Molecular dynamics simulations of lipid bilayers

Computer simulation methods are becoming increasingly widespread as tools for studying the structure and dynamics of lipid bilayer membranes. The length scale and time scale accessible to atomic-level molecular dynamics simulations are rapidly increasing, providing insight into the relatively slow motions of molecular reorientation and translation and demonstrating that effects due to the finite size of the simulation cell can influence simulation results. Additionally, significant advances have been made in the complexity of membrane systems studied, including bilayers with cholesterol, small solute molecules, and lipid-protein and lipid-DNA complexes. Especially promising is the progress that continues to be made in the comparison of simulation results with experiment, both to validate the simulation algorithms and to aid in the interpretation of existing experimental data.     

Molecular dynamics simulations of cardiolipin bilayers

Cardiolipin is a key lipid component in the inner mitochondrial membrane, where the lipid is involved in energy production, cristae structure, and mechanisms in the apoptotic pathway. In this article we used molecular dynamics computer simulations to investigate cardiolipin and its effect on the structure of lipid bilayers. Three cardiolipin/POPC bilayers with different lipid compositions were simulated: 100, 9.2, and 0% cardiolipin. We found strong association of sodium counterions to the carbonyl groups of both lipid types, leaving in the case of 9.2% cardiolipin virtually no ions in the aqueous compartment. Although binding occurred primarily at the carbonyl position, there was a preference to bind to the carbonyl groups of cardiolipin. Ion binding and the small headgroup of cardiolipin gave a strong ordering of the hydrocarbon chains. We found significant effects in the water dipole orientation and water dipole potential which can compensate for the electrostatic repulsion that otherwise should force charged lipids apart. Several parameters relevant for the molecular structure of cardiolipin were calculated and compared with results from analyses of coarse-grained simulations and available X-ray structural data.     

Microscopic structure of phospholipid bilayers: comparison between molecular dynamics simulations and wide-angle X-ray spectra

We present results of molecular dynamics simulations of fully hydrated dipalmitoylphosphatidylcholine and dimyristoylphosphatidylcholine bilayers in the disordered liquid crystalline phase (Lalpha) and compare them to wide-angle X-ray scattering experiments. Though we find a generally good agreement between the simulated and experimental spectra, there are some deviations whose origin has been investigated by a reparametrization of the aliphatic chains' force field. A detailed analysis of the various contribution to the X-ray spectra shows that a non-negligible contribution to the total scattered intensity comes from the headgroups and the head-tail cross correlation.     

Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers

Four 20 ns molecular dynamic simulations of rhodopsin embedded in different one-component lipid bilayers have been carried out to ascertain the importance of membrane lipids on the protein structure. Specifically, dimyristoyl phosphatidylcholine (DMPC), dipalmitoyl phosphatidylcholine (DPPC), palmitoyl oleoyl phosphatidylcholine (POPC), and palmitoyl linoleyl phosphatidylcholine (PLPC) lipid bilayers have been considered for the present work. The results reported here provide information on the hydrophobic matching between the protein and the bilayer and about the differential effects of the protein on the thickness of the different membranes. Furthermore, a careful analysis of the individual protein-lipid interactions permits the identification of residues that exhibit permanent interactions with atoms of the lipid environment that may putatively act as hooks of the protein to the membrane. The analysis of the trajectories also provides information about the effect of the bilayer on the protein structure, including secondary structural elements, salt bridges, and rigid-body motions.     

Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles

Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the aggregation process occurs on a nanosecond time scale, with bicelles and cuplike vesicles formed at intermediate stages. Formation of hemifused vesicles is also observed at higher lipid concentration. With either 25% dipalmitoylphosphatidylethanolamine (DPPE) or lysoPC mixed into the system, the final stages of the aggregation process occur significantly faster. The structure of the spontaneously formed vesicles is analyzed in detail. Microsecond simulations of isolated vesicles reveal significant differences in the packing of the lipids between the inner and outer monolayers, and between PC, PE, and lysoPC. Due to the small size of the vesicles they remain almost perfectly spherical, undergoing very limited shape fluctuations or bilayer undulations. The lipid lateral diffusion rate is found to be faster in the outer than in the inner monolayer. The water permeability coefficient of the pure DPPC vesicles is of the order of 10(-)(3) cm s(-)(1), in agreement with experimental measurements.     

