Effect of NaCl and KCl on phosphatidylcholine and phosphatidylethanolamine lipid membranes: insight from atomic-scale simulations for understanding salt-induced effects in the plasma membrane

Computer modelling studies of the bilayer/water interface

This review summarises high resolution studies on the interface of lamellar lipid bilayers composed of the most typical lipid molecules which constitute the lipid matrix of biomembranes. The presented results were obtained predominantly by computer modelling methods. Whenever possible, the results were compared with experimental results obtained for similar systems. The first and main section of the review is concerned with the bilayer-water interface and is divided into four subsections. The first describes the simplest case, where the interface consists only of lipid head groups and water molecules and focuses on interactions between the lipid heads and water molecules; the second describes the interface containing also mono- and divalent ions and concentrates on lipid-ion interactions; the third describes direct inter-lipid interactions. These three subsections are followed by a discussion on the network of direct and indirect inter-lipid interactions at the bilayer interface. The second section summarises recent computer simulation studies on the interactions of antibacterial membrane active compounds with various models of the bacterial outer membrane. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Force Field Development for Lipid Membrane Simulations

With the rapid development of computer power and wide availability of modelling software computer simulations of realistic models of lipid membranes, including their interactions with various molecular species, polypeptides and membrane proteins have become feasible for many research groups. The crucial issue of the reliability of such simulations is the quality of the force field, and many efforts, especially in the latest several years, have been devoted to parametrization and optimization of the force fields for biomembrane modelling. In this review, we give account of the recent development in this area, covering different classes of force fields, principles of the force field parametrization, comparison of the force fields, and their experimental validation. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Biophysical insights into the membrane interaction of the core amyloid-forming Aβ40fragment K16–K28 and its role in the pathogenesis of Alzheimer's disease

Role of central hydrophobic region of Aβ40 in membrane interaction.

Free energy landscapes of sodium ions bound to DMPC–cholesterol membrane surfaces at infinite dilution

Typical configuration of two DMPC lipids and one cholesterol molecule solvating one sodium ion, together with two additional water molecules.

Molecular-level insight into the interactions of DNA with phospholipid bilayers: barriers and triggers

A zwitterionic phospholipid bilayer represents a repulsive barrier for DNA binding; this barrier can be overcome through adsorption of divalent cations to the bilayer surface.

Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers

The behavior of electrolytes in molecular dynamics simulations of zwitterionic phospholipid bilayers is very sensitive to the force field parameters used. Here, several 200 ns molecular dynamics of simulations of dipalmitoyl phosphotidylcholine (PC) bilayers in 0.2 M sodium or potassium chloride using various common force field parameters for the cations are presented. All employed parameter sets give a larger number of Na(+) ions than K(+) ions that bind to the lipid heads, but depending on the parameter choice quite different results are seen. A wide range of coordination numbers for the Na(+) and K(+) ions is also observed. These findings have been analyzed and compared to published experimental data. Some simulations produce aggregates of potassium chloride, indicating (in accordance with published simulations) that these force fields do not reproduce the delicate balance between salt and solvated ions. The differences between the force fields can be characterized by one single parameter, the electrostatic radius of the ion, which is correlated to σMO (M represents Na(+)/K(+)), the Lennard-Jones radius. When this parameter exceeds a certain threshold, binding to the lipid heads is no longer observed. One would, however, need more accurate experimental data to judge or rank the different force fields precisely. Still, reasons for the poor performance of some of the parameter sets are clearly demonstrated, and a quality control procedure is provided.

