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Effect of Monovalent Salt on Cationic Lipid Membranes As Revealed by Molecular Dynamics Simulations
Abstract
An atomic-scale understanding of cationic lipid membranes is required for development of gene delivery agents based on cationic liposomes. To address this problem, we recently performed molecular dynamics (MD) simulations of mixed lipid membranes comprised of cationic dimyristoyltrimethylammonium propane (DMTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC) (Biophys. J. 2004, 86, 3461-3472). Given that salt ions are always present under physiological conditions, here we focus on the effects of monovalent salt (NaCl) on cationic (DMPC/DMTAP) membranes. Using atomistic MD simulations, we found that salt-induced changes in membranes depend strongly on their composition. When the DMTAP mole fraction is small (around 6%), the addition of monovalent salt leads to a considerable compression of the membrane and to a concurrent enhancement of the ordering of lipid acyl chains. That is accompanied by reorientation of phosphatidylcholine headgroups in the outward normal direction and slight changes in electrostatic properties. We attribute these changes to complexation of DMPC lipids with Na(+) ions which penetrate deep into the membrane and bind to the carbonyl region of the DMPC lipids. In contrast, at medium and high molar fractions of cationic DMTAP (50 and 75%) a substantial positive surface charge density of the membranes prevents the binding of Na(+) ions, making such membranes almost insensitive to monovalent salt. Finally, we compare our results to the Poisson-Boltzmann theory. With the exception of the immediate vicinity of the bilayer plane, we found excellent agreement with the theory. This is as expected since unlike in the theoretical description the surface is now structured due to its atomic scale nature.
... To support this statement, molecular dynamic simulation was applied to illustrate the position of ions with respect to phospholipids molecules (Böckmann & Grubmüller 2004;Gurtovenko et al. 2005). In addition, ionic strength of the medium also affects the frictional properties of PC bilayers (Oncins et al. 2005) as measured with conventional AFM. ...
... Histogram of membrane thickness measured with CM-AFM at sliding velocity 200 -2000 µm/s for each DOPC SLB prepared on different cations (Li + , Na + , and K + ) with concentration 150mM. Li + : 4.09+ 1.45 nm; Na + : 4.9+ 1.1 nm; K + : 4.95 +1.31 nm.Many scientific articles report that alkali and alkaline ions affect the mechanical resistance of PC membranes(Haverstick & Glaser 1987; López Cascales & García de la Torre 1997;Bockmann et al. 2003;Gurtovenko et al. 2005;Garcia-Manyes et al. 2005;Cordomí et al. 2008;Gurtovenko & Vattulainen 2008;Vácha et al. 2009;Vácha et al. 2010). In general, cations can reduce the intermolecular distance in the bilayers promoted by polar headgroup screening enhancement(Garcia-Manyes et al. 2005). ...
Cell membranes are involved in many cellular processes: drugs and ions diffusion, signal transduction, energy generation, cell development (fusion and fission). Phospholipid bilayers are the main components of cell membranes, they act as a dynamic barrier protecting cellular biochemical reactions. The determination of biochemical and mechanical properties of lipid bilayers and their evolution with environmental conditions is necessary to study the nature of cellular processes and the influence of external agents (mechanical resistance, permeability, and biological response). To conduct such characterizations, simplified biomimetic membrane models, such as supported lipid bilayers (SLBs), were developed. Among the available characterization techniques, atomic force microscopy (AFM) has been widely used to study the nanoscale organization of SLBs under physiological conditions. AFM can yield high resolution images and it can also be used to quantify the mechanical resistance of SLBs by means of punch through experiments. For 30 years, AFM has been through many developments. Very recently, the Circular Mode AFM (CM-AFM) has been developed at the Université de Technologie de Compiègne. CM-AFM is able to generate a sliding movement of the AFM tip on the sample at high, constant and continuous velocity and to measure the lateral friction forces fast and accurately simultaneously with the vertical forces. For the first time CM-AFM is used to characterize biological samples under physiological conditions, allowing the simultaneous measurement of both the punch-through and the friction forces as a function of the sliding velocity. It offers for the first time the ability to describe the friction behavior of SLBs in complement of the punch-through force. Due to the important need for quantitative measurement, optimization of the CM-AFM protocol has been done first. Protocol of scanner calibration has been successfully established to ensure the accuracy of sliding velocity. Besides, the protocol for tip calibration, based on wedge method and a scratched sample, is also made to determine the lateral force calibration constant. We have employed CM-AFM to measure the tribological properties of solid samples to improve the equipment under liquid medium. Then, the mechanical properties (punchthrough and friction forces) of SLBs were measured as function of the sliding velocity. Pure and mixed SLBs were prepared by the vesicle fusion method. Various media were also used to study the effect of monovalent cations to the mechanical properties of SLBs. In all cases, the friction force increases linearly with the sliding velocity allowing us to deduce the friction viscous coefficient. As expected both the punchthrough force and the friction viscous coefficient are influenced by the composition of lipid mixtures, by the nature of cations in liquid medium, and by the length of hydrocarbon chains but not in a similar fashion. The interpretation of the evolution of the viscous friction force coefficient with the studied system is particularly tricky as the friction force could be influenced by interface or volume properties. This problematic will be the challenge for the next studies. Nevertheless, our results illustrate how powerful the CM-AFM technique is and it opens wide opportunities to characterize other biological samples (cells and tissues) to gain a better understanding of the elementary mechanisms of friction.
... Among which, the transition in size and shape from spherical to rodlike micelles with increasing concentration or addition of salt in the ionic surfactant systems is a well-known phenomenon [3]. Furthermore, salt ions play a significant role in biomolecular systems [4]. For an anionic surfactant, the repulsion between head groups determines the shape and size of micelles formed by different amphiphiles [5]. ...
... where U angle is bond angle bending potential described by a harmonic function in the form of U( ) 0.5K(cos cos 0 ) 2 , 0 the balance bond angle [21] and the bond bending force constant K 520 kJ·mol 1 [22]. U nonbonded is modeled using a cut and shifted Lennard-Jones (LJ) potential nonbonded 12 6 cut cut nonbonded cut 4 , ...
The presence of salt has a profound effect on the size, shape and structure of sodium dodecyl sulfate (SDS) micelles. There have been a great number of experiments on SDS micelles in the presence and absence of salt to study this complex problem. Unfortunately, it is not clear yet how electrolyte ions influence the structure of micelles. By describing the compromise between dominant mechanisms, a simplified atomic model of SDS in presence of salt has been developed and the molecular dynamics (MD) simulations of two series of systems with different concentrations of salt and charges of ion have been performed. Polydispersity of micelle size is founded at relatively high concentration of SDS and low charge of cation. Although the counter-ion pairs with head groups are formed, the transition of micelle shape is not observed because the charge of cation is not enough to neutralize the polar of micelle surface.
... However, ionic leakage through the pore is found to be sensitive to the type of cation: K ions permeate through a lipid membrane much easier than Na ions do. The origin of such a difference is most likely in the strong interactions of sodium ions with lipid headgroups lining the pore walls [43][44][45][46][47]. In contrast, potassium ions interact only weakly with the carbonyl regions of phospholipids [11,47]. ...
... This finding can readily be explained in terms of interactions of cations with lipid headgroups: sodium ions demonstrate much stronger interactions with zwitterionic phosphatidylcholine lipids than potassium ions [11,47]. More specifically, sodium ions are known to bind strongly to carbonyl oxygens of phosphatidylcholines, leading to the formation of tight complexes between neighboring lipids [11,[43][44][45][46][47], thus weakening the desorption of lipids out of membrane leaflets toward the membrane interior. Overall, the molecular mechanism of lipid flip-flop discussed here consists of two steps [34]. ...
Biological membranes are excellent examples of biologically relevant soft interfaces. They mediate or even govern a large
variety of cellular functions [1–3]. Membranes serve as a host for membrane proteins to carry out their functions, and numerous
signaling processes are either conducted inside membranes or mediated by them. Additionally, cellular membranes act as a permeability
barrier, allowing only desired particles to permeate through the membrane into and out of the cell, besides which membranes
are also involved in a variety of large-scale functions such as in maintaining the osmotic pressure and ion density gradients
across the plasma membrane. The biological relevance of membranes is emphasized by the rather recently proposed lipid raft
model [4–7], which essentially stresses the importance of understanding the interplay between lipids and proteins: membrane
proteins function together with lipids. Consequently, lipid membrane structures, lipid domain coexistence, and especially
the role of cholesterol in the structural properties of membranes have been paid a considerable amount of attention recently.
Meanwhile, the dynamics of membranes [3,8,9] has received much less attention despite its substantial importance in, e.g.,
signaling, domain formation, and diffusion of lipids and proteins in the plane of the membrane.
... Biological membranes are electrostatically charged entities that physiologically coexist with electrolyte solutions. Thus, specific interactions with ions are a matter of considerable interest (2)(3)(4)(5)(6)(7). The distribution of ions in the solution and their interaction with the membranes are factors that substantially modify the structure and dynamics of the cell membranes (8)(9)(10). ...
... Studies have shown that ion binding to lipid bilayers provokes an increased ordering in the membrane structure, and it was reported that ions reduce the area per lipid for both negatively charged and zwitterionic phospholipids (6,21). Detailed information about the location of ions with respect to the polar headgroups and hydrocarbon chains of the phospholipid membranes was obtained from moleculardynamics (MD) simulations (4,6,(22)(23)(24)(25)(26)(27), which showed that ion binding modifies the area per lipid, lipid ordering, orientation of the lipid head dipole, and the charge distribution along the system, among other effects. One of the most studied ions, partly because of its biological relevance, is K þ , which has been a subject of controversy in the literature. ...
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.
... To improve the results, we incorporated the order parameter of decanoic acid molecules from every trajectory. The measurement was performed by reorientating each compound to the z axis to avoid the curvature for normal calculation [31,32]. ...
The origin of life possibly required processes in confined systems that facilitated simple chemical reactions and other more complex reactions impossible to achieve under the condition of infinite dilution. In this context, the self-assembly of micelles or vesicles derived from prebiotic amphiphilic molecules is a cornerstone in the chemical evolution pathway. A prime example of these building blocks is decanoic acid, a short-chain fatty acid capable of self-assembling under ambient conditions. This study explored a simplified system made of decanoic acids under temperatures ranging from 0 °C to 110 °C to replicate prebiotic conditions. The study revealed the first point of aggregation of decanoic acid into vesicles and examined the insertion of a prebiotic-like peptide in a primitive bilayer. The information gathered from this research provides critical insights into molecule interactions with primitive membranes, allowing us to understand the first nanometric compartments needed to trigger further reactions that were essential for the origin of life.
... Despite the simple membrane structures built from phosphatidylcholine lipid molecules, these representations have proved to be remarkable test systems that provide very useful insights into the inherent physics, mechanisms, and to probe the physical properties of membranes. While most membrane models are consisted of fully hydrated, pure phospholipid bilayers, more complicated organization and account of external ions (e.g., the effect of salt concentrations) have emerged (Hofsäß et al. 2003;Gurtovenko et al. 2005). For such systems, the average structure of the lipid-water interface at the atomic scale may be provided by the density distributions of different atom types along the bilayer normal. ...
This book presents an overview of the current state of research on ultrashort electric field pulses of high intensity and their use in biology and medicine. It examines in detail the most recent and exciting advances in how nanosecond and picosecond electric pulse research has grown and expanded into new areas of biology and medicine.
Further, the book specifically focuses on electric pulses in the time domain, on intracellular effects as opposed to plasma membrane electroporation, and highlights the biological and medical applications of these unique pulse effects. Since the authors were initial innovators exploring nanosecond and picosecond pulses, their unique perspectives foreshadowed directions the research took, expanding into new areas that they continue to investigate today.
... Despite the simple membrane structures built from phosphatidylcholine lipid molecules, these representations have proved to be remarkable test systems that provide very useful insights into the inherent physics, mechanisms, and to probe the physical properties of membranes. While most membrane models are consisted of fully hydrated, pure phospholipid bilayers, more complicated organization and account of external ions (e.g., the effect of salt concentrations) have emerged (Hofsäß et al. 2003;Gurtovenko et al. 2005). For such systems, the average structure of the lipid-water interface at the atomic scale may be provided by the density distributions of different atom types along the bilayer normal. ...
Externally applied nanosecond electric pulses are useful to trigger and tailor bioeffects in cells and tissues. However, the parameter space is large given the different types of cells, and the wide range of potential electrical parameters (such as pulse durations and waveforms, field intensities, and number of pulses) that are available for use. To maximize benefits, tailor a desired response, and devise an efficient system, it becomes necessary to first understand and quantify the biological behavior driven by the electrical input. Model development based on the inherent biophysical processes is an elegant and cost-effective option to help advance this technology. Given the merits and need for modeling then, this chapter focuses on the various schemes for analysis and simulations of the electrically driven bioeffects. Schemes ranging from molecular level descriptions to an averaged continuum analyses are presented and discussed in this chapter. Relevant examples and illustrative result are also given in this context of cellular bioelectrics.
