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

Giant vesicles form in physiological saline and encapsulate pDNA by the modified electroformation method

Giant vesicles (GVs) are used to study the structures and functions of cells and cell membranes. Electroformation is the most commonly used method for GV preparation. However, the electroformation of GVs is hindered in highly concentrated ionic solutions, limiting their application as cell models for research under physiological conditions. In this study, giant multilayer vesicles were successfully generated in physiological saline using a modified electroformation device by adding an insulating layer between the two electrode plates. The influence of the electric frequency and strength on the electroformation of GVs in physiological saline was explored, and a possible mechanism for this improvement was assessed. It has been shown that an insulating layer between the two electrodes can improve the electroformation of GVs in physiological saline by increasing the electrical impedance, which is weakened by the saline solution, thereby restoring the reduced effective electric field strength. Furthermore, macromolecular plasmid DNA (pDNA) was successfully encapsulated in the electroformed GVs of the modified device. This modified electroformation method may be useful for generating eukaryotic cell models under physiological conditions.

Effect of K+ Force Fields on Ionic Conductivity and Charge Dynamics of KOH in Ethylene Glycol

Predicting ionic conductivity is crucial for developing efficient electrolytes for energy storage and conversion and other electrochemical applications. An accurate estimate of ionic conductivity requires understanding complex ion-ion and ion-solvent interactions governing the charge transport at the molecular level. Molecular simulations can provide key insights into the spatial and temporal behavior of electrolyte constituents. However, such insights depend on the ability of force fields to describe the underlying phenomena. In this work, molecular dynamics simulations were leveraged to delineate the impact of force field parameters on ionic conductivity predictions of potassium hydroxide (KOH) in ethylene glycol (EG). Four different force fields were used to represent the K+ ion. Diffusion-based Nernst-Einstein and correlation-based Einstein approaches were implemented to estimate the ionic conductivity, and the predicted values were compared with experimental measurements. The physical aspects, including ion-aggregation, charge distribution, cluster correlation, and cluster dynamics, were also examined. A force field was identified that provides reasonably accurate Einstein conductivity values and a physically coherent representation of the electrolyte at the molecular level.

Molecular dynamics simulation of phosphatidylcholine membrane in low ionic strengths of sodium chloride

The one-microsecond molecular dynamics simulations of a membrane-protein complex investigate the influence of the aqueous sodium chloride solutions on the structure and dynamics of a palmitoyl-oleoyl-phosphatidylcholine bilayer membrane. The simulations were performed on five different concentrations (40, 150, 200, 300, and 400 mM) in addition to a salt-free system by using the charmm36 force field for all atoms. Four biophysical parameters, (membrane thicknesses of annular and bulk lipids, and the area per lipid of both leaflets), were computed separately. Nevertheless, the area per lipid was expressed by using the Voronoi algorithm. All time-independent analyses were carried out for the last 400 ns trajectories. Different concentrations revealed dissimilar membrane dynamics before equilibration. The biophysical properties of the membrane (thickness, area-per-lipid, and order parameter) have non-significant changes with increasing ionic strength, however, the 150 mM system had exceptional behavior. Sodium cations were dynamically penetrating the membrane forming weak coordinate bonds with single or multiple lipids. Nevertheless, the binding constant was unaffected by the cation concentration. The electrostatic and Van der Waals energies of lipid-lipid interactions were influenced by the ionic strength. On the other hand, the Fast Fourier Transform was performed to figure out the dynamics at the membrane-protein interface. The nonbonding energies of membrane-protein interactions and order parameters explained the differences in the synchronization pattern. All results were consensus with experimental and theoretical works.Communicated by Ramaswamy H. Sarma.

Structure of POPC Lipid Bilayers in OPLS3e Force Field

It is crucial for molecular dynamics simulations of biomembranes that the force field parameters give a realistic model of the membrane behavior. In this study, we examined the OPLS3e force field for the carbon-hydrogen order parameters S_CH of POPC (1-palmitoyl-2-oleoylphosphatidylcholine) lipid bilayers at varying hydration conditions and ion concentrations. The results show that OPLS3e behaves similarly to the CHARMM36 force field and relatively accurately follows the experimentally measured S_CH for the lipid headgroup, the glycerol backbone, and the acyl tails. Thus, OPLS3e is a good choice for POPC bilayer simulations under many biologically relevant conditions. The exception are systems with an abundancy of ions, as similarly to most other force fields OPLS3e strongly overestimates the membrane-binding of cations, especially Ca²⁺. This leads to undesirable positive charge of the membrane surface and drastically lowers the concentration of Ca²⁺ in the surrounding solvent, which might cause issues in systems sensitive to correct charge distribution profiles across the membrane.