Effects of truncating van der Waals interactions in lipid bilayer simulations

In membrane simulations, it is known that truncating electrostatic interactions results in artificial ordering of lipids at the truncation distance. However, less attention has been paid to the effect of truncating van der Waals (VDW) interactions. Since the VDW potential decays as r(-6), it is frequently neglected beyond a cutoff of around 1 nm. In some cases, analytical dispersion corrections appropriate for isotropic systems are applied to the pressure and the potential energy. In this work, we systematically study the effect of truncating VDW interactions at different cutoffs in 1,2-Dipalmitoyl-sn-glycero-3-phosphocholine bilayers with the Berger force field. We show that the area per lipid decreases systematically when the VDW cutoff (r(c)) increases. This dependence persists even when dispersion corrections are applied. Since the analytical form of the dispersion correction is only appropriate for isotropic systems, we suggest that a long VDW cutoff should be used in preference over a short VDW cutoff. To determine the appropriate cutoff, we simulate liquid pentadecane with the Berger parameters and find that r(c) ≥ 1.4 nm is sufficient to reproduce the density and the heat of vaporization of pentadecane. Bilayers simulated with r(c) ≥ 1.4 nm show an improved agreement with experiments in both the form factors and the deuterium order parameters. Finally, we report that the VDW cutoff has a significant impact on the lipid flip-flop energetics and an inappropriate short VDW cutoff results in a bilayer that is prone to form water defects across the bilayer.

Effect of Supporting Polyelectrolyte Multilayers and Deposition Conditions on the Formation of 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine Lipid Bilayers

The formation of complete supported lipid bilayers by vesicle adsorption and rupture was studied in relation to deposition conditions of vesicles and underlying cushion formed from various polyelectrolytes. Lipid vesicles were formed from zwitterionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and negatively charged 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) in phosphate buffer of various pH with or without NaCl addition. Polyelectrolyte multilayer films (PEM) were constructed by sequential adsorption of alternately charged polyelectrolytes from their solutions-layer-by-layer deposition (LBL). The mechanism of the formation of supported lipid bilayer on polyelectrolyte films was studied by quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM). QCM-D allowed following the adsorption kinetics while AFM measurements verified the morphology of lipid vesicles and isolated bilayer patches on the PEM cushions providing local topological images in terms of lateral organization. Additionally, polyelectrolyte cushions were characterized with ellipsometry to find thickness and swelling properties, and their roughness was determined using AFM. It has been demonstrated that the pH value and an addition of NaCl in the buffer solution as well as the type of the polyelectrolyte cushion influence the kinetics of bilayer formation and the quality of formed bilayer patches.

Ionic liquid matrix-based dispersive liquid-liquid microextraction for enhanced MALDI-MS analysis of phospholipids in soybean

Ionic liquid matrix (ILM) is found to be a very versatile substance for analysis of broad range of organic molecules in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) due to good solubility for a variety of analytes, formation of homogenous crystals and high vacuum stability of the matrix. In the present work, an ILM, cyno-4-hydroxycinnamic acid-butylamine (CHCAB) was employed in dispersive liquid-liquid microextraction (DLLME) as sample probe and matrix for extraction and ionization of phospholipids from food samples (soybean) prior to MALDI-MS analysis. With the employed technique, 8-125 fold improvement in signal intensity and limit of detection were achieved for the analysis of phospholipids. The best extraction efficiency of phospholipids in ILM-DLLME was obtained with 5min extraction time in presence 30mg/mL CHCAB and 1.2% NaCl using chloroform as an extracting solvent and methanol as a dispersing solvent. Further, the developed ILM-DLLME procedure has been successfully applied for the analysis of phospholipids in soybean samples in MALDI-MS.

Anomalous surface diffusion of protons on lipid membranes

The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of -13.0 ± 0.5 kJ mol(-1). The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery.

Membrane permeation of a peptide: it is better to be positive

A joint experimental and computational study investigates the translocation of a tryptophan molecule through a phospholipid membrane. Time dependent spectroscopy of the tryptophan side chain determines the rate of permeation into 150 nm phospholipid vesicles. Atomically detailed simulations are conducted to calculate the free energy profiles and the permeation coefficient. Different charging conditions of the peptide (positive, negative, or zwitterion) are considered. Both experiment and simulation reproduce the qualitative trend and suggest that the fastest permeation is when the tryptophan is positively charged. The permeation mechanism, which is revealed by molecular dynamics simulations, is of a translocation assisted by a local defect. The influence of long-range electrostatic interactions, such as the membrane dipole potential on the permeation process, is not significant.