... Despite the simple membrane structures built from phosphatidylcholine lipid molecules, these representations have proved to be remarkable test systems that provide very useful insights into the inherent physics, mechanisms, and to probe the physical properties of membranes. While most membrane models are consisted of fully hydrated, pure phospholipid bilayers, more complicated organization and account of external ions (e.g., the effect of salt concentrations) have emerged (Hofsäß et al. 2003;Gurtovenko et al. 2005). For such systems, the average structure of the lipid-water interface at the atomic scale may be provided by the density distributions of different atom types along the bilayer normal. ...
Generally, in studies of the bioelectric effects of nanosecond pulses, thermal effects are not considered. While this is certainly true for the delivery of single or a small number of pulses, developments in medical treatment based on tissue ablation have been based pulse trains applied at a high repetition rate. In fact, temperature increases may trigger thermally activated bioeffects. This suggests technological opportunities for electro-manipulation that takes advantage of synergisms between thermal and electrically driven processes. Even with modest temperature changes, large thermal gradients could be established, which in itself can lead to additive electric field creation. The focus in this chapter is on thermal aspects and the possible synergies with electrical stimulation for bio-effects.
... Another aspect that could contribute to explain this anomalous result could be the high concentration of the sodium cation (abundant in the buffer) in the region of the polar headgroups and its strong interaction with the carbonyl region of the phospholipid membrane [46]. It is reasonable to hypothesize that Na + could also interact electrostatically with the oxygen of the N-oxide moiety, thus partially shielding its negative charge and bringing to a higher potential than the expected one. ...
The influence of the presence of synthetic structurally related N-oxide and corresponding cationic surfactants with different chain lengths on the properties of 1,2-dimyristoyl-sn-glycero-3-phosphocholine liposomes was investigated. Their potentiality as delivery systems of (+)-usnic acid was also evaluated by studying its entrapment efficiency and its antioxidant activity. In fact, (+)-usnic acid has many pharmacological properties that, as many natural substances, are often strictly linked to their antioxidant power. N-oxide surfactants can enhance this property and improve the efficacy of the system. Based on this premise, we verified how and to what extent the molecular structure of liposomes components affects this effect: the best antioxidant effectiveness was observed when (+)-usnic acid was included in liposomes containing the N-oxide surfactant with C14 alkyl chain. Our results underline the importance of the hydrophilic/hydrophobic balance of the monomer in determining the properties of the aggregates in which it is included.
... Besides DOTMA and DOTAP, there are also other monovalent cationic lipids such as DC-Chol and DDAB. DC-Chol-based lipoplexes have a lower gene silencing efficiency than that of DOTMA and DOTAP [25,37]. ...
Liposomes are one of the most widely investigated carriers for CRISPR/Cas9 delivery. The surface properties of liposomal carriers, including the surface charge, PEGylation, and ligand modification can significantly affect the gene silencing efficiency. Three barriers of systemic CRISPR/Cas9 delivery (long blood circulation, efficient tumor penetration, and efficient cellular uptake/endosomal escape) are analyzed on liposomal carriers with different surface charges, PEGylations, and ligand modifications. Cationic formulations dominate CRISPR/Cas9 delivery and neutral formulations also have good performance while anionic formulations are generally not proper for CRISPR/Cas9 delivery. The PEG dilemma (prolonged blood circulation vs. reduced cellular uptake/endosomal escape) and the side effect of repeated PEGylated formulation (accelerated blood clearance) were discussed. Effects of ligand modification on cationic and neutral formulations were analyzed. Finally, we summarized the achievements in liposomal CRISPR/Cas9 delivery, outlined existing problems, and provided some future perspectives. Liposomes are one of the most widely investigated carriers for CRISPR/Cas9 delivery. The surface properties of liposomal carriers, including the surface charge, PEGylation, and ligand modification can significantly affect the gene silencing efficiency. Three barriers of systemic siRNA delivery (long blood circulation, efficient tumor penetration, and efficient cellular uptake/endosomal escape) are analyzed on liposomal carriers with different surface charges, PEGylations, and ligand modifications. Cationic formulations dominate CRISPR/Cas9 delivery and neutral formulations also have good performance while anionic formulations are generally not proper for CRISPR/Cas9 delivery. The PEG dilemma (prolonged blood circulation vs. reduced cellular uptake/endosomal escape) and the side effect of repeated PEGylated formulation (accelerated blood clearance) were discussed. Effects of ligand modification on cationic and neutral formulations were analyzed. Finally, we summarized the achievements in liposomal CRISPR/Cas9 delivery, outlined existing problems, and provided some future perspectives.
... Similar procedure has been followed in other studies, see e.g. ref. 24. ...
Cellulose can be phosphorylated to produce organic matrices with highly adsorptive properties for, e.g., biocompatible materials for biomedical applications. We focus on the effects of phosphorylation of surfaces of crystalline nanocellulose and, in particular, on the competitive adsorption of mono- and divalent cations (Na+ and Ca2+) typically contained in mineralizing salt mixtures using all-atom molecular dynamics (MD) simulations. Phosphorylation was applied at 12% and 25% both in water and CaCl2 solutions. Our main result shows that Na+ and Ca2+ cations are concentrated in different interfacial layers with Na+ ions penetrating much closer to the surface. This behavior cannot be described by the Poisson-Boltzmann theory or implicit solvent simulations. Our analysis shows that the physical origin of this observation is due to a balance between the electrostatic interactions and hydration free energy associated with the ions. Adsorption levels of the different ions also respond differently to changes in the degree of phosphorylation. We show that the number of adsorbed Na+ ions per phosphate group increases whereas the number of adsorbed Ca2+ ions decreases with an increasing degree of phosphorylation (or when the number of binding sites increases). The decrease in the number of adsorbed Ca2+ ions can be explained by an increasing charge-charge repulsion between the Ca2+ ions attracted by the charged surface. Importantly, our results demonstrate the existence of an optimum degree of phosphorylation in terms of adsorbed Ca2+ ions and can be used as a guideline in materials design, for example, when choosing the cellulose matrix or with other similarly structured biomolecular and polymer surfaces.
... Moreover, experiments show that ions and their concentration have a pivotal role not only in the structure, dynamics, and stability of membranes but also in the binding and insertion of proteins, membrane fusion, water-membrane interface interactions, and transport across membranes [3,[16][17][18][19][20][21][22][23][24][25][26]. Considerable MD simulations have been devoted to studying the biologically relevant ions including Na + , K + , Ca 2+ , and Cl − at the bilayer interface [27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43]. These studies elucidate that Na + ions locate at the water-membrane interface in the carbonyl groups region and strongly interact with both carbonyl and phosphate oxygen atoms. ...
Molecular dynamics (MD) simulations of a dipalmitoylphosphatidylcholine (DPPC) bilayer and its neutral inverse-phosphocholine equivalent (DPCPe) were performed to find salt-induced effects on their surface structure and the nature of ion-lipid interactions. We found that the area per lipid is not considerably affected by the inversion, but the deuterium order parameter of carbon atoms in the region of carbonyl carbons changes dramatically. MD simulations indicate that Ca2+ ions can bind to the surface of both DPPC and DPCPe membranes, but K+ ions do not bind to them. In the case of Na+, however, the ions can bind to natural lipids but not to the inverse ones. Also, our results demonstrate that the hydration level of CPe bilayers is substantially lower than PC bilayers and the averaged orientation of water dipoles in the region of CPe headgroups is effectively inverted compared to PC lipids. This might be important in the interaction of the bilayer with its biological environment. Furthermore, it was found for the CPe bilayers that the enhanced peaks of the electrostatic potential profiles shift further away from the bilayer center relative to those of PC bilayers. This behavior makes the penetration of cations into the bilayer more difficult and possibly explains the experimentally observed enhanced release rates of anionic compounds in the CPe membrane.
... In Figure 2, we show also the headgroup P−N vector angle as a function of the mole fraction of the cationic surfactant. As suggested previously 30 and observed in MD simulations, 18,19,97,98 the headgroup orients more toward the water phase with the increasing amount of positive charge in the PC lipid bilayer. The effect is more pronounced in the Lipid14 model than in the ECC-POPC model. ...
Binding affinities and stoichiometries of Na+and Ca2+ions to phospholipid bilayers are of paramount significance in the properties and functionality of cellular membranes. Current estimates of binding affinities and stoichiometries of cations are, however, inconsistent due to limitations in the available experimental and computational methods. In this work, we improve the description of the binding details of Na+and Ca2+ions to the 1-Palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer by implicitly including electronic polarization as a mean field correction, known as the electronic continuum correction (ECC). This is applied by scaling the partial charges of a selected state-of-the-art POPC lipid model for molecular dynamics simulations. Our improved ECC-POPC model reproduces not only the experimentally measured structural parameters for the ion-free membrane, but also the response of lipid head group to a strongly bound cationic amphiphile, as well as the binding affinities of Na+and Ca2+ions. With our new model we observe on the one side negligible binding of Na+ions to POPC bilayer, while on the other side stronger interactions of Ca2+primarily with phosphate oxygens, which is in agreement with the previous interpretations of the experimental spectroscopic data. The present model results in Ca2+ions forming complexes with one to three POPC molecules with almost equal probabilities, suggesting more complex binding stoichiometries than those from simple models used to interpret the NMR data previously. The results of this work pave the way to quantitative molecular simulations with realistic electrostatic interactions of complex biochemical systems at cellular membranes.
... Several works have addresed the computer simulation of systems containing cationic lipids with the interest of undestanding the interactions with nucleic acids and drugs that can potentially be transported. As a result of these studies, new knowledgement was acquired about the organization, phase behaviour, segregation of lipid components and properties of the electric double layer in cationic interfaces [20][21][22][23][24]. ...
The fatty acid-binding proteins L-BABP and Rep1-NCXSQ bind to anionic lipid membranes by electrostatic interactions. According to Molecular Dynamics (MD) simulations, the interaction of the protein macrodipole with the membrane electric field is a driving force for protein binding and orientation in the interface. To further explore this hypothesis, we studied the interactions of these proteins with cationic lipid membranes. As in the case of anionic lipid membranes, we found that both proteins, carrying a negative as well as a positive net charge, were bound to the positively charged membrane. Their major axis, those connecting the bottom of the β-barrel with the α-helix portal domain, were rotated about 180 degrees as compared with their orientations in the anionic lipid membranes. Fourier transform infrared (FTIR) spectroscopy of the proteins showed that the positively charged membranes were also able to induce conformational changes with a reduction of the β-strand proportion and an increase in α-helix secondary structure. Fatty acid-binding proteins (FABPs) are involved in several cell processes, such as maintaining lipid homeostasis in cells. They transport hydrophobic molecules in aqueous medium and deliver them into lipid membranes. Therefore, the interfacial orientation and conformation, both shown herein to be electrostatically determined, have a strong correlation with the specific mechanism by which each particular FABP exerts its biological function.
... According to molecular dynamics simulation studies by Gurtovenko et al., the addition of Na + ions to 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)/ 1,2-dipalmitoyl-3trimethylammonium-propane (DPTAP) lipid membranes decreased the hydration level of lipids as Na + ions held water molecules instead of lipids, hence required 1.5 fold increased number of water molecules to reach the hydration equilibrum. 29 Interesting experimental results obtained by infrared spectroscopy indicated that divalent ions differ in their binding ability to lipids, affecting the local environment of water molecules near lipid headgroups. For instance, Zn 2+ ions interact with lipid headgroups strongly, thereby reducing the number of water molecules near headgroups. ...
Lipids and nucleic acids (NAs) can hierarchically self-organize into a variety of nanostructures of increasingly complex geometries such as the 1D lamellar, 2D hexagonal, and 3D bicontinuous cubic phases. The diversity and complexity of those lipid–NA assemblies are interesting from a fundamental perspective as well as being relevant to the performance in gene delivery and gene silencing applications. The finding that not only the chemical make of the lipid-NA constructs, but their actual supramolecular organization, affects their gene transfection and silencing efficiencies has inspired physicists, chemists, and engineers to this field of research. At the moment it remains an open question how exactly the different lipid-NA structures interact with cells and organelles in order to output an optimal response. This article reviews our current understanding of the structures of different lipid–NA complexes and the corresponding cellular interaction mechanisms. The recent advances in designing optimal lipid–based NA carriers will be introduced with an emphasis on the structure–function relations.
... Ion binding to lipid membrane surfaces has been explored through computational techniques, e.g., molecular dynamics simulations (Gurtovenko et al. 2005) and experimental methods, e.g., nuclear magnetic resonance (Roux and Neumann 1986;Huster et al. 2000), electrochemical impedance spectroscopy (Naumowicz and Figaszewski 2005), chronoamperometry (Naumowicz and Figaszewski 2014) and microelectrophoresis (Tatulian 1987;Huster et al. 2000;Sinn et al. 2006;Klasczyk et al. 2010). In particular, microelectrophoresis enables indirect measurements of electrophoretic mobility and membrane surface charge density values. ...
