Molecular dynamics simulation of a dye molecule in the interior of a bilayer: 1,6-diphenyl-1,3,5-hexatriene in dipalmitoylphosphatidylcholine

Effect of Ionic Strength on Ibuprofenate Adsorption on a Lipid Bilayer of Dipalmitoylphosphatidylcholine from Molecular Dynamics Simulations

In this work, the free energy change in the process of transferring ibuprofenate from the bulk solution to the center of a model of the dipalmitoylphosphatidylcholine bilayer at different NaCl concentrations was calculated. Two minima were found in the free energy profile: a local minimum, located in the vicinity of the membrane, and the global free energy minimum, found near the headgroup region. The downward shift of free energy minima with increasing NaCl concentration is consistent with the results of previous works. Conversely, the upward shift of the free energy maximum with increasing ionic strength is due to the competition of sodium ions and lipids molecules to coordinate with ibuprofenate and neutralize its charge. In addition, normal molecular dynamics simulations were performed to study the effects of the ibuprofenate on the lipid bilayer and in the presence of a high ibuprofenate concentration. The effect of ionic strength on the properties of the lipid bilayer and on lipid-drug interactions was analyzed. The area per lipid shrinking with increasing ionic strength, volume of lipids, and thickness of the bilayer is consistent with the experimental results. At a very high ibuprofenate concentration, the lipid bilayer dehydrates, and it consequently transforms into the gel phase, thus blocking the permeation.

Influence of Lipid Composition on the Insertion Process of Glyphosate into Membranes: A Thermodynamic Study

In this work, molecular dynamics simulations were applied to investigate the influence of lipid composition of the model membrane on the insertion of glyphosate (in its charged state, GLYP2-). The profiles of free energy, entropy and enthalpy were obtained through umbrella sampling calculations, for lipid bilayers composed by only 1,2-dipalmitoyl-sn-glycerol-3-phosphocholine (DPPC), only 1,2-dipalmitoyl-sn-glycerol-3-phosphoserine (DPPS) or a symmetric binary mixture of DPPC and DPPS. In general, the location, the values of minima and maxima of the free energy, and the trend of free energy profiles are influenced by the lipid composition of the lipid bilayer. The driving force in the glyphosate insertion process depends on the lipid composition of the membrane model. If the lipid bilayer is composed solely of DPPS or DPPC, GLYP2- insertion is driven by a favorable enthalpic change. However, if the membrane is composed of a mixture of both lipids, this process is driven by a favorable entropic change. In the lipid bilayer containing DPPS, the glyphosate was found to penetrate hydrated and coordinated with Na+ ions, in contrast to the pure zwitterionic lipid bilayer which penetrated only hydrated. This effect is independent of the concentration of sodium ions present in the bulk solution.

The Secret Lives of Fluorescent Membrane Probes as Revealed by Molecular Dynamics Simulations

Fluorescent probes have been employed for more than half a century to study the structure and dynamics of model and biological membranes, using spectroscopic and/or microscopic experimental approaches. While their utilization has led to tremendous progress in our knowledge of membrane biophysics and physiology, in some respects the behavior of bilayer-inserted membrane probes has long remained inscrutable. The location, orientation and interaction of fluorophores with lipid and/or water molecules are often not well known, and they are crucial for understanding what the probe is actually reporting. Moreover, because the probe is an extraneous inclusion, it may perturb the properties of the host membrane system, altering the very properties it is supposed to measure. For these reasons, the need for independent methodologies to assess the behavior of bilayer-inserted fluorescence probes has been recognized for a long time. Because of recent improvements in computational tools, molecular dynamics (MD) simulations have become a popular means of obtaining this important information. The present review addresses MD studies of all major classes of fluorescent membrane probes, focusing in the period between 2011 and 2020, during which such work has undergone a dramatic surge in both the number of studies and the variety of probes and properties accessed.

Molecular dynamics simulations of glyphosate in a DPPC lipid bilayer

Extensive molecular dynamics simulations have been performed to study the effect of glyphosate (in their neutral and charged forms, GLYP and GLYP2-, respectively) on fully hydrated DiPalmitoylPhosphatidylCholine (DPPC) lipid bilayer. First, we calculated the free energy profile (using the Umbrella Sampling technique) for both states of charge of glyphosate. The minimum value for the free energy for GLYP is ∼-60 kJ mol-1 located at z = ±1.7 nm (from the lipid bilayer center), and there is almost no maximum at the center of the lipid bilayer. By contrast, the minimum for GLYP2- is ∼-35 kJ mol-1 located at z = ± 1.4 nm (from the lipid bilayer center), and the maximum reaches ∼35 kJ mol-1 at the center of the lipid bilayer. Then, different lipid bilayer properties were analyzed for different glyphosate:lipid (G:L) ratios. The mean area per lipid was slightly affected, increasing only 5% (in the presence of glyphosate at high concentrations), which is in agreement with the slight decrease in deuterium order parameters. As for the thickness of the bilayer, it is observed that the state of charge produces opposite effects. On one hand, the neutral state produces an increase in the thickness of the lipid bilayer; on the other, the charged form produces a decrease in the thickness, which not depend linearly on the G:L ratios, either. The orientation of the DPPC head groups is practically unaffected throughout the range of the G:L ratios studied. Finally, the mobility of the lipids of the bilayer is strongly affected by the presence of glyphosate, considerably increasing its lateral diffusion coefficient noteworthy (one order of magnitude), with increasing G:L ratio.

Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

Fluorescence spectroscopy and microscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in these membranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3-4Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using them as membrane reporters.

Computational and spectral studies of 1,6-diphenyl-1,3,5-hexatriene (DPH) multicomponent solutions

The multicomponent 1,6-diphenyl-1,3,5-hexatriene+tetrahydrofuran+water+ethanol (DPH+THF+W+E) solutions with variable content in water were studied by computational and spectral means. The computational results that indicate micelle formation in multicomponent solutions at high water content were correlated by the independence of the wavenumber in the maximum of the fluorescence on the solvent composition.

Recent developments in molecular dynamics simulations of fluorescent membrane probes

Due to their sensitivity and versatility, the use of fluorescence techniques in membrane biophysics is widespread. Because membrane lipids are non-fluorescent, extrinsic membrane probes are widely used. However, the behaviour of these probes when inserted in the bilayer is often poorly understood, and it can be hard to distinguish between legitimate membrane properties and perturbation resulting from probe incorporation. Atomistic molecular dynamics simulations present a convenient way to address these issues and have been increasingly used in recent years in this context. This article reviews the application of molecular dynamics to the study of fluorescent membrane probes, focusing on recent work with complex design fluorophores and ordered bilayer systems.

The impact of Texas red on lipid bilayer properties

We investigated the impact of fluorescent labeling on the properties of a lipid bilayer using atomistic molecular dynamics simulation. The system consisted of 24 Texas Red-1,2-dihexadecanoyl-sn-glycero-3-phophoethanolamine (TR-DHPE) in a bilayer of 488 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipids. We found binding between TR-DHPE and DPPC caused by electrostatic interactions. On average, TR-DHPE is bound to 1.2 DPPC molecules. Binding reduced the diffusion coefficient of TR-DHPE by 34% relative to unlabeled DPPC molecules. We estimate that binding would lead to a ∼ 5 °C increase in the liquid to liquid-ordered transition temperature of a ternary lipid system. These results emphasize the importance of considering the impact of fluorescence labeling when interpreting experimental results.

Fluorescent membrane probes' behavior in lipid bilayers: insights from molecular dynamics simulations

Fluorescence spectroscopy and microscopy have been used as tools to study membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Two major points of concern arise regarding this matter, namely the incomplete understanding of the probe behavior inside the bilayer and the perturbation of the latter resulting from probe incorporation. To this effect, molecular dynamics (MD) simulations, by providing detailed atomic-scale information, represent a valuable way to characterize the location and dynamics of bilayer-inserted membrane probes, as well as the magnitude of perturbation they induce on the host lipid structure, and several important classes of reporter molecules have been studied in recent years. This article reviews the state of the art of MD simulations of bilayer-inserted fluorescent probes, focusing on the information that has been obtained from previous studies and hinting at future perspectives in this rapidly emerging field.

Statistical thermodynamics of biomembranes

An overview of the major issues involved in the statistical thermodynamic treatment of phospholipid membranes at the atomistic level is summarized: thermodynamic ensembles, initial configuration (or the physical system being modeled), force field representation as well as the representation of long-range interactions. This is followed by a description of the various ways that the simulated ensembles can be analyzed: area of the lipid, mass density profiles, radial distribution functions (RDFs), water orientation profile, deuterium order parameter, free energy profiles and void (pore) formation; with particular focus on the results obtained from our recent molecular dynamic (MD) simulations of phospholipids interacting with dimethylsulfoxide (Me(2)SO), a commonly used cryoprotective agent (CPA).

Time-dependent stokes shifts of fluorescent dyes in the hydrophobic backbone region of a phospholipid bilayer: combination of fluorescence spectroscopy and ab initio calculations

We explored the time-dependent Stokes shifts of fluorescent dyes containing an anthroyloxy chromophore (2-AS, 9-AS, and 16-AP) in bilayers composed of palmitoyl-oleoyl-phosphatidylcholine. The obtained data revealed a nontrivial solvation response of these dyes, which are located in the backbone region of the bilayer with a gradually increasing depth. For comparison, steady-state emission spectra in the neat solvents of various polarities and viscosities were also recorded. The results indicate that on the short picosecond time scale the AS dyes undergo complex photophysics including formation of states with a charge-transfer character. This observation is supported by ab initio calculations of the excited states of 9-methylanthroate. The slower nanosecond part of the relaxation process can be attributed to the solvation response of the dyes. A slowdown in solvent relaxation is observed upon moving toward the center of the bilayer. A mechanism similar to preferential solvation present in the mixture of a polar and nonpolar solvent is considered to explain the obtained data.

