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Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions
Abstract
Positively charged lipid bilayer systems are a promising class of nonviral vectors for safe and efficient gene and drug delivery. Detailed understanding of these systems is therefore not only of fundamental but also of practical biomedical interest. Here, we study bilayers comprising a binary mixture of cationic dimyristoyltrimethylammoniumpropane (DMTAP) and zwitterionic (neutral) dimyristoylphosphatidylcholine (DMPC) lipids. Using atomistic molecular dynamics simulations, we address the effects of bilayer composition (cationic to zwitterionic lipid fraction) and of NaCl electrolyte concentration on the dynamical properties of these cationic lipid bilayer systems. We find that, despite the fact that DMPCs form complexes via Na(+) ions that bind to the lipid carbonyl oxygens, NaCl concentration has a rather minute effect on lipid diffusion. We also find the dynamics of Cl(-) and Na(+) ions at the water-membrane interface to differ qualitatively. Cl(-) ions have well-defined characteristic residence times of nanosecond scale. In contrast, the binding of Na(+) ions to the carbonyl region appears to lack a characteristic time scale, as the residence time distributions displayed power-law features. As to lateral dynamics, the diffusion of Na(+) ions within the water-membrane interface consists of two qualitatively different modes of motion: very slow diffusion when ions are bound to DMPC, punctuated by fast rapid jumps when detached from the lipids. Overall, the prolonged dynamics of the Na(+) ions are concluded to be interesting for the physics of the whole membrane, especially considering its interaction dynamics with charged macromolecular surfaces.
... Thus, specific interactions with ions are a matter of considerable interest (Bockmann et al. 2003, Pandit et al. 2003, Bockmann and Grubmuller 2004. The distribution of ions in the solution and their interaction with the membrane are factors that substantially modify the structure and dynamics of the cell membranes , Miettinen et al. 2009). Furthermore, signaling processes are modified by the membrane capability of retaining ions (Berkowitz et al. 2006). ...
... Despite the current computational resources, the dynamics simulations of ions within a lipid bilayer cannot be as long as they should in order to fully understand the interaction between the ion and the surrounding phospholipids. Nevertheless, differences in the residence times and binding behavior between different ion species were observed (Cordomi et al. 2008, Miettinen et al. 2009). ...
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.
... 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). Furthermore, signaling processes are modified by the membrane's ability to retain ions (11). ...
... Another drawback of MD simulations is that, despite the current computational resources, simulations of ions within a lipid bilayer cannot be of sufficient duration to fully elucidate the interaction between the ion and the surrounding phospholipids. Nevertheless, differences in the residence times and binding behaviors of different ion species have been observed (8,26,27). ...
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.
... ,118,120,121 Charges on molecules interact with proteins and lipids,117,[122][123][124][125][126] while primary aliphatic amines interact with several compounds including DNA.106,118,120,121 Through lipid bilayer, protein, or DNA interactions, Tris is thought to synergize with arginine to inactivate enveloped viruses.At optimal solution conditions and synergistic abilities, arginine is an effective means of inactivating some enveloped viruses.High concentrations (0.7-1 M) and a time of 60 min combined with the synergistic factor of high temperature, low pH, or Tris buffer are needed for maximum virus inactivation. ...
Arginine synergistically inactivates enveloped viruses at a pH or temperature that does little harm to proteins, making it a desired process for therapeutic protein manufacturing. However, the mechanisms and optimal conditions for inactivation are not fully understood, and therefore, arginine viral inactivation is not used industrially. Optimal solution conditions for arginine viral inactivation found in the literature are high arginine concentrations (0.7–1 M), a time of 60 min, and a synergistic factor of high temperature (≥40°C), low pH (≤pH 4), or Tris buffer (5 mM). However, at optimal conditions full inactivation does not occur over all enveloped viruses. Enveloped viruses that are resistant to arginine often have increased protein stability or membrane stabilizing matrix proteins. Since arginine can interact with both proteins and lipids, interaction with either entity may be key to understanding the inactivation mechanism. Here, we propose three hypotheses for the mechanisms of arginine induced inactivation. Hypothesis 1 describes arginine‐induced viral inactivation through inhibition of vital protein function. Hypothesis 2 describes how arginine destabilizes the viral membrane. Hypothesis 3 describes arginine forming pores in the virus membrane, accompanied by further viral damage from the synergistic factor. Once the mechanisms of arginine viral inactivation are understood, further enhancement by the addition of functional groups, charges, or additives may allow the inactivation of all enveloped viruses in mild conditions.
... Sodium chloride ions were added to neutralize excess lipid charges and set the salt concentration to $0.2 M in the 0, 7, 10, 15 mol% systems. The 2 mol% system was only charge neutralized with Na þ ions; although this gives the 2 mol% system slightly different ionic conditions than the other model systems, based on previous studies (59,60), we expect this difference in ion conditions to have a negligible effect on the properties reported in this study. Interactions were modeled using the CHARMM36 force field (61) with the TIP3P water model (62). ...
Cardiolipin is an anionic lipid found in the mitochondrial membranes of eukaryotes ranging from unicellular microorganisms to metazoans. This unique lipid contributes to various mitochondrial functions, including metabolism, mitochondrial membrane fusion and/or fission dynamics, and apoptosis. However, differences in cardiolipin content between the two mitochondrial membranes, as well as dynamic fluctuations in cardiolipin content in response to stimuli and cellular signaling events, raise questions about how cardiolipin concentration affects mitochondrial membrane structure and dynamics. Although cardiolipin’s structural and dynamic roles have been extensively studied in binary mixtures with other phospholipids, the biophysical properties of cardiolipin in higher number lipid mixtures are still not well resolved. Here, we used molecular dynamics simulations to investigate the cardiolipin-dependent properties of ternary lipid bilayer systems that mimic the major components of mitochondrial membranes. We found that changes to cardiolipin concentration only resulted in minor changes to bilayer structural features but that the lipid diffusion was significantly affected by those alterations. We also found that cardiolipin position along the bilayer surfaces correlated to negative curvature deflections, consistent with the induction of negative curvature stress in the membrane monolayers. This work contributes to a foundational understanding of the role of cardiolipin in altering the properties in ternary lipid mixtures composed of the major mitochondrial phospholipids, providing much-needed insights to help understand how cardiolipin concentration modulates the biophysical properties of mitochondrial membranes.
... Sodium chloride ions were added to neutralize excess lipid charges and set the salt concentration to $0.2 M in the 0, 7, 10, 15 mol% systems. The 2 mol% system was only charge neutralized with Na þ ions; although this gives the 2 mol% system slightly different ionic conditions than the other model systems, based on previous studies (59,60), we expect this difference in ion conditions to have a negligible effect on the properties reported in this study. Interactions were modeled using the CHARMM36 force field (61) with the TIP3P water model (62). ...
Cardiolipin is a unique anionic lipid found in mitochondrial membranes where it contributes to various mitochondrial functions, including metabolism, mitochondrial membrane fusion/fission dynamics, and apoptosis. Dysregulation of cardiolipin synthesis and remodeling have also been implicated in several diseases, such as diabetes, heart disease and Barth Syndrome. Although cardiolipin's structural and dynamic roles have been extensively studied in binary mixtures with other phospholipids, the biophysical properties of cardiolipin in ternary lipid mixtures are still not well resolved. Here, we used molecular dynamics simulations to investigate the cardiolipin-dependent properties of ternary lipid bilayer systems that mimic the major components of mitochondrial membranes. We found that changes to cardiolipin concentration only resulted in minor changes to bilayer structural features, but that the lipid diffusion was significantly affected by those alterations. We also found that cardiolipin position along the bilayer surfaces correlated to negative curvature deflections, consistent with the induction of negative curvature stress in the membrane monolayers. This work contributes to a foundational understanding of the role of CL in altering the properties in ternary lipid mixtures composed of the major mitochondrial phospholipids, providing much needed insights to help understand how cardiolipin concentration modulates the biophysical properties of mitochondrial membranes.
