DMPC Bilayers Research Articles

Ripple and Gel Phases of Saturated Phosphocholine Bilayers Investigated with Simulations

Lipid bilayers with saturated acyl chains typically are in a liquid crystalline (Lα) phase, but can condense to a ripple (Pβ) or gel (Lβ) phase. We focused on 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dipalmitoyl-sn-glycero-phosphocholine (DPPC) lipid bilayers and their mixtures to characterize these lipid phases. MD simulations with the CHARMM36 lipid force field accurately predict the main transition temperature of DMPC and DPPC bilayers. Our MD simulations focused on the less-characterized Pβ phase and compared to x-ray experiments. The Pβ major arm has similar structure to that of the Lβ, while the thinner minor arm has interdigitated chains and the transition region between these two regions has large chain splay and disorder. The length of these major/minor arms are in reasonable agreement with x-ray experiments based on several μs of simulation. The Lβ phase form a chain tilt and lipid packing in good agreement with experiment. This work demonstrates that the CHARMM36 lipid force field can accurately represent more condensed phases and provides insight into the complex structure of the ripple phase.

Simulations of general anaesthetics in membranes at raised pressures: the search for mechanisms for pressure reversal of general anaesthetics

ABSTRACT Experiments have shown that general anaesthetics lose their efficacy at pressures of around 20 MPa, but their efficacy is recovered at pressures of around 40 MPa. Molecular dynamics simulations of the general anaesthetic halothane in DMPC or POPC bilayers show that halothane aggregates inside the membrane at 20 MPa, but not at atmospheric pressure, nor at 40 MPa. The parallelism in effects suggests that aggregation could conceivably be the mechanism for pressure reversal. Further molecular dynamics simulations of another general anaesthetic, isoflurane, in POPC show that isoflurane does not aggregate at 20 MPa. This and other quantitative considerations show that general anaesthetic aggregation inside the membrane could not be the mechanism for pressure reversal.

Effect of Cholesterol and Curcumin on Ordering of DMPC Bilayers

In this work, we compared the effects of curcumin and cholesterol directly competing to insert into the DMPC lipid bilayer during bilayer formation from an initially non-ordered state. 2H and 14N nuclear magnetic resonance spectroscopy showed that curcumin is not embedded deep in the lipid bilayer and interacts mainly with the head group of the lipid. In a more complex system of DMPC/CHOL/CUR, curcumin amplifies the effect of cholesterol on the ordering of lipid acyl chains.

Effect of polyols on the DMPC lipid monolayers and bilayers

In this study, the effect of polyols, erythritol, xylitol, mannitol, on a model membrane systems composed of DMPC was investigated using differential scanning calorimetry and Fourier transform infrared spectroscopy. Generally, it is considered that polyols possess strong hydrophilic properties, and either does not interact with the hydrophobic environment at all, or these interactions are very weak. To better understand the mutual interactions between polyols and the lipid system, the Langmuir technique was used to examine the molecular organization of monolayers and to calculate their thickness in the presence of polyols at the subphase. The detailed description of the interactions between polyols and DMPC molecules was complemented by the analysis of the morphology of monolayers with the application of Brewster angle microscopy. From ATR FTIR, the significant spectral shift is observed only for the PO2− stretching band, which correlates strongly with the polyol chain-length. The longer the polyol chain, the weaker the observed interactions with lipid molecules. The most important findings, obtained from thickness measurements, reveal that short-chain polyols may prevent the formation of bilayers by the DMPC molecules under high surface pressure. The changes in the organization of DMPC monolayers on the surface, as visualized by Brewster angle microscopy, showed that the domains observed for phospholipid film spread on pure water differ substantially from those containing polyols in the subphase.

Interaction of the Saponin Aescin with Ibuprofen in DMPC Model Membranes.