Interactions of alkali metal cations (Li(+), Na(+), K(+), Cs(+)) with phosphatidylcholine (PC) liposomal membranes were investigated through experimental studies and theoretical considerations. Using a microelectrophoresis technique, charge densities of experimental membrane surfaces were measured as a function of the pH of electrolyte solutions. Equilibria between the PC liposomal membranes and monovalent ions were mathematically analyzed and described quantitatively through a previously proposed theoretical model. Association constants between functional groups of PC and the studied ions were determined and used to define theoretical curves of membrane surface charge density versus pH. Theoretical and experimental data were compared to verify the model. The PC membrane was found to have the highest affinity for lithium ions, among the ions tested.
... Such liposomes have the ability to bind both genetic material and cell membranes, that both have negative charge, i.e. are anionic and are used in this capacity as delivery vehicles for gene therapy. Hence, several groups [447,448,449,450] have computationally modeled the membrane of a positively charged LDS, i.e. cationic liposomes. The composition of the lipid membrane was found to determine the fashion in which the ...
Combined experimental and computational study of lipid membranes and liposomes, with the aim to attain mechanistic understanding, results in a synergy that makes possible the rational design of liposomal drug delivery system (LDS) based therapies. The LDS is the leading form of nanoscale drug delivery platform, an avenue in drug research, known as “nanomedicine", that holds the promise to transcend the current paradigm of drug development that has led to diminishing returns. Unfortunately this field of research has, so far, been far more successful in generating publications than new drug therapies. This partly results from the trial and error based methodologies used. We discuss experimental techniques capable of obtaining mechanistic insight into LDS structure and behavior. Insight obtained purely experimentally is, however, limited; computational modeling using molecular dynamics simulation can provide insight not otherwise available. We review computational research, that makes use of the multiscale modeling paradigm, simulating the phospholipid membrane with all atom resolution and the entire liposome with coarse grained models. We discuss in greater detail the computational modeling of liposome PEGylation. Overall, we wish to convey the power that lies in the combined use of experimental and computational methodologies; we hope to provide a roadmap for the rational design of LDS based therapies. Computational modeling is able to provide mechanistic insight that explains the context of experimental results and can also take the lead and inspire new directions for experimental research into LDS development. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
... Such liposomes have the ability to bind both genetic material and cell membranes, that both have negative charge, i.e. are anionic and are used in this capacity as delivery vehicles for gene therapy. Hence, several groups [447,448,449,450] have computationally modeled the membrane of a positively charged LDS, i.e. cationic liposomes. The composition of the lipid membrane was found to determine the fashion in which the ...
Sterically stabilized liposomes (SSLs) (PEGylated liposomes) are applied as effective drug delivery vehicles. Understanding the interactions between hydrophobic compounds and PEGylated membranes is therefore important to determine the effectiveness of PEGylated liposomes for delivery of drugs or other bioactive substances. In this study, we have combined fluorescence quenching analysis (FQA) experiments and all-atom molecular dynamics (MD) simulations to study the effect of membrane PEGylation on the location and orientation of 5,10,15,20-tetrakis(4-hydroxyphenyl)porphyrin (p-THPP) that has been used in our study as a model hydrophobic compound. First, we consider the properties of p-THPP in the presence of different fluid phosphatidylcholine bilayers that we use as model systems for protein-free cell membranes. Next, we studied the interaction between PEGylated membranes and p-THPP. Our MD simulation results indicated that the arrangement of p-THPP within zwitterionic membranes is dependent on their free volume, and p-THPP solubilized in PEGylated liposomes is localized in two preferred positions: deep within the membrane (close to the center of the bilayer) and in the outer PEG corona (p-THPP molecules being wrapped with the polymer chains). Fluorescence quenching methods confirmed the results of atomistic MD simulations and showed two populations of p-THPP molecules as in MD simulations. Our results provide both an explanation for the experimental observation that PEGylation improves the drug-loading efficiency of membranes and also a more detailed molecular-level description of the interactions between porphyrins and lipid membranes.
... nm 2 in NaCl solutions. 40,41 Thus the parameter SF (= v/(a 0 l C )) of GLH-20 could be estimated to be between 0.35 and 0.30. 38 Recalling that for SF < 1/2 surfactants are expected to pack into micelles, this estimate seems to agree with the cryo-TEM and DLS results. ...
Bolaamphiphiles-based biomimetic membranes for water purification Y.Kaufman, S.Grinberg, C.Linder, J.Gilron, and V.Freger
The high water permeability and selectivity of aquaporins (water channel proteins found in biological membranes) makes aquaporin-based biomimetic membranes potentially attractive for water purification and green-energy production. In our previous report (Kaufman et al., Langmuir 2010) we showed that a supported lipid bilayer can be prepared on NF membrane under acidic conditions (pH 2). Herein, we show that supported biomimetic membrane can be prepared on a NF substrate under milder conditions (pH 7) by replacing previously used phospholipids with positively charged bolaamphiphiles.
The main advantage of using positively charged lipids, such as the bolaamphiphile used here, is their facile adsorption on negatively charged surfaces of NF membranes. An important parameter is the aggregate structure of the bola prior to absorption onto the membrane surface. We found that the cationic bolas tend to self-assemble into micelles, with surface of a significantly curvature as compared to larger nano-sized vesicles with an aqueous core as we studied with liposomal phospholipids. It was found that these micelles can undergo fusion on the membranes surfaces similar to vesicles, thus the lipid adhering to NF membrane surface forms a continuous supported layer. Moreover, aquaporins solubilized with micellar aggregates in solution, analogous to vesicular proteoliposomes the case of regular phospholipids, may be incorporation into the supported bolaamphiphile monolayer through a similar fusion process. To the best of our knowledge, this is the first demonstration Aquaporin-Z can be incorporated in structures with a substantial spontaneous curvature such as micelles.
The water permeability and ion rejection of the supported membranes with and without aquaporins were measured using a recently developed microfluidic NF cell. Compared with bench-scale cells, the microfluidic cell allows in situ preparation of biomimetic membranes using minimal amount of the expensive lipids and proteins and measuring their performance in cross flow conditions. Fig. 1 showing typical pristine membrane permeability reveals the following: 1) The monolayer of bolaamphiphiles effectively seals the surface of the supporting NF membranes and 2) The incorporation of aquaporinZ increases the permeability of the supported bola-amphiphile layer. These results will be discussed in detail during the talk.
Figure 1: Water permeability of commercial NF membrane covered by bolaamphiphiles with different concentration of aquaporins
Keywords: bolaamphiphile, biomimetic membrane, microfluidic, water purification
... Indeed, the majority of lipid bilayers studied by MD simulation are uncharged single-component bilayers built predominantly of PC [26] with only a few built of PE [20,[27][28][29] . Only recently the bilayers [30][31][32][33][34][35] and monolayers [25] composed of charged or mixtures of uncharged and charged lipids have also been simulated. Those simulations demonstrated that the properties of such bilayers are dominated by electrostatic interactions among lipid head groups, ions, and water at the membrane/ water interface. ...
... Such liposomes have the ability to bind both genetic material and cell membranes, that both have negative charge, i.e. are anionic and are used in this capacity as delivery vehicles for gene therapy. Hence, several groups [447,448,449,450] have computationally modeled the membrane of a positively charged LDS, i.e. cationic liposomes. The composition of the lipid membrane was found to determine the fashion in which the ...
We summarize our recent work, using all atom molecular dynamics simulation to study the role of poly(ethylene glycol) (PEG) in drug delivery. We have simulated the drug delivery liposome membrane, in both the Gel and Liquid crystalline states. The simulations of the PEGylated membrane have been carried out in the presence of a physiological concentration of NaCl, and two other salts encountered in physiological conditions, KCL and CaCl2. We also simulated targeting moieties on the PEGylated membrane, comparing the behavior of two targeting moieties. We also simulated PEG with three drug molecules for which it is used as a delivery aid: paclitaxel, piroxicam, and hematoporphyrin. We found that the specific properties of PEG, its solubility in both polar and non-polar solvents, and its acting as a polymer electrolyte, have a significant e_ect on its behavior when used in drug delivery.
... nm 2 in NaCl solutions. 40,41 Thus the parameter SF (= v/(a 0 l C )) of GLH-20 could be estimated to be between 0.35 and 0.30. 38 Recalling that for SF < 1/2 surfactants are expected to pack into micelles, this estimate seems to agree with the cryo-TEM and DLS results. ...
Supported biomimetic membranes (SBM) on solid substrates have been commonly prepared from vesicle-forming double-tail lipids, such as zwitterionic phospholipids, using the method of vesicle fusion. Here we report on the preparation of SBMs on silica surfaces via a similar process of "micelle fusion" from a cationic single-tail bolaamphiphile GLH-20 that forms spherical and elongated thread-like micelles in solution. We demonstrate that in contrast to zwitterionic phospholipids, GLH-20 self-assembles into a stable contiguous SBM at both low and high ionic strengths. The cationic charge of GLH-20 promotes the formation of a stable SBM through enhanced double-layer interactions with the negatively charged silica surface. It is also shown that spinach aquaporin PM-28 was successfully incorporated within bolaamphiphile SBM in a manner similar to SBMs prepared by vesicle/proteoliposome fusion; thereby the inherent curvature of the micelle surface does not inhibit protein reconstitution. The results suggest that SBMs based on charged bolaamphiphiles might be an attractive platform for applications such as water purification and biosensors, where the stability and low defect rate of SBMs in diverse conditions are crucial for achieving desired performance.
... In addition to the simulation temperature, T, and the simulation time, t, the columns display the area per lipid, A, the bilayer thickness, d pp , and the estimated numbers of hydrogen bonds, N. a Peak-to-peak distance of electron density plot. simple membrane systems and even considerably longer times may be needed e.g. in systems with ions [35,434445464748. All publications on SM simulations have extensively concentrated on analyzing hydrogen bond patterns. ...
We review the relationship between molecular interactions and the properties of lipid environments. A specific focus is given on bilayers which contain sphingomyelin (SM) and sterols due to their essential role for the formation of lipid rafts. The discussion is based on recent atom-scale molecular dynamics simulations, complemented by extensive comparison to experimental data. The discussion is divided into four sections. The first part investigates the properties of one-component SM bilayers and compares them to bilayers with phosphatidylcholine (PC), the focus being on a detailed analysis of the hydrogen bonding network in the two bilayers. The second part deals with binary mixtures of sterols with either SM or PC. The results show how the membrane properties may vary substantially depending on the sterol and SM type available, the membrane order and interdigitation being just two of the many examples of this issue. The third part concentrates on the specificity of intermolecular interactions in three-component mixtures of SM, PC and cholesterol (CHOL) under conditions where the concentrations of SM and CHOL are dilute with respect to that of PC. The results show how SM and CHOL favor one another, thus acting as nucleation sites for the formation of highly ordered nanosized domains. Finally, the fourth part discusses the large-scale properties of raft-like membrane environments and compares them to the properties of non-raft membranes. The differences turn out to be substantial. As a particularly intriguing example of this, the lateral pressure profiles of raft-like and non-raft systems indicate that the lipid composition of membrane domains may have a major impact on membrane protein activation.
... Their presence in the membrane affects the binding of ions significantly because they prevent the positively charged ions from tight binding to the heads of neutral lipids. Thus, the high mole fractions of the DMTAP lipids in mixed DMPC/DMTAP bilayers (50-75%) suppress the changes in bilayer structure and electrostatic properties induced by the monovalent salt (Gurtovenko et al., 2005a). ...
Electrostatic fields generated on and inside biological membranes are recognized to play a fundamental role in key processes of cell functioning. Their understanding requires an adequate description on the level of elementary charges and the reconstruction of electrostatic potentials by integration over all elementary interactions. Out of all the available research tools, only molecular dynamics simulations are capable of this, extending from the atomic to the mesoscopic level of description on the required time and space scale. A complementary approach is that offered by molecular probe methods, with the application of electrochromic dyes. Highly sensitive to intermolecular interactions, they generate integrated signals arising from electric fields produced by elementary charges at the sites of their location. This review is an attempt to provide a critical analysis of these two approaches and their present and potential applications. The results obtained by both methods are consistent in that they both show an extremely complex profile of the electric field in the membrane. The nanoscopic view, with two-dimensional averaging over the bilayer plane and formal separation of the electrostatic potential into surface (Ψs), dipole (Ψd) and transmembrane (Ψt) potentials, is constructive in the analysis of different functional properties of membranes.
... Although this thermostat does not reproduce the correct statistical ensemble, this option was chosen since it is commonly used in membrane simulations. 31,34,45,46 Moreover, it was originally used for the parameterization of the Berger force field for the lipids. 39 All bond lengths of the lipid molecules were constrained using the LINCS algorithm 47 whereas the SETTLE algorithm 48 was used for water molecules. ...
