Self-induced docking site of a deeply embedded peripheral membrane protein

As a first step toward understanding the principles of the targeting of C2 domains to membranes, we have carried out a molecular dynamics simulation of the C2 domain of cytosolic phospholipase A2 (cPLA2-C2) in a 1-palmitoyl-2-oleoyl-phosphatidylcholine bilayer at constant pressure and temperature (NPT, 300 K and 1 atm). Using the high-resolution crystal structure of cPLA2-C2 as a starting point, we embedded two copies of the C2 domain into a pre-equilibrated membrane at the depth and orientation previously defined by electron paramagnetic resonance (EPR). Noting that in the membrane-bound state the three calcium binding loops are complexed to two calcium ions, we initially restrained the calcium ions at the membrane depth determined by EPR. But the depth and orientation of the domains remained within EPR experimental errors when the restraints were later removed. We find that the thermally disordered, chemically heterogeneous interfacial zones of phosphatidylcholine bilayers allow local lipid remodeling to produce a nearly perfect match to the shape and polarity of the C2 domain, thereby enabling the C2 domain to assemble and optimize its own lipid docking site. The result is a cuplike docking site with a hydrophobic bottom and hydrophilic rim. Contrary to expectations, we did not find direct interactions between the protein-bound calcium ions and lipid headgroups, which were sterically excluded from the calcium binding cleft. Rather, the lipid phosphate groups provided outer-sphere calcium coordination through intervening water molecules. These results show that the combined use of high-resolution protein structures, EPR measurements, and molecular dynamics simulations provides a general approach for analyzing the molecular interactions between membrane-docked proteins and lipid bilayers.     

The binding of a neutral aromatic molecule to a negatively-charged lipid membrane. I. Thermodynamics and mode of binding

This paper presents a detailed study of the binding of the fluorescent dye N-phenyl naphthylamine (NPN) to bilayers composed of the negatively-charged phospholipid methylphosphatidic acid. Binding to the liquid-crystalline membrane is enthalpy-driven. It is shown by determination of the binding constant and confirmed by n.m.r. that most of the dye ("guest") molecules reside between the lipid hydrocarbon chains at a fixed distance from the head-group, and are not distributed uniformly throughout the hydrocarbon phase. Each guest molecule is surrounded by about four lipid molecules. Transition of the membrane from the liquid-crystalline to the crystalline state results in almost total expulsion of the bound NPN into the water phase. Electrostatic theory is developed to find the effect of electrostatics upon the binding of a neutral molecule to charged membranes. Although the charge product is zero, electrostatic interactions play a part in determining the strength of binding, if each guest molecule incorporated increases the area of the membrane. For NPN this increase was found to be ca. 41 A(2).     

Abrogation of the selectivity of adriamycin for negatively-charged phospholipids by 14-valerate side chain substitution

The impressive affinity of Adriamycin and related anthracycline antibiotics for negatively-charged phospholipids has been implicated in the mechanism of the cardiac toxicity of these drugs. In this report we employ the method of fluorescence anisotropy titration to examine the manner in which 14-valerate side chain substitution modulates anthracycline drug associations with electroneutral vesicles composed of dimyristoyl phosphatidylcholine as well as negatively-charged vesicles composed of dimyristoyl phosphatidylglycerol or a binary mixture of dimyristoyl phosphatidylcholine and cardiolipin. Equilibrium binding data gathered on several anthracycline analogs indicate that incorporation of a hydrophobic valerate side chain abolished the high levels of preferential drug binding to negatively-charged membranes. Thus, we propose that 14-O-acyl substitution may prove to be a useful synthetic modification to prevent the selective accumulation of positively-charged anthracyclines in tissues or membrane domains rich in negatively-charged lipid.     

The pre-transmembrane region of the HCV E1 envelope glycoprotein: interaction with model membranes

The previously identified membranotropic regions of the HCV E1 envelope glycoprotein, a class II membrane fusion protein, permitted us to identify different sequences which might be implicated in viral membrane fusion, membrane interaction and/or protein-protein binding. HCV E1 glycoprotein presents a membrano-active region immediately adjacent to the transmembrane segment, which could be involved in membrane destabilization similarly to the pre-transmembrane domains of class I fusion proteins. Consequently, we have carried out a study of the binding and interaction with the lipid bilayer of a peptide corresponding to segment 309-340, peptide E1PTM, as well as the structural changes which take place in both the peptide and the phospholipid molecules induced by the binding of the peptide to the membrane. Here we demonstrate that peptide E1(PTM) strongly partitions into phospholipid membranes, interacts with negatively-charged phospholipids and locates in a shallow position in the membrane. These data support its role in HCV-mediated membrane fusion and suggest that the mechanism of membrane fusion elicited by class I and II fusion proteins might be similar.     

