Structural aspects of lipid monolayers: computer simulation analyses

Influence of the dimensionality of the periodic boundary conditions on the transport of a drug-peptide complex across model cell membranes

Many research efforts are devoted to improving the efficiency of chemotherapy. One of the aspects is to facilitate the transport of drugs across the cell membranes by attaching the therapeutics to a carrier molecule. The current study focuses on computational investigation of such a system with doxorubicin as the model drug, which is covalently bound to a cell-penetrating peptide. The correct description of its membrane translocation at the molecular level requires proper choice of the model membrane and of the simulation parameters. For the purpose, two phospholipid bilayers are built, one containing solely DPPC and another with mixed lipid content mimicking the composition of a human erythrocyte membrane. Atomistic molecular dynamics simulations are carried out in two types of periodic boundary conditions (2D and 3D PBC), in order to assess the effect of the periodicity dimensionality on the intermolecular interactions. The evolution of some basic characteristics of the bilayers and of the drug-peptide complex is tracked: mass density profiles, electrostatic potentials, lateral diffusion coefficients and areas per lipid, lipid-complex radial distribution functions, secondary structure of the peptide and orientation of the drug relative to the membrane. Thus, the influence of the periodic boundary conditions is quantified and it shows that the mixed system in 3D PBC is the most suitable for analysis of the translocation of the transporting moiety across cell membranes.

Comprehensive Study of the Liquid Expanded-Liquid Condensed Phase Transition in 1,2-Dimyristoyl-sn-glycero-3-phospho-l-serine Monolayers: Surface Pressure, Volta Potential, X-ray Reflectivity, and Molecular Dynamics Modeling

An integrated approach is applied to reveal fine changes in the surface-normal structure of 1,2-dimyristoyl-sn-glycero-3-phospho-l-serine (DMPS) monolayers at the air-lipid-water interface occurring in a liquid expanded (LE)-liquid condensed (LC) transition. The combination of the Langmuir monolayer technique, X-ray reflectometry, and molecular dynamics (MD) modeling provides new insight into the molecular nature of electrostatic phenomena in different stages of lipid compression. A homemade setup with a laboratory X-ray source (λ = 1.54 Å) offers a nondestructive way to reveal the structural difference between the LE and LC phases of the lipid. The electron density profile in the direction normal to the interface is recovered from the X-ray reflectivity data with the use of both model-independent and model-based approaches. MD simulations of the DMPS monolayer are performed for several areas per lipid using the all-atom force field. Using the conventional theory of capillary waves, a comparison is made between the electron density profiles reconstructed from the X-ray data and those calculated directly from MD modeling, which demonstrates remarkable agreement between the experiment and simulations for all selected lipid densities. This confirms the validity of the simulations and allows an analysis of the contributions of the hydrophobic tails and hydrated polar groups to the electron density profile and to the dipole component of the electric field at the interface. According to the MD data, the dependence of the Volta potential on the area per lipid in the monolayer has a different molecular nature below and above the phase transition. In the LE state of the monolayer, the potential is determined mostly by the oriented water molecules in the polar region of the lipid. In the LE-LC transition, these molecules are displaced to the bulk, and their effect on the Volta potential becomes insignificant compared with the contribution of the hydrophobic tails. The hydrophobic tails are highly ordered in the state of the liquid crystal so that their dipole moments entirely determine the growth of the potential upon compression up to the monolayer collapse.

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.

Simulating G protein-coupled receptors in native-like membranes: from monomers to oligomers

G protein-coupled receptors (GPCRs) are one of the most relevant superfamilies of transmembrane proteins as they participate in an important variety of biological events. Recently, the scientific community is witnessing an advent of a GPCR crystallization age along with impressive improvements achieved in the field of computer simulations during the last two decades. Computer simulation techniques such as molecular dynamics (MD) simulations are now frequent tools to study the dynamic behavior of GPCRs and, more importantly, to model the complex membrane environment where these proteins spend their lifetime. Thanks to these tools, GPCRs can be simulated not only longer but also in a more "physiological" fashion. In this scenario, scientists are taking advantage of such advances to approach certain phenomena such as GPCR oligomerization occurring only at timescales not reachable until now. Thus, despite current MD simulations having important limitations today, they have become an essential tool to study key biophysical properties of GPCRs and GPCR oligomers.

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.

Molecular dynamics study of the electric and dielectric properties of model DPPC and dicaprin insoluble monolayers: size effect

Atomistic modeling of insoluble monolayers is currently used to inspect their organization and electric characteristics, providing a link between theory and experiment. Extensive molecular dynamics simulations at 300 K were carried out for model films of the lipids dipalmitoylphosphatidylcholine (DPPC) and dicaprin (DC) at the air/water interface. Surface concentrations corresponding to a set of points along the surface pressure/area isotherms of the surfactants were considered. The models contained 25 or 81 lipid molecules in hexagonal arrangement and explicit aqueous media (TIP3P) treated in periodic boundary conditions. Molecular dynamics simulations based on a classical force field (CHARMM27) were carried out and key characteristics of the studied films were estimated. The dielectric properties of the films in normal and tangential direction were quantified by means of dipole moment magnitude and orientation analysis and by monolayer dielectric permittivity. The contributions of lipids and interfacial water to each component of the considered characteristics were assessed and their variations upon film compression were discussed and compared for the two monolayers and to earlier results. The dielectric permittivity tensors were analyzed. Electrostatic potential profiles across the layers and surface pressure values were used for more detailed clarification of experimental measurements. The results show dissimilar behavior of the two lipids at the air-water interface. While the average electric and dielectric properties of DPPC monolayers result from opposite surfactant and water contributions, the two subsystems are synergetic in the DC films. The anisotropy of the monolayer dipole moment and dielectric permittivity is explained by domination of a different subsystem in the various components. Tangential characteristics turn out to be more sensitive to the size of the model and to the degree of film compression.