Cell membranes are constitutively composed of thousands of different lipidic species, whose specific organization leads to functional heterogeneities. In particular, sphingolipids, cholesterol and some proteins associate among them to form stable nanoscale domains involved in recognition, signaling, membrane trafficking, etc. Atomic-detail information in the nanometer/second scale is still elusive to experimental techniques. In this context, molecular simulations on membrane systems have provided useful insights contributing to bridge this gap. Here we present the results of a series of simulations of biomembranes representing non-raft and raft-like nano-sized domains in order to analyze the particular structural and dynamical properties of these domains. Our results indicate that the smallest (5 nm) raft domains are able to preserve their distinctive structural and dynamical features, such as an increased thickness, higher ordering, lower lateral diffusion, and specific lipid-ion interactions. The insertion of a transmembrane protein helix into non-raft, extended raft-like, and raft-like nanodomain environments result in markedly different protein orientations, highlighting the interplay between the lipid-lipid and lipid-protein interactions.
This study aimed to explore the effect of ion on the interaction between soy hull polysaccharides (SHP) and glycocholic acid (GCA). The determination of bile acids (BAs) binding rate, FT-IR, and zeta potential revealed that the binding rate of SHP to GCA (fell about 14 %), hydrogen bond peak area (fell about 149), and zeta potential (fell about 13 %) showed a sharp downward trend after K ⁺ and Mg ²⁺ treatment. However, the apparent viscosity increased and the chain structure became closer, as detected by shear rheology and AFM analysis. The root mean square deviation, radius of gyration, and root mean square fluctuation levels were estimated through molecular dynamic simulations, revealing that adding mixed ions decreased the stability of the SHP–GCA complex at 50 ns. Therefore, it was meaningful to study the effect of ion species in the intestinal environment on the binding of dietary fibers to BAs. The findings might guide the selection of other food types during polysaccharide intake.
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
Though liposome-based drugs are in clinical use, the mechanism of cell internalization of liposomes is yet an object of controversy. The present experimental investigation, carried out on human glioblastoma cells, indicated different internalization routes for two diastereomeric liposomes. Molecular dynamics simulations of the lipid bilayers of the two formulations indicated that the different stereochemistry of a lipid component controls some parameters such as area per lipid molecule and fluidity of lipid membranes, surface potential and water organization at the lipid/water interface, all of which affect the interaction with biomolecules and cell components.
The ubiquity of aqueous solutions in contact with charged surfaces and the realization that the molecular-level details of water–surface interactions often determine interfacial functions and properties relevant in many natural processes have led to intensive research. Even so, many open questions remain regarding the molecular picture of the interfacial organization and preferential alignment of water molecules, as well as the structure of water molecules and ion distributions at different charged interfaces. While water, solutes and charge are present in each of these systems, the substrate can range from living tissues to metals. This diversity in substrates has led to different communities considering each of these types of aqueous interface. In this Review, by considering water in contact with metals, oxides and biomembranes, we show the essential similarity of these disparate systems. While in each case the classical mean-field theories can explain many macroscopic and mesoscopic observations, it soon becomes apparent that such theories fail to explain phenomena for which molecular properties are relevant, such as interfacial chemical conversion. We highlight the current knowledge and limitations in our understanding and end with a view towards future opportunities in the field. What do a rock in a river, a red blood cell in our body and the electrodes inside a car battery have in common? Charged surfaces in contact with water. Although a unified approach to study such a variety of systems is not available yet, the current understanding — even with its limitations — paves the road to the development of new concepts and techniques.
As efforts to move a renewable economy grow, it will be necessary to make use of microbial conversion strategies for the production of novel materials or the upgrading of waste to high-value products. One critical technical challenge currently limiting waste upgrading remains the difficulty in obtaining single-pot conversion techniques where physical, chemical, and biological conversion are performed in a single step. To overcome this challenge, a detailed understanding of how different stresses impact microbial membrane stability will be necessary. Using all-atom molecular dynamics simulations, we examine the impacts of moderate concentrations of NaCl and CaCl2on a model yeast plasma membrane. Weak, though statistically significant, changes in membrane morphology and dynamics functions are observed that are consistent with swelling and stiffening. Additionally, an examination of the ion-lipid contacts and the behavior of water at the water-membrane interface suggests that the impacts of these common salts may, in part, be mediated through changes to water-membrane hydrogen-bonding and hydration water dynamics.
Cationic lipids have attracted much attention due to their potential for biomedical applications, such as gene delivery. The gene transfection efficiency of cationic lipids is greatly influenced by the counterions as well as salt ions. We have systematically investigated the interaction of different monovalent sodium salts with positively charged membrane, composed of DOPC/DOTAP and DOTAP, using dynamic light scattering, zeta potential, isothermal titration calorimetry and fluorescence spectroscopy techniques. Our results reveal that the affinity of anions with cationic membranes follows the sequence I - >> Br - > Cl - according to descending order of their sizes and is consistent with the Hofmeister series. Interestingly, the electrostatic behavior of the DOTAP membrane in the presence of monovalent anions differs significantly from the DOPC/DOTAP membrane. This difference is due to the strong interplay between PC and TAP headgroup leading to the reorientation of TAP group in the membrane. The binding constant of anions, derived from zeta potential and ITC is in agreement with the affinity of anions mentioned above. Among all anions, I - shows strongest affinity, as evidenced from the rapid increase in hydrodynamic radius which eventually leads to the formation of large aggregates. The fluorescence spectroscopy of a lypophilic probe nile red in the presence of cationic vesicles containing ions complements the I - adsorption onto the membrane. Non linear Stern-Volmer plot, consisting of accessible and inaccessible nile red to I - is consistent with the zeta potential as well as ITC results.
In this work, the effects of the anti-hypertensive drug amlodipine in native and PEGylated forms on the malfunctioning of negatively charged lipid bilayer cell membranes constructed from DMPS or DMPS + DMPC were studied by molecular dynamics simulation. The obtained results indicate that amlodipine alone aggregates and as a result its diffusion into the membrane is retarded. In addition, due to their large size aggregates of the drug can damage the cell, rupturing the cell membrane. It is shown that PEGylation of amlodipine prevents this aggregation and facilitates its diffusion into the lipid membrane. The interaction of the drug with negatively charged membranes in the presence of an aqueous solution of NaCl, as the medium, is investigated and its effects on the membrane are considered by evaluating the structural properties of the membrane such as area per lipid, thickness, lipid chain order and electrostatic potential difference between bulk solution and lipid bilayer surface. The effect of these parameters on the diffusion of the drug into the cell is critically examined and discussed.
Despite the vast amount of experimental and theoretical studies on the binding affinity of cations - especially the biologically relevant Na(+) and Ca(2+) - for phospholipid bilayers, there is no consensus in the literature. Here we show that by interpreting changes in the choline headgroup order parameters according to the 'molecular electrometer' concept [Seelig et al., Biochemistry, 1987, 26, 7535], one can directly compare the ion binding affinities between simulations and experiments. Our findings strongly support the view that in contrast to Ca(2+) and other multivalent ions, Na(+) and other monovalent ions (except Li(+)) do not specifically bind to phosphatidylcholine lipid bilayers at sub-molar concentrations. However, the Na(+) binding affinity was overestimated by several molecular dynamics simulation models, resulting in artificially positively charged bilayers and exaggerated structural effects in the lipid headgroups. While qualitatively correct headgroup order parameter response was observed with Ca(2+) binding in all the tested models, no model had sufficient quantitative accuracy to interpret the Ca(2+):lipid stoichiometry or the induced atomistic resolution structural changes. All scientific contributions to this open collaboration work were made publicly, using nmrlipids.blogspot.fi as the main communication platform.
The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To probe these nanodomains in soft matter is a challenging task both experimentally and theoretically. This work addresses the effects of cholesterol, lipid composition, lipid charge, and lipid phase on the monolayer structure and the electrical surface potential distribution. Atomic Force Microscopy (AFM) was used to resolve topographical nanodomains and Kelvin Probe Force Microscopy (KPFM) to resolve electrical surface potential of these nanodomains in lipid monolayers. Model monolayers composed of dipalmitoylphosphatidylcholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(3-lysyl(1-glycerol))] (DOPG), sphingomyelin, and cholesterol were studied. It is shown that cholesterol changes nanoscale domain formation, affecting both topography and electrical surface potential. The molecular basis for differences in electrical surface potential was addressed with atomistic molecular dynamics (MD). MD simulations qualitatively match the experimental results, with 100s of mV difference in electrostatic potential between liquid-disordered bilayer (Ld, less cholesterol and lower chain order) and a liquid-ordered bilayer (Lo, more cholesterol and higher chain order). Importantly, the difference in electrostatic properties between Lo and Ld phases suggests a new mechanism by which membrane composition couples to membrane function.
Monovalent ions play fundamental roles in many biological processes in organisms. Modeling these ions in molecular simulations continues to be a challenging problem. The 12-6 Lennard-Jones (LJ) nonbonded model is widely used to model monovalent ions in classical molecular dynamics simulations. A lot of parameterization efforts have been reported for these ions with a number of experimental endpoints. However, some reported parameter sets don’t have a good balance between the two Lennard-Jones parameters (the van der Waals radius and potential well depth), which affects their transferability. In the present work, via the use of a noble gas curve we fitted in former work (JCTC 2013, 9, 2733), we re-optimized the 12-6 LJ parameters for 15 monovalent ions (11 positive and 4 negative ions) for three extensively used water models (TIP3P, SPC/E and TIP4PEW). Since the 12-6 LJ nonbonded model can perform poorly in some instances for these ions we have also parameterized the 12-6-4 LJ-type nonbonded model (JCTC, 2014, 10, 289) using the same three water models. The three derived parameter sets focused on reproducing the hydration free energies (the HFE set) and the ion-oxygen distance (the IOD set) using the 12-6 LJ nonbonded model and the 12-6-4 LJ-type nonbonded model overall give improved results. In particular, the final parameter sets showed better agreement with quantum mechanically calculated VDW radii and improved transferability to ion-pair solutions when compared to previous parameter sets.
Time-dependent fluorescence shift (TDFS) of Laurdan embedded in phospholipid bilayers reports on hydration and mobility of the phospholipid acylgroups. Exchange of H2O with D2O prolongs the lifetime of lipid-water and lipid-water-lipid interactions, which is reflected in a significantly slower TDFS kinetics. Combining TDFS measurements in H2O and D2O hydrated bilayers with atomistic molecular dynamics (MD) simulations provides a unique tool for characterization of the hydrogen bonding at the acylgroup level of lipid bilayers. In this work, we use this approach to study the influence of fluoride anions on the properties of cationic bilayers composed of trimethylammonium-propane (DOTAP). The results obtained for DOTAP are confronted with those for neutral phosphatidylcholine (DOPC) bilayers. Both in DOTAP and DOPC H2O/D2O exchange prolongs hydrogen-bonding lifetime and does not disturb bilayer structure. These results are confirmed by MD simulations. TDFS experiments show, however, that for DOTAP this effect is cancelled in the presence of fluoride ions. We interpret these results as evidence that strongly hydrated fluoride is able to steal water molecules that bridge lipid carbonyls. Consequently, when attracted to DOTAP bilayer, fluoride disrupts the local hydrogen-bonding network, and the differences in TDFS kinetics between H2O and D2O hydrated bilayers are no longer observed. A distinct behavior of fluoride is also evidenced by MD simulations, which show different lipid-ion binding for Cl(-) and F(-).
Infrared (IR) spectroscopy was used to quantify the ion mixture effect of seawater (SW), particularly the contribution of Mg2+ and Ca2+ as dominant divalent cations, on the thermotropic phase behaviour of 1,2-dimyristoyl-sn-glycero-3-posphocholine (DMPC) bilayers. The changed character of the main transition at 24 °C from sharp to gradual in films and the 1 °C shift of the main transition temperature in dispersions reflect the interactions of lipid headgroups with the ions in SW. Force spectroscopy was used to quantify the nanomechanical hardness of a DMPC supported lipid bilayer (SLB). Considering the electrostatic and ion binding equilibrium contributions while systematically probing the SLB in various salt solutions, we showed that ionic strength had a decisive influence on its nanomechanics. The mechanical hardness of DMPC SLBs in the liquid crystalline phase linearly increases with the increasing fraction of all ion-bound lipids in a series of monovalent salt solutions. It also linearly increases in the gel phase but almost three times faster (the corresponding slopes are 4.9 nN/100 mM and 13.32 nN/100 mM, respectively). We also showed that in the presence of divalent ions (Ca2+ and Mg2+) the bilayer mechanical hardness was unproportionally increased, and that was accompanied with the decrease of Na+ ion and increase of Cl− ion bound lipids. The underlying process is a cooperative and competitive ion binding in both the gel and the liquid crystalline phase. Bilayer hardness thus turned out to be very sensitive to ionic strength as well as to ionic composition of the surrounding medium. In particular, the indicated correlation helped us to emphasize the colligative properties of SW as a naturally occurring complex ion mixture.
In this paper, we characterized the interactions between two-component liposomal membranes and monovalent electrolyte ions. Liposomes were formed from neutral (phosphatidylcholine) and anionic (phosphatidylglycerol) lipids mixed in various ratios. Microelectrophoresis was used to determine the dependence of the membrane surface charge density on the p H of the electrolyte solution. Changes in the membrane electric charge caused by the adsorption of Na+ , Cl- , H+ , and OH- ions were observed, and the equilibria among these ions and the phosphatidylcholine-phosphatidylglycerol membrane surface were quantified. We proposed a mathematical model for characterizing these equilibria. Using this model, together with experimental data of the membrane surface charge density, we determined association constants characterizing the equilibria. Knowledge of these parameters was necessary to calculate the theoretical curves of the model. We validated the model by curve-fitting the experimental data points to simulated data generated by the model.