Ion specific effects: decoupling ion-ion and ion-water interactions

Ion-specific effects in aqueous solution, known as the Hofmeister effect, are prevalent in diverse systems ranging from pure ionic to complex protein solutions. The objective of this paper is to explicitly demonstrate how complex ion-ion and ion-water interactions manifest themselves in the Hofmeister effect based on a series of recent experimental observations. These effects are not considered in the classical descriptions of ion effects, such as the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, and therefore they fail to describe the origin of the phenomenological Hofmeister effect. However, given that models considering the basic forces of electrostatic and van der Waals interactions can offer rationalization for the core experimental observations, a universal interaction model stands a chance of being developed. In this perspective, we separately derive the contribution from ion-ion electrostatic interactions and ion-water interactions from second harmonic generation (SHG) data at the air-ion solution interface, which yields an estimate of the ion-water interactions in solution. The Hofmeister ion effect observed for biological solutes in solution should be similarly influenced by contributions from ion-ion and ion-water interactions, where the same ion-water interaction parameters derived from SHG data at the air-ion solution interface could be applicable. A key experimental data set available from solution systems to probe ion-water interactions is the modulation of water diffusion dynamics near ions in a bulk ion solution, as well as near biological liposome surfaces. This is obtained from Overhauser dynamic nuclear polarization (ODNP), a nuclear magnetic resonance (NMR) relaxometry technique. The surface water diffusivity is influenced by the contribution from ion-water interactions, both from localized surface charges and adsorbed ions, although the relative contribution of the former is larger on liposome surfaces. In this perspective, ion-water interaction energy values derived from experimental data for various ions are compared with theoretical values in the literature. Ultimately, quantifying ion-induced changes in the surface energy for the purpose of developing valid theoretical models for ion-water interactions will be critical to rationalizing the Hofmeister effect.

Interfacial water screens the protein-induced transmembrane voltage

Transmembrane proteins are crucial in cellular traffic, signal transduction, and energy storage in a form of transmembrane voltage. These proteins are stabilized by hydrophobic and hydrophilic interactions, in which cytoplasmic and exoplasmic water plays a special role. Water structural ordering generates the dipole potential that typically overcompensates for an intrinsic membrane-protein potential gradient, and thus it modifies and sustains an overall cellular electrostatics. Although the transmembrane voltage has been extensively studied, the dipole potential has attracted very little attention. Here, by using molecular dynamics, we examined water electrostatic response to the transmembrane charge, field, and potential asymmetry introduced by the presence of four integral membrane proteins: typical of inner (α-helix) and outer membrane (β-barrel). In all cases, the protein presence introduces electrostatic directionality in the transmembrane dipole field and voltage. In particular, water generates a deep potential sink if strongly polar residues are densely packed on one side of bilayer, as frequently occurs in a selectivity filter of the K(+) channel. We also found that protein secondary structure is less important than the polar residue distribution along the protein channel. Our findings are relevant for understanding the driving force behind biomembrane conductivity: the ability of biological water to electrostatically screen the transmembrane voltage.

Behaviour of NBD-head group labelled phosphatidylethanolamines in POPC bilayers: a molecular dynamics study

An NBD-diC₁₆PE/POPC bilayer with typical fluorophore inverted-snorkelling configurations, and mass density profiles across the membrane. The wide distribution of the NBD fluorophore lies at the origin of its complex emission kinetics.

Influence of the sterol aliphatic side chain on membrane properties: a molecular dynamics study

Cholesterol provides best hydrophobic matching, induces maximal membrane ordering, and displays highest preference for saturated phospholipid acyl chains, among a homologous ser ies of sterols with side chains of varying lengths.

