A molecular dynamics simulation study of C60 fullerenes inside a dimyristoylphosphatidylcholine lipid bilayer

We have carried out atomistic molecular dynamics simulations of C60 fullerenes inside a dimyristoylphosphatidylcholine lipid bilayer and an alkane melt. Simulations reveal that the preferred position of a single C60 fullerene is about 6-7 A off of the center plane, allowing the fullerene to take advantage of strong dispersion interactions with denser regions of the bilayer. Further displacement (>8 A) of the fullerene away from the center plane results in a rapid increase in free energy likely due to distortion of the lipid head group layer. The effective interaction between fullerenes (direct interaction plus environment (bilayer)-induced interaction), measured as the potential of mean force (POMF) between two fullerenes as a function of their separation, was found to be significantly less attractive in the lipid bilayer than in an alkane melt of the same molecular weight as the lipid tails. Only part of this difference can be accounted for by the more favorable interaction of the fullerene with the relatively denser bilayer. Additionally, our POMF studies indicate that the bilayer is less able to accommodate the larger aggregated fullerene pair than isolated single fullerenes, again likely due to distortion of the bilayer structure. The implications of these effects on aggregation of fullerenes within lipid bilayer are considered.     

Tuning the dynamics and molecular distribution of the self-spreading lipid bilayer

The self-spreading dynamics of lipid bilayers were investigated at controlled electrolyte concentrations. The self-spreading velocity increased when the concentration of NaCl was increased from 1 to 100 mM. Comparing the experimentally determined spreading energy with that estimated from theoretical models, we found that the self-spreading dynamics were well explained by considering the van der Waals interaction, double layer interaction and hydration interaction energies between the self-spreading bilayer and the substrate. The characteristic behavior at high concentration is attributable to the increase in the density of the lipid layer, originating from the effective shielding of the molecular charges by the electrolyte ions in solution. The distribution of doped dye-labeled molecule within the spreading bilayer was also controllable by tuning the electrolyte concentration. All of these findings were explained by systematic changes in bilayer-substrate or inter-molecular interactions depending on the electrolyte concentration.     

Enhanced hydrophobicity of fluorinated lipid bilayer: a molecular dynamics study

A molecular dynamics simulation of a partially fluorinated phospholipid bilayer has been carried out to understand the effects of fluorination of the hydrophobic chains on the structure and water permeability across the membrane. Fluorocarbon chains typically have an all-trans conformation, showing a highly ordered structure in the membrane core compared to ordinary hydrocarbon chains. The free energy profiles of water across the bilayers were successfully estimated by a revised cavity insertion Widom method. The fluorinated bilayer showed a higher free energy barrier than an ordinary nonfluorinated lipid bilayer by about 1.2 kcal/mol, suggesting a lower water permeability of the fluorinated bilayer membrane. A cavity distribution analysis elucidated the reduced free volume in the fluorinated membrane due to the neatly packed chains, which should account for the higher free energy barrier.     

Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer

We describe a new equilibration procedure for the atomic level simulation of a hydrated lipid bilayer. The procedure consists of alternating molecular dynamics trajectory calculations in a constant surface tension and temperature ensemble with configurational bias Monte Carlo moves to different regions of the configuration space of the bilayer, in a constant volume and temperature ensemble. The procedure is described in detail and is applied to a bilayer of 100 molecules of dipalmitoyl phosphatidylcholine (DPPC) and 3205 water molecules. We find that the hybrid simulation procedure enhances the equilibration of the bilayer as measured by the convergence of the area per molecule and the segmental order parameters, as compared with a simulation using only molecular dynamics (MD). Progress toward equilibration is almost three times as fast in CPU time, compared with a purely MD simulation. Equilibration is complete, as judged by the lack of energy drift in three separate 200-ps runs of continuous MD started from different initial states. Results of the simulation are presented and compared with experimental data and with other recent simulations of DPPC. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1153–1164, 1999     

Cannabinoid CB1 receptor recognition of endocannabinoids via the lipid bilayer: molecular dynamics simulations of CB1 transmembrane helix 6 and anandamide in a phospholipid bilayer