In the present work, we study the interaction of the saponin aescin with the nonsteroidal anti-inflammatory drug (NSAID) ibuprofen at concentrations of 1.2-2.5 mM. These amounts are higher than those usually used for medication (10-300 μM) to show possible structures and formulations for orally absorbed drug delivery systems. It is shown how the interaction of both substances, separately or together, alters the thermotropic phase behavior of the 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) bilayer in the presence of different amounts of aescin, ranging from 20 μM to 1 mM. The methods of choice are differential scanning calorimetry (DSC), and additionally wide-angle (WAXS) and small-angle X-ray scattering (SAXS). We found that these two additives, aescin and ibuprofen, alter the temperature-dependent structural appearance of the DMPC membrane depending on the aescin and drug content. The presence of the saponin and the drug become visible on different length scales, i.e., ranging from a global structural change to inner-membrane interactions. DSC reveals that the drug and saponin alter the cooperativity of the DMPC phase transition in a concentration-dependent manner. Furthermore, there is a significant difference between the drug-containing compared to the drug-free systems. By WAXS, we could resolve that aescin reverses the strong impact of ibuprofen on the diffraction peak of DMPC. Both molecules interact strongly with the phospholipid headgroups. This becomes visible in a changing area per lipid and shifting phase transition to higher temperatures. SAXS experiments reveal that the addition of ibuprofen leads to major morphological changes in the phospholipid bilayer. SAXS experiments performed on representative samples do not only cover the drug-saponin interaction within the bilayer from the structural perspective but also confirm the visually observed macroscopic concentration and temperature-dependent phase behavior. Vesicular shape of extruded samples is conserved at low aescin contents. At intermediate aescin content, aggregation between vesicles occurs, whereby the strength of aggregation is reduced by ibuprofen. At high aescin contents, DMPC bilayers are solubilized. The kind of formed structures depends on temperature and drug content. At low temperature, separated bilayer sheets are formed. Their size increases with ibuprofen in a concentration-dependent manner. At high temperature, the drug-free system reorganizes into stacked sheets. Whereas sheets at 5 mol % ibuprofen close to vesicles, the ones with 10 mol % of the drug increase massively in size. Altogether, ibuprofen was found to rather enhance than inhibit structural and thermotropic membrane modifications induced by the aescin on the DMPC model membrane.

Confocal-Raman Microscopy Characterization of Supported Phospholipid Bilayers Deposited on the Interior Surfaces of Chromatographic Silica.

A common approach to exploring the structure and dynamics of biological membranes is through the deposition of model lipid bilayers on planar supports by Langmuir-trough or vesicle-fusion methods. Planar-supported lipid bilayers have been shown to exhibit structure and properties similar to those of lipid-vesicle membranes and are suitable for biosensing applications. Investigations using these planar-membrane models are limited to high-sensitivity methods capable of detecting a small population of molecules at the interface between a planar support and aqueous solution. In this work, we present evidence that supported-lipid bilayers can be deposited by vesicle fusion onto the interior surfaces throughout the wide-pore network of chromatographic silica particles. The thickness of a 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) film and headgroup spacing are consistent with a single bilayer of DMPC deposited onto the pore surfaces. The high specific surface area of these materials generates phospholipid concentrations easily detected by confocal-Raman microscopy within an individual particle, which allows the structure of these supported bilayers to be investigated. Raman spectra of porous-silica-supported DMPC bilayers are equivalent to spectra of DMPC vesicle membranes, both above and below their melting phase transitions, suggesting comparable phospholipid organization and bilayer structure. These porous-silica-supported model membranes could share benefits that planar-supported lipid bilayers bring to biosensing applications, but in a material that overcomes the limited surface area of a planar support. To test this concept, the potential of these porous-silica-supported lipid bilayers as high-surface-area platforms for label-free Raman-scattering-based protein biosensing is demonstrated with detection of concanavalin A selectively binding to a lipid-immobilized mannose target.