Amphiphilic interactions of ionic liquids with lipid biomembranes: a molecular simulation study

Current bottlenecks in the large-scale commercial use of many ionic liquids (ILs) include their high costs, low biodegradability, and often unknown toxicities. As a proactive effort to better understand the molecular mechanisms of ionic liquid toxicities, the work herein presents a comprehensive molecular simulation study on the interactions of 1-n-alkyl-3-methylimidazolium-based ILs with a phosphatidylcholine (PC) lipid bilayer. We explore the effects of increasing alkyl chain length (n = 4, 8, and 12) in the cation and anion hydrophobicity on the interactions with the lipid bilayer. Bulk atomistic molecular dynamics (MD) simulations performed at millimolar (mM) IL concentrations show spontaneous insertion of cations into the lipid bilayer regardless of the alkyl chain length and a favorable orientational preference once a cation is inserted. Cations also exhibit the ability to "flip" inside the lipid bilayer (as is common for amphiphiles) if partially inserted with an unfavorable orientation. Moreover, structural analysis of the lipid bilayer show that cationic insertion induces roughening of the bilayer surface, which may be a precursor to bilayer disruption. To overcome the limitation in the timescale of our simulations, free energies for a single IL cation and anion insertion have been determined based on potential of mean force calculations. These results show a decrease in free energy in response to both short and long alkyl chain IL cation insertion, and likewise for a single hydrophobic anion insertion, but an increase in free energy for the insertion of a hydrophilic chloride anion. Both bulk MD simulations and free energy calculations suggest that toxicity mechanisms toward biological systems are likely caused by ILs behaving as ionic surfactants. [Yoo et al., Soft Matter, 2014].

Ionic strength and composition govern the elasticity of biological membranes. A study of model DMPC bilayers by force- and transmission IR spectroscopy

Infrared (IR) spectroscopy was used to quantify the ion mixture effect of seawater (SW), particularly the contribution of Mg(2+) and Ca(2+) as dominant divalent cations, on the thermotropic phase behaviour of 1,2-dimyristoyl-sn-glycero-3-posphocholine (DMPC) bilayers. The changed character of the main transition at 24 °C from sharp to gradual in films and the 1 °C shift of the main transition temperature in dispersions reflect the interactions of lipid headgroups with the ions in SW. Force spectroscopy was used to quantify the nanomechanical hardness of a DMPC supported lipid bilayer (SLB). Considering the electrostatic and ion binding equilibrium contributions while systematically probing the SLB in various salt solutions, we showed that ionic strength had a decisive influence on its nanomechanics. The mechanical hardness of DMPC SLBs in the liquid crystalline phase linearly increases with the increasing fraction of all ion-bound lipids in a series of monovalent salt solutions. It also linearly increases in the gel phase but almost three times faster (the corresponding slopes are 4.9 nN/100 mM and 13.32 nN/100 mM, respectively). We also showed that in the presence of divalent ions (Ca(2+) and Mg(2+)) the bilayer mechanical hardness was unproportionally increased, and that was accompanied with the decrease of Na(+) ion and increase of Cl(-) ion bound lipids. The underlying process is a cooperative and competitive ion binding in both the gel and the liquid crystalline phase. Bilayer hardness thus turned out to be very sensitive to ionic strength as well as to ionic composition of the surrounding medium. In particular, the indicated correlation helped us to emphasize the colligative properties of SW as a naturally occurring complex ion mixture.

Electric Field Effect on Phospholipid Monolayers at an Aqueous-Organic Liquid-Liquid Interface

