Calculation of the electrostatic potential of lipid bilayers from molecular dynamics simulations: methodological issues

Structure and Dynamics of Aqueous 2-Aminothiazole/NaCl Electrolytes at Electrified Interfaces

A computational study was performed to investigate the dynamics of aqueous electrolytes containing organic corrosion inhibitors near electrified interfaces by using the constant-charge model in classical molecular dynamics simulations. The results showed that when inhibitors form films at the interface, the surface charge of the electrode causes displacement of the molecules, referred to as electroporation. The hydrophobicity of the inhibitor molecules affects both the stability of the films and their recovery time. This study highlights the value of computational investigations of the dynamics within inhibitor films as a complementary approach to the traditional focus on inhibitor-substrate interactions, leading to deeper insights into the mechanisms of corrosion inhibition mechanisms.

Cryo-EM images of phase-separated lipid bilayer vesicles analyzed with a machine-learning approach

Lateral lipid heterogeneity (i.e., raft formation) in biomembranes plays a functional role in living cells. Three-component mixtures of low- and high-melting lipids plus cholesterol offer a simplified experimental model for raft domains in which a liquid-disordered (Ld) phase coexists with a liquid-ordered (Lo) phase. Using such models, we recently showed that cryogenic electron microscopy (cryo-EM) can detect phase separation in lipid vesicles based on differences in bilayer thickness. However, the considerable noise within cryo-EM data poses a significant challenge for accurately determining the membrane phase state at high spatial resolution. To this end, we have developed an image-processing pipeline that utilizes machine learning (ML) to predict the bilayer phase in projection images of lipid vesicles. Importantly, the ML method exploits differences in both the thickness and molecular density of Lo compared to Ld, which leads to improved phase identification. To assess accuracy, we used artificial images of phase-separated lipid vesicles generated from all-atom molecular dynamics simulations of Lo and Ld phases. Synthetic ground-truth data sets mimicking a series of compositions along a tieline of Ld + Lo coexistence were created and then analyzed with various ML models. For all tieline compositions, we find that the ML approach can correctly identify the bilayer phase with >90% accuracy, thus providing a means to isolate the intensity profiles of coexisting Ld and Lo phases, as well as accurately determine domain-size distributions, number of domains, and phase-area fractions. The method described here provides a framework for characterizing nanoscopic lateral heterogeneities in membranes and paves the way for a more detailed understanding of raft properties in biological contexts.

Counter-ion adsorption and electrostatic potential in sodium and choline dodecyl sulfate micelles - a molecular dynamics simulation study

CONTEXT

Choline-based surfactants are interesting both from the practical point of view to obtaining environmental-friendly surfactants as well as from the theoretical side since the interactions between the choline and surfactants can help to understand self-assembly phenomena in deep eutectic solvents. Although no significant change was noticed in the micelle size and shape due to the exchange of the sodium counter-ion by choline in our simulations, the adsorption of the choline cation over the micelle surface is stronger than the adsorption of the sodium, which leads to a reduction of the exposed surface area of the micelle and remarkable effects over the electrostatic potential. The choline neutralizes the surface charge of the surfactant better than sodium; however, this is partially compensated by a stronger water orientation around the SDS micelle. The balance between the contributions from the surfactant, the counter-ion, and water to the electrostatic potential leads to a complex pattern with alternate regions of positive and negative potential at the micelle/water interface which can be important to the incorporation of other charged species at the micelle surface as well as for the interaction between micelles in solution.

METHODS

To evaluate the effects of the counter-ion substitution, micelles of sodium dodecyl sulfate (SDS) and choline dodecyl sulfate (ChDS) were studied and compared by means of molecular dynamics simulations in aqueous solution. In both cases, the simulations started from pre-assembled micelles with 60 dodecyl sulfate ions and 240-ns simulations were performed at NPT ensemble at T = 323.15 K and P = 1 bar using the Gromacs software with the OPLS-AA force field to describe dodecyl sulfate and choline, Åqvist parameters for sodium, and SPC model for water molecules.

Structure and Elasticity of Mitochondrial Membranes: A Molecular Dynamics Simulation Study

Mitochondria are known as the powerhouse of the cell because they produce energy in the form of adenosine triphosphate. They also have other crucial functions such as regulating apoptosis, calcium homeostasis, and reactive oxygen species production. To perform these diverse functions, mitochondria adopt specific structures and frequently undergo dynamic shape changes, indicating that their mechanical properties play an essential role in their functions. To gain a detailed understanding at the molecular level of the structure and mechanical properties of mitochondria, we carry out atomistic molecular dynamics simulations for three inner mitochondrial membranes and three outer mitochondrial membrane models. These models take into account variations in cardiolipin and cholesterol concentrations as well as the symmetry/asymmetry between the two leaflets. Our simulations allow us to calculate various structural quantities and the bending, twisting, and tilting elastic moduli of the membrane models. Our results indicate that the structures of the inner and outer mitochondrial membranes are quite similar and do not depend much on the variation in lipid compositions. However, the bending modulus of the membranes increases with increasing concentrations of cardiolipin or cholesterol but decreases with a membrane asymmetry. Notably, we found that the dipole potential of the membrane increases with an increasing cardiolipin concentration. Finally, possible roles of cardiolipin in regulating ion and proton currents and maintaining the cristate are discussed in some details.

