Center Of Bilayer Research Articles

Free Energetics and the Role of Water in the Permeation of Methyl Guanidinium across the Bilayer–Water Interface: Insights from Molecular Dynamics Simulations Using Charge Equilibration Potentials

Combining umbrella sampling molecular dynamics (MD) simulations, the weighted histogram analysis method (WHAM) for unbiasing probabilities, and polarizable charge equilibration force fields, we compute the potential of mean force for the reversible transfer of methyl guanidinium from bulk solution to the center of a model DPPC bilayer. A 5 kcal/mol minimum in the potential of mean force profile for membrane permeation suggests that the analogue will preferentially reside in the headgroup region of the lipid, qualitatively in agreement with previously published results. We find the potential of mean force for permeation to be approximately 28 kcal/mol (relative to the minimum in the headgroups), within the range of values reported for similar types of simulations using fixed-charge force fields. From analysis of the lipid structure, we find that the lipid deformation leads to a substantial destabilizing contribution to the free energy of the methyl guanidinium as it resides in the bilayer center, though this deformation allows more efficient stabilization by water defects and transient pores. Water in the bilayer core stabilizes the charged residue. The role of water in stabilizing or destabilizing the solute as it crosses the bilayer depends on bulk electrolyte concentration. In 1 M KCl solution, the water contribution to the potential of mean force is stabilizing over the entire range of the permeation coordinate, with the sole destabilizing force originating from the anionic species in solution. Conversely, methyl guanidinium experiences net destabilization from water in the absence of electrolyte. The difference in solvent contributions to permeation free energy is traced to a local effect arising from differences in water density in the bilayer-water solution interface, thus leading to starkly opposite net forces on the permeant. The origin of the local water density differential rests with the penetration of hydrated chloride anions into the solution-bilayer interface. Finally, water permeation into the bilayer is required for the deformation of individual lipid molecules and permeation of ions into the membrane. From simulations where water is first excluded from the bilayer center where methyl guanidinium is restrained and then, after equilibration, allowed to enter the bilayer, we find that in the absence of any water defects/permeation into the bilayer, the lipid headgroups do not follow the methyl guanidinium. Only when water enters the bilayer do we see deformation of individual lipid molecules to associate with the amino acid analogue at bilayer center.

Computer simulation of cell entry of graphene nanosheet

Recent studies suggest the great promise of functionalized nanosized graphene in biomedical applications, but the transmembrane translocation mechanisms of this two-dimensional nanomaterial have remained poorly understood. Understanding how graphene interacts with cell membrane is related to the fundamental biological responses and cytotoxicity, and is thereby one critical issue to be resolved before further applications of graphene in nanomedicine. Here, by using computer simulations, we explore the translocation of graphene nanosheet (GN) across lipid bilayer membrane and the roles of size and edge of GN in the process. We discover the permeation of small GN into bilayer center through insertion and rotation driven by transbilayer lateral pressure. For large GNs, the translocation undergoes a vesiculation process driven by complicated energetic contributions. Circular GNs with smooth edge show faster translocation but similar mechanisms with square GNs. Our results are fundamentally essential for optimized design of GNs towards extensively biological and biomedical applications.