Reorganization Free Energy of Copper Proteins in Solution, in Vacuum, and on Metal Surfaces

Metalloproteins, known to efficiently transfer electronic charge in biological systems, recently found their utilization in nanobiotechnological devices where the protein is placed into direct contact with metal surfaces. The feasibility of oxidation/reduction of the protein redox sites is affected by the reorganization free energies, one of the key parameters determining the transfer rates. While their values have been measured and computed for proteins in their native environments, i.e., in aqueous solution, the reorganization free energies of dry proteins or proteins adsorbed to metal surfaces remain unknown. Here, we investigate the redox properties of blue copper protein azurin, a prototypical redox-active metalloprotein previously probed by various experimental techniques both in solution and on metal/vacuum interfaces. We used a hybrid QM/MM computational technique based on DFT to explore protein dynamics, flexibility, and corresponding reorganization free energies in aqueous solution, vacuum, and on vacuum gold interfaces. Somewhat surprisingly, the reorganization free energy only slightly decreases when azurin is dried because the loss of the hydration shell leads to larger flexibility of the protein near its redox site. At the vacuum gold surfaces, the energetics of the structure relaxation depends on the adsorption geometry, however, significant reduction of the reorganization free energy was not observed. These findings have important consequences for the charge transport mechanism in vacuum devices, showing that the free energy barriers for protein oxidation remain significant even under ultra-high vacuum conditions.

High-Dimensional Parameter Search Method to Determine Force Field Mixing Terms in Molecular Simulations

Molecular dynamics (MD) force fields for lipids and ions are typically developed independently of one another. In simulations consisting of both lipids and ions, lipid-ion interaction energies are estimated using a predefined set of mixing rules for Lennard-Jones (LJ) interactions. This, however, does not guarantee their reliability. In fact, compared to the quantum mechanical reference data, Lorentz-Berthelot mixing rules substantially underestimate the binding energies of Na⁺ ions with small-molecule analogues of lipid headgroups, yielding errors on the order of 80 and 130 kJ/mol, respectively, for methyl acetate and diethyl phosphate. Previously, errors associated with mixing force fields have been reduced using approaches such as "NB-fix" in which LJ interactions are computed using explicit cross terms rather than those from mixing rules. Building on this idea, we derive explicit lipid-ion cross terms that also may implicitly include many-body cooperativity effects. Additionally, to account for the interdependency between cross terms, we optimize all cross terms simultaneously by performing high-dimensional searches using our ParOpt software. The cross terms we obtain reduce the errors due to mixing rules to below 10 kJ/mol. MD simulation of the lipid bilayer conducted using these optimized cross terms resolves the structural discrepancies between our previous simulations and small-angle X-ray and neutron scattering experiments. These results demonstrate that simulations of lipid bilayers with ions that are accurate up to structural data from scattering experiments can be performed without explicit polarization terms. However, it is worth noting that such NB-fix cross terms are not based on any physical principle; a polarizable lipid model would be more realistic and is still desired. Our approach is generic and can be applied to improve the accuracies of simulations employing mixed force fields.

Learning to Model G-Quadruplexes: Current Methods and Perspectives

G-quadruplexes have raised considerable interest during the past years for the development of therapies against cancer. These noncanonical structures of DNA may be found in telomeres and/or oncogene promoters, and it has been observed that the stabilization of such G-quadruplexes may disturb tumor cell growth. Nevertheless, the mechanisms leading to folding and stabilization of these G-quadruplexes are still not well established, and they are the focus of much current work in this field. In seminal works, stabilization was observed to be produced by cations. However, subsequent studies showed that different kinds of small molecules, from planar and nonplanar organic molecules to square-planar and octahedral metal complexes, may also lead to the stabilization of G-quadruplexes. Thus, the comprehension and rationalization of the interaction of these small molecules with G-quadruplexes are also important topics of current interest in medical applications. To shed light on the questions arising from the literature on the formation of G-quadruplexes, their stabilization, and their interaction with small molecules, synergies between experimental studies and computational works are needed. In this review, we mainly focus on in silico approaches and provide a broad compilation of different leading studies carried out to date by different computational methods. We divide these methods into twomain categories: (a) classical methods, which allow for long-timescale molecular dynamics simulations and the corresponding analysis of dynamical information, and (b) quantum methods (semiempirical, quantum mechanics/molecular mechanics, and density functional theory methods), which allow for the explicit simulation of the electronic structure of the system but, in general, are not capable of being used in long-timescale molecular dynamics simulations and, therefore, give a more static picture of the relevant processes.

