Steered molecular dynamics simulations of cobra cytotoxin interaction with zwitterionic lipid bilayer: no penetration of loop tips into membranes

Cobra cytotoxins, small proteins of three-fingered toxin family, unspecifically damage membranes in different cells and artificial vesicles. However, the molecular mechanism of this damage is not yet completely understood. We used steered molecular dynamics simulations to study the interaction of cardiotoxin A3 from Naja atra cobra venom with hydrated 1-palmitoyl-2-oleoyl-1-sn-3-phosphatidylcholine (POPC) bilayer. The studied system included one cytotoxin molecule, 64 lipid molecules (32 molecules in each monolayer) and 2500 water molecules. It was found that the toxin interacted with zwitterionic bilayer formed by POPC. During first nanosecond of simulation the toxin molecule was oriented toward membrane surface by loops' basement including cytotoxin regions Cys14-Asn19 and Cys38-Ser46. This orientation was stable enough and was not changed during next 6 ns of simulation. The obtained data suggest that cytotoxin molecule cannot penetrate into membrane composed of zwitterionic lipids without some auxiliary interaction.     

Interaction of zervamicin IIB with lipid bilayers. Molecular dynamics study

In this work we have studied the interaction of zervamicin IIB (ZrvIIB) with the model membranes of eukaryotes and prokaryotes using all-atom molecular dynamics. In all our simulations zervamicin molecule interacted only with lipid headgroups but did not penetrate the hydrophobic core of the bilayers. During the interaction with the prokaryotic membrane zervamicin placed by its N-termini towards the lipids and rotated at an angle of 40° relatively to the bilayer surface. In the case of eukaryotic membrane zervamicin stayed in the water and located parallel to the membrane surface. We compared hydrogen bonds between peptide and lipids and concluded that interactions of ZrvIIB with prokaryotic membrane are stronger than those with eukaryotic one. Also it was shown that two zervamicin molecules formed dimer and penetrated deeper in the area of lipid headgroups.     

Dissipative particle dynamics simulation study of the bilayer-vesicle transition

A bilayer structure is an important immediate for the vesicle formation. However,the mechanism for the bilayer-vesicle transition remains unclear. In this work,a dissipative particle dynamics(DPD) simulation method was employed to study the mechanism of the bilayer-vesicle transition. A coarse-grained model was built based on a lipid molecule termed dimyristoylphosphatidylcholine(DMPC). Simulations were performed from two different initial configurations:a random dispersed solution and a tensionless bilayer. It was found that the bilayer-vesicle transition was driven by the minimization of the water-tail hydrophobic interaction energy,and was accompanied with the increase of the position entropy due to the redistribution of water molecules. The bulk pressure was reduced during the bilayer-vesicle transition,suggesting the evolved vesicle morphology was at the relatively low free energy state. The membrane in the product vesicle was a two-dimensional fluid. It can be concluded that the membrane of a vesicle is not interdigitated and most of the bonds in lipid chains are inclined to orient along the radical axis of the vesicle.     

Free Energy of Bare and Capped Gold Nanoparticles Permeating through a Lipid Bilayer

Herein, we study the permeation free energy of bare and octane‐thiol‐capped gold nanoparticles (AuNPs) translocating through a lipid membrane. To investigate this, we have pulled the bare and capped AuNPs from bulk water to the membrane interior and estimated the free energy cost. The adsorption of the bare AuNP on the bilayer surface is energetically favorable but further loading inside it requires energy. However, the estimated free‐energy barrier for loading the capped AuNP into the lipid membrane is much higher compared to bare AuNP. We also demonstrate the details of the permeation process of bare and capped AuNPs. Bare AuNP induces the curvature in the lipid membrane whereas capped AuNP creates an opening in the interacting monolayer and get inserted into the membrane. The insertion of capped AuNP induces a partial unzipping of the lipid bilayer, which results in the ordering of the local lipids interacting with the nanoparticle. However, bare AuNP disrupts the lipid membrane by pushing the lipid molecules inside the membrane. We also analyze pore formation due to the insertion of capped AuNP into the membrane, which results in water molecules penetrating the hydrophobic region.     