Dynamics imaging of lipid phases and lipid-marker interactions in model biomembranes

Biomembranes are complex systems that regulate numerous biological processes. Lipid phases that constitute these membranes influence their properties and transport characteristics. Here, we demonstrate the potential of short-range dynamics imaging (excited-state lifetime, rotational diffusion, and order parameter) as a sensitive probe of lipid phases in giant unilamellar vesicles (GUVs). Liquid-disordered and gel phases were labeled with Bodipy-PC at room temperature. Two-photon fluorescence lifetime imaging microscopy of single-phase GUVs reveals more heterogeneity in fluorescence lifetimes of Bodipy in the gel phase (DPPC: 3.8+/-0.6 ns) as compared with the fluid phase (DOPC: 5.2+/-0.2 ns). The phase-specificity of excited-state lifetime of Bodipy-PC is attributed to the stacking of ordered lipid molecules that possibly enhances homo-FRET. Fluorescence polarization anisotropy imaging also reveals distinctive molecular order that is phase specific. The results are compared with DiI-C12-labeled fluid GUVs to investigate the sensitivity of our fluorescence dynamics assay to different lipid-marker interactions. Our results provide a molecular perspective of lipid phase dynamics and the nature of their microenvironments that will ultimately help our understanding of the structure-function relationship of biomembranes in vivo. Furthermore, these ultrafast excited-state dynamics will be used for molecular dynamics simulation of lipid-lipid, lipid-marker and lipid-protein interactions.

Influence of DPH on the structure and dynamics of a DPPC bilayer

We have conducted extensive molecular dynamics (MD) simulations together with differential scanning calorimetry (DSC) and nuclear magnetic resonance (NMR) experiments to quantify the influence of free 1,6-diphenyl-1,3,5-hexatriene (DPH) fluorescent probes on the structure and dynamics of a dipalmitoylphosphatidylcholine bilayer. Atomistic MD simulations show that in the membrane-water interface the influence of DPH is minor, whereas in the acyl-chain region DPH gives rise to major perturbations. In the latter case, DPH is found to influence a wide range of membrane properties, such as the packing and ordering of hydrocarbon tails and the lateral diffusion of lipid molecules. The effects are prominent but of local nature, i.e., the changes observed in the properties of lipid molecules are significant in the vicinity of DPH, but reduce rapidly as the distance from the probe increases. Long-range perturbations due to DPH are hence not expected. Detailed DSC and (2)H NMR measurements support this view. DSC shows only subtle perturbation to the cooperative behavior of the membrane system in the presence of DPH, and (2)H NMR shows that DPH gives rise to a slight increase in the lipid chain order, in agreement with MD simulations. Potential effects of other probes such as pyrene are briefly discussed.

Molecular dynamic simulation of the hydration and diffusion of chloride ions from bulk water to polypyrrole matrix

A molecular dynamic simulation of wet polypyrrole film was carried out, in both oxidized and reduced state. The system was modeled by two layers of polypyrrole, water and chloride ions (as counterions required for charge balance in the oxidized state) in atomic detail to provide an insight into some dynamic and steady properties of the system. Our simulations pointed to a swelling of the polymer matrix after oxidation due to electrostatic repulsions between charged sites of the oxidized polypyrrole, followed by penetration of the polypyrrole by counterions to maintain the electroneutrality of the system. Associated with this penetration of counterions toward the core of the oxidized polypyrrole, dehydration of the counterions was observed. This dehydration was compensated (in part) by a strong coordination with the charged sites of the polymer. The remaining hydrophobicity inside the polymer also contributed to the dehydration of these counterions. The translational diffusion coefficient of chloride ions was also calculated at different positions of the polypyrrole/water interface, from bulk water to the inner polymer matrix. A value of 4.1 x 10(-5) cm(2) s(-1) was measured in the bulk water compared to 5 x 10(-7) cm(2) s(-1) inside the polymer, representing a diminution of two orders of magnitude for the translational diffusion coefficient from bulk water to the core of a oxidized polypyrrole matrix. These results were in good agreement with experimental data.

Simulation of the distribution and diffusion of a rigid amphipathic particle embedded in a model membrane

We simulate, by Brownian dynamics, the distribution, orientation and diffusion of a rigid molecule, represented as a dumbbell, with amphipathic nature, embedded in a model membrane. The significant features of a biological membrane are reproduced by means of a Maier-Saupe orienting potential, an enclosing potential and a lipophobic potential. We also evaluate the equilibrium quantities, such as order parameter, and dynamic features, such as rotational or translational diffusivity, of the embedded molecule in terms of the system parameters and compare the obtained results with those obtained from model independent theory.