The phospholipid bilayer plays a central role in the lifecycle of the endogenous cannabinoid, N-arachidonoylethanolamine (anandamide, AEA). Therefore, the orientation and location of AEA in the phospholipid bilayer with respect to key membrane associated proteins, is a central issue in understanding the mechanism of endocannabinoid signaling. In this paper, we report a test of the hypothesis that a βXXβ motif (formed by beta branching amino acids, V6.43 and I6.46) on the lipid face of the cannabinoid CB1 receptor in its inactive state may serve as an initial CB1 interaction site for AEA. Eight 6 ns NAMD2 molecular dynamics simulations of AEA were conducted in a model system composed of CB1 transmembrane helix 6 (TMH6) in a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayer. In addition, eight 6 ns NAMD2 molecular dynamics simulations of a low CB1 affinity (20:2, n−6) analog of AEA were conducted in the same model system. AEA was found to exhibit a higher incidence of V6.43/I6.46 groove insertion than did the (20:2, n−6) analog. In certain cases, AEA established a high energy of interaction with TMH6 by first associating with the V6.43/I6.46 groove and then molding itself to the lipid face of TMH6 to establish a hydrogen bonding interaction with the exposed backbone carbonyl of P6.50. Based upon these results, we propose that the formation of this hydrogen bonded AEA/TMH6 complex may be the initial step in CB1 recognition of AEA in the lipid bilayer.     

Control of dynamics and molecular distribution in a self-spreading lipid bilayer using surface-modified metal nanoarchitectures

The molecular distribution and spreading dynamics of self-spreading lipid bilayers can be tuned by surface-modified metallic nanoarchitectures. Interactions between lipids and molecules in the surface modification alter the self-spreading behavior at the gate regions between adjacent nanoarchitectures, leading to molecular filtering/concentrating effects and modification of the dynamics. The hydrophilic surface can tune the spreading velocity without changing the molecular distribution in the spreading bilayer, whereas the hydrophobic surface provides a molecular concentrating function to the nanogates. This indicates that a combination of unmodified/hydrophobic/hydrophilic nanoarchitectures has a wide range of potential applications since it can be used to independently control the self-spreading dynamics and the molecular distribution.     

Molecular dynamics simulation of an archaeal lipid bilayer with sodium chloride

We have performed molecular dynamics simulations of a bilayer formed by the synthetic archaeal lipid, diphytanyl phosphatidylcholine, in NaCl electrolyte solution at four different concentrations (0-4 M) to investigate how structural and dynamic properties of the model archaeal membrane are changed due to the ionic strength of the solution. The archaeal lipid bilayer shows minor changes in their physical properties, indicating the unusual high stability of the membrane against salt, though small reductions of molecular area and lateral diffusion of the lipid are detected at the highest electrolyte concentration of 4 M. Sodium ions penetrate to the ether-rich region, where the ions are likely bound to the ether oxygen in the sn-1 chain rather than to that in the sn-2 chain. The observed salt bridges among two or three neighboring lipids account for the small reduction in the molecular area. The bound ions together with the counter (chloride) ions give rise to a diffusive electric double layer; as a result, the membrane dipole potential is slightly increased with increasing NaCl concentration.     

Effect of ions on a dipalmitoyl phosphatidylcholine bilayer. a molecular dynamics simulation study

The effect of physiological concentrations of different chlorides on the structure of a dipalmitoyl phosphatidylcholine (DPPC) bilayer has been investigated through atomistic molecular dynamics simulations. These calculations provide support to the concept that Li+, Na+, Ca2+, Mg2+, Sr2+, Ba2+, and Ac3+, but not K+, bind to the lipid-head oxygens. Ion binding exhibits an influence on lipid order, area per lipid, orientation of the lipid head dipole, the charge distribution in the system, and therefore the electrostatic potential across the head-group region of the bilayer. These structural effects are sensitive to the specific characteristics of each cation, i.e., radius, charge, and coordination properties. These results provide evidence aimed at shedding some light into the apparent contradictions among different studies reported recently regarding the ordering effect of ions on zwitterionic phosphatidylcholine lipid bilayers.     