Peptide Power: Mechanistic Insights into the Effect of Mitochondria-Targeted Tetrapeptides on Membrane Electrostatics from Molecular Simulations

Mitochondrial dysfunction is implicated in nine of the ten leading causes of death in the US, yet there are no FDA-approved therapeutics to treat it. Synthetic mitochondria-targeted peptides (MTPs), including the lead compound SS-31, offer promise, as they have been shown to restore healthy mitochondrial function and treat a variety of common diseases. At the cellular level, research has shown that MTPs accumulate strongly at the inner mitochondrial membrane (IMM), slow energy sinks (e.g., proton leaks), and improve ATP production. Modulation of electrostatic fields around the IMM has been implicated as a key aspect in the mechanism of action (MoA) of these peptides; however, molecular and mechanistic details have remained elusive. In this study, we employed all-atom molecular dynamics simulations (MD) to investigate the interactions of four MTPs with lipid bilayers and calculate their effect on structural and electrostatic properties. In agreement with previous experimental findings, we observed the modulation of the membrane surface and dipole potentials by MTPs. The simulations reveal that the MTPs achieve a reduction in the dipole potential by acting to disorder both lipid head groups and water layers proximal to the bilayer surface. We also find that MTPs decrease the bilayer thickness and increase the membrane's capacitance. These changes suggest that MTPs may enhance how much potential energy can be stored across the IMM at a given transmembrane potential difference. The MTPs also displace cations away from the bilayer surface, modulating the surface potential and offering an alternative mechanism for how these MTPs reduce mitochondrial energy sinks like proton leaks and mitigate Ca2+ accumulation stress. In conclusion, this study highlights the therapeutic potential of MTPs and underlines how interactions of MTPs with lipid bilayers serve as a fundamental component of their MoA.

Building Asymmetric Lipid Bilayers for Molecular Dynamics Simulations: What Methods Exist and How to Choose One?

The compositional asymmetry of biological membranes has attracted significant attention over the last decade. Harboring more differences from symmetric membranes than previously appreciated, asymmetric bilayers have proven quite challenging to study with familiar concepts and techniques, leaving many unanswered questions about the reach of the asymmetry effects. One particular area of active research is the computational investigation of composition- and number-asymmetric lipid bilayers with molecular dynamics (MD) simulations. Offering a high level of detail into the organization and properties of the simulated systems, MD has emerged as an indispensable tool in the study of membrane asymmetry. However, the realization that results depend heavily on the protocol used for constructing the asymmetric bilayer models has sparked an ongoing debate about how to choose the most appropriate approach. Here we discuss the underlying source of the discrepant results and review the existing methods for creating asymmetric bilayers for MD simulations. Considering the available data, we argue that each method is well suited for specific applications and hence there is no single best approach. Instead, the choice of a construction protocol-and consequently, its perceived accuracy-must be based primarily on the scientific question that the simulations are designed to address.

The Effect of Cholesterol in SOPC Lipid Bilayers at Low Temperatures

We study the behavior of lipid bilayers composed of SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) with different concentrations of cholesterol, ranging from 10 mol% to 50 mol% at 273 K. To this end, we carry out extensive atomistic molecular dynamic simulations with the aid of the Slipid force field aiming at computing basic bilayer parameters, as well as thermodynamic properties and structural characteristics. The obtained results are compared to available relevant experimental data and the outcome of atomistic simulations performed on bilayers composed of analogous phospholipids. Our results show a good quantitative, as well as qualitative, agreement with the main trends associated with the concentration increase in cholesterol. Moreover, it comes out that a change in the behavior of the bilayer is brought about at a concentration of about 30 mol% cholesterol. At this very concentration, some of the bilayer properties are found to exhibit a saturation and a significant long-range ordering of the lipid molecules in the membrane shows up.

Cholesterol promotes clustering of PI(4,5)P2 driving unconventional secretion of FGF2

FGF2 is a cell survival factor involved in tumor-induced angiogenesis that is secreted through an unconventional secretory pathway based upon direct protein translocation across the plasma membrane. Here, we demonstrate that both PI(4,5)P2-dependent FGF2 recruitment at the inner plasma membrane leaflet and FGF2 membrane translocation into the extracellular space are positively modulated by cholesterol in living cells. We further revealed cholesterol to enhance FGF2 binding to PI(4,5)P2-containing lipid bilayers. Based on extensive atomistic molecular dynamics (MD) simulations and membrane tension experiments, we proposed cholesterol to modulate FGF2 binding to PI(4,5)P2 by (i) increasing head group visibility of PI(4,5)P2 on the membrane surface, (ii) increasing avidity by cholesterol-induced clustering of PI(4,5)P2 molecules triggering FGF2 oligomerization, and (iii) increasing membrane tension facilitating the formation of lipidic membrane pores. Our findings have general implications for phosphoinositide-dependent protein recruitment to membranes and explain the highly selective targeting of FGF2 toward the plasma membrane, the subcellular site of FGF2 membrane translocation during unconventional secretion of FGF2.