A computer simulation study of water drying at the interface of protein chains

This study investigated the water drying (cavitation) in the interfacial region of two chains of a dimeric protein by nanosecond molecular dynamics simulations using explicit water representation. Separation-induced cavity of water was directly observed in the region. We evaluated the separation length scale of two chains on which the drying transition occurs, and the average number of water molecules that are expelled from the interfacial region during the transition. The obtained values can be rationalized by Kelvin equation for finite lateral size of confinement [K. Lum and A. Luzar, Phys. Rev. E 56, R6283 (1997)]. Also, we found that the drying transition is accompanied by an exponential reduction in the average hydrogen-bond number per interfacial water molecule. The results of this study may deepen the understanding of how hydrophobic interaction drives the assembly of protein chains.     

十二烷基磺基甜菜碱与铂电极支撑的磷脂双层膜作用的电化学研究

以铂电极支撑的磷脂双层膜(Supported Bilayer Lipid Membrane,s-BLM)作为生物膜的模型,以Fe(CN)36-和Fe(CN)64-为探针分子,利用循环伏安法(CV)和交流阻抗谱(EIS)研究两性表面活性剂十二烷基磺基甜菜碱(Dodecyl Sulfobetaine,DSB)对s-BLM相互作用。结果显示,DSB可以嵌入到s-BLM的疏水区,容易使其表面分子的排列发生变化,产生缺陷或孔洞,探针分子Fe(CN)63-和Fe(CN)64-可以通过这些微孔接近电极,产生氧化还原响应。并且作用时间、DSB的浓度以及胆固醇的存在与否对二者的相互作用有直接影响。此外作用后的双层膜在0.1mol/LKCl溶液中能够自我修复,这表明DSB与s-BLM的相互作用是可逆的。     

Passive transport of C60 fullerenes through a lipid membrane: a molecular dynamics simulation study

To investigate the implications of the unique properties of fullerenes on their interaction with and passive transport into lipid membranes, atomistic molecular dynamics simulations of a C60 fullerene in a fully hydrated di-myristoyl-phoshatidylcholine lipid membrane have been carried out. In these simulations the free energy and the diffusivity of the fullerene were obtained as a function of its position within the membrane. These properties were utilized to calculate the permeability of fullerenes through the lipid membrane. Simulations reveal that the free energy decreases as the fullerene passes from the aqueous phase, through the head group layer and into the hydrophobic core of the membrane. This decrease in free energy is not due to hydrophobic interactions but rather to stronger van der Waals (dispersion) interactions between the fullerene and the membrane compared to those between the fullerene and (bulk) water. It was found that there is no free energy barrier for transport of a fullerene from the aqueous phase into the lipid core of the membrane. In combination with strong partitioning of the fullerenes into the lipidic core of the membrane, this "barrierless" penetration results in an astonishingly large permeability of fullerenes through the lipid membrane, greater than observed for any other known penetrant. When the strength of the dispersion interactions between the fullerene and its surroundings is reduced in the simulations, thereby emulating a nanometer sized hydrophobic particle, a large free energy barrier for penetration of the head group layer emerges, indicating that the large permeability of fullerenes through lipid membranes is a result of their unique interaction with their surrounding medium.     

Redox activity and diffusion of hydrophilic, hydrophobic, and amphiphilic redox active molecules in a bicontinuous cubic phase

The objective was to examine how a bicontinuous cubic phase influences the diffusion and electrochemical activity of dissolved molecules. The cubic phase is a structure with three-dimensional continuous channels of water separated by an apolar membrane. A redox active molecule can dissolve in three different environments. A hydrophobic molecule will prefer the interior of the membrane, a hydrophilic molecule will prefer the water channels, and an amphiphilic molecule will be situated with its headgroup at the surface of the membrane and its tail in the interior. The electrochemical activity was measured with cyclic voltammetry and the transport behavior with chronocoulometry. All the molecules were redox active in the cubic phase; that is, all the molecules could reach the surface of the electrode and react. The cubic phase made the kinetics of the charge transfer slower, showing a quasi-reversible behavior. The reason may be that a layer of the membrane adheres to the hydrophobic electrode surface. The diffusion experiment showed that the diffusion was slower than in solution. The molecules that were restricted to diffuse within the membrane gave particularly low mass transport rates.     