Graphical abstract
Abstract Atomic force microscopy (AFM) has become an invaluable tool for studying the micro- and nanoworlds. As a stand-alone, high-resolution imaging technique and force transducer, it defies most other surface instrumentation in ease of use, sensitivity and versatility. The main strength of AFM relies on the possibility to operate in an aqueous environment on a wide variety of biological samples, from single molecules - DNA or proteins - to macromolecular assemblies like biological membranes. Understanding the effect of mechanical stress on membranes is of primary importance in biophysics, since cells are known to perform their function under a complex combination of forces. In the later years, AFM-based force-spectroscopy (AFM-FS) has provided a new vista on membrane mechanics in a confined area within the nanometer realm, where most of the specific molecular interactions take place. Lipid membranes are electrostatically charged entities that physiologically coexist with electrolyte solutions. Thus, specific interactions with ions are a matter of considerable interest. The distribution of ions in the solution and their interaction with the membranes are factors that substantially modify the structure and dynamics of the cell membranes. Furthermore, signaling processes are modified by the membrane capability of retaining ions. Supported lipid bilayers (SLBs) are a versatile tool to investigate phospholipid membranes mimicking biological surfaces. In the present contribution, we review selected experiments on the mechanical stability of SLBs as models of lipid membranes by means of AFM-FS, with special focus on the effect of cations and ionic strength in the overall nanomechanical stability.
The applicability of the replica Ornstein-Zernike (ROZ) method, often used to explore the partly quenched systems, for studying ionic equilibria in membrane-like systems was investigated. A simple +1:-1 electrolyte solution was modelled as a primitive model electrolyte on the McMillan-Mayer level of approximation. The particles mimicking membrane were modelled as permeable hard spheres frozen in space in their positions. The ion-membrane potential was chosen to conform as closely as possible to the experimental data. The density profiles of ions near the membrane, as well as adsorption isotherms, were calculated using the ROZ equations complemented by the hypernetted chain (HNC) approximation. The method provides reasonable results in qualitative agreement with experimental observations.
Detergents, amphiphilic molecules used to separate and dissolve molecular aggregates and also as cleaning agents, consist of a polar head group and one or more hydrophobic tails. Above a critical concentration, they self-aggregate in an aqueous solution to form micelles. While industrially extremely important, surprisingly little is known about molecular details of the self-assembly of detergents. Here we extend our previous work of modeling and model construction of charged soft-matter systems [1] by a description of an anionic detergent, sodium dodecyl sulfate (SDS) [2]. We present the results of large-scale Molecular Dynamics simulations of the formation dynamics and structure of SDS micelles. We demonstrate that temperature affects micelle morphologies through the packing and discuss the effect of SDS concentration on the micellization. [1] M. Patra et al., Biophys. J. 84, 3636 (2003); A. A. Gurtovenko et al., J. Phys. Chem. B 109, 21126 (2005); A. A. Gurtovenko et al., Biophys. J. 86, 3461 (2004). [2] The SDS parameters are available at www.softsimu.org.
Proteins perform various biological functions in the cell by interacting and binding to other proteins, DNA, or other small molecules. These interactions occur in cellular compartments with different salt concentrations, which may also vary under different physiological conditions. The goal of this study is to investigate the effect of salt concentration on the electrostatic component of the binding free energy (hereafter, salt effect) based on a large set of 1482 protein-protein complexes, a task that has never been done before. Since the proteins are irregularly shaped objects, the calculations have been carried out by a means of finite-difference algorithm that solves Poisson- Boltzmann equation (PB) numerically. We performed simulations using both linear and non-linear PB equations and found that non-linearity, in general, does not have significant contribution into salt effect when the net charges of the protein monomers are of different polarity and are less than five electron units. However, for complexes made of monomers carrying large net charges non-linearity is an important factor, especially for homo-complexes which are made of identical units carrying the same net charge. A parameter reflecting the net charge of the monomers is proposed and used as a flag distinguishing between cases which should be treated with non-linear Poisson-Boltzmann equation and cases where linear PB produces sound results. It was also shown that the magnitude of the salt effect is not correlated with macroscopic parameters (such as net charge of the monomers, corresponding complexes, surface and number of interfacial residues) but rather is a complex phenomenon that depends on the shape and charge distribution of the molecules.
Polyunsaturated lipids are major targets of free radicals forming oxidized lipids through the lipid peroxidation process. Thus, oxidized lipids play a significant role in cell membrane damage. Using atomistic molecular dynamics (MD) simulations to investigate the dynamics of oxidized lipid bilayers, we examined the effects of NaCl on them. Lipid bilayer systems of 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLPC) and 4 oxidation products, namely 9-tc-hydroperoxide linoleic acid, 13-tc-hydroperoxide linoleic acid, 9-oxononanoic acid, and 12-oxo-9-didecadienoic acid in 0, 0.06, and 1 M NaCl solution were studied. These 51 systems, combined over 15 µs of total simulation time, show Cl- anions remaining in the water phase and Na+ cations permeating into the head group region of the bilayer leading to membrane packing. The effects of NaCl on thickness and area per molecule were found to be independent of the concentration of oxidized lipids. NaCl disturbed the bilayers with aldehyde lipids more than those with peroxide lipids. The key finding is that oxidized lipids bend their polar tails toward the water interface. This behavior was monitored by following the time evolution of hydrogen bonds between the oxidized functional groups of different lipids, and the concomitant increase of hydrogen bonds between oxidized functional groups and water molecules. Our results also show that the number of hydrogen bonds should be considered as an equilibration parameter: Very long simulations are needed to equilibrate systems with high NaCl concentrations.
The influence of monovalent salts (NaF, NaCl, NaBr, NaClO4, KCl) on the properties of lipid bilayers composed of binary mixtures of zwitterionic DOPC (dioleoylphosphatidylcholine) and cationic DOTAP (dioleoyltrimethylammoniumpropane) is experimentally measured and numerically simulated. Both approaches report a specific adsorption of the studied anions at the cationic bilayer. The adsorption is enhanced for higher content of DOTAP in DOPC/DOTAP mixtures and for larger anions (Br and ClO4-). The nonmonotonic dependence of the lipid headgroup mobility, determined using time-dependent fluorescence shifts of Laurdan located at the bilayer carbonyl level, on the content of cationic lipid is preserved in all examined salt solutions. Its maximum, however, is shifted towards higher DOTAP concentrations in the row: NaF < NaCl < NaBr. The same ordering of salts is found for the simulated area per lipid and the measured rigidification of pure DOTAP bilayers. Simulations reveal that Br strongly binds to the cationic headgroups of DOTAP neutralising the bilayer, which induces lateral inhomogeneities in the form of hydrophilic and hydrophobic patches at the membrane-water interface for pure DOTAP. In the equimolar DOPC/DOTAP mixture the neutralising effect of Br results in bending of the PC headgroups to a bilayer-parallel orientation. F-, while attracted to the DOTAP bilayer, has an opposite effect to that of Br-, i.e. it increases local mobility at the lipid carbonyl level. We attribute this effect to the disruption of the hydrogen-bonded structure of the molecules of lipids and water caused by the presence of the adsorbed F-.
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.
Phospholipid membranes are useful in the field of biocatalysis because a supported phospholipid membrane can create a biomimetic platform where biocatalytic processes can readily occur. In this work, supported bilayer formation from sonicated phospholipid vesicles containing 1,2-dielaidoyl-sn-glycero-3-phosphocholine and 1,2-dimyristoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] was studied using a quartz crystal microbalance with dissipation monitoring and an atomic force microscope. The molar percentages of DEPC and DMPG were varied to determine the effect of overall lipid composition on supported bilayer formation. This work also explored the effect that calcium ion concentration had on supported bilayer formation. Results show that vesicles with up to 50 mol% dimyristoylphosphoglycerol can form a supported bilayer without the presence of calcium ions; however, supported bilayer formation in calcium buffer was inhibited as the anionic (negatively charged) lipid concentration increased. Data suggest that supported phospholipid bilayer formation in the absence of Ca2+ from vesicles containing negatively charged lipids is specific to phosphatidylglycerol.
High-surface-area nanoparticles often cluster, with unknown effects on their cellular uptake and environmental impact. In the presence of vesicles or cell membranes, lipid adsorption can occur on the nanoparticles, resulting in the formation of supported lipid bilayers (SLBs), which tend to resist cellular uptake. When the amount of lipid available is in excess compared with that required to form a single-SLB, large aggregates of SLBs enclosed by a close-fitting lipid bilayer sheath are shown to form. The proposed mechanism for this process is one where small unilamellar vesicles (SUVs) adsorb to aggregates of SLBs just above the gel-to-liquid phase transition temperature, T(m) , of the lipids (as observed by dynamic light scattering), and then fuse with each other (rather than to the underlying SLBs) upon cooling below T(m) . The sacks of SLB nanoparticles that are formed are encapsulated by the contiguous close-fitting lipid sheath, and precipitate below T(m) , due to reduced hydration repulsion and the absence of undulation/protrusion forces for the lipids attached to the solid support. The single-SLBs can be released above T(m) , where these forces are restored by the free lipid vesicles. This mechanism may be useful for encapsulation/release of drugs/DNA, and has implications for the toxic effects of nanoparticles, which may be mitigated by lipid sequestration.
FTIR spectroscopy is used to study structural aspects of ternary complexes formed by the cationic lipid
dimyristoyltrimethylammoniumpropane (DMTAP), the zwitterionic lipid dimyristoylphosphatidylcholine (DMPC), and deoxyribonucleic acid (DNA). Spectra of the single components are compared with those obtained for both equimolar DMPC–DMTAP mixture and lipid–DNA complex. The IR spectra of mixed lipid–DNA
phases are strongly dominated by the lipidic absorption bands. This allows one to easily monitor, in particular, the thermotropic phase behaviour of lipid within the complex. The IR spectra of DNA intercalated
between cationic lipid bilayers are determined by subtracting corresponding pure lipid spectra from lipid–DNA complex spectra. These difference spectra indicate deviations of lipid–associated DNA from B-form DNA. Furthermore, two additional water bands arise at positions different from those known for lipid- and DNA-bound water which are indicative of two distinct states of hydration in lipid–DNA complexes. The pure
lipid DMTAP exhibits unusual spectroscopic features at the temperature of chain melting, Tm, near 53°C, which are attributed to the existence of a crystalline, headgroup-interdigitated phase existing at temperatures below Tm, in accordance
with X-ray diffraction and differential scanning calorimetry (DSC) data.
We report on a synchrotron x-ray diffraction study of saturated cationic lipid complexed with DNA. In the lipid gel phase Lcbeta' the complexes exhibit Bragg reflections due to lamellar lipid bilayer stacking and three nonintegral peaks in agreement with an intercalated centered rectangular columnar superlattice of DNA. The diffuse broadening of the DNA peaks is caused by in-plane translational disorder of the DNA strands and is approximated by Lorentzians with positional correlation lengths of xiy~250 Å out of plane and xix>2000 Å in plane. We interpret our results in terms of a system of interacting two-dimensional smectic layers.
The thermotropic phase behavior of zwitterionic/cationic binary lipid mixtures is investigated and compared to its corresponding lipidic phase diagram of mixtures complexed with DNA. We focus on isoelectric cationic lipid−DNA condensates where the number of cationic lipids equals the number of phosphate groups on the DNA. Using differential scanning calorimetry, X-ray scattering, freeze fracture electron microscopy, and film balance, we studied mixtures of di-myristoyl-phosphatidyl-choline (DMPC) and the cationic lipid, di-myristoyl-tri-methyl-ammonium-propane (DMTAP). The lipid phase diagram shows the well-known Lα, Lβ‘, and Pβ‘ ripple phase with peritectic behavior at a low molar fraction of cationic lipid, χTAP < 0.12. Beyond χTAP = 0.8 crystalline phases appear. A systematic variation in the hydrocarbon chain tilt in the prevailing Lβ‘ phase is measured by wide-angle X-ray scattering. Most importantly, the Lβ‘ phase shows strong nonideal mixing with an azeotropic point at about 1:1 molar stoichiometry. This finding is related to the reduced headgroup area for equimolar mixtures found in monolayer pressure−area isotherms. The intercalation of DNA in cationic lipid−DNA complexes affects the lipid-phase behavior 2-fold: (i) the chain-melting transition temperature shifts to higher temperatures and (ii) a demixing gap with coexistence of lipid vesicles and lipid−DNA complexes arises at a low cationic fraction, χTAP < 0.25. In agreement with experiments we present a thermodynamic model that describes the shift of the melting transition temperatures by DNA-induced electrostatic screening of the cationic membrane.