Discrete Helmholtz model: a single layer of correlated counter-ions. Metal oxides and silica interfaces, ion-exchange and biological membranes

The mechanism by which interfaces in solution can be polarised depends on the nature of the charge carriers. In the case of a conductor, the charge carriers are electrons and the polarisation is homogeneous in the plane of the electrode. In the case of an insulator covered by ionic moieties, the polarisation is inhomogeneous and discrete in the plane of the interface. Despite these fundamental differences, these systems are usually treated in the same theoretical framework that relies on the Poisson-Boltzmann equation for the solution side. In this perspective, we show that interfaces polarised by discrete charge distributions are rather ubiquitous and that their associated potential drop significantly differs from those of conductor-electrolyte interfaces. We show that these configurations, spanning liquid-liquid interfaces, charged silica-water interfaces, metal oxide interfaces, supercapacitors, ion-exchange membranes and even biological membranes can be uniformly treated under a common "Discrete Helmholtz" model where the discrete charges are compensated by a single layer of correlated counter-ions, thereby generating a sharp potential drop at the interface.

Salt parameterization can drastically affect the results from classical atomistic simulations of water desalination by MoS2 nanopores

Water scarcity is a reality in our world, and scenarios predicted by leading scientists in this area indicate that it will worsen in the next decades. However, new technologies based on low-cost seawater desalination can prevent the worst scenarios, providing fresh water for humanity. With this goal, membranes based on nanoporous materials have been suggested in recent years. One of the materials suggested is MoS₂, and classical Molecular Dynamics (MD) simulation is one of the most powerful tools to explore these nanomaterials. However, distinct force fields employed in MD simulations are parameterized based on distinct experimental quantities. In this paper, we compare two models of salt that were built based on distinct properties of water-salt mixtures. One model fits the hydration free energy and lattice properties, and the second fits the crystal density and the density and the dielectric constant of water and salt mixtures. To compare the models, MD simulations for salty water flow through nanopores of two sizes were used - one pore big enough to accommodate hydrated ions, and one smaller in which the ion has to dehydrate to enter - and two rigid water models from the TIP4P family - TIP4P/2005 and TIP4P/ε. Our results indicate that the water permeability and salt rejection by the membrane are more influenced by the salt model than by the water model, especially for the narrow pore. In fact, completely distinct mechanisms were observed, and they are related to the characteristics employed in the ion model parameterization. The results show that not only can the water model influence the outcomes, but the ion model plays a crucial role when the pore is small enough.

Algal Toxin Goniodomin A Binds Potassium Ion Selectively to Yield a Conformationally Altered Complex with Potential Biological Consequences

The marine toxin goniodomin A (GDA) is a polycyclic macrolide containing a spiroacetal and three cyclic ethers as part of the macrocycle backbone. GDA is produced by three species of the Alexandrium genus of dinoflagellates, blooms of which are associated with "red tides", which are widely dispersed and can cause significant harm to marine life. The toxicity of GDA has been attributed to stabilization of the filamentous form of the actin group of structural proteins, but the structural basis for its binding is not known. Japanese workers, capitalizing on the assumed rigidity of the heavily substituted macrolide ring, assigned the relative configuration and conformation by relying on NMR coupling constants and NOEs; the absolute configuration was assigned by degradation to a fragment that was compared with synthetic material. We have confirmed the absolute structure and broad features of the conformation by X-ray crystallography but have found GDA to complex with alkali metal ions in spite of two of the heterocyclic rings facing outward. Such an arrangement would have been expected to impair the ability of GDA to form a crown-ether-type multidentate complex. GDA shows preference for K⁺, Rb⁺, and Cs⁺ over Li⁺ and Na⁺ in determinations of relative affinities by TLC on metal-ion-impregnated silica gel plates and by electrospray mass spectrometry. NMR studies employing the K⁺ complex of GDA, formed from potassium tetrakis[pentafluorophenyl]borate (KBArF₂₀), reveal a major alteration of the conformation of the macrolide ring. These observations argue against the prior assumption of rigidity of the ring. Alterations in chemical shifts, coupling constants, and NOEs indicate the involvement of most of the molecule other than ring F. Molecular mechanics simulations suggest K⁺ forms a heptacoordinate complex involving O_A, O_B, O_C, O_D, O_E, and the C-26 and C-27 hydroxy groups. We speculate that complexation of K⁺ with GDA electrostatically stabilizes the complex of GDA with filamentous actin in marine animals due to the protein being negatively charged at physiological pH. GDA may also cause potassium leakage through cell membranes. This study provides insight into the structural features and chemistry of GDA that may be responsible for significant ecological damage associated with the GDA-producing algal blooms.