Access this preprint on bioRxiv: https://www.biorxiv.org/content/10.1101/557744v1
... 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.
... 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.
... 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.
... There are several comprehensive articles describing the effect of mono-and divalent ions on zwitterionic and charge lipid bilayers, e.g. [122,[140][141][142][143][144][145]. MD simulations with atomic resolution have provided a very detailed picture of the ion-lipid interactions. ...
This review summarises high resolution studies on the interface of lamellar lipid bilayers composed of the most typical lipid molecules which constitute the lipid matrix of biomembranes. The presented results were obtained predominantly by computer modelling methods. Whenever possible, the results were compared with experimental results obtained for similar systems. The first and main section of the review is concerned with the bilayer-water interface and is divided into four subsections. The first describes the simplest case, where the interface consists only of lipid head groups and water molecules and focuses on interactions between the lipid heads and water molecules; the second describes the interface containing also mono- and divalent ions and concentrates on lipid-ion interactions; the third describes direct inter-lipid interactions. These three subsections are followed by a discussion on the network of direct and indirect inter-lipid interactions at the bilayer interface. The second section summarises recent computer simulation studies on the interactions of antibacterial membrane active compounds with various models of the bacterial outer membrane. This article is part of a Special Issue entitled: Biosimulations. Guest Editors: Ilpo Vattulainen and Dr. 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.
... The lipid composition of the membrane is one of the determining factors in membrane interactions with surrounding molecules or ions which further alter the structure, stability and functions of the membrane itself. Membrane properties such as the surface potential (Eisenberg et al., 1979), the dipole potential (Clarke and Lüpfert, 1999), structure and mechanical strength (Sachs et al., 2004;Miettinen et al., 2009) are tightly associated with ions that are present in the cell interior and its environment as well. Therefore, the study of interactions of ions with the lipid bilayer, e.g. ...
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.
... A Mass density plot including the Cl 2 ion distribution is included in the supplementary materials as supplementary figure S4. The distribution of Cl 2 ions is in qualitative agreement with previous results 16,23 , and, as shown in supplementary figure S10 and S11, there is no evidence of chlorine ions binding to the membrane headgroups. We also measured the water ordering along the membrane normal, and showed this in figure S13. ...
Cholesterol is an important component of all biological membranes as well as drug delivery liposomes. We show here that increasing the level of cholesterol in a phospholipid membrane decreases surface charge in the physiological environment. Through molecular dynamics simulation we have shown that increasing the level of cholesterol decreases Na(+) ion binding. Complementary experimental ζ - potential measurements have shown a decreased ζ - potential with increasing cholesterol content, indicative of reduced surface charge. Both experiments and simulations have been carried out on both saturated 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and monounsaturated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes. This result is particularly important because membrane surface charge plays an important role in the interactions of biomembranes with peripheral membrane proteins and drug delivery liposomes with the immune system.
... 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.
... 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.
... The evidence that this phenomenon occurs is strong; however, there is significant quantitative disagreement regarding the strength of this binding from competing atomic potential sets. 91 In Figure 4, the mass density profile of PEG, the Na þ and Cl À ions, and phosphate atoms along the membrane normal is shown for DSPC/DSPE-PEG 2000 , DLPC/DLPE-PEG 2000 , and the two pure systems from our previously published work. 64 The presence of PEG strongly affects the behavior of the ions. ...
We have combined Langmuir monolayer film experiments and all-atom molecular dynamics (MD) simulation of a bilayer to study the surface structure of a PEGylated liposome and its interaction with the ionic environment present under physiological conditions. Lipids that form both gel and liquid-crystalline membranes have been used in our study. By varying the salt concentration in the Langmuir film experiment and including salt at the physiological level in the simulation, we have studied the effect of salt ions present in the blood plasma on the structure of the poly(ethylene glycol) (PEG) layer. We have also studied the interaction between the PEG layer and the lipid bilayer in both the liquid-crystalline and gel states. The MD simulation shows two clear results: (a) The Na(+) ions form close interactions with the PEG oxygens, with the PEG chains forming loops around them and (b) PEG penetrates the lipid core of the membrane for the case of a liquid-crystalline membrane but is excluded from the tighter structure of the gel membrane. The Langmuir monolayer results indicate that the salt concentration affects the PEGylated lipid system, and these results can be interpreted in a fashion that is in agreement with the results of our MD simulation. We conclude that the currently accepted picture of the PEG surface layer acting as a generic neutral hydrophilic polymer entirely outside the membrane, with its effect explained through steric interactions, is not sufficient. The phenomena we have observed may affect both the interaction between the liposome and bloodstream proteins and the liquid-crystalline-gel transition and is thus relevant to nanotechnological drug delivery device design.
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.
A molecular-level insight into the interactions of phospholipid molecules with cellulose is crucial for the development of novel cellulose-based materials for wound dressing. Here we employ the state-of-the-art computer simulations to unlock for a first time the molecular mechanisms behind such interactions. To this end, we performed a series of atomic-scale molecular dynamics simulations of phospholipid bilayers on a crystalline cellulose support at various hydration levels of the bilayer leaflets next to the cellulose surface. Our findings clearly demonstrate the existence of strong interactions between polar lipid head groups and the hydrophilic surface of a cellulose crystal. We identified two major types of interactions between phospholipid molecules and cellulose chains: (i) direct attractive interactions between lipid choline groups and oxygens of hydroxyl (hydroxymethyl) groups of cellulose and (ii) hydrogen bonding between phosphate groups of lipids and cellulose’s hydroxymethyl/hydroxyl groups. When the hydration level of the interfacial bilayer/support region is low, these interactions lead to a pronounced asymmetry in the properties of the opposite bilayer leaflets. In particular, the mass density profiles of the proximal leaflets are split into two peaks and lipid head groups become more horizontally oriented with respect to the bilayer surface. Furthermore, the lateral mobility of lipids in the leaflets next to the cellulose surface is found to slow down considerably. Most of these cellulose-induced effects are likely due to hydrogen bonding between lipid phosphate groups and hydroxymethyl/hydroxyl groups of cellulose: the lipid phosphate groups are pulled towards the water/lipid interface due to the formation of hydrogen bonds. Overall, our findings shed light on the molecular details of the interactions between phospholipid bilayers and cellulose nanocrystals and can be used for identifying possible strategies for improving the properties of cellulose-based dressing materials via e.g. chemical modification of their surface.
We have carried out molecular dynamics simulations using NAMD to study the diffusivity of Na and Cl ions across a POPC lipid bilayer membrane. We show that an imbalance of positively and negatively charged ions on either side of the membrane leads to the diffusion of ions and water molecules. We considered the cases of both weak and very strong charge imbalance across the membrane. The diffusion coefficients of the ions have been determined from the mean square displacements of the particles as a function of time. We find that for strong electrochemical gradients, both the Na and Cl ions diffuse rapidly through pores in the membrane with diffusion coefficients up to ten times larger than in water. Rather surprisingly, we found that although the Na ions are the first to begin the permeation process due to the lower potential barrier that they experience compared to the Cl ions, the latter complete the permeation across the barrier more quickly due to their faster diffusion rates.
