Unperturbed Bilayer Research Articles

Landau levels in deformed bilayer graphene at low magnetic fields

We review the effect of uniaxial strain on the low-energy electronic dispersion and Landau level structure of bilayer graphene. Based on the tight-binding approach, we derive a strain-induced term in the low-energy Hamiltonian and show how strain affects the low-energy electronic band structure. Depending on the magnitude and direction of applied strain, we identify three regimes of qualitatively different electronic dispersions. We also show that in a weak magnetic field, sufficient strain results in the filling factor ν = ± 4 being the most stable in the quantum Hall effect measurement, instead of ν = ± 8 in unperturbed bilayer at a weak magnetic field. To mention, in one of the strain regimes, the activation gap at ν = ± 4 is, down to very low fields, weakly dependent on the strength of the magnetic field.

Exploring Hydrophobic Mismatch using Molecular Dynamics Simulations of Gramicidin A in Lipid Bilayers

Gramicidin A (gA) is a 15-amino acid peptide antibiotic with an alternating L-D sequence, which forms bilayer-spanning, monovalent cation permeable channels in biological membranes and synthetic bilayers. Due to its relatively small size and extensive documentation of its function, it is a perfect candidate for molecular dynamics (MD) simulations to understand not only ion permeation but also channel-bilayer interactions. In this study, we have performed MD simulations of gA in all-atom, explicit dilauroylphosphatidylcholine (DLPC), dimyristoylphosphatidylcholine (DMPC), dioleoyl-phosphatidylcholine (DOPC), and 1-palmitoyl,2-oleoylphosphatidylcholine (POPC) bilayers. The variation in acyl chain length in these different phospholipids provides a way to alter protein-membrane interactions as a function of bilayer hydrophobic thickness. A particular goal of the study is to determine whether the predicted and observed local membrane thinning and thickening occurs adjacent to the channel. Furthermore, what is the profile of the bilayer deformation, how far does the perturbation extend radially, and does the extent of the perturbation vary as a function of the unperturbed bilayer thickness. In addition, does the channel distort in order to minimize the hydrophobic restraints imposed by the channel-bilayer hydrophobic mismatch. All of the work will be categorized based on energetic favorability, building a model for the prediction of protein-membrane interactions. Currently each system has been simulated for 10 ns.

Simulation Studies of Protein-Induced Bilayer Deformations, and Lipid-Induced Protein Tilting, on a Mesoscopic Model for Lipid Bilayers with Embedded Proteins

Biological membranes are complex and highly cooperative structures. To relate biomembrane structure to their biological function it is often necessary to consider simpler systems. Lipid bilayers composed of one or two lipid species, and with embedded proteins, provide a model system for biological membranes. Here we present a mesoscopic model for lipid bilayers with embedded proteins, which we have studied with the help of the dissipative particle dynamics simulation technique. Because hydrophobic matching is believed to be one of the main physical mechanisms regulating lipid-protein interactions in membranes, we considered proteins of different hydrophobic length (as well as different sizes). We studied the cooperative behavior of the lipid-protein system at mesoscopic time- and lengthscales. In particular, we correlated in a systematic way the protein-induced bilayer perturbation, and the lipid-induced protein tilt, with the hydrophobic mismatch (positive and negative) between the protein hydrophobic length and the pure lipid bilayer hydrophobic thickness. The protein-induced bilayer perturbation was quantified in terms of a coherence length, ξP, of the lipid bilayer hydrophobic thickness profile around the protein. The dependence on temperature of ξP, and the protein tilt-angle, were studied above the main-transition temperature of the pure system, i.e., in the fluid phase. We found that ξP depends on mismatch, i.e., the higher the mismatch is, the longer ξP becomes, at least for positive values of mismatch; a dependence on the protein size appears as well. In the case of large model proteins experiencing extreme mismatch conditions, in the region next to the so-called lipid annulus, there appears an undershooting (or overshooting) region where the bilayer hydrophobic thickness is locally lower (or higher) than in the unperturbed bilayer, depending on whether the protein hydrophobic length is longer (or shorter) than the pure lipid bilayer hydrophobic thickness. Proteins may tilt when embedded in a too-thin bilayer. Our simulation data suggest that, when the embedded protein has a small size, the main mechanism to compensate for a large hydrophobic mismatch is the tilt, whereas large proteins react to negative mismatch by causing an increase of the hydrophobic thickness of the nearby bilayer. Furthermore, for the case of small, peptidelike proteins, we found the same type of functional dependence of the protein tilt-angle on mismatch, as was recently detected by fluorescence spectroscopy measurements.

