Simulations files for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"

<p>Simulations files for the article "Molecular Conformation and Bilayer Pores in a Nonionic Surfactant Lamellar Phase Studied with 1H–13C Solid-State NMR and Molecular Dynamics Simulations"</p> <p>Ferreira et al. Langmuir, 2014, 30 (2), pp 461–469</p> <p>http://dx.doi.org/10.1021/la404684r</p> <p>The simulation trajectories can be found from:</p> <p>60 wt% C12E5, T=298K   http://dx.doi.org/10.5281/zenodo.28595</p> <p>60 wt% C12E5, T=320K   http://dx.doi.org/10.5281/zenodo.28637</p> <p>60 wt% C12E5, T=333K   http://dx.doi.org/10.5281/zenodo.28638</p> <p>70 wt% C12E5, T=298K   http://dx.doi.org/10.5281/zenodo.20368</p> <p>70 wt% C12E5, T=320K   http://dx.doi.org/10.5281/zenodo.20561</p> <p>70 wt% C12E5, T=333K   http://dx.doi.org/10.5281/zenodo.20664</p> <p>80 wt% C12E5, T=298K  http://dx.doi.org/10.5281/zenodo.20221 </p> <p> </p

Cyclic and Linear Monoterpenes in Phospholipid Membranes: Phase Behavior, Bilayer Structure, and Molecular Dynamics

Monoterpenes are abundant in essential oils extracted from plants. These relatively small and hydrophobic molecules have shown important biological functions, including antimicrobial activity and membrane penetration enhancement. The interaction between the monoterpenes and lipid bilayers is considered important to the understanding of the biological functions of monoterpenes. In this study, we investigated the effect of cyclic and linear monoterpenes on the structure and dynamics of lipids in model membranes. We have studied the ternary system 1,2-dimyristoyl-<i>sn</i>-glycero-3-phosphocholine–monoterpene–water as a model with a focus on dehydrated conditions. By combining complementary techniques, including differential scanning calorimetry, solid-state nuclear magnetic resonance, and small- and wide-angle X-ray scattering, bilayer structure, phase transitions, and lipid molecular dynamics were investigated at different water contents. Monoterpenes cause pronounced melting point depression and phase segregation in lipid bilayers, and the extent of these effects depends on the hydration conditions. The addition of a small amount of thymol to the fluid bilayer (volume fraction of 0.03 in the bilayer) leads to an increased order in the acyl chain close to the bilayer interface. The findings are discussed in relation to biological systems and lipid formulations

Time-resolved 3D mapping of the breakdown of MLVs to other lamellar morphologies.

<p>Spectral deconvolution of spatially resolved NMR spectra gives estimates of the fraction of MLVs and peak width of the MLV singlet. Histograms of and are shown in panels (a) and (b), respectively, for the times  = 1.5 (blue), 3 (green) and 12 (red) days after MLV preparation. The dashed line in (a) indicates the value used for separating between voxels dominated by MLVs () or other lamellar morphologies (). The counts in (b) are weighted by the values of . (c) 3D rendering of the contour (green surface) at the times  = 1.5, 3 and 12 days. The surface at represents with gray scale given by the bar on the -axis in panel (a).</p

Time-resolved 3D mapping of the formation of a macroscopically oriented lamellar phase.

<p>Panels (a) and (b) show histograms of the planar diffusion anisotropy index CP and the ²H quadrupolar splitting at the times 3 (blue), 6 (green), and 36 (red) days after a temperature quench from 67 to 25°C. The vertical dashed line in (a) indicates the value of CP for segmenting the 3D image into oriented (CP ) and non-oriented (CP ) lamellar phase. Insets in (b) show maps at , gray-scale coded according to the bar below the -axis. (c) 3D rendering of the contour (red surface) for the times 3, 6, and 36 days after the temperature quench. The surface at indicates the value of CP according to the gray-scale bar in (a).</p