Making Soft Magnetically-Orientable Membranes: An Alternative to Bicelles

Model lipid membranes have long been employed in a variety of biophysical techniques to circumvent the complexity of natural membranes when studying their constituents or interactions. The development of magnetically-oriented bilayers, such as DMPC/DHPC bicelles, has been notably important in solid-state NMR where they facilitate the study of membrane interactions, or provide valuable information on the structure and orientation of membrane peptides. Bicelles can be prepared through PC bilayer stabilisation by a variety of detergents, providing that physicochemical requirements are met by adjusting detergent to lipid ratio, concentration, and temperature. In this work we propose an alternative to bicelles, obtained by softening PC liposomes with a gentle surfactant. We show that polysorbate 80 (Tween 80) mixed to DMPC and DPPC bilayers leads to elongated oriented structures which maintain their alignment over a wide range of lipid-to-detergent molar ratios (2<q<13) and temperatures (∼25-80oC), as demonstrated by 31P and 2H solid-state NMR. The orientation quality of these “elastosomes”, determined by spectral simulations, is comparable to traditional bicelles, although they display a different morphology. Moreover, we show that the magnetic orientation can also be flipped by addition of lanthanides, and that transmembrane peptides can be studied. The Tween-based approach for oriented model membranes preparation is promising, and it should in principle be applicable to membrane bilayers of higher complexity - including native membranes - thus bridging the gap between model and intact membranes.

A molecular dynamics model for glycosylphosphatidyl-inositol anchors: "flop down" or "lollipop"?

We present a computational model of glycosylphosphatidyl-inositol (GPI) anchors for molecular dynamics studies. The model is based on state-of-the-art biomolecular force fields from the AMBER family, employing GLYCAM06 for carbohydrates and Lipid14 to represent fatty acid tails. We construct an adapted glycero-phosphatidyl-inositol unit to establish a seamless transition between the two domains of atom types. This link can readily be extended into a broad variety of GPI variants by applying either domain's building block scheme. As test cases, selected GPI fragments inserted into DMPC and POPC bilayer patches are considered. Our results suggest that the glycan part of the GPI anchor interacts strongly with the lipid head groups, partially embedding the carbohydrate moieties. This behaviour is supported by the conformational preferences of the GPI anchor, which in particular are conveyed by the strong interactions between the proximal amine and phosphate groups. In a similar way we can conclude that the extension of the anchor away from the lipid bilayer surface that could prevent the contact of the membrane with an attached protein ("lollipop picture") is quite unfavorable. Indeed, when attaching green fluorescent protein to the GPI anchor, it is found to reside close to bilayer surface all the time, and the rather flexible phosphoethanolamine linker governs the extent to which the protein directly interacts not only with the head groups, but also with its own GPI core.

Confocal mapping of myelin figures with micro-Raman spectroscopy

We employ confocal micro-Raman spectroscopy (CMRS) with submicron spatial resolution to study the myelin structures (cylindrical lamellae) composed of nested surfactant C12E3 or lipid DMPC bilayers. The CMRS mapping indicates that for a straight C12E3 myelin, the surfactant concentration increases with the myelin width and is higher in the center region than in the peripheral region. For a curved C12E3 myelin, the convex side has a higher surfactant concentration than the corresponding concave side. The spectrum of DMPC myelins undergoes a qualitative change as the temperature increases above 60 °C, suggesting that the surfactant molecules may be damaged. Our work demonstrates the utility of CMRS in bio-soft material research.

Surface charge and overlayer pH influence the dynamics of supported phospholipid films

Understanding the thermodynamics and kinetics of interactions between model lipid bilayers and planar supports is of critical importance in the furtherance of biosensing and the creation of biomimetic devices. Evaluating these properties can be accomplished through understanding the diffusional properties of the bilayer constituents. In this report, the dynamics of a model DMPC bilayer supported on a phosphorylated silica surface are studied in the presence and absence of interfacial Ca2+ as a function of pH of the aqueous overlayer. The data for this system reveal the importance of the balance of ionic interactions between the interfacial species, and the dependence of the diffusional, kinetic and thermodynamic properties of the system on pH. The thermodynamic data suggest that interactions between the bilayer and surface are mediated enthalpically rather than entropically.