The electric potential difference across cell membranes, known as the membrane potential, plays an important role in the activation of many biological processes. To investigate the effect of the membrane potential on the molecular ordering of lipids within a biomimetic membrane, a self-assembled monolayer of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC) lipids at an electrified 1,2-dichloroethane/water interface is studied with X-ray reflectivity and interfacial tension. Measurements over a range of electric potential differences, -150 to +130 mV, that encompass the range of typical biomembrane potentials demonstrate a nearly constant and stable structure whose lipid interfacial density is comparable to that found in other biomimetic membrane systems. Measurements at higher positive potentials, up to 330 mV, illustrate a monotonic decrease in the lipid interfacial density and accompanying variations in the interfacial configuration of the lipid. Molecular dynamics simulations, designed to mimic the experimental conditions, show that the measured changes in lipid configuration are due primarily to the variation in area per lipid with increasing applied electric field. Rotation of the SOPC dipole moment by the torque from the applied electric field appears to be negligible, except at the highest measured potentials. The simulations confirm in atomistic detail the measured potential-dependent characteristics of SOPC monolayers. Our hybrid study sheds light on phospholipid monolayer stability under different membrane potentials, which is important for understanding membrane processes. This study also illustrates the use of X-ray surface scattering to probe the ordering of surfactant monolayers at an electrified aqueous-organic liquid-liquid interface.

Molecular insight into the effect of lipid bilayer environments on thrombospondin-1 and calreticulin interactions

Thrombospondin-1 (TSP1) binding to cell surface calreticulin (CRT) stimulates the association of CRT with low-density lipoprotein (LDL) receptor-related protein (LRP1) to signal focal adhesion disassembly and engagement of cellular activities. A recent study demonstrated that membrane rafts are necessary for TSP1-mediated focal adhesion disassembly, but the molecular role of membrane rafts in mediating TSP1-CRT-LRP1 signaling is unknown. In this study, we investigated the effect of lipid bilayer environments on TSP1 and CRT interactions via atomically detailed molecular dynamics simulations. Results showed that the microscopic structural properties of lipid molecules and mesoscopic mechanical properties and electrostatic potential of the bilayer were significantly different between a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer and a raftlike lipid bilayer [a POPC/cholesterol (CHOL) raftlike lipid bilayer or a POPC/CHOL/sphingomyelin (SM) raftlike lipid bilayer], and the difference was enhanced by SM lipids in a raftlike lipid bilayer. These bilayer property differences affect the interactions of CRT with the bilayer, further influencing CRT conformation and TSP1-CRT interactions. A raftlike lipid bilayer stabilized CRT conformation as compared to a POPC bilayer environment. TSP1 binding to CRT resulted in a conformation for the CRT N-domain more "open" than that of the CRT P-domain in a raftlike lipid bilayer environment, which could facilitate binding of CRT to LRP1 to engage downstream signaling. The open conformational changes of CRT by binding to TSP1 in a raftlike lipid bilayer were enhanced by SM lipids in a lipid bilayer. The direct interactions of both the N- and P-domains of CRT with the bilayer contribute to the more open conformation of CRT in the TSP1-CRT complex on a raftlike lipid bilayer as compared to that on a POPC bilayer. The interactions of CRT or the TSP1-CRT complex with the lipid bilayer also caused CHOL molecules and/or lipids to be more coordinated and to aggregate into patchlike regions in the raftlike lipid bilayers. The lipid and CHOL molecule coordination and aggregation could in turn affect the interactions of CRT with the membrane raft, thereby altering TSP1-CRT interactions and CRT conformational changes that potentially regulate its interactions with LRP1. This study provides molecular insights into the role of lipid bilayer environments in TSP1-CRT interactions and in the CRT conformational changes that are predicted to facilitate binding of CRT to LRP1 to engage downstream signaling events.

Ion-induced defect permeation of lipid membranes

We have explored the mechanisms of uncatalyzed membrane ion permeation using atomistic simulations and electrophysiological recordings. The solubility-diffusion mechanism of membrane charge transport has prevailed since the 1960s, despite inconsistencies in experimental observations and its lack of consideration for the flexible response of lipid bilayers. We show that direct lipid bilayer translocation of alkali metal cations, Cl(-), and a charged arginine side chain analog occurs via an ion-induced defect mechanism. Contrary to some previous suggestions, the arginine analog experiences a large free-energy barrier, very similar to those for Na(+), K(+), and Cl(-). Our simulations reveal that membrane perturbations, due to the movement of an ion, are central for explaining the permeation process, leading to both free-energy and diffusion-coefficient profiles that show little dependence on ion chemistry and charge, despite wide-ranging hydration energies and the membrane's dipole potential. The results yield membrane permeabilities that are in semiquantitative agreement with experiments in terms of both magnitude and selectivity. We conclude that ion-induced defect-mediated permeation may compete with transient pores as the dominant mechanism of uncatalyzed ion permeation, providing new understanding for the actions of a range of membrane-active peptides and proteins.