Structural Adaptation of Proteins to Different Biological Membranes

Transmembrane polarity profiles and distributions of different protein groups that interact directly with lipids were calculated for 3D structuresof 187 α-helical and 73 β-barrel proteins from eight types of biological membranes. The polarity profiles were represented by H-bonding donor and acceptor capacities (α and β) and polarizability parameter (π∗) calculated for protein surface. The proteins from the set have different hydrophobic thicknesses, with average values of 23.1, 27.3 and 32.5 Å for outer bacterial, inner mitochondrial and eukaryotic plasma membranes, respectively, and 29.5 to 30.6Å for endoplasmic reticulum, thylakoid and different bacterial membranes. The proteins have three distinct polarity regions: lipid head group area with peaks for positively charged groups and crystallized water (15 to 25Å from the bilayer center); interfacial “mid-polar” region with peaks for Tyr and Trp (8 to 15Å); and aliphatic hydrocarbon core (±8Å). Polarity of the core region was nearly identical for different membranes (α∼0.01, β∼0.04, π∗=0.09-0.14). Main changes in polarity occur at the level of lipid carbonyl groups (∼15±5Å), but the changes are more gradual than in DOPC bilayer. The locations and amplitudes of peaks for Trp, Tyr, and Phe are frequently asymmetric and dependent on the type of membrane. The distributions of crystallized water have two peaks at ±20Å. Head groups of crystallized lipids are shitted closer to the hydrocarbon boundary, especially in mitochondrial membrane and on the inner side of eukaryotic plasma membrane. All proteins have a peak of positive net charge at ∼20 Å on the inner side, consistent with the “positive inside” rule, except single-chain β-barrels that follow “negative inside” rule. All curves are shifted inwards in β-barrels, consistent with their smaller thickness. Computational modeling of membrane proteins can be improved using hydrophobic thicknesses and asymmetric polarity profiles for different membranes.

Residue-specific membrane location of peptides and proteins using specifically and extensively deuterated lipids and 13C–2H rotational-echo double-resonance solid-state NMR

Residue-specific location of peptides in the hydrophobic core of membranes was examined using (13)C-(2)H REDOR and samples in which the lipids were selectively deuterated. The transmembrane topology of the KALP peptide was validated with this approach with substantial dephasing observed for deuteration in the bilayer center and reduced or no dephasing for deuteration closer to the headgroups. Insertion of β sheet HIV and helical and β sheet influenza virus fusion peptides into the hydrophobic core of the membrane was validated in samples with extensively deuterated lipids.

Drug permeability prediction using PMF method

Drug permeability determines the oral availability of drugs via cellular membranes. Poor permeability makes a drug unsuitable for further development. The permeability may be estimated as the free energy change that the drug should overcome through crossing membrane. In this paper the drug permeability was simulated using molecular dynamics method and the potential energy profile was calculated with potential of mean force (PMF) method. The membrane was simulated using DPPC bilayer and three drugs with different permeability were tested. PMF studies on these three drugs show that doxorubicin (low permeability) should pass higher free energy barrier from water to DPPC bilayer center while ibuprofen (high permeability) has a lower energy barrier. Our calculation indicates that the simulation model we built is suitable to predict drug permeability.

Accommodation of a Central Arginine in a Transmembrane Peptide by Changing the Placement of Anchor Residues

Both Trp and Arg in transmembrane protein domains make important interactions with lipids at the membrane/water interface, but at different depths. Derivatives of the designed peptide GWALP23, acetyl-GGALW(5)LALALALALALALW(19)LAGA-amide, with single Trp anchors, have proven useful for characterizing such interactions. Indeed, previous work revealed quite different effects emanating from Arg substitutions at positions 12 and 14 within GWALP23, with the R12 peptide exhibiting multiple positions and orientations with respect to DOPC bilayer membranes (Vostrikov et al. J. Am. Chem. Soc. 2010, 132, 5803-5811). To gain further understanding of the multistate behavior, we moved the Trp "anchor" residues to more outer positions 3 and 21 in GWALP23 itself, and in the R12 and R14 derivatives. The locations and orientations of the peptides with respect to lipid bilayer membranes of differing thickness were investigated by means of solid-state (2)H NMR spectroscopy, using labeled alanines, and coarse-grained molecular dynamics simulations. Interestingly, relatively intense and narrow (2)H resonances from selected backbone C(α) deuterons were observed over quite narrow ranges of frequency and sample orientation. The backbone resonances reflect dynamic complexities and at the same time provide important contributions for the analysis of peptide transmembrane orientation. With the Trp(3,21) anchors relatively far from the peptide and bilayer center, the results indicate significantly large apparent tilt angles, for example, close to 30° for the new R12 and R14 peptides with respect to the bilayer normal of DLPC membranes. The R12 side chain indeed is "rescued" to a stable position, where it is accommodated within the transmembrane helix, when the Trp anchors are moved outward and to another face of the helix. At the same time, the R14 side chain of transmembrane GW(3,21)ALP23 also retains a stable favored position.