Bilayer in small bicelles revealed by lipid-protein interactions using NMR spectroscopy

Intermolecular nuclear Overhauser effects (NOEs) between the integral outer membrane protein OmpX from Escherichia coli and small bicelles of dihexanoyl phosphatidylcholine (DHPC) and dimyristoyl phosphatidylcholine (DMPC) give insights into protein-lipid interactions. Intermolecular NOEs between hydrophobic tails of lipid and protein in the bicelles cover the surface area of OmpX forming a continuous cylindric jacket of approximately 2.7 nm in height. These NOEs originate only from DMPC molecules, and no NOEs from DHPC are observed. Further, these NOEs are mainly from methylene groups of the hydrophobic tails of DMPC, and only a handful of NOEs arise from methyl groups of the hydrophobic tails. The observed contacts indicate that the hydrophobic tails of DMPC are oriented parallel to the surface of OmpX and thus DMPC molecules form a bilayer in the vicinity of the protein. Thus, a bilayer exists in the small bicelles not only in the absence of but also in the presence of a membrane protein. In addition, the number of NOEs between the polar head groups of lipid molecules and protein is increased in the bicelles compared with those in micelles. This observation may be due to the closely packed head groups of the bilayer. Moreover, irregularity of hydrophobic interactions in the middle of the bilayer environment was observed. This observation together with the interactions between polar head groups and proteins gives a possible rationale for structural and functional differences of membrane proteins solubilized in micelles and in bilayer systems and hints at structural differences between protein-free and protein-loaded bilayers.     

Structure of small associates of glycyrrhizic acid with cholesterol in aqueous solution: Molecular dynamics simulation

In a recent work by Zelikman et al.(J. Struct. Chem., 2015, 56(1)), the molecular dynamics simulation of dimers of glycyrrhizic acid (GA) arising from the spontaneous collision of two GA molecules in water is performed. Several relatively stable dimer structures are found, and when a cholesterol molecule is inserted, associates are observed constituting a GA dimer with a cholesterol molecule “stuck” to it. Here, we simulate the associates consisting of three and four GA molecules and a cholesterol molecule. It appears that the cholesterol molecule, as a rule, also locates at the surface of the GA associate. Therewith, the trimers do not form any clear characteristic structures, as dimers do, and the tetramers can be two stuck dimers.     

Protegrin‐1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations

Protegrin‐1 (PG‐1) belongs to the family of antimicrobial peptides. It interacts specifically with the membrane of a pathogen and kills the pathogen by releasing its cellular contents. To fully understand the energetics governing the orientation of PG‐1 in different membrane environments and its effects on the physicochemical properties of the peptide and membrane bilayers, we have performed the potential of mean force (PMF) calculations as a function of its tilt angle at four distinct rotation angles in explicit membranes composed of either DLPC (1,2‐dilauroylphosphatidylcholine) or POPC (1‐palmitoyl‐2‐oleoylphosphatidylcholine) lipid molecules. The resulting PMFs in explicit lipid bilayers were then used to search for the optimal hydrophobic thickness of the EEF1/IMM1 implicit membrane model in which a two‐dimensional PMF in the tilt and rotation space was calculated. The PMFs in explicit membrane systems clearly reveal that the energetically favorable tilt angle is affected by both the membrane hydrophobic thickness and the PG‐1 rotation angle. Local thinning of the membrane around PG‐1 is observed upon PG‐1 tilting. The thinning is caused by both hydrophobic mismatch and arginine‐lipid head group interactions. The two‐dimensional PMF in the implicit membrane is in good accordance with those from the explicit membrane simulations. The ensemble‐averaged Val16 ¹⁵N and ¹³CO chemical shifts weighted by the two‐dimensional PMF agree fairly well with the experimental values, suggesting the importance of peptide dynamics in calculating such ensemble properties for direct comparison with experimental observables. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

The Effect of Bacterial Signal Indole on the Electrical Properties of Lipid Membranes

Indole is an important biological signalling molecule produced by many Gram positive and Gram negative bacterial species, including Escherichia coli. Here we study the effect of indole on the electrical properties of lipid membranes. Using electrophysiology, we show that two indole molecules act cooperatively to transport charge across the hydrophobic core of the lipid membrane. To enhance charge transport, induced by indole across the lipid membrane, we use an indole derivative, 4 fluoro‐indole. We demonstrate parallels between charge transport through artificial lipid membranes and the function of complex eukaryotic membrane systems by showing that physiological indole concentrations increase the rate of mitochondrial oxygen consumption. Our data provide a biophysical explanation for how indole may link the metabolism of bacterial and eukaryotic cells.     