Free-energy landscapes and insertion pathways for peptides in membrane environment

Free-energy landscapes for short peptides-specifically for variants of the pH low insertion peptide (pHLIP)-in the heterogeneous environment of a lipid bilayer or cell membrane are constructed, taking into account a set of dominant interactions and the conformational preferences of the peptide backbone. Our methodology interprets broken internal H-bonds along the backbone of a polypeptide as statistically interacting quasiparticles, activated from the helix reference state. The favored conformation depends on the local environment (ranging from polar to nonpolar), specifically on the availability of external H-bonds (with H_{2}O molecules or lipid headgroups) to replace internal H-bonds. The dominant side-chain contribution is accounted for by residue-specific transfer free energies between polar and nonpolar environments. The free-energy landscape is sensitive to the level of pH in the aqueous environment surrounding the membrane. For high pH, we identify pathways of descending free energy that suggest a coexistence of membrane-adsorbed peptides with peptides in solution. A drop in pH raises the degree of protonation of negatively charged residues and thus increases the hydrophobicity of peptide segments near the C terminus. For low pH, we identify insertion pathways between the membrane-adsorbed state and a stable trans-membrane state with the C terminus having crossed the membrane.

The role of structural order in heterogeneous ice nucleation

The freezing of water into ice is a key process that is still not fully understood. It generally requires an impurity of some description to initiate the heterogeneous nucleation of the ice crystals. The molecular structure, as well as the extent of structural order within the impurity in question, both play an essential role in determining its effectiveness. However, disentangling these two contributions is a challenge for both experiments and simulations. In this work, we have systematically investigated the ice-nucleating ability of the very same compound, cholesterol, from the crystalline (and thus ordered) form to disordered self-assembled monolayers. Leveraging a combination of experiments and simulations, we identify a “sweet spot” in terms of the surface coverage of the monolayers, whereby cholesterol maximises its ability to nucleate ice (which remains inferior to that of crystalline cholesterol) by enhancing the structural order of the interfacial water molecules. These findings have practical implications for the rational design of synthetic ice-nucleating agents.

The freezing of water into ice is still not fully understood. Here, we investigate the role of structural disorder within the biologically relevant impurities that facilitate this fundamental phase transition.

Influence of Substrate Hydrophilicity on Structural Properties of Supported Lipid Systems on Graphene, Graphene Oxides, and Silica

Pristine graphene, a range of graphene oxides, and silica substrates were used to investigate the effect of surface hydrophilicity on supported lipid bilayers by means of all-atom molecular dynamics simulations. Supported 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayers were found in close-contact conformations with hydrophilic substrates with as low as 5% oxidation level, while self-assembled monolayers occur on pure hydrophobic graphene only. Lipids and water at the surface undergo large redistribution to maintain the stability of the supported bilayers. Deposition of bicelles on increasingly hydrophilic substrates shows the continuous process of reshaping of the supported system and makes intermediate stages between self-assembled monolayers and supported bilayers. The bilayer thickness changes with hydrophilicity in a complex manner, while the number of water molecules per lipid in the hydration layer increases together with hydrophilicity.

How to control interactions of cellulose-based biomaterials with skin: the role of acidity in the contact area

Being able to control the interactions of biomaterials with living tissues and skin is highly desirable for many biomedical applications. This is particularly the case for cellulose-based materials which provide one of the most versatile platforms for tissue engineering due to their strength, biocompatibility and abundance. Achieving such control, however, requires detailed molecular-level knowledge of the dominant interaction mechanisms. Here, we employed both biased and unbiased atomic-scale molecular dynamics simulations to explore how cellulose crystals interact with model stratum corneum bilayers, ternary mixtures of ceramides, cholesterol, and free fatty acids. Our findings show that acidity in the contact area directly affects binding between cellulose and the stratum corneum bilayer: Protonation of free fatty acids in the bilayer promotes attractive cellulose-bilayer interactions. We identified two major factors that control the cellulose-skin interactions: (i) the electrostatic repulsion between a cellulose crystal and the charged (anionic due to deprotonated fatty acids) surface of a stratum corneum bilayer and (ii) the cellulose-stratum corneum hydrogen bonding. When less than half of the fatty acids in the bilayer are protonated, the first factor dominates and there is no binding to skin. At a larger degree of fatty acid protonation the cellulose-stratum corneum hydrogen bonding prevails yielding a tight binding. Remarkably, we found that ceramide molecules are the key component in hydrogen bonding with cellulose. Overall, our findings highlight the critical role of fatty acid protonation in biomaterial-stratum corneum interactions and can be used for optimizing the surface properties of cellulose-based materials aimed at biomedical applications such as wound dressings.