Experimental and theoretical studies of emodin interacting with a lipid bilayer of DMPC.

Emodin is one of the most abundant anthraquinone derivatives found in nature. It is the active principle of some traditional herbal medicines with known biological activities. In this work, we combined experimental and theoretical studies to reveal information about location, orientation, interaction and perturbing effects of Emodin on lipid bilayers, where we have taken into account the neutral form of the Emodin (EMH) and its anionic/deprotonated form (EM-). Using both UV/Visible spectrophotometric techniques and molecular dynamics (MD) simulations, we showed that both EMH and EM- are located in a lipid membrane. Additionally, using MD simulations, we revealed that both forms of Emodin are very close to glycerol groups of the lipid molecules, with the EMH inserted more deeply into the bilayer and more disoriented relative to the normal of the membrane when compared with the EM-, which is more exposed to interfacial water. Analysis of several structural properties of acyl chains of the lipids in a hydrated pure DMPC bilayer and in the presence of Emodin revealed that both EMH and EM- affect the lipid bilayer, resulting in a remarkable disorder of the bilayer in the vicinity of the Emodin. However, the disorder caused by EMH is weaker than that caused by EM-. Our results suggest that these disorders caused by Emodin might lead to distinct effects on lipid bilayers including its disruption which are reported in the literature.

Understanding the Enhanced Magnetic Response of Aminocholesterol Doped Lanthanide-Ion-Chelating Phospholipid Bicelles.

Cholesterol (Chol-OH) and its conjugates are powerful molecules for engineering the physicochemical and magnetic properties of phospholipid bilayers in bicelles. Introduction of aminocholesterol (3β-amino-5-cholestene, Chol-NH2) in bicelles composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and the thulium-ion-chelating phospholipid 1,2-dimyristoyl-sn-glycero-3-phospho-ethanolamine-diethylene triaminepentaacetate (DMPE-DTPA/Tm3+) results in unprecedented high magnetic alignments by selectively tuning the magnetic susceptibility Δχ of the bilayer. However, little is known on the underlying mechanisms behind the magnetic response and, more generally, on the physicochemical forces governing a Chol-NH2 doped DMPC bilayer. We tackled this shortcoming with a multiscale bottom-up comparative investigation of Chol-OH and Chol-NH2 mixed with DMPC. First, simplified monolayer models on a Langmuir trough were employed to compare the two steroid molecules at various contents in DMPC. In a second step, a molecular dynamics (MD) simulation allowed for a more representative model of the bicelle bilayer while monitoring the amphiphiles and their interactions on the molecular level. In a final step, we moved away from the models and investigated the effect of temperature on the structure and magnetic alignment of Chol-NH2 doped bicelles by SANS. The DMPC/steroid monolayer studies showed that Chol-OH induces a larger condensation effect than Chol-NH2 at steroid contents of 16 and 20 mol %. However, this tendency was inversed at steroid contents of 10, 30, and 40 mol %. Although the MD simulation with 16 mol % steroid revealed that both compounds induce a liquid-ordered state in DMPC, the bilayer containing Chol-NH2 was much less ordered than the analogous system containing Chol-OH. Chol-NH2 underwent significantly more hydrogen bonding interactions with neighboring DMPC lipids than Chol-OH. It seems that, by altering the dynamics of the hydrophilic environment of the bicelle, Chol-NH2 changes the crystal field and angle of the phospholipid-lanthanide DMPE-DTPA/Tm3+ complex. These parameters largely determine the magnetic susceptibility Δχ of the complex, explaining the SANS results, which show significant differences in magnetic alignment of the steroid doped bicelles. Highly magnetically alignable DMPC/Chol-NH2/DMPE-DTPA/Tm3+ (molar ratio 16:4:5:5) bicelles were achieved up to temperatures of 35 °C before a thermoreversible rearrangement into nonalignable vesicles occurred. The results confirm the potential of Chol-NH2 doped bicelles to act as building blocks for the development of the magnetically responsive soft materials of tomorrow.

Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations

Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant. An extended sampling simulation provided qualitative results and showed the same orientation to be a global minimum of free energy. The secondary structure of HZ was characterized, and it was found to be located in the 310-helical family. The specific challenges of computer simulation of nonpolar peptides are discussed briefly.

On the structure and dynamics of water associated with single-supported zwitterionic and anionic membranes.

We have used high-resolution quasielastic neutron scattering (QENS) to investigate the dynamics of water molecules (time scale of motion ∼10-11-10-9 s) in proximity to single-supported bilayers of the zwitterioniclipid DMPC (1,2-dimyristoyl-sn-glycero-3-phosphorylcholine) and the anionic lipid DMPG (1,2-dimyristoyl-sn-glycero-3-phosphoglycerol) in the temperature range 160-295 K. For both membranes, the temperature dependence of the intensity of neutronsscattered elastically and incoherently from these samples indicates a series of freezing/melting transitions of the membrane-associated water, which have not been observed in previous studies of multilayer membranes. We interpret these successive phase transitions as evidence of different types of water that are common to the two membranes and which are defined by their local environment: bulk-like water located furthest from the membrane and two types of confined water in closer proximity to the lipids. Specifically, we propose a water type termed "confined 2" located within and just above the lipid head groups of the membrane and confined 1 water that lies between the bulk-like and confined 2 water. Confined 1 water is only present at temperatures below the freezing point of bulk-like water. We then go on to determine the temperature dependence of the translational diffusion coefficient of the water associated with single-supported DMPG membranes containing two different amounts of water as we have previously done for DMPC. To our knowledge, there have been no previous studies comparing the dynamics of water in proximity to zwitterionic and anionic membranes. Our analysis of the water dynamics of the DMPG and DMPC membranes supports the classification of water types that we have inferred from their freezing/melting behavior. However, just as we observe large differences in the freezing/melting behavior between these model membranes for the same water type, our measurements demonstrate variation between these membranes in the dynamics of their associated water over a wide temperature range. In particular, there are differences in the diffusive motion of water closest to the lipid head groups. Previously, QENS spectra of the DMPC membranes have revealed the motion of water bound to the lipid head groups. For the DMPG membrane, we have found some evidence of such bound water molecules; but the signal is too weak for a quantitative analysis. However, we observe confined 2 water in the DMPG membrane to undergo slow translational diffusion in the head group region, which was unobserved for DMPC. The weak temperature dependence of its translational diffusion coefficient allows extrapolation to physiological temperatures for comparison with molecular dynamics simulations.

Interaction of Different Divalent Metal Ions with Lipid Bilayer: Impact on the Encapsulation of Doxorubicin by Lipid Bilayer and Lipoplex Mediated Deintercalation.

In this article, we investigate the influence of different metal ions (Ca2+, Mg2+, and Zn2+) on binding of an anticancer drug doxorubicin (DOX) to DMPC bilayer and lipoplex mediated deintercalation of DOX from DOX-DNA complex. Our study reveals that lipid bilayer in the presence of different metal ions displays much higher binding affinity toward DOX than bare lipid bilayer does. Further, this affinity for a particular metal ion increases linearly with metal ion concentration. The steady state and time-resolved fluorescence studies reveal that binding of DOX with lipid bilayer in the presence of different metal ions varies in the order of Ca2+> Mg2+> Zn2+. The rotational relaxation of DOX in the presence of different metal ions takes place in the same order. We explain these phenomena in the light of alteration of the physical properties brought about by metal ions. Moreover, we find that binding pattern of metal ions with lipid head groups influences the intake of DOX in lipid bilayer. We exploit the binding of DOX with bilayer to study the deintercalation of DOX from DOX-DNA complex. We observe that with increase in metal ion concentration the deintercalation increases. Among all metal ions, Ca2+ appears to be most effective in deintercalation compared to other metal ions. The time-resolved fluorescence anisotropy and circular dichroism measurements indicate that in the presence of Ca2+, lipid bilayer offer strongest interaction with DNA while the same is weakest for Zn2+. This explains the highest percentage of deintercalation of DOX from drug-DNA complex in the presence of Ca2+. Overall the present study demonstrates a new strategy that binding of drug molecules with lipid bilayer and deintercalation of the same from drug-DNA complex can be tuned by modulation of lipid bilayer with different metal ions and their concentration.