The alterations of lipid bilayer fluidity induced by newly synthesized phenothiazine derivative

Using fluorescence spectroscopy, calorimetry and ESR the interactions of the phenothiazine derivative 2-trifluoromethyl-10-(4-[methylsulfonylamid]buthyl)-phenothiazine (FPhMS) with lipids were studied. Calorimetry showed biphasic effect of FPhMS on main phase transition of DPPC. At molar ratios up to 0.06 drug induced decrease of transition temperature and enthalpy, while at higher concentrations it caused subsequent increase of these parameters. For all concentrations studied we observed gradual broadening of transition peaks. Fluorescence polarization revealed that in FPhMS/lipid mixtures, order in bilayers is decreased in the gel state and increased in the liquid crystalline state. ESR experiment showed that at molar ratio of 0.06, FPhMS reduces the mobility of spin probes located in both polar and hydrophobic regions. Comparing observed effects with those reported for cholesterol/lipid mixtures, we conclude that at higher concentrations FPhMS presumably induces a new mode of bilayer packing. This structure is less co-operative than an unperturbed bilayer, but locally the mobility of lipid molecules is decreased.

Molecular Theory of Lipid-Protein Interaction and the Lα- HII Transition

We present a molecular-level theory for lipid-protein interaction and apply it to the study of lipid-mediated interactions between proteins and the protein-induced transition from the planar bilayer ( L α ) to the inverse-hexagonal ( H II) phase. The proteins are treated as rigid, membrane-spanning, hydrophobic inclusions of different size and shape, e.g., “cylinder-like,” “barrel-like,” or “vase-like.” We assume strong hydrophobic coupling between the protein and its neighbor lipids. This means that, if necessary, the flexible lipid chains surrounding the protein will stretch, compress, and/or tilt to bridge the hydrophobic thickness mismatch between the protein and the unperturbed bilayer. The system free energy is expressed as an integral over local molecular contributions, the latter accounting for interheadgroup repulsion, hydrocarbon-water surface energy, and chain stretching-tilting effects. We show that the molecular interaction constants are intimately related to familiar elastic (continuum) characteristics of the membrane, such as the bending rigidity and spontaneous curvature, as well as to the less familiar tilt modulus. The equilibrium configuration of the membrane is determined by minimizing the free energy functional, subject to boundary conditions dictated by the size, shape, and spatial distribution of inclusions. A similar procedure is used to calculate the free energy and structure of peptide-free and peptide-rich hexagonal phases. Two degrees of freedom are involved in the variational minimization procedure: the local length and local tilt angle of the lipid chains. The inclusion of chain tilt is particularly important for studying noncylindrical (for instance, barrel-like) inclusions and analyzing the structure of the H II lipid phase; e.g., we find that chain tilt relaxation implies strong faceting of the lipid monolayers in the hexagonal phase. Consistent with experiment, we find that only short peptides (large negative mismatch) can induce the L α → H II transition. At the transition, a peptide-poor L α phase coexists with a peptide-rich H II phase.

Spring Constants for Channel-Induced Lipid Bilayer Deformations Estimates Using Gramicidin Channels

Hydrophobic interactions between a bilayer and its embedded membrane proteins couple protein conformational changes to changes in the packing of the surrounding lipids. The energetic cost of a protein conformational change therefore includes a contribution from the associated bilayer deformation energy ( ΔG def 0), which provides a mechanism for how membrane protein function depends on the bilayer material properties. Theoretical studies based on an elastic liquid-crystal model of the bilayer deformation show that ΔG def 0 should be quantifiable by a phenomenological linear spring model, in which the bilayer mechanical characteristics are lumped into a single spring constant. The spring constant scales with the protein radius, meaning that one can use suitable reporter proteins for in situ measurements of the spring constant and thereby evaluate quantitatively the ΔG def 0 associated with protein conformational changes. Gramicidin channels can be used as such reporter proteins because the channels form by the transmembrane assembly of two nonconducting monomers. The monomer↔dimer reaction thus constitutes a well characterized conformational transition, and it should be possible to determine the phenomenological spring constant describing the channel-induced bilayer deformation by examining how ΔG def 0 varies as a function of a mismatch between the hydrophobic channel length and the unperturbed bilayer thickness. We show this is possible by analyzing experimental studies on the relation between bilayer thickness and gramicidin channel duration. The spring constant in nominally hydrocarbon-free bilayers agrees well with estimates based on a continuum analysis of inclusion-induced bilayer deformations using independently measured material constants.

Lipid bilayer electrostatic energy, curvature stress, and assembly of gramicidin channels.