Interaction Profiles and Stability of Rigid and Polymer-Tethered Lipid Bilayer Models at Highly Charged and Highly Adhesive Contacts

Understanding interaction force versus distance profiles of supported lipid bilayers (SLBs) is relevant to a number of areas, which rely on these model systems, including, e.g., characterization of ligand/receptor interactions or bacterial adhesion. Here, the stability of 4 different SLB architectures was compared using the surface forces apparatus (SFA) and atomic force microscopy (AFM). Specifically, the outer envelope of the bilayer systems remained constant as 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). The inner layer was varied between DPPC and 1,2-dipalmitoyl-3-trimethylammonium-propane (DPTAP) both on mica, and self-assembled monolayers (SAMs) of hexadecanethiol and the polymer-tethered diphytanylglycerol-tetraethylene glycol-lipoid acid (DPhyTL) on smooth gold surfaces. In that same order these gave an increasing strength of interaction between the inner layer and the supporting substrate and hence improved stability under highly adhesive conditions. Detachment profiles from highly charged and highly adhesive contacts were characterized, and approach characteristics were fitted to DLVO models. We find increasing stability under highly adhesive loads, approaching the hydrophobic limit of the adhesive energy between the inner and outer layers for the SAM-based systems. For all four SLBs we further compare AFM surface topographies, which strongly depend on preparation conditions, and the DLVO fitting of the SFA approach curves finds a strong charge regulation behavior during interaction, dependent on the particular model system. In addition, we find undulation characteristics during approach and separation. The increased stability of the complex architectures on a gold support makes these model systems an ideal starting point for studying more complex strongly adhesive/interacting systems, including, for example, ligand/receptor interactions, biosensing interactions, or cell/surface interactions.

Competing for the same space: protons and alkali ions at the interface of phospholipid bilayers

Maintaining gradients of solvated protons and alkali metal ions such as Na⁺ and K⁺ across membranes is critical for cellular function. Over the last few decades, both the interactions of protons and alkali metal ions with phospholipid membranes have been studied extensively and the reported interactions of these ions with phospholipid headgroups are very similar, yet few studies have investigated the potential interdependence between proton and alkali metal ion binding at the water-lipid interface. In this short review, we discuss the similarities between the proton-membrane and alkali ion-membrane interactions. Such interactions include cation attraction to the phosphate and carbonyl oxygens of the phospholipid headgroups that form strong lipid-ion and lipid-ion-water complexes. We also propose potential mechanisms that may modulate the affinities of these cationic species to the water-phospholipid interfacial oxygen moieties. This review aims to highlight the potential interdependence between protons and alkali metal ions at the membrane surface and encourage a more nuanced understanding of the complex nature of these biologically relevant processes.

Perturbation of Hydrogen-Bonding Networks over Supported Lipid Bilayers by Poly(allylamine hydrochloride)

Water is vital to many biochemical processes and is necessary for driving fundamental interactions of cell membranes with their external environments, yet it is difficult to probe the membrane/water interface directly and without the use of external labels. Here, we employ vibrational sum frequency generation spectroscopy to understand the role of interfacial water molecules above bilayers formed from zwitterionic (phosphatidylcholine) and anionic (phosphatidylglycerol, PG, and phosphatidylserine, PS) lipids as they are exposed to the common polycation poly(allylamine hydrochloride) (PAH) in 100 mM NaCl. We show that as the concentration of PAH is increased, the interfacial water molecules are irreversibly displaced and find that it requires 10 times more PAH to displace interfacial water molecules from membranes formed from purely zwitterionic lipids when compared to membranes that contain the anionic PG and PS lipids. This outcome is likely due to the difference in (1) the energy with which water molecules are bound to the lipid headgroups, (2) the number of water molecules bound to the headgroups, which is related to the headgroup area, and (3) the electrostatic interactions between the PAH molecules and the negatively charged lipids that are favored when compared to the zwitterionic lipid headgroups. The findings presented here contribute to establishing causal relationships in nanotoxicology and to understanding, controlling, and predicting the initial steps that lead to the lysis of cells exposed to membrane-disrupting polycations or to transfection.

Electrostatics of Tau Protein by Molecular Dynamics

Tau is a microtubule-associated protein that promotes microtubule assembly and stability. This protein is implicated in several neurodegenerative diseases, including Alzheimer’s. To date, the three-dimensional (3D) structure of tau has not been fully solved, experimentally. Even the most recent information is sometimes controversial in regard to how this protein folds, interacts, and behaves. Predicting the tau structure and its profile sheds light on the knowledge about its properties and biological function, such as the binding to microtubules (MT) and, for instance, the effect on ionic conductivity. Our findings on the tau structure suggest a disordered protein, with discrete portions of well-defined secondary structure, mostly at the microtubule binding region. In addition, the first molecular dynamics simulation of full-length tau along with an MT section was performed, unveiling tau structure when associated with MT and interaction sites. Electrostatics and conductivity were also examined to understand how tau affects the ions in the intracellular fluid environment. Our results bring a new insight into tau and tubulin MT proteins, their characteristics, and the structure–function relationship.