A molecular dynamics study on heat conduction characteristics in DPPC lipid bilayer

In this paper, nonequilibrium molecular dynamics simulations were performed on a single component 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine lipid bilayer in order to investigate the thermal conductivity and its anisotropy. To evaluate the thermal conductivity, we applied a constant heat flux to the lipid bilayer along and across the membrane with ambient water. The contribution of molecular interaction to the heat conduction was also evaluated. Along the bilayer plane, there is little transfer of thermal energy by the interaction between lipid molecules as compared with the interaction between water molecules. Across the bilayer plane, the local thermal conductivity depends on the constituents (i.e., water, head group, and tail group of lipid molecule) that occupy the domain. Although the intramolecular transfer of thermal energy in the tail groups of lipid molecules works efficiently to promote high local thermal conductivity in this region, the highest thermal resistance appears at the center of lipid bilayer where acyl chains of lipid molecules face each other due to a loss of covalent-bond and low number density. The overall thermal conductivities of the lipid bilayer in the directions parallel and perpendicular to the lipid membrane have been compared, and it was found that the thermal conductivity normal to the membrane is higher than that along the membrane, but it is still smaller than that of bulk water.     

Structure of gramicidin a in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data

Two different high-resolution structures recently have been proposed for the membrane-spanning gramicidin A channel: one based on solid-state NMR experiments in oriented phospholipid bilayers (Ketchem, R. R.; Roux, B.; Cross, T. A. Structure 1997, 5, 1655-1669; Protein Data Bank, PDB:1MAG); and one based on two-dimensional NMR in detergent micelles (Townsley, L. E.; Tucker, W. A.; Sham, S.; Hinton, J. F. Biochemistry 2001, 40, 11676-11686; PDB:1JNO). Despite overall agreement, the two structures differ in peptide backbone pitch and the orientation of several side chains; in particular that of the Trp at position 9. Given the importance of the peptide backbone and Trp side chains for ion permeation, we undertook an investigation of the two structures using molecular dynamics simulation with an explicit lipid bilayer membrane, similar to the system used for the solid-state NMR experiments. Based on 0.1 micros of simulation, both backbone structures converge to a structure with 6.25 residues per turn, in agreement with X-ray scattering, and broad agreement with SS backbone NMR observables. The side chain of Trp 9 is mobile, more so than Trp 11, 13, and 15, and undergoes spontaneous transitions between the orientations in 1JNO and 1MAG. Based on empirical fitting to the NMR results, and umbrella sampling calculations, we conclude that Trp 9 spends 80% of the time in the 1JNO orientation and 20% in the 1MAG orientation. These results underscore the utility of molecular dynamics simulations in the analysis and interpretation of structural information from solid-state NMR.     

Molecular dynamics simulation of nonsteroidal antiinflammatory drugs,naproxen and relafen,in a lipid bilayer membrane

Naproxen and relafen, as nonsteroidal antiinflammatory drugs, were simulated in neutral and charged forms and their effects on a lipid bilayer membrane were investigated by molecular dynamics simulation using Groningen machine for chemical simulations software (GROMACS). Simulation of 10 systems was performed, which included different dosages of the drug molecules, naproxen and Relafen, in charged and neutral forms, and a mixture of naproxen and Relafen in neutral forms. The effects of the mixture and the individual drugs' dosages on membrane properties, such as electrostatic potential, order parameter, diffusion coefficients, and hydrogen bond formation, were analyzed. Hydration of the drugs in the membrane system was investigated using radial distribution function analysis. Using fully hydrated dimyristoylphosphatidylcholine (DMPC) as a reference system, 128 lipid molecules and water molecules were simulated exclusively, and the same simulation technique was performed on 10 other systems, including drug mixtures and a DMPC membrane. Angular distributions of lipid chains of the membrane were calculated, and the effects of the drug insertion and chain orientation in the membrane were evaluated. © 2013 Wiley Periodicals, Inc.     