Specific ions modulate diffusion dynamics of hydration water on lipid membrane surfaces

Effects of specific ions on the local translational diffusion of water near large hydrophilic lipid vesicle surfaces were measured by Overhauser dynamic nuclear polarization (ODNP). ODNP relies on an unpaired electron spin-containing probe located at molecular or surface sites to report on the dynamics of water protons within ∼10 Å from the spin probe, which give rise to spectral densities for electron–proton cross-relaxation processes in the 10 GHz regime. This pushes nuclear magnetic resonance relaxometry to more than an order of magnitude higher frequencies than conventionally feasible, permitting the measurement of water moving with picosecond to subnanosecond correlation times. Diffusion of water within ∼10 Å of, i.e., up to ∼3 water layers around the spin probes located on hydrophilic lipid vesicle surfaces is ∼5 times retarded compared to the bulk water translational diffusion. This directly reflects on the activation barrier for surface water diffusion, i.e., how tightly water is bound to the hydrophilic surface and surrounding waters. We find this value to be modulated by the presence of specific ions in solution, with its order following the known Hofmeister series. While a molecular description of how ions affect the hydration structure at the hydrophilic surface remains to be answered, the finding that Hofmeister ions directly modulate the surface water diffusivity implies that the strength of the hydrogen bond network of surface hydration water is directly modulated on hydrophilic surfaces.

Unveiling the membrane-binding properties of N-terminal and C-terminal regions of G protein-coupled receptor kinase 5 by combined optical spectroscopies

G protein-coupled receptor kinase 5 (GRK5) is thought to associate with membranes in part via N- and C-terminal segments that are typically disordered in available high-resolution crystal structures. Herein we investigate the interactions of these regions with model cell membrane using combined sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. It was found that both regions associate with POPC lipid bilayers but adopt different structures when doing so: GRK5 residues 2-31 (GRK5(2-31)) was in random coil whereas GRK5(546-565) was partially helical. When the subphase for the GRK5(2-31) peptide was changed to 40% TFE/60% 10 mM phosphate pH 7.4 buffer, a large change in the SFG amide I signal indicated that GRK5(2-31) became partially helical. By inspecting the membrane behavior of two different segments of GRK5(2-31), namely, GRK5(2-24) and GRK5(25-31), we found that residues 25-31 are responsible for membrane binding, whereas the helical character is imparted by residues 2-24. With SFG, we deduced that the orientation angle of the helical segment of GRK5(2-31) is 46 ± 1° relative to the surface normal in 40% TFE/60% 10 mM phosphate pH = 7.4 buffer but increases to 78 ± 11° with higher ionic strength. We also investigated the effect of PIP2 in the model membrane and concluded that the POPC:PIP2 (9:1) lipid bilayer did not change the behavior of either peptide compared to a pure POPC lipid bilayer. With ATR-FTIR, we also found that Ca(2+)·calmodulin is able to extract both peptides from the POPC lipid bilayer, consistent with the role of this protein in disrupting GRK5 interactions with the plasma membrane in cells.