Interactions Between Natural Herbicides and Lipid Bilayers Mimicking the Plant Plasma Membrane

Natural phytotoxic compounds could become an alternative to traditional herbicides in the framework of sustainable agriculture. Nonanoic acid, sarmentine and sorgoleone are such molecules extracted from plants and able to inhibit the growth of various plant species. However, their mode of action is not fully understood and despite clues indicating that they could affect the plant plasma membrane, molecular details of such phenomenon are lacking. In this paper, we investigate the interactions between those natural herbicides and artificial bilayers mimicking the plant plasma membrane. First, their ability to affect lipid order and fluidity is evaluated by means of fluorescence measurements. It appears that sorgoleone has a clear ordering effect on lipid bilayers, while nonanoic acid and sarmentine induce no or little change to these parameters. Then, a thermodynamic characterization of interactions of each compound with lipid vesicles is obtained with isothermal titration calorimetry, and their respective affinity for bilayers is found to be ranked as follows: sorgoleone > sarmentine > nonanoic acid. Finally, molecular dynamics simulations give molecular details about the location of each compound within a lipid bilayer and confirm the rigidifying effect of sorgoleone. Data also suggest that mismatch in alkyl chain length between nonanoic acid or sarmentine and lipid hydrophobic tails could be responsible for bilayer destabilization. Results are discussed regarding their implications for the phytotoxicity of these compounds.

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.

Discovery of 8-Trifluoromethyl-3-cyclopropylmethyl-7-[(4-(2,4-difluorophenyl)-1-piperazinyl)methyl]-1,2,4-triazolo[4,3-a]pyridine (JNJ-46356479), a Selective and Orally Bioavailable mGlu2 Receptor Positive Allosteric Modulator (PAM)

Positive allosteric modulators of the metabotropic glutamate 2 receptor have generated great interest in the past decade. There is mounting evidence of their potential as therapeutic agents in the treatment of multiple central nervous system disorders. We have previously reported substantial efforts leading to potent and selective mGlu2 PAMs. However, finding compounds with the optimal combination of in vitro potency and good druglike properties has remained elusive, in part because of the hydrophobic nature of the allosteric binding site. Herein, we report on the lead optimization process to overcome the poor solubility inherent to the advanced lead 6. Initial prototypes already showed significant improvements in solubility while retaining good functional activity but displayed new liabilities associated with metabolism and hERG inhibition. Subsequent subtle modifications efficiently addressed those issues leading to the identification of compound 27 (JNJ-46356479). This new lead represents a more balanced profile that offers a significant improvement on the druglike attributes compared to previously reported leads.

Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface

We used molecular dynamics simulations to explore the effects of asymmetric transbilayer distribution of anionic phosphatidylserine (PS) lipids on the structure of a protein on the membrane surface and subsequent protein-lipid interactions. Our simulation systems consisted of an amyloidogenic, beta-sheet rich dimeric protein (D42) absorbed to the phosphatidylcholine (PC) leaflet, or protein-contact PC leaflet, of two membrane systems: a single-component PC bilayer and double PC/PS bilayers. The latter comprised of a stable but asymmetric transbilayer distribution of PS in the presence of counterions, with a 1-component PC leaflet coupled to a 1-component PS leaflet in each bilayer. The maximally asymmetric PC/PS bilayer had a non-zero transmembrane potential (TMP) difference and higher lipid order packing, whereas the symmetric PC bilayer had a zero TMP difference and lower lipid order packing under physiologically relevant conditions. Analysis of the adsorbed protein structures revealed weaker protein binding, more folding in the N-terminal domain, more aggregation of the N- and C-terminal domains and larger tilt angle of D42 on the PC leaflet surface of the PC/PS bilayer versus the PC bilayer. Also, analysis of protein-induced membrane structural disruption revealed more localized bilayer thinning in the PC/PS versus PC bilayer. Although the electric field profile in the non-protein-contact PS leaflet of the PC/PS bilayer differed significantly from that in the non-protein-contact PC leaflet of the PC bilayer, no significant difference in the electric field profile in the protein-contact PC leaflet of either bilayer was evident. We speculate that lipid packing has a larger effect on the surface adsorbed protein structure than the electric field for a maximally asymmetric PC/PS bilayer. Our results support the mechanism that the higher lipid packing in a lipid leaflet promotes stronger protein-protein but weaker protein-lipid interactions for a dimeric protein on membrane surfaces.

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.