Structure and Dynamics of Nanopore-Confined Membrane Proteins are Affected by Bilayer Lipid Composition

Self-assembled nanotubular lipid bilayers confined within macroscopically aligned high-density homogeneous nanopore array structure of anodic aluminum oxide (AAO) membranes exhibit a high degree of macroscopic alignment that facilitates their studies by oriented sample solid state (OS SS) NMR and spin-labeling EPR methods. The principal advantages of the lipid nanotube arrays are in the applicability of this method to essentially any lipid composition and a tolerance of the macroscopic alignment to a wide range of environmental conditions such as, e.g., temperature, pH, and ionic strength. Here we describe 1) a recent progress in reconstructing small pore-forming and transmembrane peptides as well as large membrane protein complexes, such as photosynthetic reaction center (RC) protein in inorganic nanopores and 2) utilization of this technology to study lipid-induced changes in protein conformations by magnetic resonance methods. Specifically, by using OS SS NMR we have shown that the tilt and α-helix kink angles of Pf1 coat protein are affected by the bilayer composition on example of DOPC, POPC and DMPC bilayers. Effects of unsaturated lipids on Pf1 dynamics as evidenced by the changes in the linewidths in the Pf1 spectra are also reported. We relate these changes to the bilayer fluidity and its effects on the uniaxial rotational diffusion of the protein within the membrane. Further, we demonstrate the use of DEER spectroscopy to obtain long-range distance constraints for membrane protein systems incorporated into lipid nanotubes. The improved nanopore alignment technique described here provides a general method for studying lipid-induced structural conformations of membrane proteins under physiologically relevant conditions by magnetic resonance. Supported by U.S. DOE contract No. DE-FG02-02ER15354 to A.I.S. and NSF MRI 1229547 to A.A.N.

The Interplay of Structure and Dynamics in Mixed Lipid Bilayers

The implication of lipids in membrane mediated processes has motivated significant theoretical and experimental research interest to understand the functional significance of lipid chemical structure variations on the biomembrane structure and dynamics. In particular, hydrophobic mismatch between lipids with different acyl chain lengths is expected to play an important role in determining the local membrane structure and collective membrane dynamics. Herein we investigated these phenomena in large unilamellar vesicles composed of binary mixtures of lipids with a 4 carbon mismatch in tail length, dimyristoylphosphatidylcholine (DMPC, 14:0 C) and distearoylphosphatidycholine (DSPC, 18:0 C), using neutron scattering techniques. Structural studies using small angle neutron scattering (SANS) revealed that the mixed lipid bilayers were thinner than expected for a simple composition-weighted average of the pure component bilayers. The structural differences were accompanied by dramatic differences in the mixed lipid membrane dynamics. Neutron spin echo spectroscopy (NSE) experiments showed that the mixed lipid bilayers were more dynamic than their single component analogs, with the mixed bilayers having a lower bending modulus and increased thickness fluctuation amplitude than the pure DMPC or DSPC bilayers. Both of these enhanced dynamics were consistent with a decrease in the area expansion modulus of the mixed systems. Together our results demonstrate the influence of lipid composition on the bilayer biophysical properties and highlight the complex interplay between structure and dynamics in lipid membranes.