Structure and dynamics of a fluid phase bilayer on a solid support as observed by a molecular dynamics computer simulation

Simulations of a 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine lipid bilayer interacting with a solid surface of hydroxylated nanoporous amorphous silica have been carried out over a range of lipid-solid substrate distances. The porous solid surface allowed the water layer to dynamically adjust its thickness, maintaining equal pressures above and below the membrane bilayer. Qualitative estimates of the force between the surfaces leads to an estimated lipid-silicon distance in very good agreement with the results of neutron scattering experiments. Detailed analysis of the simulation at the separation suggested by experiment shows that for this type of solid support the water layer between surfaces is very narrow, consisting only of bound waters hydrating the lipid head groups and hydrophilic silica surface. The reduced hydration, however, has only minor effects on the head group hydration, the orientation of water molecules at the interface, and the membrane dipole potential. Whereas these structural properties were not sensitive to the presence of the solid substrate, the calculated diffusion coefficient for translation of the lipid molecules was altered significantly by the silica surface.     

Probing the molecular-scale lipid bilayer response to shear flow using nonequilibrium molecular dynamics

A nonequilibrium molecular dynamics simulation of the response of dimyristoylphosphatidylcholine (DMPC) bilayers to a solvent shear flow is presented. Application of shear flow to planar, stationary DMPC bilayers results in a redistribution of the membrane density profile along the bilayer normal due to the alignment of the lipids in the direction of flow and an increase in average lipid chain length. An increase in the intermolecular and intramolecular order of the lipids in response to the shear flow is also observed. This study provides groundwork for understanding the mechanism of the full response of lipid bilayers to externally imposed solvent shear flows, beginning with the response in the absence of collective lipid motions such as undulations and bilayer flow.     

Conformational dynamics of the nicotinic acetylcholine receptor channel: a 35-ns molecular dynamics simulation study

The nicotinic acetylcholine receptor (AChR) is the paradigm of ligand-gated ion channels, integral membrane proteins that mediate fast intercellular communication in response to neurotransmitters. A 35-ns molecular dynamics simulation has been performed to explore the conformational dynamics of the entire membrane-spanning region, including the ion channel pore of the AChR. In the simulation, the 20 transmembrane (TM) segments that comprise the whole TM domain of the receptor were inserted into a large dipalmitoylphosphatidylcholine (DPPC) bilayer. The dynamic behavior of individual TM segments and their corresponding AChR subunit helix bundles was examined in order to assess the contribution of each to the conformational transitions of the whole channel. Asymmetrical and asynchronous motions of the M1-M3 TM segments of each subunit were revealed. In addition, the outermost ring of five M4 TM helices was found to convey the effects exerted by the lipid molecules to the central channel domain. Remarkably, a closed-to-open conformational shift was found to occur in one of the channel ring positions in the time scale of the present simulations, the possible physiological significance of which is discussed.     

Spin-labeled alkylphospholipids in a dipalmitoylphosphatidylcholine bilayer: molecular dynamics simulations

Molecular dynamics simulation has been performed to investigate the structural properties of perifosine and its synthetic spin-labeled alkylphospholipid analogues. The conformations adopted by these compounds in water and in a dipalmitoylphosphatidylcholine bilayer as a function of the presence and position of the N-oxyl-4',4'-dimethyloxazolidine ring (doxyl group) have been investigated by all-atom molecular dynamics. No predominant conformation was observed in water, but the molecules adopt specific orientations and conformations in the lipid bilayer. As is expected, alkyl chains tend to insert into the hydrophobic core, while charged groups stay at the lipid-water interface. A doxyl group in the middle of the alkyl chain moves up to the interface region, thus preventing adoption of the extended conformation. Compounds with a doxyl group close to the polar head group adopt conformations similar to that of unlabeled perifosine within the first nanoseconds of simulation. When the doxyl group is at the end of alkyl chain, the spin-labeled molecule needs more time to reach equilibrium. These results indicate a considerable effect of the doxyl position within the alkyl chain on its localization in the lipid bilayer and can be extended further to other similar spin probes used in the electron paramagnetic resonance spectroscopy of biological membranes.     