The binding of calcium, magnesium, lithium, potassium, and sodium to membrane bilayers of 5 to 1 (M/M) 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) and 1-palmitoyl- 2-oleoylphosphatidylserine (POPS) was investigated by using deuterium nuclear magnetic resonance (2H NMR). Both lipids were deuteriated on their polar headgroups, and spectra were obtained at 25 degrees C in the liquid-crystalline phase as a function of salt concentration. The spectra obtained with calcium were correlated with 45CaCl2 binding studies to determine the effective membrane-bound calcium at low calcium binding, up to 0.78 calcium per POPS. Deuterium quadrupolar splittings of both POPC and POPS headgroups were shown to be very sensitive to calcium binding. The behavior of these two headgroups over a wide range of CaCl2 concentrations suggests that Ca2+ binding occurs in at least two steps, the first step being achieved with 0.5 M CaCl2, with a stoichiometry of 0.5 Ca2+ per POPS. Correlations of the deuterium Ca2+ binding data with related data obtained after incorporation of a cationic integral peptide showed that the effects of these two cationic molecules of the POPS headgroup are qualitatively similar, and provided further support for two-step Ca2+ binding to the POPC/POPS 5:1 membranes. The corresponding data obtained with magnesium, lithium, and potassiummore » indicate that these cations interact with both the choline and serine headgroups. The amplitudes of headgroup perturbations could be partly correlated to the relative affinities of the metallic cations for the lipid membrane. The two-step binding described with Ca2+ appears to be relevant to the Mg2+ data, and in certain limits to the Li+ data. The data were interpreted in terms of conformational changes of the lipid headgroups induced by an electric field due to the charges of the membrane-bound metallic cations.« less
The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors. This reformulation allows a natural extension of the method to potentials of the form 1/r p with p≥1. Furthermore, efficient calculation of the virial tensor follows. Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy. We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N). For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 Å or less.
For molecular dynamics simulations of hydrated proteins a simple yet reliable model for the intermolecular potential for water is required. Such a model must be an effective pair potential valid for liquid densities that takes average many-body interactions into account. We have developed a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6–12 potential on the oxygen positions only. Parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion. Both potential energy and pressure were required to coincide with experimental values. The model has very satisfactory properties, is easily incorporated into protein-water potentials, and requires only 0.25 sec computertime per dynamics step (for 216 molecules) on a CRAY-1 computer.
In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD. A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling. The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints. The influence of coupling time constants on dynamical variables is evaluated. A leap‐frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath.
Gene therapy is based on the vectorization of genes to target cells and their subsequent expression. Cationic amphiphile-mediated delivery of plasmid DNA is the nonviral gene transfer method most often used. We examined the supramolecular structure of lipopolyamine/plasmid DNA complexes under various condensing conditions. Plasmid DNA complexation with lipopolyamine micelles whose mean diameter was 5 nm revealed three domains, depending on the lipopolyamine/plasmid DNA ratio. These domains respectively corresponded to negatively, neutrally, and positively charged complexes. Transmission electron microscopy and x-ray scattering experiments on complexes originating from these three domains showed that although their morphology depends on the lipopolyamine/plasmid DNA ratio, their particle structure consists of ordered domains characterized by even spacing of 80 A, irrespective of the lipid/DNA ratio. The most active lipopolyamine/DNA complexes for gene transfer were positively charged. They were characterized by fully condensed DNA inside spherical particles (diameter: 50 nm) sandwiched between lipid bilayers. These results show that supercoiled plasmid DNA is able to transform lipopolyamine micelles into a supramolecular organization characterized by ordered lamellar domains.
To characterize the specificity of ion binding to phospholipids in terms of headgroup structure, hydration and lyotropic phase behavior we studied 1-palmitoyl-2-oleoyl-phosphatidylcholine as a function of relative humidity (RH) at 25 degrees C in the presence and absence of Li+, Na+, K+, Be2+, Mg2+, Ca2+, Sr2+, Ba2+, Zn2+ and Cu2+ ions by means of infrared (IR) spectroscopy. All divalent cations and Li+ shift the gel-to-liquid crystalline phase transition towards bigger RH values indicating stabilization of the gel state. The observed shift correlates in a linearly fashion with the electrostatic solvation free energy for most of the ions in water that in turn, is inversely related to the ionic radius. This interesting result was interpreted in terms of the excess chemical potential of mixing of hydrated ions and lipids. Calcium, zinc and partially lithium, cause a positive deviation from the linear relationship. IR spectral analysis shows that the carbonyl groups become more accessible to the water in the presence of Mg2+, Ca2+, Sr2+ and Ba2+ probably because of their involvement into the hydration shell of the ions. In contrast, Be2+, Zn2+ and Cu2+ dehydrate the carbonyl groups at small and medium RH. The ability of the lipid to take up water is distinctly reduced in the presence of Zn2+ and, partially, of Cu2+ meaning that the headgroups have become less hydrophilic. The binding mode of Be2+ to lipid headgroups involves hydrolyzed water. Polarized IR spectra show that complex formation of the phosphate groups with divalent ions gives rise to conformational changes and immobilization of the headgroups. The results are discussed in terms of the lyotropic Hofmeister series and of fusogenic activity of the ionic species.
To investigate the microscopic interactions between cholesterol and lipids in biological membranes, we have performed a series of molecular dynamics simulations of large membranes with different levels of cholesterol content. The simulations extend to 10 ns, and were performed with hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers. The bilayers contain 1024 lipids of which 0-40% were cholesterol and the rest DPPC. The effects of cholesterol on the structure and mesoscopic dynamics of the bilayer were monitored as a function of cholesterol concentration. The main effects observed are a significant ordering of the DPPC chains (as monitored by NMR type order parameters), a reduced fraction of gauche bonds, a reduced surface area per lipid, less undulations--corresponding to an increased bending modulus for the membrane, smaller area fluctuations, and a reduced lateral diffusion of DPPC-lipids as well as cholesterols.
We compared Molecular Dynamics simulations of a bilayer of 128 fully hydrated phospholipid (DPPC) molecules, using different parameters and macroscopic boundary conditions. The same system was studied under constant pressure, constant volume and constant surface tension boundary conditions, with two different sets of charges, the single point charge (SPC) and extended single point charge (SPC/E) water model and two different sets of Lennard Jones parameters for the interaction between water and methyl/methylene. Some selected properties of the resulting bilayer systems are compared to each other, previous simulations and experimental data. It is concluded that in relatively high water concentration it is possible to use ab initio derived charges with constant pressure boundary conditions. The SPC water model gives a larger area per headgroup and a broader interface than the SPC/E model. Increasing the repulsion between water oxygens and CH 2 /CH 3 groups has a large effect on the width...
An N·log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms. Timings and accuracies are presented for three large crystalline ionic systems. The Journal of Chemical Physics is copyrighted by The American Institute of Physics.
Lipid−DNA complexes are of topical interest because of their potential for use as vectors in gene therapy. Herein, molecular dynamics simulations have been carried out to probe the nature of lipid−DNA interactions and thereby provide a complement to recent experimental and theoretical studies. Specifically, we have investigated the DNA duplex d(CCAACGTTGG)2, in its canonical B-form, intercalated into a lipid bilayer consisting of a neutralizing binary mixture of cationic (dimyristoyltrimethylammonium propaneDMTAP) and zwitterionic (dimyristoylphosphatidylcholineDMPC) lipids. Surprisingly, both lipids are involved in neutralizing the anionic DNA phosphate groups. The electrostatic interactions between the cationic trimethylammonium (TAP) and zwitterionic phosphocholine (PC) headgroups of the two lipids allow the PC headgroups to orient out of the bilayer plane and thereby also become available to screen the negative charges on the DNA.
Monolayers of the naturally occurring cationic lipid sphingosine and its mixtures with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) were studied using a Langmuir balance. More specifically, we measured the force−area (π−A) isotherms and determined the monolayer dipole potential Ψ as a function of the mole fraction of sphingosine (XSph) with and without a charge-saturating concentration of DNA in the subphase. Both sphingosine and POPC exhibited smooth compression isotherms, indicating their monolayers to be in the liquid expanded state. Even low contents (XSph = 0.05) of sphingosine in a POPC monolayer condensed the film dramatically, by 20% at 20 mN/m. This effect is suggested to reflect a reorientation of the P-−N+ dipole of the POPC headgroup (Säily, V. M. J.; Ryhänen, S. J.; Holopainen, J. M.; Borocci, S.; Mancini, G.; Kinnunen, P. K. J. Biophys. J. 2001, 81, 2135), in keeping with a simultaneous and pronounced increase in Ψ. Mixed monolayers of sphingosine and POPC exhibited three critical mole fractions XSph of sphingosine, viz., 0.25, 0.6, and 0.83, at which the area/molecule reached a local minimum, followed by a pronounced expansion of the film. This suggests energetically favorable ordering, which allows the positively charged sphingosines to maximize their distance, so as to minimize the Coulombic repulsion. The presence of DNA affected the mixed POPC/sphingosine monolayers differently depending on the constituent lipid stoichiometry, yet the same discontinuities were evident as in the presence of DNA.
We provide compelling evidence that different treatments of electrostatic interactions in molecular dynamics simulations may dramatically affect dynamic properties of lipid bilayers. To this end, we consider a fully hydrated pure dipalmitoylphosphatidylcholine bilayer through 50-ns molecular dynamics simulations and study various dynamic properties of individual lipids in a membrane, including the velocity autocorrelation function, the lateral and rotational diffusion coefficients, and the autocorrelation function for the area per molecule. We compare the results based on the Particle-Mesh Ewald (PME) and reaction field (RF) techniques with those obtained by an approach where the electrostatic interactions are truncated at rcut = 1.8, 2.0, and 2.5 nm. We find that the overall performance of PME is very good; its results are consistent with the expected behavior. The RF method performs rather well, too, despite certain inherent problems and the fact that its results differ from those obtained by PME. Nevertheless, the largest differences are found for the truncation methods, for which all examined truncation methods lead to results distinctly different from those obtained by PME. The lateral diffusion coefficients obtained by PME and truncation at 1.8 nm, for example, differ by a factor of 10, while the PME results are consistent with experimental values. The observed deviations can be interpreted in terms of artificial ordering due to truncation and highlight the important role of electrostatic interactions in the dynamics of systems composed of lipids and other biologically relevant molecules such as proteins and DNA.
This chapter discusses some of the basic considerations underlying the behavior of charged membranes in aqueous solutions. The chapter also describes the electrostatic interactions of membranes. After some general considerations of charged surfaces in liquids and the derivation of the Poisson–Boltzmann equation, the chapter presents specific solutions of several electrostatic problems starting with a single flat and rigid membrane, and then generalizing it to two flat membranes. Then, it considers the possibility of having a flexible membrane in various situations: a single membrane, two membranes, and a stack of membranes. Special emphasis is given to the coupling between the electrostatic and the elastic properties. By considering the membrane as a flexible (and homogeneous) interface, the contribution of the charges to the bending moduli has been found in various electrostatic regimes. Electrostatics tends to rigidify the membranes and also suppresses the out-of-plane fluctuations of a lamellar phase composed of a stack of membranes. However, when the membrane is heterogeneous, electrostatics can induce shape instabilities in relation to a lateral segregation of the two components.