Molecular electrometer and binding of cations to phospholipid bilayers

The molecular electrometer – reorientation of lipid head due to bound charge – allows direct quantitative vetting of simulations against noninvasive NMR experiments; most simulation models overestimated lipid–cation affinities.

Evaluating Force Fields for the Computational Prediction of Ionized Arginine and Lysine Side-Chains Partitioning into Lipid Bilayers and Octanol

Abundant peptides and proteins containing arginine (Arg) and lysine (Lys) amino acids can apparently permeate cell membranes with ease. However, the mechanisms by which these peptides and proteins succeed in traversing the free energy barrier imposed by cell membranes remain largely unestablished. Precise thermodynamic studies (both theoretical and experimental) on the interactions of Arg and Lys residues with model lipid bilayers can provide valuable clues to the efficacy of these cationic peptides and proteins. We have carried out molecular dynamics simulations to calculate the interactions of ionized Arg and Lys side-chains with the zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid bilayer for 10 widely used lipid/protein force fields: CHARMM36/CHARMM36, SLIPID/AMBER99SB-ILDN, OPLS-AA/OPLS-AA, Berger/OPLS-AA, Berger/GROMOS87, Berger/GROMOS53A6, GROMOS53A6/GROMOS53A6, nonpolarizable MARTINI, polarizable MARTINI, and BMW MARTINI. We performed umbrella sampling simulations to obtain the potential of mean force for Arg and Lys side-chains partitioning from water to the bilayer interior. We found significant differences between the force fields, both for the interactions between side-chains and bilayer surface, as well as the free energy cost for placing the side-chain at the center of the bilayer. These simulation results were compared with the Wimley-White interfacial scale. We also calculated the free energy cost for transferring ionized Arg and Lys side-chains from water to both dry and wet octanol. Our simulations reveal rapid diffusion of water molecules into octanol whereby the equilibrium mole fraction of water in the wet octanol phase was ∼25%. Surprisingly, our free energy calculations found that the high water content in wet octanol lowered the water-to-octanol partitioning free energies for cationic residues by only 0.6 to 0.7 kcal/mol.

Ligand binding determinants for angiotensin II type 1 receptor from computer simulations

The ligand binding determinants for the angiotensin II type 1 receptor (AT1R), a G protein-coupled receptor (GPCR), have been characterized by means of computer simulations. As a first step, a pharmacophore model of various known AT1R ligands exhibiting a wide range of binding affinities was generated. Second, a structural model of AT1R was built making use of the growing set of crystal structures of GPCRs, which was further used for the docking of the AT1R ligands based on the devised pharmacophore model. Next, ligand-receptor-lipid bilayer systems were studied by means of molecular dynamics (MD) simulations. Overall, the present study has permitted, combining the pharmacophore model with binding free energy calculations obtained from the MD simulations, to propose the molecular mechanisms by which sartans interact with AT1R.

Another Piece of the Membrane Puzzle: Extending Slipids Further

To be able to model complex biological membranes in a more realistic manner, the force field Slipids (Stockholm lipids) has been extended to include parameters for sphingomyelin (SM), phosphatidylglycerol (PG), phosphatidylserine (PS) lipids, and cholesterol. Since the parametrization scheme was faithful to the scheme used in previous editions of Slipids, all parameters are consistent and fully compatible. The results of careful validation of a number of key structural properties for one and two component lipid bilayers are in excellent agreement with experiments. Potentials of mean force for transferring water across binary mixtures of lipids and cholesterol were also computed in order to compare water permeability rates to experiments. In agreement with experimental and simulation studies, it was found that the permeability and partitioning of water is affected by cholesterol in lipid bilayers made of saturated lipids to the largest extent. With the extensions of Slipids presented here, it is now possible to study complex systems containing many different lipids and proteins in a fully atomistic resolution in the isothermic-isobaric (NPT) ensemble, which is the proper ensemble for membrane simulations.

Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids

An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The parametrization has been largely based on high-level ab initio calculations in order to keep the empirical input to a minimum. Parameters for the lipid chains have been developed based on knowledge about bulk alkane liquids, for which thermodynamic and dynamic data are excellently reproduced. The FFs ability to simulate lipid bilayers in the liquid crystalline phase in a tensionless ensemble was tested in simulations of three lipids: 1,2-diauroyl-sn-glycero-3-phospocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1,2-dipalmitoyl-sn-glycero-3-phospcholine (DPPC). Computed areas and volumes per lipid, and three different kinds of bilayer thicknesses, have been investigated. Most importantly NMR order parameters and scattering form factors agree in an excellent manner with experimental data under a range of temperatures. Further, the compatibility with the AMBER FF for biomolecules as well as the ability to simulate bilayers in gel phase was demonstrated. Overall, the FF presented here provides the important balance between the hydrophilic and hydrophobic forces present in lipid bilayers and therefore can be used for more complicated studies of realistic biological membranes with protein insertions.

