous solution. The unmodified peptide takes on an orientation within lipid bilayers that is tilted approximately 30° away from an in-plane position. Tryptophan oxidation causes significant modifications to the peptide-lipid interactions, and the peptide likely shifts to a more in-plane orientation within the lipids. Interestingly, the character of the disruptions to peptide-lipid interactions caused by tryptophan oxidation was highly dependent on the charge of the lipid headgroup.

The effect of PAMAM G6 dendrimers on the structure of lipid vesicles

Dendrimers are polymers with unique properties that make them promising in a variety of applications such as potential drug and gene delivery systems. PAMAM dendrimers, in particular, have been widely investigated and are efficiently translocated into the cell. The mechanism of translocation, however, is still unknown. Recently it was proposed that PAMAM dendrimers are able to open holes in lipid bilayers by stealing lipid from the bilayer and forming "dendrisomes". The present work intends to contribute in the clarification of this question: why are dendrimers able to translocate into the cell? We create simple models for cell membranes by using small lipid vesicles that present a single lipid phase at physiologically relevant conditions. We then follow the effect that dendrimers have on the structure of the vesicles by using a combination of various techniques: dynamic light scattering, cryo-TEM and small angle X-ray scattering. We discuss our results with respect to the previous findings and reflect on their possible implications for real translocation in living cells.

Structural aspects of lipid monolayers: computer simulation analyses

Extensive molecular dynamics simulations at room temperature were carried out for model films of two dissimilar lipids (DPPC and dicaprin) at the air/water interface. To study the peculiarities of the organization patterns at different average areas per molecule, surface concentrations corresponding to five almost equally spaced points along the isotherms of the two surfactants were considered. A variable of prime interest was the density distribution in a direction normal to the interface of the monolayer components: interfacial water and surfactant on one hand and the separate moieties of the lipids on the other hand. The packing pattern and cluster size dispersion were studied by means of Voronoi tessellation and radial distribution functions. Speculations regarding structural changes upon phase-state changes during film compression were made. Individual characteristics for surfactant heads and tails as well as for interfacial water were outlined and related to the available experimental data. An analysis of the diffusion coefficients revealed the limiting factors for lipid lateral and normal diffusion. Structural arguments in support of changes in monolayer dielectric properties with the area per molecule were provided.