Molecular basis of cannabinoid CB1 receptor coupling to the G protein heterotrimer Gαiβγ: identification of key CB1 contacts with the C-terminal helix α5 of Gαi

The cannabinoid (CB1) receptor is a member of the rhodopsin-like G protein-coupled receptor superfamily. The human CB1 receptor, which is among the most expressed receptors in the brain, has been implicated in several disease states, including drug addiction, anxiety, depression, obesity, and chronic pain. Different classes of CB1 agonists evoke signaling pathways through the activation of specific subtypes of G proteins. The molecular basis of CB1 receptor coupling to its cognate G protein is unknown. As a first step toward understanding CB1 receptor-mediated G protein signaling, we have constructed a ternary complex structural model of the CB1 receptor and Gi heterotrimer (CB1-Gi), guided by the x-ray structure of β2-adrenergic receptor (β2AR) in complex with Gs (β2AR-Gs), through 824-ns duration molecular dynamics simulations in a fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer environment. We identified a group of residues at the juxtamembrane regions of the intracellular loops 2 and 3 (IC2 and IC3) of the CB1 receptor, including Ile-218(3.54), Tyr-224(IC2), Asp-338(6.30), Arg-340(6.32), Leu-341(6.33), and Thr-344(6.36), as potential key contacts with the extreme C-terminal helix α5 of Gαi. Ala mutations of these residues at the receptor-Gi interface resulted in little G protein coupling activity, consistent with the present model of the CB1-Gi complex, which suggests tight interactions between CB1 and the extreme C-terminal helix α5 of Gαi. The model also suggests that unique conformational changes in the extreme C-terminal helix α5 of Gα play a crucial role in the receptor-mediated G protein activation.

Molecular dynamics simulations of ion conductance in field-stabilized nanoscale lipid electropores

Molecular dynamics (MD) simulations of electrophoretic transport of monovalent ions through field-stabilized electropores in POPC lipid bilayers permit systematic characterization of the conductive properties of lipid nanopores. The radius of the electropore can be controlled by the magnitude of the applied sustaining external electric field, which also drives the transport of ions through the pore. We examined pore conductances for two monovalent salts, NaCl and KCl, at physiological concentrations. Na(+) conductance is significantly less than K(+) and Cl(-) conductance and is a nonlinear function of pore radius over the range of pore radii investigated. The single pore electrical conductance of KCl obtained from MD simulation is comparable to experimental values measured by chronopotentiometry.

Impact of oxidized phospholipids on the structural and dynamic organization of phospholipid membranes: a combined DSC and solid state NMR study

Membranes undergo severe changes under oxidative stress conditions due to the creation of oxidized phospholipid (OxPL) species, which possess molecular properties quite different from their parental lipid components. These OxPLs play crucial roles in various pathological disorders and their occurrence is involved in the onset of intrinsic apoptosis, a fundamental pathway in programmed mammalian cell death. However, the molecular mechanisms by which these lipids can exert their apoptotic action via their host membranes (e.g., altering membrane protein function) are poorly understood. Therefore, we studied the impact of OxPLs on the organization and biophysical properties of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) based lipid membranes by differential scanning calorimetry (DSC) and solid state nuclear magnetic resonance (NMR) spectroscopy. Incorporation of defined OxPLs with either a carboxyl group (1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PazePC)) or aldehyde (1-palmitoyl-(9'oxononanoyl)-sn-glycero-3-phosphocholine (PoxnoPC)) at their truncated sn-2-chain ends enabled us to reveal OxPL species-dependent differences. The calorimetric studies revealed significant effects of OxPLs on the thermotropic phase behavior of DMPC bilayers, especially at elevated levels where PazePC induced more pronounced effects than PoxnoPC. Temperature-dependent changes in the solid state 31P NMR spectra, which provided information of the lipid headgroup region in these mixed membrane systems, reflected this complex phase behavior. In the temperature region between 293 K (onset of the Lalpha-phase) and 298 K, two overlapping NMR spectra were visible which reflect the co-existence of two liquid-crystalline lamellar phases with presumably one reflecting OxPL-poor domains and the other OxPL-rich domains. Deconvolution of the DSC profiles also revealed these two partially overlapping thermal events. In addition, a third thermal, non-NMR-visible, event occurred at low temperatures, which can most likely be associated to a solid-phase mixing/demixing process of the OxPL-containing membranes. The observed phase transitions were moved to higher temperatures in the presence of heavy water due its condensing effect, where additional wideline 2H-NMR studies revealed a complex hydration pattern in the presence of OxPLs.