How cholesterol is distributed between monolayers in asymmetric lipid membranes

The distribution of cholesterol in asymmetric lipid bilayers was studied by extensive coarse-grained molecular dynamics simulations. The effects of the lipid head group charge, acyl chain saturation, spontaneous membrane curvature and surface tension of the membrane were investigated. Four asymmetric bilayers containing DOPC, DOPS, DSPC or DSPS lipids were simulated on a time scale extended to tens of microseconds. We show that cholesterol strongly prefers anionic lipids to neutral and saturated lipid tails to unsaturated with a distribution ratio of ~0.7 in neutral/anionic bilayers and of ~0.4 in unsaturated/saturated bilayers. Multiple flip-flop transitions of cholesterol were observed directly, and their mean times ranged from 80 to 250 ns. It was shown that the distribution of cholesterol in the asymmetric membrane depends not only on the type of lipid, but also on the local membrane curvature and the surface tension. The membrane curvature enhances the influence of the lipid head groups on cholesterol distribution, while non-optimal surface tension caused by different areas per lipid in different monolayers increases the effect of the lipid tail saturation. It was clearly seen that the monolayers of asymmetric bilayers are interdependent. Mean distances from the bilayer center to cholesterol molecules depend not only on the type of the lipid in the considered monolayer but also on the composition of the opposite monolayer.

Effect of Calcium and Magnesium on Phosphatidylserine Membranes: Experiments and All-Atomic Simulations

It is known that phosphatidylserine (PS−) lipids have a very similar affinity for Ca2+ and Mg2+ cations, as revealed by electrokinetic and stability experiments. However, despite this similar affinity, experimental evidence shows that the presence of Ca2+ or Mg2+ induces very different aggregation behavior for PS− liposomes as characterized by their fractal dimensions. Also, turbidity measurements confirm substantial differences in aggregation behavior depending on the presence of Ca2+ or Mg2+ cations. These puzzling results suggest that although these two cations have a similar affinity for PS− lipids, they induce substantial structural differences in lipid bilayers containing each of these cations. In other words, these cations have strong ion-specific effects on the structure of PS− membranes. This interpretation is supported by all-atomic molecular-dynamics simulations showing that Ca2+ and Mg2+ cations have different binding sites and induce different membrane hydration. We show that although both ions are incorporated deep into the hydrophilic region of the membrane, they have different positions and configurations at the membrane. Absorbed Ca2+ cations present a peak at a distance ∼2 nm from the center of the lipid bilayer, and their most probable binding configuration involves two oxygen atoms from each of the charged moieties of the PS molecule (phosphate and carboxyl groups). In contrast, the distribution of absorbed Mg2+ cations has two different peaks, located a few angstroms before and after the Ca2+ peak. The most probable configurations (corresponding to these two peaks) involve binding to two oxygen atoms from carboxyl groups (the most superficial binding peak) or two oxygen atoms from phosphate groups (the most internal peak). Moreover, simulations also show differences in the hydration structure of the membrane: we obtained a hydration of 7.5 and 9 water molecules per lipid in simulations with Ca2+ and Mg2+, respectively.

Unassisted transport of N-acetyl-L-tryptophanamide through membrane: experiment and simulation of kinetics.

Cellular transport machinery, such as channels and pumps, is working against the background of unassisted material transport through membranes. The permeation of a blocked tryptophan through a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membrane is investigated to probe unassisted or physical transport. The transport rate is measured experimentally and modeled computationally. The time scale measured by parallel artificial membrane permeation assay (PAMPA) experiments is ~8 h. Simulations with the milestoning algorithm suggest mean first passage time (MFPT) of ~4 h and the presence of a large barrier at the center of the bilayer. A similar calculation with the solubility-diffusion model yields a MFPT of ~15 min. This permeation rate is 9 orders of magnitude slower than the permeation rate of only a tryptophan side chain (computed by us and others). This difference suggests critical dependence of transport time on permeant size and hydrophilicity. Analysis of the simulation results suggests that the permeant partially preserves hydrogen bonding of the peptide backbone to water and lipid molecules even when it is moving closer to the bilayer center. As a consequence, defects of the membrane structure are developed to assist permeation.