Influence of Membrane Phase on the Optical Properties of DPH

The fluorescent molecule diphenylhexatriene (DPH) has been often used in combination with fluorescence anisotropy measurements, yet little is known regarding the non-linear optical properties. In the current work, we focus on them and extend the application to fluorescence, while paying attention to the conformational versatility of DPH when it is embedded in different membrane phases. Extensive hybrid quantum mechanics/molecular mechanics calculations were performed to investigate the influence of the phase- and temperature-dependent lipid environment on the probe. Already, the transition dipole moments and one-photon absorption spectra obtained in the liquid ordered mixture of sphingomyelin (SM)-cholesterol (Chol) (2:1) differ largely from the ones calculated in the liquid disordered DOPC and solid gel DPPC membranes. Throughout the work, the molecular conformation in SM:Chol is found to differ from the other environments. The two-photon absorption spectra and the ones obtained by hyper-Rayleigh scattering depend strongly on the environment. Finally, a stringent comparison of the fluorescence anisotropy decay and the fluorescence lifetime confirm the use of DPH to gain information upon the surrounding lipids and lipid phases. DPH might thus open the possibility to detect and analyze different biological environments based on its absorption and emission properties.

The Voltage-Dependent Deactivation of the KvAP Channel Involves the Breakage of Its S4 Helix

Voltage-gated potassium channels (Kv) allow ion permeation upon changes of the membrane electrostatic potential (Vm). Each subunit of these tetrameric channels is composed of six transmembrane helices, of which the anti-parallel helix bundle S1-S4 constitutes the voltage-sensor domain (VSD) and S5-S6 forms the pore domain. Here, using 82 molecular dynamics (MD) simulations involving 266 replicated VSDs, we report novel responses of the archaebacterial potassium channel KvAP to membrane polarization. We show that the S4 α-helix, which is straight in the experimental crystal structure solved under depolarized conditions (Vm ∼ 0), breaks into two segments when the cell membrane is hyperpolarized (Vm << 0), and reversibly forms a single straight helix following depolarization (Vm = 0). The outermost segment of S4 translates along the normal to the membrane, bringing new perspective to previously paradoxical accessibility experiments that were initially thought to imply the displacement of the whole VSD across the membrane. The novel model is applied through steered and unbiased MD simulations to the recently solved whole structure of KvAP. The simulations show that the resting state involves a re-orientation of the S5 α-helix by ∼ 5-6 degrees in respect to the normal of the bilayer, which could result in the constriction and closure of the selectivity filter. Our findings support the idea that the breakage of S4 under (hyper)polarization is a general feature of Kv channels with a non-swapped topology.

Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description

Membranes are a crucial component of both bacterial and mammalian cells, being involved in signaling, transport, and compartmentalization. This versatility requires a variety of lipid species to tailor the membrane’s behavior as needed, increasing the complexity of the system. Molecular dynamics simulations have been successfully applied to study model membranes and their interactions with proteins, elucidating some crucial mechanisms at the atomistic detail and thus complementing experimental techniques. An accurate description of the functional interplay of the diverse membrane components crucially depends on the selected parameters that define the adopted force field. A coherent parameterization for lipids and proteins is therefore needed. In this work, we propose and validate new lipid head group parameters for the GROMOS 54A8 force field, making use of recently published parametrizations for key chemical moieties present in lipids. We make use additionally of a new canonical set of partial charges for lipids, chosen to be consistent with the parameterization of soluble molecules such as proteins. We test the derived parameters on five phosphocholine model bilayers, composed of lipid patches four times larger than the ones used in previous studies, and run 500 ns long simulations of each system. Reproduction of experimental data like area per lipid and deuterium order parameters is good and comparable with previous parameterizations, as well as the description of liquid crystal to gel-phase transition. On the other hand, the orientational behavior of the head groups is more realistic for this new parameter set, and this can be crucial in the description of interactions with other polar molecules. For that reason, we tested the interaction of the antimicrobial peptide lactoferricin with two model membranes showing that the new parameters lead to a weaker peptide–membrane binding and give a more realistic outcome in comparing binding to antimicrobial versus mammal membranes.

Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study

This review gives an overview about the some of the most important possible analyzes, technical challenges, and existing protocols that can be performed on the biological membrane by the molecular dynamics simulation.

Molecular dynamics simulation of potentiometric sensor response: the effect of biomolecules, surface morphology and surface charge

The silica-water interface is critical to many modern technologies in chemical engineering and biosensing. One technology used commonly in biosensors, the potentiometric sensor, operates by measuring the changes in electric potential due to changes in the interfacial electric field. Predictive modelling of this response caused by surface binding of biomolecules remains highly challenging. In this work, through the most extensive molecular dynamics simulation of the silica-water interfacial potential and electric field to date, we report a novel prediction and explanation of the effects of nano-morphology on sensor response. Amorphous silica demonstrated a larger potentiometric response than an equivalent crystalline silica model due to increased sodium adsorption, in agreement with experiments showing improved sensor response with nano-texturing. We provide proof-of-concept that molecular dynamics can be used as a complementary tool for potentiometric biosensor response prediction. Effects that are conventionally neglected, such as surface morphology, water polarisation, biomolecule dynamics and finite-size effects, are explicitly modelled.