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.
Temperature dependence of the zeta potential (ZP) is proposed as a tool to analyze the thermotropic behavior of unilamellar liposomes prepared from binary mixtures of phosphatidylcholines in the absence or presence of ions in aqueous suspensions. Since the lipid phase transition influences the surface potential of the liposome reflecting a sharp change in the ZP during the transition, it is proposed as a screening method for transition temperatures in complex systems, given its high sensitivity and small amount of sample required, that is, 70% less than that required in the use of conventional calorimeters. The sensitivity is also reflected in the pre-transition detection in the presence of ions. Plots of phase boundaries for these mixed-lipid vesicles were constructed by plotting the delimiting temperatures of both main phase transition and pre-transition vs. the lipid composition of the vesicle. Differential scanning calorimetry (DSC) studies, although subject to uncertainties in interpretation due to broad bands in lipid mixtures, allowed the validation of the temperature dependence of the ZP method for determining the phase transition and pre-transition temperatures. The system chosen was dipalmitoylphosphatidylcholine/dimyristoyl phosphatidylcholine (DMPC/DPPC), the most common combination in biological membranes. This work may be considered as a starting point for further research into more complex lipid mixtures with functional biological importance.
Phospholipids are essential building blocks of biological membranes. Despite of vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data - but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files (https://zenodo.org/collection/user-nmrlipids) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.
Potassium phosphate buffer solution has been widely used in the biological experiments, which represents an important process of the interaction between ions and biomolecules, yet the influences of potassium phosphate on biomolecules such as the cell membrane are still poorly understood at the molecular level. In this work, we have applied sum frequency generation vibrational spectroscopy and carried out a detailed study on the interaction between potassium phosphate buffer solution (PBS) and negative 1,2-dimyristoyl-d54-sn-glycero-3-[phospho-rac-(1-glycerol)] (d54-DMPG) lipid bilayer in real time. The PBS-induced dynamic change in the molecular structure of d54-DMPG lipid bilayer was monitored using the spectral features of CD2, CD3, lipid head phosphate, and carbonyl groups for the first time. It is found that K+ can bind to the cell membrane and cause the signal change of CD2, CD3, lipid head phosphate, and carbonyl groups quickly. Potassium PBS interacts with lipid bilayers most likely by formation of toroidal pores inside the bilayer matrix. This result can provide a molecular basis for the interpretation of the effect of PBS on the ion-assisted transport of protein across the membrane.
An atomistic-level understanding of cationic lipid monolayers is essential for development of gene delivery agents based on cationic micelle-like structures. We employ molecular dynamics (MD) simulations for a detailed atomistic study of lipid monolayers composed of both pure zwitterionic dipalmitoylphosphatidylcholine (DPPC) and a mixture of DPPC and cationic cetyltrimethylammonium bromide (CTAB) at the air/water interface. We aim to investigate how the composition of the DPPC/CTAB monolayers affects their structural and electrostatic properties in the liquid-expanded phase. By varying the molar fraction of CTAB, we found the cationic CTAB lipids have significant condensing effect on the DPPC/CTAB monolayers, i.e., at the same surface tension or surface pressure, monolayers with higher CTAB molar fraction have smaller area per lipid. The DPPC/CTAB monolayers are also able to achieve negative
surface tension without introducing buckling into the monolayer structure. We also found the condensing effect is caused by the interplay between the cationic CTAB headgroups and the zwitterionic phosphatidylcholine (PC) headgroups which has electrostatic origin. With CTAB in its vicinity, the P-N vector of PC headgroups reorients from being parallel to the monolayer plane to a more vertical orientation. Moreover, detailed analysis of the structural properties of the monolayers, such as the density profile analysis, hydrogen bonding analysis, chain order parameter calculations and radial distribution function calculations were also performed for better understanding of cationic DPPC/CTAB monolayers.
Rapid development of computer power during the last decade has made molecular simulations of lipid bilayers feasible for many research groups, which, together with the growing general interest in investigations of these very important biological systems has lead to tremendous increase of the number of research on the computational modeling of lipid bilayers. In this review, we give account of the recent progress in computer simulations of lipid bilayers covering mainly the period of the last 7 years, and covering only several selected subjects: methodological (development of the force fields for lipid bilayer simulations, use of coarse-grained models) and scientific (studies of the role of lipid unsaturation, and the effect of cholesterol and other inclusions on properties of the bilayer).
The effect of viscosity on the encounter rate of two interacting membranes was investigated by combining a non-equilibrium Fokker-Planck model together with extensive Molecular Dynamics (MD) calculations. The encounter probability and stabilization of transient contact points represent the preliminary steps toward short-range adhesion and fusion of lipid leaflets. To strengthen our analytical model, we used a Coarse Grained MD method to follow the behavior of two charged palmitoyl oleoyl phosphatidylglycerol membranes embedded in a electrolyte-containing box at different viscosity regimes. Solvent friction was modulated by varying the concentration of a neutral, water-soluble polymer, polyethylene glycol, while contact points were stabilized by divalent ions that form bridges among juxtaposed membranes. While a naïve picture foresees a monotonous decrease of the membranes encounter rate with solvent viscosity, both the analytical model and MD simulations show a complex behavior. Under particular conditions, the encounter rate could exhibit a maximum at a critical viscosity value or for a critical concentration of bridging ions. These results seem to be confirmed by experimental observations taken from the literature.
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.
Given the increasing interest in the characterization of new biosurfactants, in this work we have carried out a physicochemical study of a monorhamnolipid (monoRL) produced by Pseudomonas aeruginosa MA01 in aqueous media. The detailed knowledge of the physicochemical properties of these monoRL biosurfactant is of importance for the validation of this particular P. aeruginosa strain as a useful biosurfactant producer. A pKa value for monoRL of 5.9 was consistently obtained, as well as the indication that the presence of one or two rhamnose rings does not have a notorious influence on the pKa of the carboxyl group. The critical micelle concentration (cmc) of the negatively charged monoRL is dependent on the ionic strength, whereas that of the protonated form is not, whereas the charge of the polar head of monoRL has little effect on the surface area. Dynamic light scattering showed that in the vicinity of the cmc structures with an average diameter of 50nm are present, whereas at concentrations well above the cmc the size increases to about 200nm. Taken together our results show that monoRL presents a monomer-to-micelle transition, which depends on pH and ionic strength, similar to that described before for the diRL species. However the formation of lamellar vesicles described for diRL at pH 7.4, was not observed here. Molecular dynamics (MD) simulations yielded a similar value for the lateral diffusion coefficient of protonated anionic monoRL, indicating that the negative charge does not affect biosurfactant mobility in the monolayer surface. The radial distribution function value is slightly higher for the protonated monoRL; therefore the number of molecules located at a particular distance is somehow higher in the case of the protonated form. On the other hand, it is clearly obtained that the carboxylate group of the anionic form moves more inside the aqueous phase as compared to the carboxyl group of the protonated form. The results obtained correspond to the expected behaviour for a biosurfactant molecule in relation to the dependence of protonation state and micelle formation, and therefore the molecular dynamics simulation appears to describe properly our molecular systems.