Structure and Elasticity of Genistein and Daidzein in Lipid Membranes using X-Ray Scattering and MD Simulations

This work reports the effects of bioflavinoids genistein and daidzein on lipid bilayers as determined by volume measurements, X-ray scattering and molecular dynamics simulations. Upon adding 20 mole% genistein or daidzein to DOPC membranes, experimental and simulated volumes are found to be in outstanding agreement. Both bioflavinoids insert into the hydrocarbon region near the carbonyls of DOPC and also DiphytanoylPC, ∼12 A from the bilayer center. In DOPC, both experiments and MD simulations show the area/unit cell equals 83 A2 for 20 mole% genistein and 80 A2 for 14 mole% daidzein (its maximum solubility in oriented samples). Both bioflavinoids thin DOPC and DPhyPC membranes proportional to their solubility. The long axes of both bioflavinoids are oriented nearly parallel to the plane of the bilayer with their carbonyl groups preferentially pointed towards the proximal surface. X-ray diffuse scattering reveals that both bioflavinoids modestly reduce KC, the bending modulus, daidzein slightly more than genistein. MD simulations determine that both bioflavinoids reduce KA, the area compressibility modulus, daidzein slightly more than genistein. These elasticity results are in general agreement with the hypothesis that bioflavinoids increase membrane flexibility, thereby overcoming hydrophobic mismatch, and increase gramicidin (gA) lifetimes1. However, the small structural and elasticity differences between genistein and daidzein cannot account for genistein's having twice the effect of daidzein in increasing gA channel lifetimes; that is apparently due to the greater solubility of genistein in membranes when equal amounts are added in gA experiments. 1Hwang, Koeppe & Andersen, Biochemistry 42:13464(2003).

Secondary Structure Formation by Bilayer-Active Peptides Studied by Freeze-Fracture Electron Microscopy: From Disc Micelles to Cochleate Cylinder

Melittin, a 26 amino acid, amphipatic peptide, is known for its hemolytic activity but some short-chain, cationic peptides show antimicrobial properties. Employing freeze-fracture transmission electron microscopy (ff-TEM) we investigated structural modifications within bilayers caused by these two membrane-active peptide groups. Ff-TEM as a cryofixation replica technique is a powerful tool to explore bilayer alterations in a probe-free mode down to a resolution limit of 2nm. Moreover, the fact that the fracture plane follows the area of weakest forces allows insides into the hydrophobic center of lipid bilayer [1]. Here we report the formation of disc micelles as a result of the reversible bilayer to micelle transformation caused by melittin in synthetic lipid bilayer [2]. Furthermore, we explored lipid domain formation in lipid films mimicking the lipid pattern of cytoplasmic membranes of Gram negative bacteria by arginine-rich antimicrobial peptides [3]. Additionally to lipid domains we observed secondary structure formation such as doughnut-type structures caused by arginine-rich peptides and cochleate cylinder (CCC) triggered by lysine-rich peptides. The new type of CCC has been proven to encapsulate and transport traditional, ineffective antibiotics such as erythromycin to resistant bacteria cells. The double-function of these antimicrobial peptides in forming CCC and promoting encapsulation and effective delivery of traditional antibiotics in/by these assemblies provides an interesting approach combating bacterial multidrug resistance [4].