Hydrophobic interactions between lipid bilayers and imbedded membrane proteins couple protein conformation to the mechanical properties of the bilayer. This coupling is widely assumed to account for the regulation of membrane protein function by the membrane lipids' propensity to form nonbilayer phases, which will produce a curvature stress in the bilayer. Nevertheless, there is only limited experimental evidence for an effect of bilayer curvature stress on membrane protein structure. We show that alterations in curvature stress, due to alterations in the electrostatic energy of dioleoylphosphatidylserine bilayers, modulate the structurally well-defined gramicidin A monomer <--> dimer reaction. Maneuvers that decrease the electrostatic energy of the unperturbed bilayer promote channel dissociation; we measure the change in interaction energy. The bilayer electrostatic energy thus can affect membrane protein structure by a mechanism that does not involve the electrostatic field across the bilayer, but rather electrostatic interactions among the phospholipid head groups in each monolayer which affect the bilayer curvature stress. These results provide further evidence for the importance of mechanical interactions between a bilayer and its imbedded proteins for protein structure and function.

The structure of lipid bilayers and the effects of general anaesthetics: An X-ray and neutron diffraction study

We have looked for the effects of three clinically used inhalational anaesthetics (nitrous oxide, halothane and cyclopropane) on the structure of lecithin/ cholesterol bilayers. The anaesthetics were delivered to the membranes in the gaseous phase, so that effects at clinical concentrations could be determined. High-resolution X-ray diffraction patterns were recorded out to 4 Å and analyzed using swelling experiments. Parallel neutron diffraction experiments were performed and analyzed using H 2O- 2H 2O exchange. Methods were developed which enabled us to obtain confidence limits for the X-ray and neutron structure factors. The resultant X-ray and neutron scattering density profiles clearly define the positions of the principal molecular groups in the unperturbed bilayer. In particular, the high-resolution electron density profiles reveal features directly attributable to the cholesterol molecule. A comparison with the neutron scattering density profiles shows that cholesterol is anchored with its hydroxyl group at the water/hydrocarbon interface, aligned with the fatty acid ester groups of the lecithin molecule. We suggest that this positioning of the cholesterol molecule allows it to act as a thickness buffer for plasma membranes. In the presence of very high concentrations of general anaesthetics, the bilayers show increased disorder while maintaining constant membrane thickness. At surgical concentrations, however, there are no significant changes in bilayer structure at 95% confidence levels. We briefly review the literature previously used to support lipid bilayer hypotheses of general anaesthesia. We conclude that the lipid bilayer per se is not the primary site of action of general anaesthetics.

Hydrocarbon phase transitions and lipid-protein interactions in the erythrocyte membrane. A 31P NMR and fluorescence study

1. 1. 31P NMR and other techniques have been employed to study various derivatives of the human erythrocyte ghost membrane, derived liposomes and liposomes composed of mixtures of synthetic phosphatidylcholines. It is shown that the previously reported (Cullis, P.R. (1976) FEBS Lett. 68, 173–176) phospholipid phase transition observed in ether extracted ghosts is also observable employing fluorescence depolarization techniques. This phase transition can be (reversibly) removed by re-addition of cholesterol. 2. 2. A new semi-biological model membrane system is described which may be obtained by proteolytic digestion of peripheral membrane protein and a subsequent ether extraction. Freeze-etch studies and other considerations indicate that these “pronase digested ether extracted ghosts” consist of segments of integral membrane protein surrounded by one or two boundary layers of lipid. 3. 3. Within the terms of the “fluid mosaic” model of biological membranes lipids may exist in at least four different environments. These include unperturbed bilayer regions, bilayer regions shielded by peripheral membrane protein, lipid experiencing strong polar interactions with membrane protein (bound lipid), and lipid associated with integral membrane protein (boundary lipid). The results obtained here are consistent with the following general conclusions. 3.1. (a). The ether extraction procedure removes most, if not all, of the unperturbed bilayer lipid. 3.2. (b). The amount of membrane phospholipid “bound” to membrane protein so as to cause immobilization in the phosphate group region (on the time scale of 10 −5 s) is at most 3% of the membrane phospholipid. 3.3. (c). Phospholipids in all three of the major classes of lipid (unperturbed bilayer, shielded bilayer and boundary lipid) exhibit 31P NMR spectra consistent with bilayer structure. 3.4. (d). The motion (on the time scale of 10 −5 s) in the phosphate group region of membrane phospholipids is not sensitive to the presence of peripheral membrane protein. 3.5. (e). The phase transition behaviour and 31P NMR lineshapes observed suggest that in the ether extracted ghost system phospholipids in bilayer regions (possibly consisting largely of sphingomyelin) enter the gel state below 20°C. Below 20°C “boundary” phospholipids also experience restricted motion. Above 20°C the results would be consistent with a model whereby boundary phospholipids experience fast exchange with lipids in liquid crystalline bilayer regions.