Molecular dynamics simulations of neutral chlorpromazine in zwitterionic phospholipid monolayers

Molecular dynamics simulations have been performed to investigate the interactions between chlorpromazine (CPZ), a neuroleptic drug used in the treatment of psychiatric disorders, and dipalmitoylphosphatidylcholine (DPPC), a zwitterionic phospholipid, in Langmuir monolayers. The results from simulations carried out at different monolayer surface densities were able to capture important features of the CPZ-lipid interaction. We find that neutral (unprotonated) CPZ is preferentially located in the lipid tail region of the phospholipids, in little contact with the aqueous phase, and that the orientation of its rigid ring structure and tail conformation vary with lipid surface density. CPZ is found to promote ordering of the lipid tails for all surface densities because of a reduction in the effective surface area per lipid upon addition of the drug. Similar effects have been observed in previous studies of cholesterol in DPPC monolayers, in which lipid tails were seen to order around the solute. This feature, however, is quite distinct from what we observe for the most dense monolayer considered here (area per lipid of 50 A(2)), for which we find that CPZ promotes a local distortion of the lipid tails in its immediate vicinity and a concomitant ordering of lipid tails located further away from the solute. This view is further supported by the results obtained for an approximated nonlinear vibrational sum frequency generation susceptibility, which showed greater tail disorder close to CPZ.     

Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers

The reliability of molecular simulations largely depends on the quality of the empirical force field parameters. Force fields used in lipid simulations continue to be improved to enhance the agreement with experiments for a number of different properties. In this work, we have carried out molecular dynamics simulations of neat DMPC bilayers using united‐atom Berger force field and three versions of all‐atom CHARMM force fields. Three different systems consisting of 48, 72, and 96 lipids were studied. Both particle mesh Ewald (PME) and spherical cut‐off schemes were used to evaluate the long‐range electrostatic interactions. In total, 21 simulations were carried out and analyzed to find out the dependence of lipid properties on force fields, system size, and schemes to calculate long‐range interactions. The acyl chain order parameters calculated from Berger and the recent versions of CHARMM simulations have shown generally good agreement with the experimental results. However, both sets of force fields deviate significantly from the experimentally observed P‐C dipolar coupling values for the carbon atoms that link the choline and glycerol groups with the phosphate groups. Significant differences are also observed in several headgroup parameters between CHARMM and Berger simulations. Our results demonstrate that when changes were introduced to improve CHARMM force field using PME scheme, all the headgroup parameters have not been reoptimized. The headgroup properties are likely to play a significant role in lipid–lipid, protein–lipid, and ligand–lipid interactions and hence headgroup parameters in phospholipids require refinement for both Berger and CHARMM force fields. © 2009 Wiley Periodicals, Inc.J Comput Chem, 2010     

Molecular dynamics simulations of bilayers containing mixtures of sphingomyelin with cholesterol and phosphatidylcholine with cholesterol

We performed six molecular dynamics simulations: three on hydrated bilayers containing pure phospholipids and three on hydrated bilayers containing mixtures of these phospholipids with cholesterol. The phospholipids in our simulations were SSM (sphingomyelin containing a saturated 18:0 acyl chain), OSM (sphingomyelin with an unsaturated 18:1 acyl chain), and POPC (palmitoyloleoylphosphatidylcholine containing one saturated and one unsaturated chain). Data from our simulations were used to study systematically the effect of cholesterol on phospholipids that differed in their headgroup and tail composition. In addition to the structural analysis, we performed an energetic analysis and observed that energies of interaction between cholesterol and neighboring SM molecules are similar to the energies of interaction between cholesterol and POPC. We also observed that the interaction energy between cholesterol and neighboring lipids cannot be used for the determination of which lipids are involved in the creation of a complex.     