J026016 超音波作用下におけるイオンの脂質膜透過の分子シミュレーション

We investigated the potential of mean force (PMF) of a potassium ion across intact or pore-containing bilayers using molecular dynamics simulations with the Weighted Histogram Analysis Method (WHAM). The pore-containing bilayer was prepared by using equibiaxial stretching and constant area simulations. The umbrella samplings for various ion positions from the bilayer center to the water layer were performed with harmonic biasing potentials. In the intact bilayer, the PMF in the center of the bilayer is significantly larger than that in the water layer (-100 kJ/mol), while the difference of the PMF in the pore of the bilayer and in the water layer are small (<1 kJ/mol). This suggests that the formation of a pore in the bilayer after ultrasound irradiations may enhance the transport of potassium ions.

An Atomic and Molecular View of the Depth Dependence of the Free Energies of Solute Transfer from Water into Lipid Bilayers

Molecular interactions and orientations responsible for differences in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayer partitioning of three structurally related drug-like molecules (4-ethylphenol, phenethylamine, and tyramine) were investigated. This work is based on previously reported molecular dynamics (MD) simulations that determined their transverse free energy profiles across the bilayer. Previously, the location where the transfer free energy of the three solutes is highest, which defines the barrier domain for permeability, was found to be the bilayer center, while the interfacial region was found to be the preferred binding region. Contributions of the amino (NH2) and hydroxyl (OH) functional groups to the transfer free energies from water to the interfacial region were found to be very small both experimentally and by MD simulation, suggesting that the interfacial binding of these solutes is hydrophobically driven and occurs with minimal loss of hydrogen-bonding interactions of the polar functional groups which can occur with either water or phospholipid head groups. Therefore, interfacial binding is relatively insensitive to the number or type of polar functional groups on the solute. In contrast, the relative solute free energy in the barrier domain is highly sensitive to the number of polar functional groups on the molecule. The number and types of hydrogen bonds formed between the three solutes and polar phospholipid atoms or with water molecules were determined as a function of solute position in the bilayer. Minima were observed in the number of hydrogen bonds formed by each solute at the center of the bilayer, coinciding with a decrease in the number of water molecules in DOPC as a function of distance away from the interfacial region. In all regions, hydrogen bonds with water molecules account for the majority of hydrogen-bonding interactions observed for each solute. Significant orientational preferences for the solutes are evident in certain regions of the bilayer (e.g., within the ordered chain region and near the interfacial region 20-25 Å from the bilayer center). The preferred orientations are those that preserve favorable molecular interactions for each solute, which vary with the solute structure.

Statistical Convergence of Equilibrium Properties in Simulations of Molecular Solutes Embedded in Lipid Bilayers.

In recent years, atomistic molecular simulations have become a method of choice for studying the interaction of small molecules, peptides, and proteins with biological membranes. Here, we critically examine the statistical convergence of equilibrium properties in molecular simulations of two amino acid side-chain analogs, leucine and arginine, in the presence of a hydrated phospholipid bilayer. To this end, the convergence of the standard binding free energy for the reversible insertion of the solutes in the bilayer is systematically assessed by evaluating dozens of separate sets of umbrella sampling calculations for a total simulation time exceeding 400 μs. We identify rare and abrupt transitions in bilayer structure as a function of solute insertion depth. These transitions correspond to the slow reorganization of ionic interactions involving zwitterionic phospholipid headgroups when the solutes penetrate the lipid-water interface and when arginine is forced through the bilayer center. These rare events are shown to constitute hidden sampling barriers that limit the rate of convergence of equilibrium properties and result in systematic sampling errors. Our analysis demonstrates that the difficulty of attaining convergence for lipid bilayer-embedded solutes has, in general, been drastically underestimated. This information will assist future studies in improving accuracy by selecting a more appropriate reaction coordinate or by focusing computational resources on those regions of the reaction coordinate that exhibit slow convergence of equilibrium properties.