Specific binding of chloride ions to lipid vesicles and implications at molecular scale

Biological membranes composed of lipids and proteins are in contact with electrolytes like aqueous NaCl solutions. Based on molecular dynamics studies it is widely believed that Na(+) ions specifically bind to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes, whereas Cl(-) ions stay in solution. Here, we present a careful comparison of recent data from electrophoresis and isothermal titration calorimetry experiments as well as molecular dynamics simulations suggesting that in fact both ions show very similar affinities. The corresponding binding constants are 0.44(±0.05) M(-1) for Na(+) and 0.40(±0.04) M(-1) for Cl(-) ions. This is highlighted by our observation that a widely used simulation setup showing asymmetric affinities of Na(+) and Cl(-) for POPC bilayers overestimates the effect of NaCl on the electrophoretic mobility of a POPC membrane by an order of magnitude. Implications for previous simulation results on the effect of NaCl on polarization of interfacial water, transmembrane potentials, and mechanisms for ion transport through bilayers are discussed. Our findings suggest that a range of published simulations results on the interaction of NaCl with phosphocholine bilayers have to be reconsidered and revised and that force field refinements are necessary for reliable simulation studies of membranes at physiological conditions on a molecular level.

Macro- versus microscopic view on the electrokinetics of a water-membrane interface

Electrophoresis is an experimental method widely used to study electrostatic properties of interfaces. Here, we question the validity of the macroscopic theory for the planar geometry by Helmholtz and Smoluchowski by considering a POPC bilayer in an aqueous solution with 500 mM NaCl, using molecular dynamics simulations. We find that POPC shows positive electrophoretic mobility due to adsorption of sodium ions at the lipid headgroups. The theory assumes that the region in which the water density undergoes a transition from the bulk value to zero (interfacial width) is small compared to the Debye screening length. This separation of length scale is not fullfilled in the present case. Hence, contrasting the theory, we observe that the surface is not sharply defined, continuum hydrodynamics is not applicable, the effective viscosity in the double layer is increased compared to the bulk, and the zeta potential is dominated by the dipole potential. Our results might have widespread implications for interpretation of electrokinetic studies in general.

Advances in the understanding of nanomaterial–biomembrane interactions and their mathematical and numerical modeling

The widespread application of nanomaterials (NMs), which has accompanied advances in nanotechnology, has increased their chances of entering an organism, for example, via the respiratory system, skin absorption or intravenous injection. Although accumulating experimental evidence has indicated the important role of NM–biomembrane interaction in these processes, the underlying mechanisms remain unclear. Computational techniques, as an alternative to experimental efforts, are effective tools to simulate complicated biological behaviors. Computer simulations can investigate NM–biomembrane interactions at the nanoscale, providing fundamental insights into dynamic processes that are challenging to experimental observation. This paper reviews the current understanding of NM–biomembrane interactions, and existing mathematical and numerical modeling methods. We highlight the advantages and limitations of each method, and also discuss the future perspectives in this field. Better understanding of NM–biomembrane interactions can benefit various fields, including nanomedicine and diagnosis.

Power-law trapping of water molecules on the lipid-membrane surface induces water retardation

Cell membranes provide unique local environments for biological reactions, where the diffusion of biomolecules as well as water molecules plays critical roles. Translational and rotational motions of water molecules near membranes are known to be slower than those in bulk. Using all-atom molecular dynamics simulations of a membrane, we show that the temperature dependence of the water molecular motions on the membrane surface is different from that in bulk. Decreasing temperature enhances the water retardation on the membrane surface, and the lateral motions of water molecules are correlated with the vertical motions. We find that trapping times of water molecules onto membrane surfaces are distributed according to a power-law distribution and that the power-law exponents depend linearly on temperature, suggesting a random energy landscape picture. Moreover, we find that water molecules on the membrane surfaces exhibit subdiffusions in translational motions.