Improved dissipative particle dynamics simulations of lipid bilayers

The authors introduce a new parameterization for the dissipative particle dynamics simulations of lipid bilayers. In this parameterization, the conservative pairwise forces between beads of the same type in two different hydrophobic chains are chosen to be less repulsive than the water-water interaction, but the intrachain bead interactions are the same as the water-water interaction. For a certain range of parameters, the new bilayer can only be stretched up to 30% before it ruptures. Membrane tension, density profiles, and the in-plane lipid diffusion coefficient of the new bilayer are discussed in detail. They find two kinds of finite size effects that influence the membrane tension: lateral finite size effects, for which larger membranes rupture at a smaller stretch, and transverse finite size effects, for which tensionless bilayers are more compact in larger systems. These finite size effects become rather small when the simulation box is sufficiently large.     

Comparative molecular dynamics study of ether- and ester-linked phospholipid bilayers

The lipid membranes found in archaea have high bilayer stability and low permeability. The molecular structure of their constituent lipids is characterized by ether-linked, branched hydrophobic chains, whereas the conventional lipids obtained from eukaryotic or eubacterial sources have ester linked straight chains. In order to elucidate the influence of the ether linkage, instead of an ester one, on the physical properties of the lipid bilayers, we have carried out comparative 10 ns molecular dynamics simulations of diphytanyl phosphatidylcholine (ether-DPhPC) and diphytanoyl phosphatidylcholine (ester-DPhPC) bilayers in water, respectively. We analyze bilayer structures, hydration of the lipids, membrane dipole potentials, and free energy profiles of water and oxygen across the bilayers. We observe that the membrane dipole potential for the ether-DPhPC bilayer, which arises mainly from the ether linkage, is about half of that of the ester-DPhPC. The calculated free energy barrier for a water molecule in the ether-DPhPC bilayer system is slightly higher than that in the ester-DPhPC counterpart, which is in accord with experimental data.     

Structure of docosahexaenoic acid-containing phospholipid bilayers as studied by (2)H NMR and molecular dynamics simulations.

Polyunsaturated phospholipids are known to be important with regard to the biological functions of essential fatty acids, for example, involving neural tissues such as the brain and retina. Here we have employed two complementary structural methods for the study of polyunsaturated bilayer lipids, viz. deuterium ((2)H) NMR spectroscopy and molecular dynamics (MD) computer simulations. Our research constitutes one of the first applications of all-atom MD simulations to polyunsaturated lipids containing docosahexaenoic acid (DHA; 22:6 cis-Delta(4,7,10,13,16,19)). Structural features of the highly unsaturated, mixed-chain phospholipid, 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PDPC), have been studied in the liquid-crystalline (L(alpha)) state and compared to the less unsaturated homolog, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). The (2)H NMR spectra of polyunsaturated bilayers are dramatically different from those of less unsaturated phospholipid bilayers. We show how use of MD simulations can aid in interpreting the complex (2)H NMR spectra of polyunsaturated bilayers, in conjunction with electron density profiles determined from small-angle X-ray diffraction studies. This work clearly demonstrates preferred helical and angle-iron conformations of the polyunsaturated chains in liquid-crystalline bilayers, which favor chain extension while maintaining bilayer flexibility. The presence of relatively long, extended fatty acyl chains may be important for solvating the hydrophobic surfaces of integral membrane proteins, such as rhodopsin. In addition, the polyallylic DHA chains have a tendency to adopt back-bended (hairpin-like) structures, which increase the interfacial area per lipid. Finally, the material properties have been analyzed in terms of the response of the bilayer to mechanical stress. Simulated bilayers of phospholipids containing docosahexaenoic acid were less sensitive to the applied surface tension than were saturated phospholipids, possibly implying a decrease in membrane elasticity (area elastic modulus, bending rigidity). The above features distinguish DHA-containing lipids from saturated or monounsaturated lipids and may be important for their biological modes of action.     