Membrane Protein Simulations Using AMBER Force Field and Berger Lipid Parameters

AMBER force fields are among the most commonly used in molecular dynamics (MD) simulations of proteins. Unfortunately, they lack a specific set of lipid parameters, thus limiting its use in membrane protein simulations. In order to overcome this limitation we assessed whether the widely used united-atom lipid parameters described by Berger and co-workers could be used in conjunction with AMBER force fields in simulations of membrane proteins. Thus, free energies of solvation in water and in cyclohexane, and free energies of water to cyclohexane transfer, were computed by thermodynamic integration procedures for neutral amino acid side-chains employing AMBER99, AMBER03, and OPLS-AA amino acid force fields. In addition, MD simulations of three membrane proteins in a POPC lipid bilayer, the β2 adrenergic G protein-coupled receptor, Aquaporin-1, and the outer membrane protein Omp32, were performed with the aim of comparing the AMBER99SB/Berger combination of force fields with the OPLS-AA/Berger combination. We have shown that AMBER99SB and Berger force fields are compatible, they provide reliable free energy estimations relative to experimental values, and their combination properly describes both membrane and protein structural properties. We then suggest that the AMBER99SB/Berger combination is a reliable choice for the simulation of membrane proteins, which links the easiness of ligand parametrization and the ability to reproduce secondary structure of AMBER99SB force field with the largely validated Berger lipid parameters.

Aqueous solutions at the interface with phospholipid bilayers

In a sense, life is defined by membranes, because they delineate the barrier between the living cell and its surroundings. Membranes are also essential for regulating the machinery of life throughout many interfaces within the cell's interior. A large number of experimental, computational, and theoretical studies have demonstrated how the properties of water and ionic aqueous solutions change due to the vicinity of membranes and, in turn, how the properties of membranes depend on the presence of aqueous solutions. Consequently, understanding the character of aqueous solutions at their interface with biological membranes is critical to research progress on many fronts. The importance of incorporating a molecular-level description of water into the study of biomembrane surfaces was demonstrated by an examination of the interaction between phospholipid bilayers that can serve as model biological membranes. The results showed that, in addition to well-known forces, such as van der Waals and screened Coulomb, one has to consider a repulsion force due to the removal of water between surfaces. It was also known that physicochemical properties of biological membranes are strongly influenced by the specific character of the ions in the surrounding aqueous solutions because of the observation that different anions produce different effects on muscle twitch tension. In this Account, we describe the interaction of pure water, and also of aqueous ionic solutions, with model membranes. We show that a symbiosis of experimental and computational work over the past few years has resulted in substantial progress in the field. We now better understand the origin of the hydration force, the structural properties of water at the interface with phospholipid bilayers, and the influence of phospholipid headgroups on the dynamics of water. We also improved our knowledge of the ion-specific effect, which is observed at the interface of the phospholipid bilayer and aqueous solution, and its connection with the Hofmeister series. Nevertheless, despite substantial progress, many issues remain unresolved. Thus, for example, we still cannot satisfactorily explain the force of interaction between phospholipid bilayers immersed in aqueous solutions of NaI. Although we try to address many issues here, the scope of the discussion is limited and does not cover such important topics as the influence of ionic solutions on phases of bilayers, the influence of salts on the properties of Langmuir monolayers containing lipid molecules, or the influence of aqueous solutions on bilayers containing mixtures of lipids. We anticipate that the future application of more powerful experimental techniques, in combination with more advanced computational hardware, software, and theory, will produce molecular-level information about these important topics and, more broadly, will further illuminate our understanding of interfaces between aqueous solutions and biological membranes.

Force spectroscopy reveals the effect of different ions in the nanomechanical behavior of phospholipid model membranes: the case of potassium cation

How do metal cations affect the stability and structure of phospholipid bilayers? What role does ion binding play in the insertion of proteins and the overall mechanical stability of biological membranes? Investigators have used different theoretical and microscopic approaches to study the mechanical properties of lipid bilayers. Although they are crucial for such studies, molecular-dynamics simulations cannot yet span the complexity of biological membranes. In addition, there are still some experimental difficulties when it comes to testing the ion binding to lipid bilayers in an accurate way. Hence, there is a need to establish a new approach from the perspective of the nanometric scale, where most of the specific molecular phenomena take place. Atomic force microscopy has become an essential tool for examining the structure and behavior of lipid bilayers. In this work, we used force spectroscopy to quantitatively characterize nanomechanical resistance as a function of the electrolyte composition by means of a reliable molecular fingerprint that reveals itself as a repetitive jump in the approaching force curve. By systematically probing a set of bilayers of different composition immersed in electrolytes composed of a variety of monovalent and divalent metal cations, we were able to obtain a wealth of information showing that each ion makes an independent and important contribution to the gross mechanical resistance and its plastic properties. This work addresses the need to assess the effects of different ions on the structure of phospholipid membranes, and opens new avenues for characterizing the (nano)mechanical stability of membranes.