Extremely rapid developments in molecular biology are making gene therapysa new medical treatment with a potential to cure diseases on the molecular levelsa promising new therapeutical modality. While appropriate plasmids (genes) can be prepared in large quantities, their efficient and safe delivery into appropriate cells in ViVo seems to be the main obstacle in successful medical applications. 1 Cationic liposomes were shown to be a promising gene delivery system. 2 Despite numerous studies and commercially available liposome kits, however, the structure of DNA-cationic liposome complexes is still not yet well understood. Several electron microscopy studies have shown either larger aggregates surrounded by thin fibers 3,4 or condensed DNA coated by a lipid bilayer. 5 Hex-agonally packed DNA coated by lipid was also proposed. 6 We have investigated the structure of these complexes using high-resolution cryo electron microscopy (EM) and small angle X-ray scattering (SAXS). Complexes were prepared by rapid mixing of DNA and liposome solutions at room temperature. 7 Precipitation behavior of DNA-cationic liposome mixtures was studied in a phase space of DNA and cationic lipid concentra-tion. Typically, complexes around charge neutralization and for lipid concentrations above 0.1 mM precipitate. Figure 1 shows phase diagram of DODAB/Chol (dioctadecyldiammo-nium bromide/cholesterol, 1:1 mol/mol) liposomes (130 nm in 5% dextrose) complexed with a 4.7 kb DNA plasmid. Figure 2 shows cryo EM micrographs of two different DNA-cationic liposome systems with the negative/positive charge ratio of F) 0.5. Typically heterogeneous particles in the size range 0.2-0.5 µm are observed, and their shapes vary from stacks of bilayers, which can be flat, concentric, or bent, to amorphous aggregates. Both systems (Figure 2A,B) show lamellar struc-tures with a periodicity of 6.5 nm. In some micrographs, a second periodicity around 3.5 nm can be observed also (arrows in Figure 2B). Exactly the same periodicities were observed by SAXS (Figure 3). A very strong reflection is observed around 6.5 nm, and second-and third-order reflections can be easily detected at positions clearly indicating lamellar symmetry, in which reflections occur at d/n (d-spacing, n-order of reflec-tion). Using the Warren-Gaussian approximation 8 for analyz-ing the line shape of the first-order reflection, we determined an average domain size of the lamellar DODAB/Chol-DNA complex (F) 0.5) to be 36 nm, corresponding to about six repeat spacings and consistent with cryo EM micrographs. A weak reflection with shorter periodicity of 3.6 nm can be also observed, in agreement with EM (Figure 2B, arrow). As controls, unreacted liposomes, unsonicated dispersion of lipid, and naked DNA did not give any reflections. Plasmid condensed by polyethylene oxide and salt showed typical hexagonal structure 9 with an interhelical periodicity of 2.5 nm. In a similar system, atomic force microscopy of DNA deposited on a supported cationic lipid bilayer has shown that DNA adsorbs in a single layer in the form of aligned helices, without any knots and crossings resembling a two-dimensional (2D) nematic phase. 10 From these data, the structure of these complexes can be estimated. We believe that DNA is adsorbed between cationic bilayers as a single layer of parallel helices with average in-plane separation consistent with the short periodicity observed by SAXS and EM. Stacks of alternating cationic lamellae and 2D DNA yield long periodicity of 6.5 nm, which is consistent Complex formation is, in addition to thermodynamic factors, kineti-cally controlled. Slow mixing at lipid concentrations >0.1 mM caused precipitation. Also, anionic complexes must be prepared by adding liposomes into DNA and vice versa for cationic ones. Using the phase diagram shown in Figure 1, we can see that that by doing so the crossing of the solubility gap (around F) 1 diagonal) is avoided. Quick mixing assures good dispersal and growth of many small complexes as opposed to the growth of a smaller number of larger ones for slow mixing, which results in precipitation. This is analogous to crystallization and preparation of inorganic colloidal particles where reactions far from equilibrium conditions ("burst of nucleation embrii") yield the smallest particles. (See: Lasic, D. D. Bull. Chem. Soc. Jpn. 1993, 66, 709.) Equivolumetric mixing and the use of small unilamellar vesicles offer the quickest reaction and best dispersal, respectively.
An analytical algorithm, called SETTLE, for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented. This method is still based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE. We implemented this algorithm in the SPASMS package of molecular mechanics and dynamics. Several series of molecular dynamics simulations were carried out to examine the performance of the new algorithm in comparison with the original RATTLE method. It was found that SETTLE is of higher accuracy and is faster than RATTLE with reasonable tolerances by three to nine times on a scalar machine. Furthermore, the performance improvement ranged from factors of 26 to 98 on a vector machine since the method presented is not iterative. © 1992 by John Wiley & Sons, Inc.
GROMACS 3.0 is the latest release of a versatile and very well optimized package for molecular simulation. Much effort has been devoted to achieving extremely high performance on both workstations and parallel computers. The design includes an extraction of virial and periodic boundary conditions from the loops over pairwise interactions, and special software routines to enable rapid calculation of x–1/2. Inner loops are generated automatically in C or Fortran at compile time, with optimizations adapted to each architecture. Assembly loops using SSE and 3DNow! Multimedia instructions are provided for x86 processors, resulting in exceptional performance on inexpensive PC workstations. The interface is simple and easy to use (no scripting language), based on standard command line arguments with selfexplanatory functionality and integrated documentation. All binary files are independent of hardware endian and can be read by versions of GROMACS compiled using different floating-point precision. A large collection of flexible tools for trajectory analysis is included, with output in the form of finished Xmgr/Grace graphs. A basic trajectory viewer is included, and several external visualization tools can read the GROMACS trajectory format. Starting with version 3.0, GROMACS is available under the GNU General Public License from http://www.gromacs.org.
A mechanism of ion-induced acidic lipid vesicle fusion is proposed. It has been reported that fusogenic ions, e.g. Ca2+, alter acidic phospholipid membrane surfaces to be more hydrophobic. The proposed theory suggests that this alteration of the membrane surface reduces repulsive hydration interaction forces exerted on two interacting membranes and eventually induces strong adhesion of the two membranes. In vesicle systems, the strong adhesion of membranes results in deformation of vesicle membranes. At the fusion threshold concentrations of fusogenic ions, the surface hydrophobicity of the deformed area (rim area) at the boundary of adhered two vesicle membranes becomes sufficiently great according to the theory so that membrane molecular exchanges can occur through these regions (fusion sites) and the two membranes fuse. The above scheme is proposed by the theory based on the experimental results of vesicle fusion and its membrane properties. It is discussed that this fusion concept of local high hydrophobic area of the membrane surface as a fusion site is not only applicable to the cases of lipid membrane fusion, but also would be applied to the final step of membrane fusion processes occurring in most biological membrane fusion systems.
The effects of alkali chlorides on multilamellar vesicles of various phosphatidylcholines in the lamellar liquid crystalline Lα-phase were investigated by using small-angle X-ray scattering. At alkali chloride concentrations above 70 mM (LiCl) a phase separation in the liquid crystalline phase of POPC is induced. The splitting of the first and second order diffraction peaks into two major discrete components indicates a separation into different lamellar liquid crystalline (smectic A) phases. Detailed data-analysis applying the modified Caillé theory proves that the phases mainly differ in the interbilayer water thickness by about two hydration layers. The lipid bilayer profile itself remains essentially the same in all liquid crystalline phases. A comparison of differently prepared samples and rapid mixing experiments in combination with simultaneous time-resolved X-ray diffraction suggest that the phase separation is osmotically driven.
A parallel message-passing implementation of a molecular dynamics (MD) program that is useful for bio(macro)molecules in aqueous environment is described. The software has been developed for a custom-designed 32-processor ring GROMACS (GROningen MAchine for Chemical Simulation) with communication to and from left and right neighbours, but can run on any parallel system onto which a a ring of processors can be mapped and which supports PVM-like block send and receive calls. The GROMACS software consists of a preprocessor, a parallel MD and energy minimization program that can use an arbitrary number of processors (including one), an optional monitor, and several analysis tools. The programs are written in ANSI C and available by ftp (information: [email protected]
/* */). The functionality is based on the GROMOS (GROningen MOlecular Simulation) package (van Gunsteren and Berendsen, 1987; BIOMOS B.V., Nijenborgh 4, 9747 AG Groningen). Conversion programs between GROMOS and GROMACS formats are included. The MD program can handle rectangular periodic boundary conditions with temperature and pressure scaling. The interactions that can be handled without modification are variable non-bonded pair interactions with Coulomb and Lennard-Jones or Buckingham potentials, using a twin-range cut-off based on charge groups, and fixed bonded interactions of either harmonic or constraint type for bonds and bond angles and either periodic or cosine power series interactions for dihedral angles. Special forces can be added to groups of particles (for non-equilibrium dynamics or for position restraining) or between particles (for distance restraints). The parallelism is based on particle decomposition. Interprocessor communication is largely limited to position and force distribution over the ring once per time step.
Methodological issues in molecular dynamics (MD) simulations, such as the treatment of long-range electrostatic interactions or the type of pressure coupling, have important consequences for the equilibrium properties observed. We report a series of long (up to 150 ns) MD simulations of dipalmitoylphosphatidylcholine (DPPC) bilayers in which the methodology of simulation is systematically varied. Comparisons of simulations with truncation schemes, Ewald summations, and modified Coulomb interactions, either by shift functions or reaction field models, to describe long-range electrostatics point out the artifacts inherent in each of these methods and above all those of straight cutoff methods. We further show that bilayer properties are less sensitive to the details of the pressure-coupling algorithm and that an increased integration time step of 5 fs can be safely used in simulations of phosphatidylcholine lipid bilayers.
In conclusion, charged membrane together with their adjacent electrolyte solution form a thermodynamic and physico-chemical entity. Their surfaces represent an exceptionally complicated interfacial system owing to intrinsic membrane complexity, as well as to the polarity and often large thickness of the interfacial region. Despite this, charged membranes can be described reasonably accurately within the framework of available theoretical models, provided that the latter are chosen on the basis of suitable criteria, which are briefly discussed in Section A. Interion correlations are likely to be important for the regular and/or rigid, thin membrane-solution interfaces. Lateral distribution of the structural membrane charge is seldom and charge distribution perpendicular to the membranes is nearly always electrostatically important. So is the interfacial hydration, which to a large extent determines the properties of the innermost part of the interfacial region, with a thickness of 2-3 nm. Fine structure of the ion double-layer and the interfacial smearing of the structural membrane charge decrease whilst the surface hydration increases the calculated value of the electrostatic membrane potential relative to the result of common Gouy-Chapman approximation. In some cases these effects partly cancel-out; simple electrostatic models are then fairly accurate. Notwithstanding this, it is at present difficult to draw detailed molecular conclusions from a large part of the published data, mainly owing to the lack of really stringent controls or calibrations. Ion binding to the membrane surface is a complicated process which involves charge-charge as well as charge-solvent interactions. Its efficiency normally increases with the ion valency and with the membrane charge density, but it is also strongly dependent on the physico-chemical and thermodynamic state of the membrane. Except in the case of the stereospecific ion binding to a membrane, the relatively easily accessible phosphate and carboxylic groups on lipids and integral membrane proteins are the main cation binding sites. Anions bind preferentially to the amine groups, even on zwitterionic molecules. Membrane structure is apt to change upon ion binding but not always in the same direction: membranes with bound ions can either expand or become more condensed, depending on the final hydrophilicity (polarity) of the membrane surface. The more polar membranes, as a rule, are less tightly packed and more fluid. Diffusive ion flow across a membrane depends on the transmembrane potential and concentration gradients, but also on the coulombic and hydration potentials at the membrane surface.(ABSTRACT TRUNCATED AT 400 WORDS)
The apparent Mn2+ binding constant for L-alpha-dipalmitoylphosphatidylcholine (DPPC) bilayers dispersed in monovalent salt and MnCl2 dispersions was determined as a function temperature using electron paramagnetic resonance (ERP). Reproducibility in the data sets requires the use of a standard salt solution and dual cavity techniques. Changes in the binding constant at different phase states and temperatures were observed and correlated to the influence of monovalent salts on the thermal properties of DPPC. The turning points (i.e. changes in slope) in the curves of the apparent Mn2+ binding constant versus temperature can be understood in terms of differences in ion binding to headgroups with different bilayer surface areas. The influence of Li+ and SCN- on Mn2+ binding is viewed as a function of their presence in the ionic media in contact with the bilayer rather than as a competitive event. Other monovalent ions studied appear to have little effect on the measured apparent Mn2+ binding constants for DPPC headgroups.
A systemic formalism is developed that shows how the results for absolute specific volumes of multilamellar lipid dispersions may be combined with results from diffraction studies to obtain quantitative characterizations of the average structure of fully hydrated lipid bilayers. Quantities obtained are the area per molecule, the thickness and volumes of the bilayer, the water layer, the hydrocarbon chain layer and the headgroup layer, and where appropriate, the tilt angle of the hydrocarbon chains. In the case of the C phase of DPPC this formalism leads to the detection of inconsistencies between three data. Results for the G phases of DPPC and DLPE are in reasonable agreement with, though more comprehensive than, previous work that used fewer data and equations. Various diffraction data for the F phase of DPPC are in disagreement and it is shown how this disagreement affects results for the bilayer structure. A recent method of McIntosh and Simon for obtaining fluid phase structure utilizing gel phase structure is slightly modified to obtain results for the F phase of DLPE. Methods of obtaining the average methylene and methyl volumes in the fluid phases are critically examined.
The dependence of electrophoretic mobility of multilamellar liposomes composed of egg phosphatidylcholine (PtdCho), dimyristoyl-glycerophosphocholine (Myr2Gro-P-Cho) and dipalmitoyl-glycerophosphocholine (Pam2-Gro-P-Cho) on the concentration of several cations and anions has been measured. Values of surface densities of binding sites and intrinsic binding constants of ions to liposome membranes were determined by processing the results in the framework of Gouy-Stern theory. Sharp reductions in the positive surface potential of Myr2Gro-P-Cho and Pam2Gro-P-Cho liposomes have been detected at the thermotropic transition of the lipids from the gel to liquid-crystalline phase. Similar alterations of liposome surface potential were revealed at the temperature of pretransition, as well as at about 50 degrees C, in the case of Pam2Gro-P-Cho. A model is suggested for ion binding to PtdCho membranes, according to which the ion-binding sites are considered as point defects (vacancies) in the structure of lipid head-groups arranged over a trigonal lattice.