Molecular Modeling of Multidrug Properties of Resistance Nodulation Division (RND) Transporters

Efflux pumps of the resistance nodulation division (RND) superfamily are among the major contributors to intrinsic and acquired multidrug resistance in Gram-negative bacteria. Structural information on AcrAB-TolC and MexAB-OprM, major efflux pumps of Escherichia coli and Pseudomonas aeruginosa respectively, boosted intensive research aimed at understanding the molecular mechanisms ruling the active extrusion processes. In particular, several studies were devoted to the understanding of the determinants behind the extraordinary broad specificity of the RND transporters AcrB and MexB. In this chapter, we discuss the ever-growing role computational methods have been playing in deciphering key structural and dynamical features of these transporters and of their interaction with substrates and inhibitors. We further discuss and illustrate examples from our lab of how molecular docking, homology modeling, all-atom molecular dynamics simulations and in silico free energy estimations can all together give precious insights into the processes of recognition and extrusion of substrates, as well as on the possible inhibition strategies.

pH Sensing Properties of Flexible, Bias-Free Graphene Microelectrodes in Complex Fluids: From Phosphate Buffer Solution to Human Serum

Advances in techniques for monitoring pH in complex fluids can have a significant impact on analytical and biomedical applications. This study develops flexible graphene microelectrodes (GEs) for rapid (<5 s), very-low-power (femtowatt) detection of the pH of complex biofluids by measuring real-time Faradaic charge transfer between the GE and a solution at zero electrical bias. For an idealized sample of phosphate buffer solution (PBS), the Faradaic current is varied monotonically and systematically with the pH, with a resolution of ≈0.2 pH unit. The current-pH dependence is well described by a hybrid analytical-computational model, where the electric double layer derives from an intrinsic, pH-independent (positive) charge associated with the graphene-water interface and ionizable (negative) charged groups. For ferritin solution, the relative Faradaic current, defined as the difference between the measured current response and a baseline response due to PBS, shows a strong signal associated with ferritin disassembly and the release of ferric ions at pH ≈2.0. For samples of human serum, the Faradaic current shows a reproducible rapid (<20 s) response to pH. By combining the Faradaic current and real-time current variation, the methodology is potentially suitable for use to detect tumor-induced changes in extracellular pH.

Gating Charge Calculations by Computational Electrophysiology Simulations

Electrical cell signaling requires adjustment of ion channel, receptor, or transporter function in response to changes in membrane potential. For the majority of such membrane proteins, the molecular details of voltage sensing remain insufficiently understood. Here, we present a molecular dynamics simulation-based method to determine the underlying charge movement across the membrane-the gating charge-by measuring electrical capacitor properties of membrane-embedded proteins. We illustrate the approach by calculating the charge transfer upon membrane insertion of the HIV gp41 fusion peptide, and validate the method on two prototypical voltage-dependent proteins, the Kv1.2 K⁺ channel and the voltage sensor of the Ciona intestinalis voltage-sensitive phosphatase, against experimental data. We then use the gating charge analysis to study how the T1 domain modifies voltage sensing in Kv1.2 channels and to investigate the voltage dependence of the initial binding of two Na⁺ ions in Na⁺-coupled glutamate transporters. Our simulation approach quantifies various mechanisms of voltage sensing, enables direct comparison with experiments, and supports mechanistic interpretation of voltage sensitivity by fractional amino acid contributions.

Effects of Lithium and Other Monovalent Ions on Palmitoyl Oleoyl Phosphatidylcholine Bilayer

Interactions of monovalent salts with lipid membranes are explored with molecular dynamics (MD) simulations. The simulations included the monovalent ions Na⁺ and K⁺, for their importance in physiology, Li⁺ for its small size and importance in several medical conditions including bipolar disorder, and Rb⁺ for its large size. All simulations included Cl^- as counterions. One bilayer was simulated without salt as a control. Palmitoyl oleoyl phosphatidylcholine (POPC) bilayers experienced reductions in area per lipid with the addition of salt; the smaller the ion the smaller the area, with the exception of Li⁺. Li⁺ exhibited unique binding affinities between phosphates and sn-2 carbonyls that lowered the order of the top part of sn-2 chain, which increased the area per lipid, compared to other ionic simulations. Further, we observe that monovalent salts alter bilayer properties through structural changes and not so much through the changes in surface potential.

What Can We Learn about Cholesterol's Transmembrane Distribution Based on Cholesterol-Induced Changes in Membrane Dipole Potential?

