Interaction of cationic antiseptics with cardiolipin-containing model bacterial membranes

Plasma membrane is one of the major targets for cationic antiseptics (CA). The study was aimed to assess molecular effects of CAs of different chemical classes on cardiolipin-containing regions of bacterial plasma membranes. The study was carried out using coarse-grained molecular modeling. Interaction of CAs, such as miramistin, chlorhexidine, picloxidine, and octenidine, with cardiolipin-containing bilayer was assessed based on the CA coarse-grained models. CAs reduced lipid lateral diffusion coefficients and increased the membrane area per lipid. All CAs, except miramistin, reduced the lipid fatty acid chain order parameters. Adding octenidine at a CA : lipid ratio of 1 : 4 resulted in cardiolipin clustering with subsequent pulling the neutral phosphatidylethanolamine molecules out of the model bilayer. It was found that CАs have the potential for sorption to lipid bilayer, causing clustering of negatively charged lipids. Antiseptic octenidine causes formation of cardiolipin microdomains. Abnormal lateral lipid distribution together with pulling out phosphatidylethanolamine molecules can result in increased lipid bilayer permeability. The most significant reduction of cardiolipin lateral diffusion coefficient by 2.8 ± 0.4 times was observed in the presence of CA chlorhexidine at an antiseptic : lipid ratio of 1 : 4.

Vesicle Viewer: Online Analysis of Small Angle Scattering from Lipid Vesicles

In this project, we developed an internet-based application, called Vesicle Viewer, to visualize and analyze small angle scattering data generated in the study of lipid bilayers. Vesicle Viewer models SAS data using the EZ-SDP model. In this way, key bilayer structural parameters, such as area per lipid and bilayer thickness, can be easily determined. This application primarily uses Django, a python package specialized for the development of robust web applications. In addition, several other libraries are used to support the more technical aspects of the project – notable examples are MatPlotLib (for graphs) and NumPy (for calculations). Without the barrier of downloading and installing software, the development of this web-based application will allow scientists all over the world to take advantage of this solution, regardless of their preferred operating system.

Vesicle Viewer: Online Analysis of Small Angle Scattering from Lipid Vesicles

In this project, we developed an internet-based application, called Vesicle Viewer, to visualize and analyze small angle scattering data generated in the study of lipid bilayers. Vesicle Viewer models SAS data using the EZ-SDP model. In this way, key bilayer structural parameters, such as area per lipid and bilayer thickness, can be easily determined. This application primarily uses Django, a python package specialized for the development of robust web applications. In addition, several other libraries are used to support the more technical aspects of the project – notable examples are MatPlotLib (for graphs) and NumPy (for calculations). Without the barrier of downloading and installing software, the development of this web-based application will allow scientists all over the world to take advantage of this solution, regardless of their preferred operating system.

Microscopic Interactions of Melatonin, Serotonin and Tryptophan with Zwitterionic Phospholipid Membranes

The interactions at the atomic level between small molecules and the main components of cellular plasma membranes are crucial for elucidating the mechanisms allowing for the entrance of such small species inside the cell. We have performed molecular dynamics and metadynamics simulations of tryptophan, serotonin, and melatonin at the interface of zwitterionic phospholipid bilayers. In this work, we will review recent computer simulation developments and report microscopic properties, such as the area per lipid and thickness of the membranes, atomic radial distribution functions, angular orientations, and free energy landscapes of small molecule binding to the membrane. Cholesterol affects the behaviour of the small molecules, which are mainly buried in the interfacial regions. We have observed a competition between the binding of small molecules to phospholipids and cholesterol through lipidic hydrogen-bonds. Free energy barriers that are associated to translational and orientational changes of melatonin have been found to be between 10–20 kJ/mol for distances of 1 nm between melatonin and the center of the membrane. Corresponding barriers for tryptophan and serotonin that are obtained from reversible work methods are of the order of 10 kJ/mol and reveal strong hydrogen bonding between such species and specific phospholipid sites. The diffusion of tryptophan and melatonin is of the order of 10−7 cm2/s for the cholesterol-free and cholesterol-rich setups.

Melittin Induces Local Order Changes in Artificial and Biological Membranes as Revealed by Spectral Analysis of Laurdan Fluorescence

Antimicrobial peptides (AMPs) are a class of molecules widely used in applications on eukaryotic and prokaryotic cells. Independent of the peptide target, all of them need to first pass or interact with the plasma membrane of the cells. In order to have a better image of the peptide action mechanism with respect to the particular features of the membrane it is necessary to better understand the changes induced by AMPs in the membranes. Laurdan, a lipid membrane probe sensitive to polarity changes in the environment, is used in this study for assessing changes induced by melittin, a well-known peptide, both in model and natural lipid membranes. More importantly, we showed that generalized polarization (GP) values are not always efficient or sufficient to properly characterize the changes in the membrane. We proved that a better method to investigate these changes is to use the previously described log-normal deconvolution allowing us to infer other parameters: the difference between the relative areas of elementary peak (ΔSr), and the ratio of elementary peaks areas (Rs). Melittin induced a slight decrease in local membrane fluidity in homogeneous lipid membranes. The addition of cholesterol stabilizes the membrane more in the presence of melittin. An opposite response was observed in the case of heterogeneous lipid membranes in cells, the local order of lipids being diminished. RS proved to be the most sensitive parameter characterizing the local membrane order, allowing us to distinguish among the responses to melittin of both classes of membrane we investigated (liposomes and cellular membranes). Molecular simulation of the melittin pore in homogeneous lipid bilayer suggests that lipids are more closely packed in the proximity of the melittin pore (a smaller area per lipid), supporting the experimental observation.