Calcium-dependence of laminin binding to phospholipid membranes

Laminin is the most abundant noncollagenous protein in basement membranes. Its selfassembly has been studied in solution, and it has been established that calcium ions induce partially reversible aggregation. The behavior at a lipid membrane surface is of greater biological significance, but it is difficult to study quantitatively binding kinetics at a surface. The present work uses a powerful new integrated optics technique to measure the absorption and aggregation of the laminin–nidogen at a bilayer lipid membrane surface. It is found that the binding of a single layer of laminin at the lipid membrane is independent of the presence of calcium, but that the building up of multilayer laminin membranes requires calcium, and that these may not be destroyed by a calcium-complexing agent. © 1993 John Wiley & Sons, Inc.     

The pre-transmembrane region of the HCV E1 envelope glycoprotein: Interaction with model membranes

The previously identified membranotropic regions of the HCV E1 envelope glycoprotein, a class II membrane fusion protein, permitted us to identify different sequences which might be implicated in viral membrane fusion, membrane interaction and/or protein-protein binding. HCV E1 glycoprotein presents a membrano-active region immediately adjacent to the transmembrane segment, which could be involved in membrane destabilization similarly to the pre-transmembrane domains of class I fusion proteins. Consequently, we have carried out a study of the binding and interaction with the lipid bilayer of a peptide corresponding to segment 309-340, peptide E1_PTM, as well as the structural changes which take place in both the peptide and the phospholipid molecules induced by the binding of the peptide to the membrane. Here we demonstrate that peptide E1_PTM strongly partitions into phospholipid membranes, interacts with negatively-charged phospholipids and locates in a shallow position in the membrane. These data support its role in HCV-mediated membrane fusion and suggest that the mechanism of membrane fusion elicited by class I and II fusion proteins might be similar.     

The crystal structure of calcium-bound annexin Gh1 from Gossypium hirsutum and its implications for membrane binding mechanisms of plant annexins

Plant annexins show distinct differences in comparison with their animal orthologues. In particular, the endonexin sequence, which is responsible for coordination of calcium ions in type II binding sites, is only partially conserved in plant annexins. The crystal structure of calcium-bound cotton annexin Gh1 was solved at 2.5 A resolution and shows three metal ions coordinated in the first and fourth repeat in types II and III binding sites. Although the protein has no detectable affinity for calcium in solution, in the presence of phospholipid vesicles, we determined a stoichiometry of four calcium ions per protein molecule using isothermal titration calorimetry. Further analysis of the crystal structure showed that binding of a fourth calcium ion is structurally possible in the DE loop of the first repeat. Data from this study are in agreement with the canonical membrane binding of annexins, which is facilitated by the convex surface associating with the phospholipid bilayer by a calcium bridging mechanism. In annexin Gh1, this membrane-binding state is characterized by four calcium bridges in the I/IV module of the protein and by direct interactions of several surface-exposed basic and hydrophobic residues with the phospholipid membrane. Analysis of the protein fold stability revealed that the presence of calcium lowers the thermal stability of plant annexins. Furthermore, an additional unfolding step was detected at lower temperatures, which can be explained by the anchoring of the N-terminal domain to the C-terminal core by two conserved hydrogen bonds.     

The effect of calcium on the properties of charged phospholipid bilayers

We have performed molecular dynamics simulations to investigate the structure and dynamics of charged bilayers as well as the distribution of counterions at the bilayer interface. For this, we have considered the negatively charged di-myristoyl-phosphatidyl-glycerol (DMPG) and di-myristoyl-phosphatidyl-serine (DMPS) bilayers as well as a protonated di-myristoyl-phosphatidyl-serine (DMPSH) bilayer. We were particularly interested in calcium ions due to their important role in biological systems. Simulations performed in the presence of calcium ions (DMPG, DMPS) or sodium ions (DMPS) were run for 45-60 ns. Simulation results for DMPG are compared with fluorescence measurements. The average areas per molecule were 47.4+/-0.5 A2 (DMPG with calcium), 47.3+/-0.5 A2 (DMPS with calcium), 51.3+/-1.0 A2 (DMPS with sodium) and 45.3+/-0.5 A2 (DMPSH). The structure of the negatively charged lipids is significantly affected by the counterions, where calcium ions have a more pronounced effect than sodium ions. Calcium ions were found to be tightly bound to the anionic groups of the lipid molecules and as such appear to constitute an integral part of the membrane interface on nanoseconds time scales. In contrast to sodium ions, calcium ions are localised in a narrow (approximately 10 A) band around the phosphate group. The interaction of calcium with the lipid molecules enhances the molecular packing of the PG and PS lipids. This observation is in good agreement with emission spectra of the membrane partitioning probe Laurdan in DMPG multilamellar vesicles that indicate an increase in the ordering of the DMPG bilayer due to the presence of calcium. Our results indicate that calcium ions, which often function as a second messengers in living cells have a pronounced effect on membrane structures, which may have implications during signal transduction events.     