Cholesterol is abundant in the plasma membranes of animal cells and is known to regulate a variety of membrane properties. Despite decades of research, the transmembrane distribution of cholesterol is still a matter of debate. Here we consider this outstanding issue through atomistic simulations of asymmetric lipid membranes, whose composition is largely consistent with eukaryotic plasma membranes. We show that the membrane dipole potential changes in a cholesterol-dependent manner. Remarkably, moving cholesterol from the extracellular to the cytosolic leaflet increases the dipole potential on the cytosolic side, and vice versa. Biologically this implies that by altering the dipole potential, cholesterol can provide a driving force for cholesterol molecules to favor the cytosolic leaflet, in order to compensate for the intramembrane field that arises from the resting potential.

Interaction of NBD-labelled fatty amines with liquid-ordered membranes: a combined molecular dynamics simulation and fluorescence spectroscopy study

A complete homologous series of fluorescent 7-nitrobenz-2-oxa-1,3-diazol-4-yl-(NBD) labelled fatty amines of varying alkyl chain lengths, NBD-Cn, inserted in 1-palmitoyl, 2-oleoyl-sn-glycero-3-phosphocholine (POPC) or N-palmitoyl sphingomyelin (SpM) bilayers, with 50 mol% and 40 mol% cholesterol (Chol), respectively, was studied using atomistic molecular dynamics simulations. For all amphiphiles in both bilayers, the NBD fluorophore locates at the interface, in a more external position than that previously observed for pure POPC bilayers. This shallower location of the NBD group agrees with the lower fluorescent quantum yield, shorter fluorescence lifetime, and higher ionisation constants (smaller pKa) determined experimentally. The more external location is also consistent with the changes measured in steady-state fluorescence anisotropy from POPC to POPC/Chol (1 : 1) vesicles. Accordingly, the equilibrium location of the NBD group within the various bilayers is mainly dictated by bilayer compositions, and is mostly unaffected by the length of the attached alkyl chain. Similarly to the behaviour observed in POPC bilayers, the longer-chained NBD-Cn amphiphiles show significant mass density near the mixed bilayers' midplanes, and the alkyl chains of the longer derivatives, mainly NBD-C16, penetrate the opposite bilayer leaflet to some extent. However, this effect is quantitatively less pronounced in these ordered bilayers than in POPC. Similarly to POPC bilayers, the effects of these amphiphiles on the structure and dynamics of the host lipid were found to be relatively mild, in comparison with acyl-chain phospholipid analogues.

Surface Electrostatic Potential and Water Orientation in the presence of Sodium Octanoate Dilute Monolayers Studied by Means of Molecular Dynamics Simulations

A series of atomistic molecular dynamics simulations were performed in the present investigation to assess the spontaneous formation of surfactant monolayers of sodium octanoate at the water-vacuum interface. The surfactant surface coverage increased until a saturation threshold was achieved, after which any further surfactant addition led to the formation of micellar aggregates within the solution. The saturated films were not densely packed, as might be expected for short-chained surfactants, and all films regardless of the surface coverage presented surfactant molecules with the same ordering pattern, namely, with the ionic heads toward the aqueous solution and the tails lying nearly parallel to the interface. The major contributions to the electrostatic surface potential came from the charged heads and the counterion distribution, which nearly canceled out each other. The balance between the oppositely charged ions rendered the electrostatic contributions from water meaningful, amounting to ca. 10% of the contributions arising from the ionic species. And even the aliphatic tails, whose atoms bear relatively small partial atomic charges as compared to the polar molecules and molecular fragments, contributed with ca. 20% of the total electrostatic surface potential of the systems under investigation. Although the aliphatic tails were not so orderly arranged as in a compact film, the C-H bonds assumed a preferential orientation, leading to an increased contribution to the electrostatic properties of the interface. The most prominent feature arising from the partitioning of the electrostatic potential into individual contributions was the long-range ordering of the water molecules. This ordering of the water molecules produced a repulsive dipole-dipole interaction between the two interfaces, which increased with the surface coverage. Only for a water layer wider than 10 nm was true bulk behavior observed, and the repulsive dipole-dipole interaction faded away.

Membrainy: a 'smart', unified membrane analysis tool

BACKGROUND

The study of biological membranes using Molecular Dynamics has become an increasingly popular means by which to investigate the interactions of proteins, peptides and potentials with lipid bilayers. These interactions often result in changes to the properties of the lipids which can modify the behaviour of the membrane. Membrainy is a unified membrane analysis tool that contains a broad spectrum of analytical techniques to enable: measurement of acyl chain order parameters; presentation of 2D surface and thickness maps; determination of lateral and axial headgroup orientations; measurement of bilayer and leaflet thickness; analysis of the annular shell surrounding membrane-embedded objects; quantification of gel percentage; time evolution of the transmembrane voltage; area per lipid calculations; and quantification of lipid mixing/demixing entropy.