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.

Validating affinities for ion-lipid association from simulation against experiment

Understanding biological membranes at physiological conditions requires comprehension of the interaction of lipid bilayers with sodium and potassium ions. These cations are adsorbed at palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayers as indicated from previous studies. Here we compare the affinity of Na(+) and K(+) for POPC in molecular dynamics (MD) simulations with recent data from electrophoresis experiments and isothermal calorimetry (ITC) at neutral pH. NaCl and KCl were described using GROMOS or parameters matching solution activities on the basis of Kirkwood-Buff theory (KBFF), and K(+) was also described using parameters by Dang et al., all in conjunction with the Berger parameters for the lipids and the SPC water model. Apparent binding constants of GROMOS-Na(+) and KBFF-K(+) are the same within error and in good agreement with values from ITC. Although these force fields yield the same number of bound ions per number of lipids for Na(+) and K(+), they give a larger number of Na(+) ions per surface area compared to K(+), in agreement with the electrophoresis experiments, because Na(+) causes a stronger reduction in the area per lipid than K(+). The intrinsic binding constants, on the other hand, are reproduced by Dang-K(+) but overestimated by GROMOS-Na(+) and KBFF-K(+). That no ion force field reproduces the intrinsic and the apparent binding constant simultaneously arises from the fact that in MD simulations, implicitly meant to mimic neutral pH, pure PC is usually modeled with zero surface charge. In contrast, POPC at neutral conditions in experiment carries a low but significant negative surface charge and is uncharged only at acidic pH as indicated from electrophoretic mobilities. Implications for future simulation and experimental studies are discussed.

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process

A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange.

Interaction of salicylate and a terpenoid plant extract with model membranes: reconciling experiments and simulations

We investigate the effects of two structurally similar small cyclic molecules: salicylic acid and perillic acid on a zwitterionic model lipid bilayer, and show that both molecules might have biological activity related to membrane thinning. Salicylic acid is a nonsteroidal antiinflammatory drug, some of the pharmacological properties of which arise from its interaction with the lipid bilayer component of the plasma membrane. Prior simulations show that salicylate orders zwitterionic lipid membranes. However, this is in conflict with Raman scattering and vesicle fluctuation analysis data, which suggest the opposite. We show using extensive molecular dynamics simulations, cumulatively >2.5 μs, that salicylic acid indeed disorders membranes with concomitant membrane thinning and that the conflict arose because prior simulations suffered from artifacts related to the sodium-ion induced condensation of zwitterionic lipids modeled by the Berger force field. Perillic acid is a terpenoid plant extract that has antiinfective and anticancer properties, and is extensively used in eastern medicine. We found that perillic acid causes large-scale membrane thinning and could therefore exert its antimicrobial properties via a membrane-lytic mechanism reminiscent of antimicrobial peptides. Being more amphipathic, perillic acid is more potent in disrupting lipid headgroup packing, and significantly modifies headgroup dipole orientation. Like salicylate, the membrane thinning effect of perillic acid is masked by the presence of sodium ions. As an alternative to sodium cations, we advocate the straightforward solution of using larger countercations like potassium or tetra-methyl-ammonium that will maintain electroneutrality but not interact strongly with, and thus not condense, the lipid bilayer.

Direct imaging of salt effects on lipid bilayer ordering at sub-molecular resolution

The interactions of salts with lipid bilayers are known to alter the properties of membranes and therefore influence their structure and dynamics. Sodium and calcium cations penetrate deeply into the headgroup region and bind to the lipids, whereas potassium ions only loosely associate with lipid molecules and mostly remain outside of the headgroup region. We investigated a dipalmitoylphosphatidylcholine (DPPC) bilayer in the gel phase in the presence of all three cations with a concentration of Ca²+ ions an order of magnitude smaller than the Na+ and K+ ions. Our findings indicate that the area per unit cell does not significantly change in these three salt solutions. However the lipid molecules do re-order non-isotropically under the influence of the three different cations. We attribute this reordering to a change in the highly directional intermolecular interactions caused by a variation in the dipole-dipole bonding arising from a tilt of the headgroup out of the membrane plane. Measurements in different NaCl concentrations also show a non-isotropic re-ordering of the lipid molecules.