We develop a semi-quantitative analytical theory to describe adhesion between two identical planar charged surfaces embedded in a polymer-containing electrolyte solution. Polymer chains are uncharged and differ from the solvent by their lower dielectric permittivity. The solution mimics physiological fluids: It contains 0.1 M of monovalent ions and a small number of divalent cations that form tight bonds with the headgroups of charged lipids. The components have heterogeneous spatial distributions. The model was derived self-consistently by combining: (a) a Poisson-Boltzmann like equation for the charge densities, (b) a continuum mean-field theory for the polymer profile, (c) a solvation energy forcing the ions toward the polymer-poor regions, and (d) surface interactions of polymers and electrolytes. We validated the theory via extensive coarse-grained Molecular Dynamics (MD) simulations. The results confirm our analytical model and reveal interesting details not detected by the theory. At high surface charges, polymer chains are mainly excluded from the gap region, while the concentration of ions increases. The model shows a strong coupling between osmotic forces, surface potential and salting-out effects of the slightly polar polymer chains. It highlights some of the key differences in the behaviour of monomeric and polymeric mixed solvents and their responses to Coulomb interactions. Our main findings are: (a) the onset of long-ranged ion-induced polymer depletion force that increases with surface charge density and (b) a polymer-modified repulsive Coulomb force that increases with surface charge density. Overall, the system exhibits homeostatic behaviour, resulting in robustness against variations in the amount of charges. Applications and extensions of the model are briefly discussed.
We study the coordination of excess NaCl to zwitterionic DPPC lipid bilayers using molecular dynamics simulations. We find that Na ions directly coordinate with the DPPC lipid carbonyl groups. As the number of excess ions increases, the number of coordinated ions increases, until it reaches a plateau at a ratio near 1 ion per every four lipids at 310 K, and 1 ion per every six lipids at 323 K. The area per lipid decreases as the number of excess ions is increased. For low number of ions per lipids (1:16 and 1:8), most Na ions are bound to the lipid carbonyls, while the Cl form an ionic cloud around the lipid choline groups. As a result of the Na binding, the lipid has an effective positive charge density. The residence time of Na ions bound to the lipid is longer than 40 ns, while Cl ions exchange faster than the nanoseconds timescale. We find that the bound Na ions replace ordered water around the carbonyls. The net linear charge density near the carbonyl groups stays positive, regardless of the presence of excess salt in the solution.
We performed atomistic molecular dynamics simulations of lipid bilayers consisting of a mixture of cationic dioleoyloxytrimethylammonium propane (DOTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC) lipids at different DOTAP fractions. Our primary focus was the specific effects of unsaturated lipid chains on structural and dynamic properties of mixed cationic bilayers. The bilayer area, as well as the ordering of lipid tails, shows a pronounced nonmonotonic behavior when TAP lipid fraction increases. The minimum in area (maximum in ordering) was observed for a bilayer with TAP fraction of 0.4, that is, at lower TAP fractions compared with saturated PC/TAP bilayers. Adding unsaturated DOTAP lipids into DMPC bilayers was found to promote lipid chain interdigitation and to fluidize lipid bilayers, as seen through enhanced lateral lipid diffusion. The speed-up in lateral diffusion at large DOTAP fractions results from increasing area per lipid, whereas at smaller DOTAP concentrations, the competing effect due to lipid-lipid complex formation results in a constant value for diffusion. We also characterize the lipid headgroup orientation and the interactions between DMPC and DOTAP lipids, which were found to form PC-PC and PC-TAP pairs, and the formation of lipid clusters.
Micellization of the ionic surfactant sodium hexyl sulfate has been studied using atomistic explicit-solvent molecular dynamics simulations with and without excess NaCl or CaCl(2). Simulations were performed at surfactant loadings near the critical micellization concentration. Equilibrium micelle size distributions and estimates of the critical micellization concentration obtained from the simulations are in agreement with experimental data. In comparison to the sodium dodecyl sulfate surfactant, the shorter alkyl chain of sodium hexyl sulfate results in increased disorder of the micellar core and water exposure of the hydrocarbon tail groups. However, water and ions do not penetrate into the micellar core even for these weakly micellizing surfactants. Excess NaCl is observed to have a minor influence on the micelle structure but excess CaCl(2) induces drastic changes both in the structure and the dynamics of the micellar system. Furthermore, in the absence of excess salt, sodium hexyl sulfate forms predominantly spherical, disorganized aggregates but an increase in ionic strength drives an increase in aggregate size and leads to prolate aggregates.
Polymer-cushioned lipid bilayers are frequently used to mimic the native environment of cellular membranes in respect to the extracellular matrix and intracellular structures. With the aim to actively tune lipid membrane characteristics, we pursue the approach to use temperature and pH responsive polymer thin films of poly(N-isopropylacrylamide-co-carboxyacrylamide) (PNIPAAm-co-carboxyAAM) as cushions for supported lipid bilayers. A cationic lipid bilayer composed of dioleoylphosphatidylcholine (DOPC) and dioleoyltrimethylammoniumpropane (DOTAP) (9:1) was formed on top of the polymer thin film in a drying/rehydration process. Fluorescence recovery after photobleaching (FRAP) yielded higher lipid diffusion coefficients (6.3-9.6 μm(2) s(-1)) on polymer cushions in comparison to solid glass supports (3.0-5.9 μm(2) s(-1)). No correlation of the lipid mobility was found with the swelling state of (PNIPAAm-co-carboxyAAM), which is ascribed to restrained interfacial electrostatic interactions and dispersion forces. The results revealed a minimal coupling of the lipid bilayer with the polymer cushions, and thus, bilayers supported by (PNIPAAm-co-carboxyAAM) provide interesting opportunities for unperturbed lipid diffusion combined with control of transmembrane protein mobility due to the impact of a tunable frictional drag.
The interactions of salts with lipid bilayers are known to alter the properties of membranes and therefore influence their structure and dynamics. Sodium and calcium cations penetrate deeply into the headgroup region and bind to the lipids, whereas potassium ions only loosely associate with lipid molecules and mostly remain outside of the headgroup region. We investigated a dipalmitoylphosphatidylcholine (DPPC) bilayer in the gel phase in the presence of all three cations with a concentration of Ca²+ ions an order of magnitude smaller than the Na+ and K+ ions. Our findings indicate that the area per unit cell does not significantly change in these three salt solutions. However the lipid molecules do re-order non-isotropically under the influence of the three different cations. We attribute this reordering to a change in the highly directional intermolecular interactions caused by a variation in the dipole-dipole bonding arising from a tilt of the headgroup out of the membrane plane. Measurements in different NaCl concentrations also show a non-isotropic re-ordering of the lipid molecules.
We performed 200 ns MD simulations of phosphatidylcholine (PC) bilayers in the liquid crystalline (L(α)) and gel (L(β)') states to compare the properties of the water-membrane interfaces in these two thermotropic bilayer phases. Our simulations show that the membrane phase determines the behavior of water, ions, and PC head groups. When the membrane was in the gel phase, we found partial dehydration (fewer PC-water interactions), particularly in the carbonyl groups region, as well as an almost complete lack of ionic penetration into this region as compared with the bilayer in the liquid-crystalline phase. In the latter case, there is an exchange of Na(+) ions between the water layer and the interfacial region. This is mainly due to the fact that the most stable binding of Na(+) in the liquid-crystalline bilayer is to the carbonyl groups. The lack of Na(+) binding to the carbonyl groups in the gel phase bilayer can be explained by the more compact structure of the bilayer in this phase.