A molecular dynamics study on heat conduction characteristics in DPPC lipid bilayer

In this paper, nonequilibrium molecular dynamics simulations were performed on a single component 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine lipid bilayer in order to investigate the thermal conductivity and its anisotropy. To evaluate the thermal conductivity, we applied a constant heat flux to the lipid bilayer along and across the membrane with ambient water. The contribution of molecular interaction to the heat conduction was also evaluated. Along the bilayer plane, there is little transfer of thermal energy by the interaction between lipid molecules as compared with the interaction between water molecules. Across the bilayer plane, the local thermal conductivity depends on the constituents (i.e., water, head group, and tail group of lipid molecule) that occupy the domain. Although the intramolecular transfer of thermal energy in the tail groups of lipid molecules works efficiently to promote high local thermal conductivity in this region, the highest thermal resistance appears at the center of lipid bilayer where acyl chains of lipid molecules face each other due to a loss of covalent-bond and low number density. The overall thermal conductivities of the lipid bilayer in the directions parallel and perpendicular to the lipid membrane have been compared, and it was found that the thermal conductivity normal to the membrane is higher than that along the membrane, but it is still smaller than that of bulk water.     

Agglutination of like-charged red blood cells induced by binding of beta2-glycoprotein I to outer cell surface

Plasma protein-mediated attractive interaction between membranes of red blood cells (RBCs) and phospholipid vesicles was studied. It is shown that beta(2)-glycoprotein I (beta(2)-GPI) may induce RBC discocyte-echinocyte-spherocyte shape transformation and subsequent agglutination of RBCs. Based on the observed beta(2)-GPI-induced RBC cell shape transformation it is proposed that the hydrophobic portion of beta(2)-GPI molecule protrudes into the outer lipid layer of the RBC membrane and increases the area of this layer. It is also suggested that the observed agglutination of RBCs is at least partially driven by an attractive force which is of electrostatic origin and depends on the specific molecular shape and internal charge distribution of membrane-bound beta(2)-GPI molecules. The suggested beta(2)-GPI-induced attractive electrostatic interaction between like-charged RBC membrane surfaces is qualitatively explained by using a simple mathematical model within the functional density theory of the electric double layer, where the electrostatic attraction between the positively charged part of the first domains of bound beta(2)-GPI molecules and negatively charged glycocalyx of the adjacent RBC membrane is taken into account.     

Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide

Several conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer-the first solvation shell-around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within this layer, water molecules show marked orientations relative to a peptide surface. Using the two-particle contribution to entropy as a measure of structural ordering of water, we found that the first solvation shell contributes 95% or more to the total water ordering around the peptide molecule. In investigating the dynamic properties of water, diffusion coefficients and lifetime of the hydrogen bond, clear differences between solvation layer and the bulk water were observed. It was found that the translational diffusion coefficient, D(T), decreases by 30% or more compared to bulk water; also, the lifetime of the water-water hydrogen bond clearly increases. The rotational diffusion coefficient, however, decreases only slightly, no more than approximately 10%. These differences correspond to the slightly higher energy of the hydrogen bond, and to its slightly distorted geometry. Analyzing the translational dynamics of water in the vicinity of the peptide molecule, it was deduced that the structure of the first solvation shell becomes more rigid than the structure of the bulk water. Investigation of a "pure hydrophobic" form of the polypeptide shows that the structure and the properties of water within the solvation shell are predominantly determined by the hydrophobic effect. The specific interactions between water molecules and various charge groups of the peptide molecule modifies this effect only slightly.     

Effects of lidocaine on the expansion of lipid monolayer at air/water interface in relation to the local anesthesia

Lidocaine compounds have widely been used as local anesthetics. Regarding the molecular mechanism for anesthesia by local anesthetics, two hypotheses have been proposed. The first one is that molecules of local anesthetics penetrate into the hydrophobic region of cell membrane and expand the membrane volume, resulting in a change of protein conformation that blocks sodium permeability. The second hypothesis is that molecules of local anesthetics are directly adsorbed into the receptors of anesthetics in the protein channel without expanding the cell membrane. However, these proposals have never been examined systematically. In this study, the expansion of cell membrane by lidocaine compounds was investigated by employing lipid monolayer at the air/water interface as the mimetic system for cell membrane. It was found that oil-soluble lidocaine contracted the area/molecule of lipids in the monolayer of phosphatidyl choline, sphingomyelin, DS-PL95E and lipoid, but expand the monolayer of phosphatidyl ethanolamine only in a certain range of mixing ratios. Thus, this study can provide an evidence that lidocaine yields anesthesia effect by adsorbing into receptors in the protein channel rather than expanding the cell membrane.     