Interactions of Carbon Nanotubes Stabilized by Selected Gemini Surfactants with Model Biomembranes

Thanks to the extraordinary mechanical strength and high electrical conductivity multiwalled carbon nanotubes are currently used in electronics, medicine (as biomedical sensors, transporters or drugs) as well as in the production of lightweight and durable construction. The aim of this study was to determine the possibility to use different cationic gemini surfactants with different spacer lengths or alkyl chain lengths in more efficient systems for dispersing nanostructures in aqueous solutions. The most important advantages of these systems are their non-immunogenic, biocompatible properties and generally low toxicity . Therefore nanotubes, surrounded by surfactants, have the potential to interact with biological membranes. For this purpose we studied the influence of dispersed CN solution on the phase behavior of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) - a phospholipid most often present in membranes of nerve cells. The microstructure of the stable suspension of carbon nanotubes was investigated using high-resolution Transmission Electron Microscopy and Atomic Force Microscopy. Fourier transform infrared (FTIR) spectroscopy and differential scanning calorimetry (DSC) were used to analyze the influence of surfactants studied, used for CN dispersion, on the phase behavior of DMPC bilayers. A series of measurements of toxicity of these systems were performed in HeLa and fibroblast cell cultures. This work was supported by the Ministry of Science and Higher Education, within the project “Najlepsi z najlepszych!” dec. DIR.5210.352016/1.

How does ytterbium chloride interact with DMPC bilayers? A computational and experimental study.

Lanthanide salts have been studied for many years, primarily in Nuclear Magnetic Resonance (NMR) experiments of mixed lipid-protein systems and more recently to study lipid flip-flop in model membrane systems. It is well recognised that lanthanide salts can influence the behaviour of both lipid and protein systems, however a full molecular level description of lipid-lanthanide interactions is still outstanding. Here we present a study of lanthanide-bilayer interactions, using molecular dynamics computer simulations, fluorescence electrostatic potential experiments and nuclear magnetic resonance. Computer simulations reveal the microscopic structure of DMPC lipid bilayers in the presence of Yb3+, and a surprising ability of the membranes to adsorb significant concentrations of Yb3+ without disrupting the overall membrane structure. At concentrations commonly used in NMR experiments, Yb3+ ions bind strongly to 5 lipids, inducing a small decrease of the area per lipid and a slight increase of the ordering of the aliphatic chains and the bilayer thickness. The area compressibility modulus increases by a factor of two, with respect to the free-salt case, showing that Yb3+ ions make the bilayer more rigid. These modifications of the bilayer properties should be taken into account in the interpretation of NMR experiments.

Energetic and Dynamic Analysis of Transport of Na+ and K+ through a Cyclic Peptide Nanotube in Water and in Lipid Bilayers.

Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na+ and K+ are calculated to elucidate the translocation of ions through a cyclic peptide nanotube, composed of 8 × cyclo[-(d-Leu-Trp)4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that favorable interactions of the cations with the CPN as well as the lipid bilayer and dehydration free energy penalties are two major competing factors which determine the free energy surface for ion transport through CPNs both in water and in lipid bilayers, and that the selectivity of CPNs to cations mainly arises from favorable interaction energies of cations with CPNs and lipid bilayers that are more dominant than the dehydration penalties. Calculations of the position-dependent diffusion coefficients and dynamic friction kernels of the cations indicate that the dehydration process along with the molecular rearrangements occurring outside the channel and the coupling of the ion motions with the chain-structured water movements inside the channel lead to a decrease of the diffusion coefficients far away from the channel entrance and also reduced coefficients inside the channel. The PMF and diffusivity profiles for Na+ and K+ reveal that the energetics of ion transport through the CPN are governed by global interactions of ions with all the components in the system, while the diffusivity of ions through the channel is mostly determined by local interactions of ions with the confined water molecules inside the channel. Comparison of Na+ and K+ ion distributions based on overdamped Brownian dynamics simulations based on the PMF and diffusivity profiles with the corresponding results from molecular dynamics shows good agreement, indicating accuracy of the Bayesian inference method for determining diffusion coefficients in this application. In addition, this work shows that position-dependent diffusion coefficients of ions are required to explain the dynamics and conductance of ions through the CPN properly.