Molecular Conformation and Bilayer Pores in a Nonionic Surfactant Lamellar Phase Studied with ¹H–¹³C Solid-State NMR and Molecular Dynamics Simulations

The structure of the lamellar phase of aqueous pentaethylene glycol mono-n-dodecyl ether (C12E5) surfactant at various temperatures and molar fractions is studied by using united atom molecular dynamics simulations and nuclear magnetic resonance measurements. Namely, the simulation model is used to interpret the magnitude and temperature dependence of experimental C–H order parameter profiles in terms of the molecular conformation and orientation. Our simulations suggest that the low order parameters that are generally measured in poly­(ethylene oxide) surfactant bilayers are due to the presence of bilayer pores throughout the entire lamellar phase region

Representative DTI and data for C₁₀E₃/water lamellar phases.

<p>(a) Selected 2D slices from a conventional -weighted ¹H 3D image for a freshly prepared sample of multi-lamellar vesicles (MLVs). (b), (c), and (d): 2D arrays of diffusion tensors (top) and spectra (bottom) for fresh MLVs, 12 days aged MLVs, and an oriented lamellar phase L_α obtained by 36 days equilibration after a temperature quench. The 2D arrays show the slices extracted from the full data sets with spatial resolution in three dimensions. Diffusion tensors are shown only for voxels with ¹H signal intensity significantly above the noise level.</p

Estimation of the fraction of MLVs () by spectral deconvolution of data.

<p>The observed spectrum is the sum of contributions from MLVs (singlet) and other lamellar morphologies (doublet). Experimental, fitted, and deconvoluted spectra are shown with black, blue, and gray lines, respectively. The deconvolution process yields the values , 0.32, and 0.14 from left to right.</p

Timing diagrams of the NMR pulse sequences.

<p>(a) Diffusion tensor imaging (DTI) pulse sequence based on a ¹H spin echo. Spatial resolution is provided by two phase-encoding gradients in the and -directions and frequency-encoding gradient in the -direction, while the diffusion gradients encode the images for translational motion. The phase and diffusion gradients are incremented independently, yielding a 4D experiment with three spatial and one diffusion dimension. The phase of the 180° RF pulse is cycled in two steps . (b) spectroscopic imaging sequence using a quadrupolar echo and three independently incremented phase-encoding gradients ( and -direction). The sequence yields a 4D data set with three spatial and one spectral dimension. The RF and receiver (rec) phases are cycled in 4 steps according to , , and .</p

Color-coded NMR and DTI data with spatial resolution in 3D.

<p>²H NMR (left) and DTI (right) for C₁₀E₃/water lamellar phases with different superstructures: (a) fresh MLVs, (b) MLVs aged 12 days, (c) and oriented L_α equilibrated 36 days after a temperature quench. The voxels of the NMR data are color-coded with the peak area (brightness) and second moment (narrow to broad peak: blue to white). The voxels of the DTI data are color-coded using RGB triplets calculated as FA.</p

Schematic lamellar phase morphologies with corresponding diffusion tensors and spectra.

<p>Column 1: Lab frame coordinate system indicating the direction of domain alignment. The main magnetic field defines the direction of the -axis. Column 2: Schematic lamellar phase domains with water and surfactant shown in blue and gray, respectively. Column 3: Diffusion tensors displayed as superquadrics <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098752#pone.0098752-Kindlmann1" target="_blank">[54]</a>. Column 4: spectra with quadrupolar splitting , see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098752#pone.0098752.e038" target="_blank">Eq. 3</a>. Rows (a), (b), and (c): Uniform orientation with non-restricted water diffusion in the , , and -planes, respectively. Rows (d), (e), and (f): Domains oriented randomly along the curved arrow with main symmetry axis along , , and -axes, respectively. Row (g): Random orientations in three dimensions. Row (h): Multi-lamellar vesicles (MLVs). Row (i): Mixture of MLVs and randomly oriented domains.</p