Water inside a hydrophobic cavitand molecule

The structure and dynamics of water inside a water-soluble, bowl-shaped cavitand molecule with a hydrophobic interior are studied using molecular dynamics computer simulations. The simulations find that the number of inside water molecules is about 4.5, but it fluctuates from being completely empty to full on a time scale of tens of nanoseconds. The transition from empty to full is energetically favorable and entropically unfavorable. The water molecules inside have fewer hydrogen bonds than the bulk and in general weaker interactions; the lower energy results from the nearest-neighbor interactions with the cavitand atoms and the water molecules at the entrance of the cavitand, interactions that are lost upon dewetting. An analysis of translational and rotational motion suggests that the lower entropy of the inside water molecules is due to decreased translational entropy, which outweighs an increased orientational entropy. The cavitand molecule acts as a host binding hydrophobic guests, and dewetting can be induced by the presence of a hydrophobic guest molecule about 3 A above the entrance. At this position, the guest displaces the water molecules which stabilize the inside water molecules and the empty cavitand becomes more stable than the full.     

Computer simulation of the distribution of hexane in a lipid bilayer: spatially resolved free energy, entropy, and enthalpy profiles

The partitioning behavior of small molecules in lipid bilayers is important in a variety of areas including membrane protein folding and pharmacology. However, the inhomogeneous nature of lipid bilayers on a nanometer length scale complicates experimental studies of membrane partitioning. To gain more insight in the partitioning of a small molecule into the lipid bilayer, we have carried out atomistic computer simulations of hexane in a dioleoyl phosphatidylcholine model membrane. We have been able to obtain spatially resolved free energy, entropy, enthalpy, and heat capacity profiles based on umbrella sampling calculations at three different temperatures. In agreement with experiment, hexane partitions preferentially to the center of the bilayer. This process is driven almost entirely by a favorable entropy change, consistent with the hydrophobic effect. In contrast, partitioning to the densest region of the acyl chains is dominated by a favorable enthalpy change with a small entropy change, which is consistent with the "nonclassical" hydrophobic effect or "bilayer" effect. We explain the features of the entropy and enthalpy profiles in terms of density and free volume in the system.     

Methotrexate interaction with a lipid membrane model of DPPC

Dipalmitoylphosphatidylcholine (DPPC) liposomes were employed as membrane models for the investigation of the interaction occurring between methotrexate (MTX) and bilayer lipid matrix. Liposomes were obtained by hydrating a lipid film with 50 mM Tris buffer (pH 7.4). The differential scanning calorimetry (DSC) evaluation of the thermotropic parameters associated with the phase transitions of DPPC liposomes gave useful information about the kind of drug-membrane interaction. The results showed an electrostatic interaction taking place with the negatively charged molecules of MTX and the phosphorylcholine head groups, constituting the outer part of DPPC bilayers. No interaction with the hydrophobic phospholipid bilayer domains was detected, revealing a poor capability of MTX to cross through lipid membranes to reach the interior compartment of a lipid bounded structure. These findings correlate well within vitro biological experiments on MTX cell susceptibility.     

Dissimilar interaction of CB1/CB2 with lipid bilayers as revealed by molecular dynamics simulation

Cannabinoid receptors CB1 and CB2 are a striking class of transmembrane proteins involved in a high number of important biological processes. In spite of the inherent similarity (40% in aminoacid sequence) these receptors are found in different cell environments. In addition to this, CB1 activity has been intimately associated with lipid rafts whereas CB2 has not. In this work we have performed a 50 nanosecond molecular dynamics simulation of the inactive conformations of both receptors inserted in a POPC lipid bilayer. Although in both cases the overall protein structure is maintained along the entire simulation we have found important differences in the protein-lipid interaction. While CB1 tends to distort the lipid bilayer regularity, especially in the extracellular moiety, CB2 has a minor influence on the lipid distribution along the plane of the bilayer. This observation is consistent with some experimental facts observed in these cannabinoid receptors with regard to lipid/protein interaction.