Interactions of different anions with phospholipid membranes in aqueous salt solutions were investigated by molecular dynamics simulations and fluorescence solvent relaxation measurements. Both approaches indicate that the anion-membrane interaction increases with the size and softness of the anion. Calculations show that iodide exhibits a genuine affinity for the membrane, which is due to its pairing with the choline group and its propensity for the nonpolar region of the acyl chains, the latter being enhanced in polarizable calculations showing that the iodide number density profile is expanded toward the glycerol level. Solvent relaxation measurements using Laurdan confirm the influence of large soft ions on the membrane organization at the glycerol level. In contrast, chloride exhibits a peak at the membrane surface only in the presence of a surface-attracted cation, such as sodium but not potassium, suggesting that this behavior is merely a counterion effect.
The action of NaCl vs KCl on the static and kinetic behavior of a fully charged and unfolded polyglutamic acid (PGA) chain is investigated by extensive explicit-water computer simulations. Ion-specific shrinking of the PGA coil size with increasing salt concentration is observed and is consistent with intrinsic viscosity measurements. The PGA relaxation kinetics is found to be nearly exponential in KCl on a Rouse/Zimm time scale (approximately 1 ns), whereas NaCl induces a 10- to 100-times slower, highly nonexponential relaxation. The slow decay can be traced back to Na(+) ions bridging anionic groups with scale-free power-law residence time distributions. This "transient cross-linking" may explain cation-specific slowing down of (bio)polymer kinetics observed in a variety of experiments. A systematic test using different force-field combinations in the simulations corroborates the qualitative trends, while quantitatively, the kinetic rates in the NaCl simulations significantly depend on the particular choice of water and ion parameters.
We employ atomistic simulations to consider how mono- (NaCl) and divalent (CaCl(2)) salt affects properties of inner and outer membranes of mitochondria. We find that the influence of salt on structural properties is rather minute, only weakly affecting lipid packing, conformational ordering, and membrane electrostatic potential. The changes induced by salt are more prominent in dynamical properties related to ion binding and formation of ion-lipid complexes and lipid aggregates, as rotational diffusion of lipids is slowed down by ions, especially in the case of CaCl(2). In the same spirit, lateral diffusion of lipids is slowed down rather considerably for increasing concentration of CaCl(2). Both findings for dynamic properties can be traced to the binding of ions with lipid head groups and the related changes in interaction patterns in the headgroup region, where the binding of Na(+) and Ca(2+) ions is clearly different. The role of cardiolipins in these phenomena turns out to be important.
Soft Condensed Matter commonly deals with materials that are mechanically soft and, more importantly, particularly prone to thermal fluctuation effects. Charged soft matter systems are especially interesting: they can be manufactured artificially as polyelectrolytes to serve as superabsorbers in dypers, as flocculation and retention agents, as thickeners and gelling agents, and as oil-recovery process aids. They are also abundant in living organisms, mostly performing important structural (e.g. membranes) and functional (e.g. DNA) tasks.
The book describes the many areas in soft matter and biophysics where electrostatic interactions play an important role. It offers in-depth coverage of recent theoretical approaches, advances in computer simulation, and novel experimental techniques.
Readership: Advanced undergraduate level in physics, physical chemistry, and theoretical biochemistry.
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
Despite its importance, the understanding of ionic cloud distribution close to a charged macroion under physiological salt conditions has remained very limited especially for strongly coupled systems with, for instance, multivalent counterions. Here we present a formalism that predicts both counterion and coion distributions in the vicinity of a charged macroion for an arbitrary amount of added salt and in both limits of mean field and strong coupling. The distribution functions are calculated explicitly for ions next to an infinite planar charged wall. We present a schematic phase diagram identifying different physical regimes in terms of electrostatic coupling parameter and bulk salt concentration.
The distribution profiles of rubidium ions near polar, zwitterionic 1,2-di stearoyl-sn-glycero-3-phospho choline (DSPC) and charged, anionic 1,2-di stearoyl-sn-glycero-3-phospho glycerol (DSPG−) membranes were determined by means of anomalous X-ray diffraction close to the K-absorption edge of Rb+, which was measured to be 15.225 keV. The samples were kept in the Lβ'-phase at 30 °C. The DSPC suspensions in 2 M RbCl were examined at 15.125 keV, 15.196 keV, 15.210 keV, the DSPG− suspensions in 0 M RbCl and 2 M RbCl at 14.667 keV and 15.196 keV. This gave up to seven peaks in the powder-like diffraction pattern and revealed, for the first time directly, different rubidium ion distributions in either of the investigated systems: rubodium ions are enriched by 100% in the proximity of the charged DSPG− headgroups and depleted by 25% from the vicinity of the zwitterionic DSPC headgroups. The latter phenomenon results in rubidium ion concentration maximum in the aqueous compartment between polar, but uncharged bilayers.
Realistic all-atom simulation of biological systems requires accurate modeling of both the biomolecules and their ionic environment. Recently, ion nucleation phenomena leading to the rapid growth of KCl or NaCl clusters in the vicinity of biomolecular systems have been reported. To better understand this phenomenon, molecular dynamics simulations of KCl aqueous solutions at three (1.0, 0.25, and 0.10 M) concentrations were performed. Two popular water models (TIP3P and SPC/E) and two Lennard-Jones parameter sets (AMBER and Dang) were combined to produce a total of 80 ns of molecular dynamics trajectories. Results suggest that the use of the Dang cation Lennard-Jones parameters instead of those adopted by the AMBER force-field produces a more accurate description of the ionic solution. In the later case, formation of salt aggregates is probably indicative of an artifact resulting from misbalanced force-field parameters. Because similar results were obtained with two different water parameter sets, the simulations exclude a water model dependency in the formation of anomalous ionic clusters. Overall, the results strongly suggest that for accurate modeling of ions in biomolecular systems, great care should be taken in choosing balanced ionic parameters even when using the most popular force-fields. These results invite a reexamination of older data obtained using available force-fields and a thorough check of the quality of current parameters sets by performing simulations at finite (>0.25 M) instead of minimal salt conditions.
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.
Atomistic molecular dynamics simulations of fully hydrated 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE), and 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG) bilayers in the liquid-crystalline state were carried out to investigate the effect of different lipid headgroups on the dynamics of water at the bilayer surface in short 80 ps time scales. Results obtained in these studies show that the hydrogen bonding amine group of POPE and the glycerol group of POPG slow water motion more than the equivalent choline group of POPC. Therefore, it is surprising that the effect of a POPC bilayer surface on water dynamics is similar to that of POPE and POPG bilayers. That result is due to a much higher number of water molecules interacting with the choline group of POPC than hydrogen-bonded molecules interacting with amine or glycerol groups of POPE and POPG.
We use a long, all-atom molecular-dynamics (MD) simulation combined with theoretical modeling to investigate the dynamics of selected lipid atoms and lipid molecules in a hydrated diyristoyl-phosphatidylcholine lipid bilayer. From the analysis of a 0.1 micros MD trajectory, we find that the time evolution of the mean-square displacement, <[deltar(t)]2>, of lipid atoms and molecules exhibits three well-separated dynamical regions: (i) ballistic, with <[deltar(t)]2> approximately t2 for t<or approximately 10 fs; (ii) subdiffusive, with <[deltar(t)]2> approximately tbeta with beta<1 for 10 ps<or approximately t<or approximately 10 ns; and (iii) Fickian diffusion, with <[deltar(t)]2> approximately t for t>or approximately 30 ns. We propose a memory-function approach for calculating <[deltar(t)]2> over the entire time range extending from the ballistic to the Fickian diffusion regimes. The results are in very good agreement with the ones from the MD simulations. We also examine the implications of the presence of the subdiffusive dynamics of lipids on the self-intermediate scattering function and the incoherent dynamic structure factor measured in neutron-scattering experiments.