Exploring a model of a chemokine receptor/ligand complex in an explicit membrane environment by molecular dynamics simulation: the human CCR1 receptor

The seven transmembrane helices G-protein-coupled receptors (GPCRs) form one of the largest superfamilies of signaling proteins found in humans. Homology modeling, molecular docking, and molecular dynamics (MD) simulation were carried out to construct a reliable model for CCR1 as one of the GPCRs and to explore the structural features and the binding mechanism of BX471 as one of the most potent CCR1 inhibitors. In this study, BX471 has been docked into the active site of the CCR1 protein. After docking, one 20 ns MD simulation was performed on the CCR1-ligand complex to explore effects of the presence of lipid membrane in the vicinity of the CCR1-ligand complex. At the end of the MD simulation, a change in the position and orientation of the ligand in the binding site was observed. This important observation indicated that the application of MD simulation after docking of ligands is useful. Explorative runs of molecular dynamics simulation on the receptor-ligand complex revealed that except for Phe85, Phe112, Tyr113, and Ile259, the rest of the residues in the active site determined by docking are changed. The results obtained are in good agreement with most of the experimental data reported by others. Our results show that molecular modeling and rational drug design for chemokine targets is a possible approach.     

Phase transition of a DPPC bilayer induced by an external surface pressure: from bilayer to monolayer behavior. a molecular dynamics simulation study

Understanding the lipid phase transition of lipid bilayers is of great interest from biophysical, physicochemical, and technological points of view. With the aim of elucidating the structural changes that take place in a DPPC phospholipid bilayer induced by an external isotropic surface pressure, five computer simulations were carried out in a range from 0.1 to 40 mN/m. Molecular dynamics simulations provided insight into the structural changes that took place in the lipid structure. It was seen that low pressures ranging from 0.1 to 1 mN/m had hardly any effect on the structure, electrical properties, or hydration of the lipid bilayer. However, for pressures above 40 mN/m, there was a sharp change in the lipid-lipid interactions, hydrocarbon lipid fluidity, and electrostatic potential, corresponding to the mesomorphic transition from a liquid crystalline state (L(alpha)) to its gel state (P'(beta)). The head lipid orientation remained almost unaltered, parallel to the lipid layer, as the surface pressure was increased, although a noticeable change in its angular distribution function was evident with the phase transition.     

Pore-spanning lipid membrane under indentation by a probe tip: a molecular dynamics simulation study

We study the indentation of a free-standing lipid membrane suspended over a nanopore on a hydrophobic substrate by means of molecular dynamics simulations. We find that in the course of indentation the membrane bends at the point of contact and the fringes of the membrane glide downward intermittently along the pore edges and stop gliding when the fringes reach the edge bottoms. The bending continues afterward, and the large strain eventually induces a phase transition in the membrane, transformed from a bilayered structure to an interdigitated structure. The membrane is finally ruptured when the indentation goes deep enough. Several local physical quantities in the pore regions are calculated, which include the tilt angle of lipid molecules, the nematic order, the included angle, and the distance between neighboring lipids. The variations of these quantities reveal many detailed, not-yet-specified local structural transitions of lipid molecules under indentation. The force-indentation curve is also studied and discussed. The results make a connection between the microscopic structure and the macroscopic properties and provide deep insight into the understanding of the stability of a lipid membrane spanning over nanopore.     

Passive transport of C60 fullerenes through a lipid membrane: a molecular dynamics simulation study

To investigate the implications of the unique properties of fullerenes on their interaction with and passive transport into lipid membranes, atomistic molecular dynamics simulations of a C60 fullerene in a fully hydrated di-myristoyl-phoshatidylcholine lipid membrane have been carried out. In these simulations the free energy and the diffusivity of the fullerene were obtained as a function of its position within the membrane. These properties were utilized to calculate the permeability of fullerenes through the lipid membrane. Simulations reveal that the free energy decreases as the fullerene passes from the aqueous phase, through the head group layer and into the hydrophobic core of the membrane. This decrease in free energy is not due to hydrophobic interactions but rather to stronger van der Waals (dispersion) interactions between the fullerene and the membrane compared to those between the fullerene and (bulk) water. It was found that there is no free energy barrier for transport of a fullerene from the aqueous phase into the lipid core of the membrane. In combination with strong partitioning of the fullerenes into the lipidic core of the membrane, this "barrierless" penetration results in an astonishingly large permeability of fullerenes through the lipid membrane, greater than observed for any other known penetrant. When the strength of the dispersion interactions between the fullerene and its surroundings is reduced in the simulations, thereby emulating a nanometer sized hydrophobic particle, a large free energy barrier for penetration of the head group layer emerges, indicating that the large permeability of fullerenes through lipid membranes is a result of their unique interaction with their surrounding medium.