Molecular dynamics simulations of PAMAM dendrimer-induced pore formation in DPPC bilayers with a coarse-grained model

We have performed 0.5-micros-long molecular dynamics (MD) simulations of 0%, 50%, and 100% acetylated third- (G3) and fifth-generation (G5) polyamidoamine (PAMAM) dendrimers in dipalmitoylphosphatidylcholine (DPPC) bilayers with explicit water using the coarse-grained (CG) model developed by Marrink et al. (J.Phys. Chem. B 2004, 108, 750-760), but with long-range electrostatic interactions included. Radii of gyration of the CG G5 dendrimers are 1.99-2.32 nm, close to those measured in the experiments by Prosa et al. (J. Polym. Sci. 1997, 35, 2913-2924) and atomistic simulations by Lee et al. (J. Phys. Chem. B 2006, 110, 4014-4019). Starting with the dendrimer initially positioned near the bilayer, we find that positively charged un-acetylated G3 and 50%-acetylated and un-acetylated G5 dendrimers insert themselves into the bilayer, and only un-acetylated G5 dendrimer induces hole formation at 310 K, but not at 277 K, which agrees qualitatively with experimental observations of Hong et al. (Bioconj. Chem. 2004, 15, 774-782) and Mecke et al. (Langmuir 2005, 21, 10348-10354). At higher salt concentration (approximately 500 mM NaCl), un-acetylated G5 dendrimer does not insert into the bilayer. The results suggest that with inclusion of long-range electrostatic interactions into coarse-grained models, realistic MD simulation of membrane-disrupting effects of nanoparticles at the microsecond time scale is now possible.     

Interface water dynamics and porating electric fields for phospholipid bilayers

Lipid bilayers, normally a barrier to charged species and large molecules, are permeabilized by electric fields, a phenomenon exploited by cell biologists and geneticists for porating and transfecting cells and tissues. Recent molecular simulation studies have advanced our understanding of electroporation, but the relative contributions of atomically local details (interface water and headgroup dipole and counterion configurations) and medium- and long-range electrostatic gradients and changes in membrane structural shifts to the initiating conditions and mechanisms of pore formation remain unclear. Molecular dynamics simulations of electroporation in several lipid systems presented here reveal the effects of lipid hydrocarbon tail length and composition on the magnitude of the field required for poration and on the location of the initial sites of field-driven water intrusion into the bilayer. Minimum porating external fields of 260 mV nm(-1), 280 mV nm(-1), 320 mV nm(-1), and 380 mV nm(-1) were found for 1,2-dilauroyl-sn-glycero-3-phosphatidylcholine (DLPC), 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), and 1,2-dioleoyl- sn-glycero-3-phosphatidylcholine (DOPC) bilayers, respectively, and correlated most strongly with the bilayer thickness. These phospholipid systems share several common features including a wide, dynamic distribution of the headgroup dipole angle with the bilayer normal ranging from 0 to 155 degrees that is only slightly shifted in a porating electric field, and similar electric field-induced shifts in water dipole orientation, although the mean water dipole moment profile at the aqueous-membrane interface is more sensitive to the electric field for DOPC than for the other phospholipids. The location of pore initiation, at the anode- or cathode-facing leaflet, varies with the composition of the bilayer and correlates with a change in the polarity of the localized electric field at the interface.     

Structure and dynamics of water at the interface with phospholipid bilayers

We have performed two molecular-dynamics simulations to study the structural and dynamical properties of water at the interface with phospholipid bilayers. In one of the simulations the bilayer contained neutral phospholipid molecules, dioleoylphosphatidylcholine (DOPC); in the second simulation the bilayer contained charged lipid molecules, dioleoylphosphatidylserine (DOPS). From the density profile of water we observe that water next to the DOPS bilayer is more perturbed as compared to water near the DOPC bilayer. Using an energetic criterion for the determination of hydrogen bonding we find that water molecules create strong hydrogen bonds with the headgroups of the phospholipid molecules. Due to the presence of these bonds and also due to the confinement of water, the translational and orientational dynamics of water at the interface are slowed down. The degree of slowing down of the dynamics depends upon the location of water molecules near a lipid headgroup.     