Effect of membrane tension on the electric field and dipole potential of lipid bilayer membrane

The dipole potential of lipid bilayer membrane controls the difference in permeability of the membrane to oppositely charged ions. We have combined molecular dynamics (MD) simulations and experimental studies to determine changes in electric field and electrostatic potential of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayer in response to applied membrane tension. MD simulations based on CHARMM36 force field showed that electrostatic potential of DOPC bilayer decreases by ~45mV in the physiologically relevant range of membrane tension values (0 to 15dyn/cm). The electrostatic field exhibits a peak (~0.8×109V/m) near the water/lipid interface which shifts by 0.9Å towards the bilayer center at 15dyn/cm. Maximum membrane tension of 15dyn/cm caused 6.4% increase in area per lipid, 4.7% decrease in bilayer thickness and 1.4% increase in the volume of the bilayer. Dipole-potential sensitive fluorescent probes were used to detect membrane tension induced changes in DOPC vesicles exposed to osmotic stress. Experiments confirmed that dipole potential of DOPC bilayer decreases at higher membrane tensions. These results are suggestive of a potentially new mechanosensing mechanism by which mechanically induced structural changes in the lipid bilayer membrane could modulate the function of membrane proteins by altering electrostatic interactions and energetics of protein conformational states.

Dioxygen Transmembrane Distributions and Partitioning Thermodynamics in Lipid Bilayers and Micelles

Cellular respiration, mediated by the passive diffusion of oxygen across lipid membranes, is key to many basic cellular processes. In this work, we report the detailed distribution of oxygen across lipid bilayers and examine the thermodynamics of oxygen partitioning via NMR studies of lipids in a small unilamellar vesicle (SUV) morphology. Dissolved oxygen gives rise to paramagnetic chemical shift perturbations and relaxation rate enhancements, both of which report on local oxygen concentration. From SUVs containing the phospholipid sn-2-perdeuterio-1-myristelaidoyl, 2-myristoyl-sn-glycero-3-phosphocholine (MLMPC), an analogue of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), we deduced the complete trans-bilayer oxygen distribution by measuring (13)C paramagnetic chemical shifts perturbations for 18 different sites on MLMPC arising from oxygen at a partial pressure of 30 bar. The overall oxygen solubility at 45 °C spans a factor of 7 between the bulk water (23.7 mM) and the bilayer center (170 mM) and is lowest in the vicinity of the phosphocholine headgroup, suggesting that oxygen diffusion across the glycerol backbone should be the rate-limiting step in diffusion-mediated passive transport of oxygen across the lipid bilayer. Lowering of the temperature from 45 to 25 °C gave rise to a slight decrease of the oxygen solubility within the hydrocarbon interior of the membrane. An analysis of the temperature dependence of the oxygen solubility profile, as measured by (1)H paramagnetic relaxation rate enhancements, reveals that oxygen partitioning into the bilayer is entropically favored (ΔS° = 54 ± 3 J K(-1) mol(-1)) and must overcome an enthalpic barrier (ΔH° = 12.0 ± 0.9 kJ mol(-1)).

Deciphering a mechanism of membrane permeabilization by α-hordothionin peptide

α-Hordothionin (αHTH) belongs to thionins, the plant antimicrobial peptides with membrane-permeabilizing activity which is associated with broad-range antimicrobial activity. Experimental data have revealed a phospholipid-binding site and indicated formation of ion channels as well as membrane disruption activity of thionin. However, the mechanism of membrane permeabilization by thionin remained unknown. Here it is shown that thionin is a small water-selective channel. Unbiased high-precision molecular modeling revealed formation of a water-selective pore running through the αHTH double α-helix core when the peptide interacted with anions. Anion-induced unfolding of the C-end of the α2-helix opened a pore mouth. The pore started at the α2 C-end between the hydrophilic and the hydrophobic regions of the peptide surface and ended in the middle of the unique hydrophobic region at the C-end of the α1-helix. Highly conserved residues including cysteines and tyrosine lined the pore walls. A large positive electrostatic potential accumulated inside the pore. The narrow pore was, nonetheless, sufficient to accommodate at least one water molecule along the channel except for two constriction sites. Both constriction sites were formed by residues participating in the phospholipid-binding site. The channel properties resembled that of aquaporins with two selectivity filters, one at the entrance, inside the α2 C-end cavity, and a second in the middle of the channel. It is proposed that the αHTH water channel delivers water molecules to the bilayer center that leads to local membrane disruption. The proposed mechanism of membrane permeabilization by thionins explains seemingly controversial experimental data.