The pH-indicator dye fluorescein was covalently bound to the surface of the purple membrane at position 72 on the extracellular side of bacteriorhopsin and at positions 101, 105, 160, or 231 on the cytoplasmic side by reacting bromomethylfluorescein with the sulfhydryl groups of cysteines introduced by site-directed mutagenesis. At position 72, on the extracellular surface, the light-induced proton release was detected 71 +/- 4 microseconds after the flash (conditions: pH 7.3, 22 degrees C, and 150 mM KCl). On the cytoplasmic side with the dye at positions 101, 105, and 160, the corresponding values were 77, 76, and 74 +/- 5 microseconds, respectively. Under the same conditions, the proton release time in the bulk medium as detected by pyranine was around 880 microseconds--i.e., slower by a factor of more than 10. The fact that the proton that is released on the extracellular side is detected much faster on the cytoplasmic surface than in the aqueous bulk phase demonstrates that it is retained on the surface and migrates along the purple membrane to the other side. These findings have interesting implications for bioenergetics and support models of local proton coupling. From the small difference between the proton detection times by labels on opposite sides of the membrane, we estimate that at 22 degrees C the proton surface diffusion constant is greater than 3 x 10(-5) cm2/s. At 5 degrees C, the proton release detection time at position 72 equals the faster of the two main rise times of the M intermediate (deprotonation of the Schiff base). At higher temperatures this correlation is gradually lost, but the curved Arrhenius plot for the proton release time is tangential to the linear Arrhenius plot for the rise of M at low temperatures. These observations are compatible with kinetic coupling between Schiff base deprotonation and proton release.
The authors review recent advances in the physics of strongly interacting charged systems functioning in water at room temperature. In these systems, many phenomena go beyond the framework of mean-field theories, whether linear Debye-Hückel or nonlinear Poisson-Boltzmann, culminating in charge inversion-a counterintuitive phenomenon in which a strongly charged particle, called a macroion, binds so many counterions that its net charge changes sign. The review discusses the universal theory of charge inversion based on the idea of a strongly correlated liquid of adsorbed counterions, similar to a Wigner crystal. This theory has a vast array of applications, particularly in biology and chemistry; for example, in the presence of positive multivalent ions (e.g., polycations), the DNA double helix acquires a net positive charge and drifts as a positive particle in an electric field. This simplifies DNA uptake by the cell as needed for gene therapy, because the cell membrane is negatively charged. Analogies of charge inversion to other fields of physics are also discussed.
The
force between silica spheres and naturally oxidised silicon wafer has been measured in calcium chloride solutions at concentrations between 1 and 5 M using an atomic force microscope. An oscillatory force, consistent
in periodicity with the expulsion of layers of ions, was found to overlay the expected van der Waals force. The extent and magnitude of the oscillations increased markedly with electrolyte concentration. Measured pull-off forces point to the oscillatory force minima being much larger in magnitude than
the maxima, and appears to confirm the existence of ion correlation forces, possibly resulting from
shared hydration waters forming an attractive network. Forces were also measured in 1 M NaCl solution. A monotonic
repulsion was observed at short-range, in contrast with the ‘
hard-wall’ of Ca2+ ions observed in 1 M CaCl2
before expulsion at a force of 3 mN m−1. These observations suggest that calcium ions are attracted to the surface
strongly enough to disrupt the hydration of the surface and/or the ions, whereas sodium ions are not. The results
demonstrate a simple
methodology
for the direct
investigation of ion-specific
surface forces at high salt concentrations.
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.
Interactions between charged surfaces immersed in aqueous calcium solutions were measured using the surface force apparatus and the atomic force microscope. With the surface force apparatus, good agreement with previously reported measurements was found for mica surfaces in dilute solutions up to 0.1 M. However, at higher concentrations large discrepancies were observed. Compared to the earlier work, the strength of the force was lower by two or three orders of magnitude and the range was diminished. Experiments using the atomic force microscope indicated similar force‐distance profiles for the interaction between silicon nitride and mica. With this technique concentrations as high as 5 M can be investigated, and owing to the small radius of curvature much higher pressures can be recorded. Results obtained by both methods confirm that the force is strongly attractive at very small surface separations, in agreement with the theoretical predictions based on calculations of ion correlations. Just outside of that interval the interaction is repulsive, and it can be quantitatively explained by taking into account the adsorption of hydrated ions onto the surface (sign reversal of the effective surface charge) and the layering of co‐ and counterions. At larger surface separations, the behavior indicates a balance between the double layer repulsion and the van der Waals attraction (the presence of a secondary minimum).
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.
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.
The Poisson-Boltzmann (PB) approach gives asymptotically exact counter-ion density profiles around macroscopic charged objects and forces between macroscopic charged objects in the weak-coupling limit of low counter-ion valency, low surface-charge density, and high temperature. In this paper we derive, using field-theoretic methods, a theory which becomes exact in the opposite limit of strong coupling (SC). Formally, it corresponds to a standard virial expansion. Long-range divergences render the virial expansion intractable for homogeneous bulk systems, giving rise to non-analyticities in the low-density expansion of the free-energy density of electrolyte solutions. We demonstrate that for the case of inhomogeneous density distribution functions at macroscopic charged bodies these divergences are renormalizable by a systematic expansion in powers of the fugacity. For a single planar charged wall, we obtain the counter-ion density profile in the SC limit, which decays exponentially, in contrast to the PB result, which predicts algebraic decay, and in agreement with previously published numerical results. Similarly and highly charged plates in the presence of multivalent counter-ions attract each other in the SC limit and form electrostatically bound states, in contrast to the PB limit, where the interaction is always repulsive. By considering next-leading corrections to both the PB and SC theories, we estimate the range of validity for both theories.
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.
The force as a function of distance between mica surfaces in aqueous KC1 solutions has been measured with particular attention given to the forces at separations below 2 nm. As previously reported, the forces in dilute electrolyte solutions are well described by the DLVO theory (i.e., repulsive double-layer forces and attractive van der Waals forces), but above a certain electrolyte concentration an additional short-range repulsive hydration force arises as hydrated cations adsorb to the mica surfaces. As more cations adsorb, the hydration force increases in both magnitude and range (attaining 4–5 nm). We now find that the repulsive hydration force is not purely monotonic, but has an oscillatory component superimposed on it which is particularly pronounced at separations below about 1 nm. The periodicity of the oscillations is 0.25 ± 0.03 nm, corresponding to the diameter of water molecules. The results are compared with those obtained using other, nonaqueous, liquids and with the crystalline swelling properties of clays. The finding that hydration forces are oscillatory at short-range carries implications for the theoretical understanding of hydration effects in general, and its significance for other systems is discussed.
The effect of ion-binding on a zwitterionic phospholipid such as 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) has been studied by measuring the zeta potential value of the unilamellar liposomes present in solution while varying the pH and the ionic strength in independent experiments. We have experimentally confirmed that DMPC binds cations, resulting in an increase of the zeta potential value. The liposome surface charge has been proved to have a strong effect on the supported bilayer formation on hydrophilic, negatively charged surfaces such as mica and silicon oxide as atomic force microscopy images reveal. Furthermore, thanks to force spectroscopy measurements we have proved that ion-binding also affects the nanomechanical response of the system, since it increases the force that has to be exerted on the membrane in order to puncture it. Last but not least, the nanomechanics of the bilayer does not depend on the substrate, thus implying that membrane properties are not influenced by the supporting material.