RESULTS

Each analytical component within Membrainy has been tested on a variety of lipid bilayer systems and was found to be either comparable to or an improvement upon existing software. For the analytical techniques that have no direct comparable software, our results were confirmed with experimental data.

CONCLUSIONS

Membrainy is a user-friendly, intelligent membrane analysis tool that automatically interprets a variety of input formats and force fields, is compatible with both single and double bilayers, and capable of handling asymmetric bilayers and lipid flip-flopping. Membrainy has been designed for ease of use, requiring no installation or configuration and minimal user-input to operate.

Electroporation threshold of POPC lipid bilayers with incorporated polyoxyethylene glycol (C12E8)

Electroporation relates to a phenomenon in which cell membranes are permeabilized after being exposed to high electric fields. On the molecular level, the mechanism is not yet fully elucidated, although a considerable body of experiments and molecular dynamic (MD) simulations were performed on model membranes. Here we present the results of a combined theoretical and experimental investigation of electroporation of palmitoy-oleoyl-phosphatidylcholine (POPC) bilayers with incorporated polyoxyethylene glycol (C12E8) surfactants. The experimental results show a slight increase of the capacitance and a 22% decrease of the voltage breakdown upon addition of C12E8 to pure POPC bilayers. These results were qualitatively confirmed by the MD simulations. They later revealed that the polyoxyethylene glycol molecules play a major role in the formation of hydrophilic pores in the bilayers above the electroporation threshold. The headgroup moieties of the latter are indeed embedded in the interior of the bilayer, which favors formation of water wires that protrude into its hydrophobic core. When the water wires extend across the whole bilayer, they form channels stabilized by the C12E8 head groups. These hydrophilic channels can transport ions across the membrane without the need of major lipid head-group rearrangements.

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].

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.

Effects of dimethyl sulfoxide on lipid membrane electroporation

Pores can be generated in lipid membranes by the application of an external electric field or by the addition of particular chemicals such as dimethyl sulfoxide (DMSO). Molecular dynamics (MD) has been shown to be a useful tool for unveiling many aspects of pore formation in lipid membranes in both situations. By means of MD simulations, we address the formation of electropores in cholesterol-containing lipid bilayers under the influence of DMSO. We show how a combination of physical and chemical mechanisms leads to more favorable conditions for generating membrane pores and, in particular, how the addition of DMSO to the medium significantly reduces the minimum electric field required to electroporate a lipid membrane. The strong alteration of membrane transversal properties and the energetic stabilization of the hydrophobic pore stage by DMSO provide the physicochemical mechanisms that explain this effect.

Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: the MEMPOT algorithm implemented in DelPhi

Four chemotypes of the rough lipopolysaccharides (LPS) membrane from Pseudomonas aeruginosa were investigated by a combined approach of explicit water molecular dynamics (MD) simulations and Poisson-Boltzmann continuum electrostatics with the goal to deliver the distribution of the electrostatic potential across the membrane. For the purpose of this investigation, a new tool for modeling the electrostatic potential profile along the axis normal to the membrane, MEMbrane POTential (MEMPOT), was developed and implemented in DelPhi. Applying MEMPOT on the snapshots obtained by MD simulations, two observations were made: (a) the average electrostatic potential has a complex profile but is mostly positive inside the membrane due to the presence of Ca(2+) ions, which overcompensate for the negative potential created by lipid phosphate groups; and (b) correct modeling of the electrostatic potential profile across the membrane requires taking into account the water phase, while neglecting it (vacuum calculations) results in dramatic changes including a reversal of the sign of the potential inside the membrane. Furthermore, using DelPhi to assign different dielectric constants for different regions of the LPS membranes, it was investigated whether a single frame structure before MD simulations with appropriate dielectric constants for the lipid tails, inner, and the external leaflet regions, can deliver the same average electrostatic potential distribution as obtained from the MD-generated ensemble of structures. Indeed, this can be attained by using smaller dielectric constant for the tail and inner leaflet regions (mostly hydrophobic) than for the external leaflet region (hydrophilic) and the optimal dielectric constant values are chemotype-specific.

Understanding the microscopic origin of gold nanoparticle anisotropic growth from molecular dynamics simulations

We use molecular dynamics simulations in order to understand the microscopic origin of the asymmetric growth mechanism in gold nanorods. We provide the first atomistic model of different surfaces on gold nanoparticles in a growing electrolyte solution, and we describe the interaction of the metal with the surfactants, namely, cetyltrimethylammonium bromide (CTAB) and the ions. An innovative aspect is the inclusion of the role of the surfactants, which are explicitly modeled. We find that on all the investigated surfaces, namely, (111), (110), and (100), CTAB forms a layer of distorted cylindrical micelles where channels among micelles provide direct ion access to the surface. In particular, we show how AuCl2(-) ions, which are found in the growth solution, can freely diffuse from the bulk solution to the gold surface. We also find that the (111) surface exhibits a higher CTAB packing density and a higher electrostatic potential. Both elements would favor the growth of gold nanoparticles along the (111) direction. These findings are in agreement with the growth mechanisms proposed by the experimental groups of Murphy and Mulvaney.