Lipid Bilayers of Ester-Modified Lipids

Lipid membranes and bilayers essentially function as barriers for cells to control the transport of substances. Since phospholipid membranes consist of a hydrophilic surface and a hydrophobic inside, the center of a phospholipid bilayer is known to contain almost no water and to prevent the transport of water-dissolving substances, such as ions. These water soluble molecules take alternate routes via ion channel protein pumps to transverse the cell membrane. Typical lipid bilayers with saturated or moderately unsaturated chains show a bilayer with a water density that decreases to zero around 10A and remains at zero at the center. Recent experimental work suggests that ester-modified lipids allow for ions and water to be present at the center of the bilayer (JACS, 128: 14034). These ester-modified phospholipid bilayers contain ester groups along their hydrocarbon chain at various positions. The addition of the ester groups to these lipids can occur naturally through a free radical reaction called lipid peroxidation. We are using molecular dynamics simulations to study two lipid bilayers with additional ester groups on the chain. One lipid contains ester groups in the upper half of the acyl chain (lipid E) and another contains ester groups towards the middle and the end (lipid G). The bilayers contain 15 lipid G (or E) and 35 POPC lipids per leaflet with a hydration of 70.5 waters per lipid. For lipid E, the water density reaches zero at ∼7A, as oppose to the standard 10A. As for lipid G, water fully penetrates the bilayer. We are currently extending these simulations to at least 100 ns, to obtain good statistics on ion permeation where longer timescales are needed to further understand this water and ion permeation mechanism.

Molecular Dynamic Simulations of Blast Waves on Bilayers

Many studies using animal models have shown that blast waves cause injuries to the brain despite the lack of a direct physical impact to the brain or skull. Such injuries are manifested as biochemical, functional, or morphological alterations that result in motor and sensory deficits in addition to behavioral changes. Primary blast due to explosions causes an intense rise of atmospheric pressure, the positive phase, followed by a broader under-pressure, the negative phase. The peak overpressure reaches pressures up to 1724 kPa and the blast wave travels at speeds up to 670 m/s. Because of this high velocity, it is difficult to study the interaction of explosive blast waves with neural tissue in real time. Accordingly, we have performed molecular dynamic (MD) simulations of blast waves on myelin membranes to understand how blast waves interact with neural tissue to cause injury. In our simulations, we have created blast overpressure using a planar wall, which exerts a forces of -K(x0 - x)2; where K is the spring force constant, and x0 and x are the starting and final positions of the wall, respectively. The intensity of the overpressure wave is controlled by the spring stiffness (K) and the duration of the wave is controlled by how far the wall moves (x0 - x). Our findings demonstrate that the velocity of the blast wave is more deleterious to membranes than is the blast overpressure. At velocities above 600 m/s the negative phase can cause bilayers containing phospholipid and cholesterol to bifurcate at the bilayer center. Such structural perturbations could result in diffuse axonal injury, which is believed to play a role in the pathology of blast injury.

Computational Characterization of DMPI and DMPI(4)P Head Groups

Results from Molecular Dynamics simulations of dimyristoyl-phosphatidylinositol (DMPI) using the C36 CHARMM lipid force field are compared with those from neutron-diffraction and 2H-NMR studies. Calculated and experimental quadrapolar splitting ratios and distances from the bilayer center to inositol deuteration sites are in good agreement. The simulations yield a large number of conformations consistent with the flexibility of the torsion angles between the glycerol and phosphate; the interpretation from diffraction indicated that the inositol ring tilt is within 30 degrees from parallel to the membrane normal, whereas the inositol ring in the simulations is within 40 degrees from perpendicular to the membrane normal, even pointing into the membrane. The results pave the way for the study of interactions between the phosphoinositides in lipid bilayers and their binding partners.