For many decades, the Gouy–Chapman model, whose cornerstone is the Poisson–Boltzmann equation, has been the traditional approach to describing the electric double layer (EDL). Since the early 1980s, a great amount of theoretical work (mostly computer simulations and integral equation theories) has proved that this classical picture of the EDL presents severe failures in the case of electrolytes with multivalent ions, as a result of neglecting ion size correlations. The overlooking of the phenomenon of charge reversal is probably one of the most representative examples of such deficiencies.This work is a critical survey on the relevance of ion size correlations in real colloidal systems (focused mainly on solutions with multivalent counterions). A sophisticated electrophoresis theory (in which ionic steric correlations are taken into account) will be applied to analyze experimental data, which will be also compared with predictions of the classical approach. In addition, we will discuss to what extent ion size correlations contribute to charge reversal in colloids of biological nature and other real colloids. Unlike the classical Poisson–Boltzmann approach, the presented theory describes the charge inversion that occurs within aqueous latexes when increasing the trivalent aqueous electrolyte concentration well above the mmolar range.
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.
This reference describes the role of various intermolecular and interparticle forces in determining the properties of simple systems such as gases, liquids and solids, with a special focus on more complex colloidal, polymeric and biological systems. The book provides a thorough foundation in theories and concepts of intermolecular forces, allowing researchers and students to recognize which forces are important in any particular system, as well as how to control these forces. This third edition is expanded into three sections and contains five new chapters over the previous edition. • starts from the basics and builds up to more complex systems • covers all aspects of intermolecular and interparticle forces both at the fundamental and applied levels • multidisciplinary approach: bringing together and unifying phenomena from different fields • This new edition has an expanded Part III and new chapters on non-equilibrium (dynamic) interactions, and tribology (friction forces).
We show that mixing zwitterionic lipids with up to 20% mole % cationic lipids produces gel-phase supported lipid bilayers that are morphologically free of defects detectable using noncontact mode atomic force microscopy (AFM). This contrasts with the observation of massive defects when anionic lipid was added, and also when no charged lipid was added. Infrared measurements of headgroup orientation in the presence of cationic lipid show that the mean headgroup orientation changes only minimally when temperature is lowered from the fluid phase to the gel phase. This is consistent with a tentative explanation, based on simple electrostatic arguments, in which cationic lipids "stitch" the bilayers together. On the functional side, this study demonstrates a simple method by which to minimize defects in gel-supported phospholipid bilayers.
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.
The diffusion coefficients D(cm2.s-1) of the sodium salts of a series of hydrophilic mono- and dicarboxylic acids, have been measured in the hydrophilic layers of phosphatidylcholine-water lamellar phases, as a function of phase hydration. At pH 9.0, the diffusion rates of the anionic (RCOO-) form of the acid exhibit a prominent increase within a narrow range of water content, specific to each anion. This high diffusion rate seems to occur when the Stokes diameter of an anion is equal to the thickness of the aqueous layer between the two planes formed by the quaternary ammonium groups of the choline phosphate dipoles of two facing layers of phosphatidylcholine molecules. This phenomenon demonstrates the importance of the spatial organization of successive binding sites in the rate constant of diffusional processes in hydrophilic channels.
The conformation of the polar headgroup of phosphatidylcholine in bilayer vesicles has been investigated using paramagnetic probes. The extended disposition of the polar group when bound to cations is maintained when anions are bound.
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 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 potassium 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. A conformational change of the serine headgroup induced by the membrane-bound charges is proposed. We propose that the metallic cations can be differentiated on the basis of their respective spatial distribution functions relative to the choline and serine headgroups. According to this interpretation, the divalent cations Ca2+ and Mg2+ are more deeply buried in the membrane than monovalent Na+ and K+, the case of Li+ being intermediate of the latter two. This conclusion is discussed in relation to fundamental theories of the spatial distribution of ions near the interface between water and smooth charged solid surfaces.
The influence of electric surface charges on the polar headgroups and the hydrocarbon region of phospholipid membranes was studied by mixing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) with charged amphiphiles. A positive surface charge was generated with dialkyldimethylammonium salts and a negative surface charge with dialkyl phosphates. The POPC:amphiphile ratio and hence the surface charge density could be varied over a large range since stable liquid-crystalline bilayers were obtained even for the pure amphiphiles in water. POPC was selectively deuterated at both methylene segments of the choline moiety and at the cis double bond of the oleic acyl chain. Additional experiments were carried out with 1,2-dipalmitoyl-rac-glycero-3-phosphocholine labeled at the C-2 position of the glycerol backbone. Deuterium, phosphorus, and nitrogen-14 nuclear magnetic resonance (NMR) spectra were recorded for liquid-crystalline bilayers with varying concentrations of amphiphiles. Although the hydrocarbon region and the glycerol backbone were not significantly influenced by the addition of amphiphiles, very large perturbations of the phosphocholine headgroup were observed. Qualitatively, these results were similar to those observed previously with other cationic and anionic molecules and suggest that the electric surface charge is the essential driving force in changing the phospholipid headgroup orientation and conformation. While the P-N dipole is approximately parallel to the membrane surface in the pure phospholipid membrane, the addition of a positively charged amphiphile or the binding of cationic molecules moves the N+ end of the dipole toward the water phase, changing the orientation of the phosphate segment by more than 30 degrees at the highest amphiphile concentration.(ABSTRACT TRUNCATED AT 250 WORDS)
Aqueous anion binding to bilayer membranes consisting of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) was investigated by using deuterium and phosphorus-31 nuclear magnetic resonance (NMR) spectroscopy. Only those anions that exhibit chaotropic properties showed significant binding to POPC membranes. A detailed investigation of thiocyanate binding to neutral POPC and to positively charged mixed POPC/dihexadecyldimethylammonium bromide (DHDMAB) (8:2 mol/mol) membranes revealed changes in the 2H NMR quadrupole splittings from POPC specifically deuteriated at either the alpha-segment or the beta-segment of the choline head group which were consistent with a progressive accumulation of excess negative charge at the membrane surface with increasing SCN- concentration. Both the 2H and 31P NMR spectra indicated the presence of fluid lipids in a bilayer configuration up to at least 1.0 M NaSCN with no indication of any phase separation of lipid domains. Calibration of the relationship between the change in the 2H NMR quadrupole splitting and the amount of SCN- binding provided thiocyanate binding isotherms. At a given SCN- concentration the positively charged membranes bound levels of SCN- 3 times that of the neutral membranes. The binding isotherms were analyzed by considering both the electrostatic and the chemical equilibrium contributions to SCN- binding. Electrostatic considerations were accounted for by using the Gouy-Chapman theory. For 100% POPC membranes as well as for mixed POPC/DHDMAB (8:2 mol/mol) membranes the thiocyanate binding up to concentrations of 100 mM was characterized by a partition equilibrium with an association constant of K approximately 1.4 +/- 0.3 M-1.(ABSTRACT TRUNCATED AT 250 WORDS)
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.