Atomistic study of lipid membranes containing chloroform: looking for a lipid-mediated mechanism of anesthesia

The molecular mechanism of general anesthesia is still a controversial issue. Direct effect by linking of anesthetics to proteins and indirect action on the lipid membrane properties are the two hypotheses in conflict. Atomistic simulations of different lipid membranes subjected to the effect of small volatile organohalogen compounds are used to explore plausible lipid-mediated mechanisms. Simulations of homogeneous membranes reveal that electrostatic potential and lateral pressure transversal profiles are affected differently by chloroform (anesthetic) and carbon tetrachloride (non-anesthetic). Simulations of structured membranes that combine ordered and disordered regions show that chloroform molecules accumulate preferentially in highly disordered lipid domains, suggesting that the combination of both lateral and transversal partitioning of chloroform in the cell membrane could be responsible of its anesthetic action.

Assessment of Common Simulation Protocols for Simulations of Nanopores, Membrane Proteins, and Channels

Molecular dynamics (MD) simulation has become a common technique to study biological systems. Transport of small molecules through carbon nanotubes and membrane proteins has been an intensely studied topic, and MD simulations have been able to provide valuable predictions, many of which have later been experimentally proven. Simulations of such systems pose challenges, and unexpected problems in commonly used protocols and methods have been found in the past few years. The two main reasons why some were not found before are that most of these newly discovered errors do not lead to unstable simulations. Furthermore, some of them manifest themselves only after relatively long simulation times. We assessed the reliability of the most common simulations protocols by MD and stochastic dynamics (SD) or Langevin dynamics, simulations of an alpha hemolysin nanochannel embedded in a palmitoyloleoylphosphatidylcholine (POPC) lipid bilayer. Our findings are that (a) reaction field electrostatics should not be used in simulations of such systems, (b) local thermostats should be preferred over global ones since the latter may lead to an unphysical temperature distribution,

Concentration dependence of NaCl ion distributions around DPPC lipid bilayers

We study the coordination of excess NaCl to zwitterionic DPPC lipid bilayers using molecular dynamics simulations. We find that Na ions directly coordinate with the DPPC lipid carbonyl groups. As the number of excess ions increases, the number of coordinated ions increases, until it reaches a plateau at a ratio near 1 ion per every four lipids at 310 K, and 1 ion per every six lipids at 323 K. The area per lipid decreases as the number of excess ions is increased. For low number of ions per lipids (1:16 and 1:8), most Na ions are bound to the lipid carbonyls, while the Cl form an ionic cloud around the lipid choline groups. As a result of the Na binding, the lipid has an effective positive charge density. The residence time of Na ions bound to the lipid is longer than 40 ns, while Cl ions exchange faster than the nanoseconds timescale. We find that the bound Na ions replace ordered water around the carbonyls. The net linear charge density near the carbonyl groups stays positive, regardless of the presence of excess salt in the solution.

Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail

Presently, most simulations of ion channel function rely upon nonatomistic Brownian dynamics calculations, indirect interpretation of energy maps, or application of external electric fields. We present a computational method to directly simulate ion flux through membrane channels based on biologically realistic electrochemical gradients. In close analogy to single-channel electrophysiology, physiologically and experimentally relevant timescales are achieved. We apply our method to the bacterial channel PorB from pathogenic Neisseria meningitidis, which, during Neisserial infection, inserts into the mitochondrial membrane of target cells and elicits apoptosis by dissipating the membrane potential. We show that our method accurately predicts ion conductance and selectivity and elucidates ion conduction mechanisms in great detail. Handles for overcoming channel-related antibiotic resistance are identified.

Dynamics and control of the two-pulse protocol in electroporation: numerical exploration

Externally applied voltages can create transient, non-selective pores in a cell's membrane, a phenomenon known as electroporation. Electroporation has reduced toxicity, is easy to perform, and does not induce the immune system. Therefore, the technique has a wide range of biological and medical applications. Previous experiments show that a two-pulse protocol, which consists of a fast, large-magnitude pulse and a slow, small-magnitude pulse, can increase the efficiency of drug delivery such as gene electrotransfer. In this work, we investigate the dynamics and control of the two-pulse protocol using a macroscopic model of electroporation. Numerical simulations show that there exists a range of pore radii that cannot be sustained using the conventional, open-loop, two-pulse protocol. As a result, one may need to use pores that are significantly larger than the sizes of the targeted molecules. Moreover, it is not possible to know the rate of delivery a priori. To ensure accurate drug delivery and avoid potential damage to the cell's membrane, we explore feedback mechanisms to eliminate the gap in sustainable pore radii and thus to precisely control the electroporation process. Numerical simulations show that a straightforward feedback algorithm can achieve robust control effects. Moreover, the control algorithm is effective without knowledge of the model and thus has the potential to be implemented in experiments.