Cholesterol promotes the interaction of Alzheimer β-amyloid monomer with lipid bilayer

Cholesterol in the plasma membrane plays an important role in the pathogenesis of Alzheimer's disease, but the exact function of cholesterol in the regulation of amyloid-β (Aβ) generation, aggregation, and toxicity remains elusive. To gain insight into the bioactivity of cholesterol, we investigate the effect of cholesterol levels on the interaction of Aβ(1-42) monomer with the zwitterionic 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) bilayer containing different mole fractions of cholesterol from χ=0, 0.2, to 0.4 using all-atom molecular dynamics simulations. Simulation results show that an increased cholesterol level alters the structure, dynamics, and surface chemistry of the lipid bilayer, leading to increased bilayer thickness, hydrophobic chain order, surface hydrophobicity, and decreased lipid mobility. All these effects significantly promote the binding of Aβ to the lipid bilayer. Mechanistically, the adsorption of Aβ on the bilayer is a cooperative process. First, charged residues act as anchors to establish the initial binding of Aβ to phosphate headgroups of the bilayer driven by electrostatic interactions, which further facilitates hydrophobic residues to reside on the bilayer. Once hydrophobic residues especially from C-terminus are locked on the bilayer, the interactions among charged residues, lipid bilayer, and calcium ions are optimized to provide additional attractive forces to stabilize Aβ adsorbed on or inserted into the lipid bilayer. Inclusion of cholesterol makes this binding process more energetically favorable. Upon adsorption on the bilayer, Aβ appears to preferentially adopt α-helical or unstructured conformation. This work supports that cholesterol acts as a promoter for Aβ--membrane interactions, which would facilitate Aβ aggregation and membrane insertion.     

The effect of HIV-1 Gag myristoylation on membrane binding

During the viral life cycle, an HIV protein, Gag, assembles at the host membrane, specifically at lipid raft regions, at very high concentrations leading to viral particle budding. Gag is post-translationally modified with an N-terminal myristate group which is thought to target Gag to lipid rafts thus aiding in assembly. Here we have analyzed the membrane binding of myristoylated HIV-1 Gag and a non-myristoylated form of HIV-1 Gag to various membrane models. After assessing the extent of myristoylation by HPLC and radiometric assays, we compared membrane binding using fluorescence methods. We found that myristoylated Gag shows a greater than twofold increase in binding affinity to model rafts. A structural model to explain these results is presented.     

Calcium-binding to non-ionic lipids: crystal structure of a calcium chloride complex of geraniol.

X-ray diffraction data were used to determine the crystal structure of a calcium chloride complex of geraniol. The geraniol molecules assume a bilayer arrangement, with channels of calcium and chloride ions separating the bilayers. Each calcium ion is coordinated to the hydroxyl groups of two symmetry-related geraniol molecules and to four chloride ions. Our results demonstrate that hydrophobic interactions within a lipid bilayer can lead to an arrangement of hydroxyl groups suitable for binding calcium ions. Similar interactions may be involved in the calcium-binding sites on membrane surfaces.     

Binding and selectivity in L-type calcium channels: a mean spherical approximation

L-type calcium channels are Ca(2+) binding proteins of great biological importance. They generate an essential intracellular signal of living cells by allowing Ca(2+) ions to move across the lipid membrane into the cell, thereby selecting an ion that is in low extracellular abundance. Their mechanism of selection involves four carboxylate groups, containing eight oxygen ions, that belong to the side chains of the "EEEE" locus of the channel protein, a setting similar to that found in many Ca(2+)-chelating molecules. This study examines the hypothesis that selectivity in this locus is determined by mutual electrostatic screening and volume exclusion between ions and carboxylate oxygens of finite diameters. In this model, the eight half-charged oxygens of the tethered carboxylate groups of the protein are confined to a subvolume of the pore (the "filter"), but interact spontaneously with their mobile counterions as ions interact in concentrated bulk solutions. The mean spherical approximation (MSA) is used to predict ion-specific excess chemical potentials in the filter and baths. The theory is calibrated using a single experimental observation, concerning the apparent dissociation constant of Ca(2+) in the presence of a physiological concentration of NaCl. When ions are assigned their independently known crystal diameters and the carboxylate oxygens are constrained, e.g., to a volume of 0.375 nm(3) in an environment with an effective dielectric coefficient of 63.5, the hypothesized selectivity filter produces the shape of the calcium binding curves observed in experiment, and it predicts Ba(2+)/Ca(2+) and Na(+)/Li(+) competition, and Cl(-) exclusion as observed. The selectivities for Na(+), Ca(2+), Ba(2+), other alkali metal ions, and Cl(-) thus can be predicted by volume exclusion and electrostatic screening alone. Spontaneous coordination of ions and carboxylates can produce a wide range of Ca(2+) selectivities, depending on the volume density of carboxylate groups and the permittivity in the locus. A specific three-dimensional structure of atoms at the binding site is not needed to explain Ca(2+) selectivity.     