Results are presented of force measurements between deposited bilayers of dimyristoylphosphatidyl glycerol (DMPG) at T greater than Tm, and distearoylphosphatidyl glycerol (DSPG) at T less than Tm. Below a bilayer separation of 100 nm, a repulsive double-layer force is measured, which can be explained through the combined screening and binding effect of the counterions in electrolyte solutions of NaCl, HCl, CaCl2, or mixtures of these. The binding of cations to bilayers in the fluid phase (DMPG) appears to be greater than to bilayers in the gel phase (DSPG). At shorter range, below approximately 3 nm, an attractive interaction is measured in solutions containing CaCl2, which was found to be slightly stronger than the theoretically expected van der Waals interaction. No hydration force was observed to exist in solutions containing CaCl2. In NaCl solutions, the measured interbilayer force can completely be accounted for by the electrostatic repulsion, down to a bilayer separation of at least 2 nm, below which no accurate measurements were possible anymore. Parallel measurements on PG monolayers show that the contraction of a DMPG monolayer following addition of CaCl2 is significantly greater than what is predicted from the change in the double-layer free energy alone. This indicates that changes in the lateral interactions between the lipid headgroups probably involve Ca2+-bridge binding and/or a possible dehydration of the lipid headgroups through Ca2+ binding. The results shed new light on both the interbilayer and intrabilayer interactions of PG and identify the possible factors responsible for the morphological behavior of PG aggregates.
We have determined the degree of binding of divalent cations to several kinds of phosphatidylcholine (PC) bilayers. This has been done by measuring the electrostatic interbilayer repuslive force that results when multilamellar lattices are exposed to Me2+Cl2 solutions. Divalent cations bind to dipalmitoylphosphatidylcholine in the sequence Ca2+ approximately equal to Cd2+ approximately equal to Mn2+ greater than Ca2+ approximately equal to Mg2+ greater than Ba2+. Among the different synthetic lipids, preference for Ca2+ is in the sequence DOPC less than DLPC less than DMPC approximately equal to DPPC approximately equal to DSPC. The density of bound charge is proportional to the density of polar groups on the bilayer surface. Phosphatidylcholines with mixed hydrocarbon chains, such as egg PC or 1:1 mixtures of synthetic PC's, form two distinct lamellar phases in CaCl2 solutions. In all cases the electrostatic force between bilayers decays exponentially with their separation but more slowly than expected from ionic double-layer theory. We suggest that the electric fields from opposing surfaces perturb the zwitterionic charge-binding polar groups and continuously modify their ion binding affinities as the bilayers approach.
Aqueous gel sieving chromatography on Sephadex G-10 of the Group IA cations (Li+, Na+, K+, Rb+, Cs+) plus NH4+ as the Cl- salts, in combination with previous results for the halide anions (F-, Cl-, Br-, I-) as the Na+ salts [Washabaugh, M.W. & Collins, K.D. (1986) J. Biol. Chem. 261, 12477-12485], leads to the following conclusions. (i) The small monovalent ions (Li+, Na+, F-) flow through the gel with water molecules attached, whereas the large monovalent ions (K+, Rb+, Cs+, Cl-, Br-, I-) adsorb to the nonpolar surface of the gel, a process requiring partial dehydration of the ion and implying that these ions bind the immediately adjacent water molecules weakly. (ii) The transition from strong to weak hydration occurs at a radius of about 1.78 A for the monovalent anions, compared with a radius of about 1.06 A for the monovalent cations (using ionic radii), indicating that the anions are more strongly hydrated than the cations for a given charge density. (iii) The anions show larger deviations from ideal behavior (an elution position corresponding to the anhydrous molecular weight) than do the cations and dominate the chromatographic behavior of the neutral salts. These results are interpreted to mean that weakly hydrated ions (chaotropes) are "pushed" onto weakly hydrated surfaces by strong water-water interactions and that the transition from strong ionic hydration to weak ionic hydration occurs where the strength of ion-water interactions approximately equals the strength of water-water interactions in bulk solution.
Since the proposal of the chemiosmotic theory there has been a continuing debate about how protons that have been pumped across membranes reach another membrane protein that utilizes the established pH gradient. Evidence has been gathered in favour of a 'delocalized' theory, in which the pumped protons equilibrate with the aqueous bulk phase before being consumed, and a 'localized' one, in which protons move exclusively along the membrane surface. We report here that after proton release by an integral membrane protein, long-range proton transfer along the membrane surface is faster than proton exchange with the bulk water phase. The rate of lateral proton diffusion can be calculated by considering the buffer capacity of the membrane surface. Our results suggest that protons can efficiently diffuse along the membrane surface between a source and a sink (for example H(+)-ATP synthase) without dissipation losses into the aqueous bulk.
Small ions of high charge density (kosmotropes) bind water molecules strongly, whereas large monovalent ions of low charge density (chaotropes) bind water molecules weakly relative to the strength of water-water interactions in bulk solution. The standard heat of solution of a crystalline alkali halide is shown here to be negative (exothermic) only when one ion is a kosmotrope and the ion of opposite charge is a chaotrope; this standard heat of solution is known to become proportionally more positive as the difference between the absolute heats of hydration of the corresponding gaseous anion and cation decreases. This suggests that inner sphere ion pairs are preferentially formed between oppositely charged ions with matching absolute enthalpies of hydration, and that biological organization arises from the noncovalent association of moieties with matching absolute free energies of solution, except where free energy is expended to keep them apart. The major intracellular anions (phosphates and carboxylates) are kosmotropes, whereas the major intracellular monovalent cations (K+; arg, his, and lys side chains) are chaotropes; together they form highly soluble, solvent-separated ion pairs that keep the contents of the cell in solution.
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.
Long-range proton transfer along the surface of black lipid bilayers was observed between two integral membrane channels (gramicidins), one operating as a proton source, the other as a sink, by patch-clamp technique. In contrast, potassium ions were shown to equilibrate with the aqueous bulk phase before being consumed. Both channels opened and closed simultaneously only if the charge between them was carried by protons. In this case an anomalous high conductance between two patched membrane fragments was measured, each of them containing one single gramicidin channel. The coupled state disappeared when the distance between these two channels was increased above the critical value. The latter was shown to increase with the channel lifetime. Our results support the idea of the 'localized' proton coupling, in which protons that have been pumped across membranes migrate along the membrane surface to reach another membrane protein that utilizes the established pH gradient.
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.
The thermotropic phase behavior of lipid bilayer model membranes composed of the cationic lipid 1,2-di-O-myristoyl-3-N,N,N-trimethylaminopropane (DM-TAP) was examined by differential scanning calorimetry, infrared spectroscopy and X-ray diffraction. Aqueous dispersions of this lipid exhibit a highly energetic endothermic transition at 38.4 degrees C upon heating and two exothermic transitions between 20 and 30 degrees C upon cooling. These transitions are accompanied by enthalpy changes that are considerably greater than normally observed with typical gel/liquid--crystalline phase transitions and have been assigned to interconversions between lamellar crystalline and lamellar liquid--crystalline forms of this lipid. Both infrared spectroscopy and X-ray diffraction indicate that the lamellar crystalline phase is a highly ordered, substantially dehydrated structure in which the hydrocarbon chains are essentially immobilized in a distorted orthorhombic subcell. Upon heating to temperatures near 38.4 degrees C, this structure converts to a liquid-crystalline phase in which there is excessive swelling of the aqueous interlamellar spaces owing to charge repulsion between, and undulations of, the positively charged lipid surfaces. The polar/apolar interfaces of liquid--crystalline DM-TAP bilayers are not as well hydrated as those formed by other classes of phospho- and glycolipids. Such differences are attributed to the relatively small size of the polar headgroup and its limited capacity for interaction with moieties in the bilayer polar/apolar interface.
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.