In this paper we report on the molecular dynamics simulation of a fluid phase hydrated dimyristoylphosphatidylcholine bilayer. The initial configuration of the lipid was the x-ray crystal structure. A distinctive feature of this simulation is that, upon heating the system, the fluid phase emerged from parameters, initial conditions, and boundary conditions determined independently of the collective properties of the fluid phase. The initial conditions did not include chain disorder characteristic of the fluid phase. The partial charges on the lipids were determined by ab initio self-consistent field calculations and required no adjustment to produce a fluid phase. The boundary conditions were constant pressure and temperature. Thus the membrane was not explicitly required to assume an area/phospholipid molecule thought to be characteristic of the fluid phase, as is the case in constant volume simulations. Normal to the membrane plane, the pressure was 1 atmosphere, corresponding to the normal laboratory situation. Parallel to the membrane plane a negative pressure of -100 atmospheres was applied, derived from the measured surface tension of a monolayer at an air-water interface. The measured features of the computed membrane are generally in close agreement with experiment. Our results confirm the concept that, for appropriately matched temperature and surface pressure, a monolayer is a close approximation to one-half of a bilayer. Our results suggest that the surface area per phospholipid molecule for fluid phosphatidylcholine bilayer membranes is smaller than has generally been assumed in computational studies at constant volume. Our results confirm that the basis of the measured dipole potential is primarily water orientations and also suggest the presence of potential barriers for the movement of positive charges across the water-headgroup interfacial region of the phospholipid.
Cationic liposomes complexed with DNA (CL-DNA) are promising synthetically based nonviral carriers of DNA vectors for gene
therapy. The solution structure of CL-DNA complexes was probed on length scales from subnanometer to micrometer by synchrotron
x-ray diffraction and optical microscopy. The addition of either linear λ-phage or plasmid DNA to CLs resulted in an unexpected
topological transition from liposomes to optically birefringent liquid-crystalline condensed globules. X-ray diffraction of
the globules revealed a novel multilamellar structure with alternating lipid bilayer and DNA monolayers. The λ-DNA chains
form a one-dimensional lattice with distinct interhelical packing regimes. Remarkably, in the isoelectric point regime, the
λ-DNA interaxial spacing expands between 24.5 and 57.1 angstroms upon lipid dilution and is indicative of a long-range electrostatic-induced
repulsion that is possibly enhanced by chain undulations.
Molecular dynamics simulations of 500 ps were performed on a system consisting of a bilayer of 64 molecules of the lipid dipalmitoylphosphatidylcholine and 23 water molecules per lipid at an isotropic pressure of 1 atm and 50 degrees C. Special attention was devoted to reproduce the correct density of the lipid, because this quantity is known experimentally with a precision better than 1%. For this purpose, the Lennard-Jones parameters of the hydrocarbon chains were adjusted by simulating a system consisting of 128 pentadecane molecules and varying the Lennard-Jones parameters until the experimental density and heat of vaporization were obtained. With these parameters the lipid density resulted in perfect agreement with the experimental density. The orientational order parameter of the hydrocarbon chains agreed perfectly well with the experimental values, which, because of its correlation with the area per lipid, makes it possible to give a proper estimate of the area per lipid of 0.61 +/- 0.01 nm2.
Anions and cations have long been recognized to be capable of modifying the functioning of various membrane-related physiological processes. Here, a fluorescent ratio method using the styrylpyridinium dyes, RH421 and di-8-ANEPPS, was applied to determine the effect of a range of anions and cations on the intramembrane dipole potential of dimyristoylphosphatidylcholine vesicles. It was found that certain anions cause a decrease in the dipole potential. This could be explained by binding within the membrane, in support of a hypothesis originally put forward by A. L. Hodgkin and P. Horowicz [1960, J. Physiol. (Lond.) 153:404-412.] The effectiveness of the anions in reducing the dipole potential was found to be ClO4- > SCN- > I- > NO3- > Br- > Cl- > F- > SO42-. This order could be modeled by a partitioning of ions between the membrane and the aqueous phase, which is controlled predominantly by the Gibbs free energy of hydration. Cations were also found to be capable of reducing the dipole potential, although much less efficiently than can anions. The effects of the cations was found to be trivalent > divalent > monovalent. The cation effects were attributed to binding to a specific polar site on the surface of the membrane. The results presented provide a molecular basis for the interpretation of the Hofmeister effect of lyotropic anions on ion transport proteins.
Molecular dynamics simulations of fully hydrated Dipalmitoylphosphatidylcholine bilayers, extending temporal and spatial scales by almost one order of magnitude, are presented. The present work reaches system sizes of 1024 lipids and times 10-60 ns. The simulations uncover significant dynamics and fluctuations on scales of several nanoseconds, and enable direct observation and spectral decomposition of both undulatory and thickness fluctuation modes. Although the former modes are strongly damped, the latter exhibit signs of oscillatory behavior. From this, it has been possible to calculate mesoscopic continuum properties in good agreement with experimental values. A bending modulus of 4 x 10(-20) J, bilayer area compressibility of 250-300 mN/m, and mode relaxation times in the nanosecond range are obtained. The theory of undulatory motions is revised and further extended to cover thickness fluctuations. Finally, it is proposed that thickness fluctuations is the explanation to the observed system-size dependence of equilibrium-projected area per lipid.
We performed a molecular dynamics simulation of dipalmitoylphosphatidylserine (DPPS) bilayer with Na+ counterions. We found that hydrogen bonding between the NH group and the phosphate group leads to a reduction in the area per headgroup when compared to the area in dipalmitoylphosphatidylcholine bilayer. The Na+ ions bind to the oxygen in the carboxyl group of serine, thus giving rise to a dipolar bilayer similar to dipalmitoylphosphatidylethanolamine bilayer. The results of the simulation show that counterions play a crucial role in determining the structural and electrostatic properties of DPPS bilayer.
Molecular dynamics simulations are performed on two hydrated dipalmitoylphosphatidylcholine bilayer systems: one with pure water and one with added NaCl. Due to the rugged nature of the membrane/electrolyte interface, ion binding to the membrane surface is characterized by the loss of ion hydration. Using this structural characterization, binding of Na(+) and Cl(-) ions to the membrane is observed, although the binding of Cl(-) is seen to be slightly weaker than that of Na(+). Dehydration is seen to occur to a different extent for each type of ion. In addition, the excess binding of Na(+) gives rise to a net positive surface charge density just outside the bilayer. The positive density produces a positive electrostatic potential in this region, whereas the system without salt shows an electrostatic potential of zero.
We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic interactions were truncated are compared to similar simulations using the particle-mesh Ewald (PME) technique. All examined truncation distances (1.8-2.5 nm) lead to major effects on the bilayer properties, such as enhanced order of acyl chains together with decreased areas per lipid. The results obtained using PME, on the other hand, are consistent with experiments. These artifacts are interpreted in terms of radial distribution functions g(r) of molecules and molecular groups in the bilayer plane. Pronounced maxima or minima in g(r) appear exactly at the cutoff distance indicating that the truncation gives rise to artificial ordering between the polar phosphatidyl and choline groups of the DPPC molecules. In systems described using PME, such artificial ordering is not present.
Two mixed bilayers containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine at a ratio of 5:1 are simulated in NaCl electrolyte solutions of different concentration using the molecular dynamics technique. Direct NH.O and CH.O hydrogen bonding between lipids was observed to serve as the basis of interlipid complexation. It is deduced from our results and previous studies that dipalmitoylphosphatidylcholine alone is less likely to form interlipid complexes than in the presence of bound ions or other bilayer "impurities" such as dipalmitoylphosphatidylserine. The binding of counterions is observed and quantitated. Based upon the calculated ion binding constants, the Gouy-Chapman surface potential (theta) is calculated. In addition we calculated the electrostatic potential profile (Phi) by twice integrating the system charge distribution. A large discrepancy between and the value of Phi at the membrane surface is observed. However, at "larger" distance from the bilayer surface, a qualitative similarity in the z-profiles of Phi and psi(GC) is seen. The discrepancy between the two potential profiles near the bilayer surface is attributed to the discrete and nonbulk-like nature of water in the interfacial region and to the complex geometry of this region.
Two 40 ns molecular dynamics simulations of a palmitoyl-oleoyl phosphatidylserine (POPS) lipid bilayer in the liquid crystalline phase with Na(+) counterions and NaCl were carried out to investigate the structure of the negatively charged lipid bilayer and the effect of salt (NaCl) on the lipid bilayer structure. Na(+) ions were found to penetrate deep into the ester region of the water/lipid interface of the bilayer. Interaction of the Na(+) ions with the lipid bilayer is accompanied by a loss of water molecules around the ion and a simultaneous increase in the number of ester carbonyl oxygen atoms binding the ion, which define an octahedral and square pyramidal geometry. The amine group of the lipid molecule is involved in the formation of inter- and intramolecular hydrogen bonds with the carboxylate and the phosphodiester groups of the lipid molecule. The area per lipid of the POPS bilayer is unaffected by the presence of 0.15M NaCl. There is a small increase in the order parameter of carbon atoms in the beginning of the alkyl chain in the presence of NaCl. This is due to a greater number of Na(+) ions being coordinated by the ester carbonyl oxygen atoms in the water/lipid interface region of the POPS bilayer.
Cationic lipid membranes are known to form compact complexes with DNA and to be effective as gene delivery agents both in vitro and in vivo. Here we employ molecular dynamics simulations for a detailed atomistic study of lipid bilayers consisting of a mixture of cationic dimyristoyltrimethylammonium propane (DMTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC). Our main objective is to examine how the composition of the DMPC/DMTAP bilayers affects their structural and electrostatic properties in the liquid-crystalline phase. By varying the mole fraction of DMTAP, we have found that the area per lipid has a pronounced nonmonotonic dependence on the DMTAP concentration, with a minimum around the point of equimolar DMPC/DMTAP mixture. We show that this behavior has an electrostatic origin and is driven by the interplay between positively charged TAP headgroups and the zwitterionic phosphatidylcholine (PC) heads. This interplay leads to considerable reorientation of PC headgroups for an increasing DMTAP concentration, and gives rise to major changes in the electrostatic properties of the lipid bilayer, including a significant increase of total dipole potential across the bilayer and prominent changes in the ordering of water in the vicinity of the membrane. Moreover, chloride counterions are bound mostly to PC nitrogens implying stronger screening of PC heads by Cl ions compared to TAP headgroups. The implications of these findings are briefly discussed.
In this article we compare different force fields that are widely used (Gromacs, Charmm-22/x-Plor, Charmm-27, Amber-1999, OPLS-AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic parameters of, in particular, sodium, and, to a lesser extent, chloride, translate into large differences in the computed radial-distribution functions. This uncertainty reflect the incomplete experimental knowledge of the structural properties of ionic aqueous solutions at finite molarity. We discuss possible implications on the computation of potential of mean force and effective potentials.
Interactions between salt ions and lipid components of biological membranes are essential for the structure, stability, and functions of the membranes. The specific ionic composition of aqueous buffers inside and outside of the cell is known to differ considerably. To model such a situation we perform atomistic molecular-dynamics (MD) simulations of a single-component phosphatidylcholine lipid bilayer which separates two aqueous reservoirs with and without NaCl salt. To implement the difference in electrolyte composition near two membrane sides, a double bilayer setup (i.e., two bilayers in a simulation box) is employed. It turns out that monovalent salt, being in contact with one leaflet only, induces a pronounced asymmetry in the structural, electrostatic, and dynamical properties of bilayer leaflets after 50 ns of MD simulations. Binding of sodium ions to the carbonyl region of the leaflet which is in contact with salt results in the formation of "Na-lipids" complexes and, correspondingly, reduces mobility of lipids of this leaflet. In turn, attractive interactions of chloride ions (mainly located in the aqueous phase close to the water-lipid interface) with choline lipid groups lead to a substantial (more vertical) reorientation of postphatidylcholine headgroups of the leaflet adjoined to salt. The difference in headgroup orientation on two sides of a bilayer, being coupled with salt-induced reorientation of water dipoles, leads to a notable asymmetry in the charge-density profiles and electrostatic potentials of bilayer constitutes of the two leaflets. Although the overall charge density of the bilayer is found to be almost insensitive to the presence of salt, a slight asymmetry in the charge distribution between the two bilayer leaflets results in a nonzero potential difference of about 85 mV between the two water phases. Thus, a transmembrane potential of the order of the membrane potential in a cell can arise without ionic charge imbalance between two aqueous compartments.
Step by step: The sequential coordination of calcium ions (yellow) to four lipid carbonyl oxygen atoms in neutral zwitterionic phospholipid bilayers has been studied by molecular dynamics simulations.
Electrostatic interactions govern structural and dynamical properties of membranes and can vary considerably with the composition of the aqueous buffer. We studied the influence of sodium chloride on a pure POPC lipid bilayer by fluorescence correlation spectroscopy experiments and molecular dynamics simulations. Increasing sodium chloride concentration was found to decrease the self-diffusion of POPC lipids within the bilayer. Self-diffusion coefficients calculated from the 100 ns simulations agree with those measured on a millisecond timescale, suggesting that most of the relaxation processes relevant for lipid diffusion are faster than the simulation timescale. As the dominant effect, the molecular dynamics simulations revealed a tight binding of sodium ions to the carbonyl oxygens of on average three lipids leading to larger complexes with reduced mobility. Additionally, the bilayer thickens by approximately 2 A, which increases the order parameter of the fatty acyl chains. Sodium binding alters the electrostatic potential, which is largely compensated by a changed polarization of the aqueous medium and a lipid dipole reorientation.
- D D Lasic
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