Channel formation in model membranes by the adenylate cyclase toxin of Bordetella pertussis: effect of calcium

Calmodulin-dependent adenylate cyclase toxin (ACT or CyaA) of Bordetella pertussis requires calcium ions for target cell binding, formation of hemolytic channels, and delivery of its enzyme component into cells. We examined the effect of calcium and calmodulin on toxin interaction with planar lipid bilayers. While calmodulin binding did not affect the properties of CyaA channels, addition of calcium ions and toxin to the same side of the membrane caused a steep increase of the channel-forming capacity of CyaA. The calcium effect was highly specific, since among other divalent cations only strontium caused some CyaA activity enhancement. The minimal stimulatory concentration of calcium ions ranged from 0.6 to 0.8 mM, depending on the ionic strength of the aqueous phase. Half-maximal channel activity of CyaA was observed at 2-4 mM, and saturation was reached at 10 mM calcium concentration, respectively. The unit size of single CyaA channels, assessed as single-channel conductance, was not affected by calcium ions, while the frequency of CyaA channel formation strongly depended on calcium concentration. The calcium effect was abrogated upon deletion of the RTX repeats of the toxin, suggesting that binding of calcium ions to the repeats modulates the propensity of CyaA to form membrane channels.     

Modulation of the in vitro activity of lysosomal phospholipase A1 by membrane lipids

Lysosomal phospholipases play a critical role for degradation of cellular membranes after their lysosomal segregation. We investigated the regulation of lysosomal phospholipase A1 by cholesterol, phosphatidylethanolamine, and negatively-charged lipids in correlation with changes of biophysical properties of the membranes induced by these lipids. Lysosomal phospholipase A1 activity was determined towards phosphatidylcholine included in liposomes of variable composition using a whole-soluble lysosomal fraction of rat liver as enzymatic source. Phospholipase A1 activity was then related to membrane fluidity, lipid phase organization and membrane potential as determined by fluorescence depolarization of DPH, 31P NMR and capillary electrophoresis. Phospholipase A1 activity was markedly enhanced when the amount of negatively-charged lipids included in the vesicles was increased from 10 to around 30% of total phospholipids and the intensity of this effect depended on the nature of the acidic lipids used (ganglioside GM1相似文献   

Evidence against Hydrogen–Calcium Competition Model for Activation of Electrically Excitable Membranes

TO explain the voltage-dependent sodium permeability of excitable membranes, Stephens¹ proposed a model in which sodium-selective channels are normally blocked by calcium ions bound to negatively charged sites located near the outer end of the channels. The calcium ions can be displaced competitively by hydrogen ions, opening the channels to sodium. According to this model, depolarization of an excitable membrane causes an outward flow of hydrogen ions across the membrane. The consequent transient increase in hydrogen ion concentration at the outer surface of the membrane displaces calcium and opens the sodium channels. This model is particularly interesting because it is sufficiently specific to allow direct tests. Stephens shows that it is in general agreement with a variety of experimental data. To test the model further, we have determined the effect of variation in the internal and external concentration of hydrogen ions on sodium currents.     

The Modulatory Effect of Calcium Ions Upon Alamethicin Monomers Uptake on Artificial Phospholipid Membranes

In this paper, we examined the influence exerted by calcium ions upon physical properties of lipids constituting an artificial membrane. Our strategy was to study changes on alamethicin oligomer kinetic features embedded into such an artificial membrane. At neutral pH and in the presence of calcium ions, we observed an increase in the number of alamethicin monomers that oligomerize within the membrane, forming a multi-substate nanopore. We make the argument that calcium ions binding within the interface between the hydrophobic and the hydrophilic regions of the biomembrane causes a sizeable alteration of the physical properties of neutral lipid membranes. This in turn is seen to influence the translocation rates of alamethicin monomers from the solution adjacent to the biomembrane and leads to an augmentation in the subunit composition of the alamethicin oligomers, leaving the electrical conductance of the substates and their kinetics mainly unchanged.     