Coarse-grained implicit solvent lipid force field with a compatible resolution to the Cα protein representation

Biological membranes have been prominent targets for coarse-grained (CG) molecular dynamics (MD) simulations. While minimal CG lipid models with three-beads per lipid and quantitative CG lipid models with >10-beads per lipid have been well studied, in between them, CG lipid models with a compatible resolution to residue-level CG protein models are much less developed. Here, we extended a previously developed three-bead lipid model into a five-bead model and parametrized it for two phospholipids, POPC and DPPC. The developed model, iSoLF, reproduced the area per lipid, hydrophobic thickness, and phase behaviors of the target phospholipid bilayer membranes at the physiological temperature. The model POPC and DPPC membranes were in liquid and gel phases, respectively, in accordance with experiments. We further examined the spontaneous formation of a membrane bilayer, the temperature dependence of physical properties, vesicle dynamics, and the POPC/DPPC two-component membrane dynamics of the CG lipid model, showing some promise. Once combined with standard Cα protein models, the iSoLF model will be a powerful tool to simulate large biological membrane systems made of lipids and proteins.

Structural Effects of Cation Binding to DPPC Monolayers

Ions at the two sides of the plasma membrane maintain the transmembrane potential, participate in signaling, and affect the properties of the membrane itself. The extracellular leaflet is particularly enriched in phosphatidylcholine lipids an under the influence of Na+, Ca2+, and Cl− ions. In this work, we combined molecular dynamics simulations performed using state-of-the-art models with vibrational sum frequency generation (VSFG) spectroscopy to study the effects of these key ions on the structure of dipalmitoylphosphatidylcholine. We used lipid monolayers as a proxy for membranes, as this approach enabled a direct comparison between simulation and experiment. We find that the effects of Na+ are minor. Ca2+, on the other hand, strongly affects the lipid head group conformations and induces a tighter packing of lipids, thus promoting the liquid condensed phase. It does so by binding to both the phosphate and carbonyl oxygens via direct and water-mediated binding modes, the ratios of which depend on the monolayer packing. Clustering analysis performed on simulation data revealed that changes in area per lipid or CaCl2 concentration both affect the head group conformations, yet their effects are anti-correlated. Cations at the monolayer surface also attract Cl−, which at large CaCl2 concentrations penetrates deep to the monolayer. This phenomenon coincides with a radical change in the VSFG spectra of the phosphate group, thus indicating the emergence of a new binding mode.

Structural Effects of Cation Binding to DPPC Monolayers

Ions at the two sides of the plasma membrane maintain the transmembrane potential, participate in signaling, and affect the properties of the membrane itself. The extracellular leaflet is particularly enriched in phosphatidylcholine lipids an under the influence of Na+, Ca2+, and Cl− ions. In this work, we combined molecular dynamics simulations performed using state-of-the-art models with vibrational sum frequency generation (VSFG) spectroscopy to study the effects of these key ions on the structure of dipalmitoylphosphatidylcholine. We used lipid monolayers as a proxy for membranes, as this approach enabled a direct comparison between simulation and experiment. We find that the effects of Na+ are minor. Ca2+, on the other hand, strongly affects the lipid head group conformations and induces a tighter packing of lipids, thus promoting the liquid condensed phase. It does so by binding to both the phosphate and carbonyl oxygens via direct and water-mediated binding modes, the ratios of which depend on the monolayer packing. Clustering analysis performed on simulation data revealed that changes in area per lipid or CaCl2 concentration both affect the head group conformations, yet their effects are anti-correlated. Cations at the monolayer surface also attract Cl−, which at large CaCl2 concentrations penetrates deep to the monolayer. This phenomenon coincides with a radical change in the VSFG spectra of the phosphate group, thus indicating the emergence of a new binding mode.

In situ, fluorescence lifetime-based measurements of cell membrane micromechanics

ABSTRACTMicroscopic in situ measurements of the mechanical properties of lipid bilayers were derived from the mean and variance of the fluorescence lifetime distributions of 1’-dioctadecyl-3,3,3’3’-tetramethylindocarbocyanine perchlorate (DiI). In this method, DiI, incorporated into membranes, acts as a membrane-targeted molecular rotor whose fluorescence lifetime is sensitive to local lipid viscosity. A new model was developed in which changes in area per lipid were derived from the first and second moments of a stretched exponential distribution of fluorescence lifetimes of DiI, which were subsequently used to compute mean area per lipid and its variance, quantities directly related to bilayer compressibility and bending moduli. This method enabled molecular scale assays of surface micromechanics of membrane-bound entities, such as nanoliposomes and human red blood cells.STATEMENT OF SIGNIFICANCEDespite the progress in cell deformability studies, and in understanding mechanical properties of purified lipid bilayers, there has not, to date, been a method to measure the mechanics of the lipid bilayer in cells in situ. The current manuscript describes such a method. Using a fluorescent molecular rotor, DiI, embedded in the membrane, along with time resolved fluorescence, we directly measure area per lipid, and its temporal and spatial variance, properties directly related to bilayer mechanical moduli. Such a method will allow investigators to start exploring the relationship between lipid bilayer mechanics and cellular health and disease.