Isomerization dynamics of photochromic spiropyran molecular switches in phospholipid bilayers

Transient absorption spectroscopy was used to investigate the dynamics of the photochromic indolinobenzospiropyran reaction in toluene solution and in phosphatidylcholine bilayers (1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)). After excitation with UV light, colorless (R/S)-2-(3',3'-dimethyl-6-nitro-3'H-spiro[chromene-2,2'-indol]-1'-yl)ethanol derivatives are converted to colored merocyanine products in high yield; Phi = 0.45 in DMPC liposomes. We find that the reaction occurs in the bilayer aliphatic region in the gel (P(beta)(')) and liquid (L(alpha)) phases. The Arrhenius activation energy for the isomerization in DMPC bilayers was approximately 3.5 times larger in the liquid phase (L(alpha), E(a) = 26.0 +/- 1.0 kJ mol(-1)) than that in the gel phase (P(beta)('), E(a) = 7.3 +/- 1.6 kJ mol(-1)). Analysis of the isomerization rate constant temperature dependence allows an estimation of the bilayer viscosity and free volume properties in the L(alpha) phase.     

Molecular dynamics simulations of semicrystalline polymers: Crystallization,melting, and reorganization

Large‐scale molecular dynamics (MD) simulations of semicrystalline entangled polymers are carried out to explore crystallization and melting processes. Semicrystalline polymers are obtained from disordered melts via homogeneous nucleation. In the early stage of the crystallization process, the collective scattering does not show the emergence of nuclei seeds. Although the crystallization process is thermodynamically simple, the melting process is complex resulting in multiple‐peaked melting endotherms. The molecular origin is found to be the different thermal stabilities of microcrystalline domains (MCDs). Coexistence of melting and growth of different MCDs during sufficiently slow heating enlarges the difference of their thermal stabilities. An increase of stem length close to the melting point is assisted by disorder effects in particular in the surface regions of the MCDs. The number of trans–trans states is decreasing, which increases the flexibility and mobility of the crystalline stems. We have also investigated self‐seeding processes, and we show how these can be used to obtain single lamellar crystals in MD simulations. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2010     

Molecular umbrella-assisted transport of an oligonucleotide across cholesterol-rich phospholipid bilayers

A series of molecular umbrella conjugates, derived from cholic acid, deoxycholic acid, spermidine, lysine, and 5-mercapto-2-nitrobenzoic acid, have been synthesized and found capable of transporting an attached 16-mer oligonucleotide (S-dT16) across liposomal membranes made from 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyldglycerol (POPG), and cholesterol [POPC/POPG/cholesterol (65/5/30; mol/mol/mol, v/v/v)] at 37 degrees C. Those molecular umbrellas containing four choloyl (or deoxycholoyl) groups resulted in significantly faster rates of transport as compared to those containing only two such moieties. A model that accounts for these membrane transport processes is proposed.     

Area compressibility and buckling of amphiphilic bilayers in molecular dynamics simulations

The elastic modulus or area compressibility of a membrane is routinely calculated in molecular dynamics simulations as the proportionality constant relating surface tension and projected surface area. Recent studies, however, have revealed a marked system size dependence of these moduli, which we attribute to the neglect of thermal undulations in the area calculation. We discuss several methods, based on the Helfrich model and on numerical triangulation, to remedy this situation, and find a satisfying agreement between them. The Helfrich model also quantitatively describes a buckling transition observed for compressed bilayers.     

Origin of short-range repulsion between hydrated phospholipid bilayers: a computer simulation study

The grand canonical Monte Carlo technique is used to simulate the pressure-distance dependence for supported dilauroylphosphatidylethanolamine (DLPE) membranes. The intra- and intermolecular interactions in the system are described with a combination of an AMBER-based force field for DLPE and a TIP4P model for water. To improve the balance between the pair interactions of like and unlike molecules, the water-lipid interaction potentials are scaled to reproduce the hydration level and intermembrane separation at full hydration. It is found that the short-range water-mediated repulsion originates from the hydration component of the intermembrane pressure, whereas the direct interaction between the membranes remains attractive throughout the pressure range studied (0-5 kbar).