Phase separations induced by melittin in negatively-charged phospholipid bilayers as detected by fluorescence polarization and differential scanning calorimetry

Interactions between melittin and a variety of negatively-charged lipid bilayers have been investigated by intrinsic fluorescence, fluorescence polarization of 1,6-diphenylhexatriene and differential scanning calorimetry. (1) Intrinsic fluorescence of the single tryptophan residue of melittin shows that binding of this peptide to negatively-charged phospholipids is directly related to the surface charge density, but is unaffected by the physical state of lipids, fluid or gel, single-shell vesicles or unsonicated dispersions. (2) Changes in the thermotropic properties of negatively-charged lipids upon melittin binding allow to differentiate two groups of lipids: (i) A progressive disappearance of the transition, without any shift in temperature, is observed with monoacid C₁₄ lipids such as dimyristoylphosphatidylglycerol and -serine (group 1). (ii) With a second group of lipids (group 2), a transition occurs even at melittin saturation, and two transitions are detected at intermediate melittin content, one corresponding to remaining unperturbed lipids, the other shifted downward by 10–20°C. This second group of lipids is constituted by monoacid C₁₆ lipids, dipalmitoylphosphatidylglycerol and -serine. Phosphatidic acids also enter this classification, but it is the net charge of the phosphate group which allows to discriminate: singly charged phosphatidic acids belong to group 2, whereas totally ionized ones behave like group 1 lipids, whatever the chain length. (3) It is concluded that melittin induces phase separations between unperturbed lipid regions which give a transition at the same temperature as pure lipid, and peptide rich domains in which the stoichiometry is 1 toxin per 8 phospholipids. The properties of such domains depend on the bilayer stability: in the case of C₁₆ aliphatic chains and singly charged polar heads, the lipid-peptide domains have a transition at a lower temperature than the pure lipid. With shorter C₁₄ chains or with two net charges by polar group, the bilayer structure is probably totally disrupted, and the new resulting phase can no longer lead to a cooperative transition.     

Characterizing the binding of annexin V to a lipid bilayer using molecular dynamics simulations

Annexins play critical roles in membrane organization, membrane trafficking and vesicle transport. The family members share the ability to bind to membranes with high affinities, but the interactions between annexins and membranes remain unclear. Here, using long‐time molecular dynamics simulations, we provide detailed information for the binding of an annexin V trimer to a POPC/POPS lipid bilayer. Calcium ions function as bridges between several negatively charged residues of annexin V and the oxygen atoms of lipids. The preferred calcium‐bridges are those formed via the carboxyl oxygen atoms of POPS lipids. H‐bonds and hydrophobic interactions formed by several critical residues have also been observed in the annexin‐membrane interface. The annexin‐membrane binding causes small changes of annexin trimer structures, while has significant effects on lipid bilayer structures. The lipid bilayer shows a bent shape and forms a concave region in the annexin‐membrane interaction interface, which provides an atomic‐level evidence to support the view that annexins could disturb the stability of lipids and bend membranes. This study provides insights into the commonly occurring PS‐dependent and calcium‐dependent binding of proteins to membranes. Proteins 2014; 82:312–322. © 2013 Wiley Periodicals, Inc.     

Determination of the contribution of the myristoyl group and hydrophobic amino acids of recoverin on its dynamics of binding to lipid monolayers

It has been postulated that myristoylation of peripheral proteins would facilitate their binding to membranes. However, the exact involvement of this lipid modification in membrane binding is still a matter of debate. Proteins containing a Ca(2+)-myristoyl switch where the extrusion of their myristoyl group is dependent on calcium binding is best illustrated by the Ca(2+)-binding recoverin, which is present in retinal rod cells. The parameters responsible for the modulation of the membrane binding of recoverin are still largely unknown. This study was thus performed to determine the involvement of different parameters on recoverin membrane binding. We have used surface pressure measurements and PM-IRRAS spectroscopy to monitor the adsorption of myristoylated and nonmyristoylated recoverin onto phospholipid monolayers in the presence and absence of calcium. The adsorption curves have shown that the myristoyl group and hydrophobic residues of myristoylated recoverin strongly accelerate membrane binding in the presence of calcium. In the case of nonmyristoylated recoverin in the presence of calcium, hydrophobic residues alone are responsible for its much faster monolayer binding than myristoylated and nonmyristoylated recoverin in the absence of calcium. The infrared spectra revealed that myristoylated and nonmyristoylated recoverin behave very different upon adsorption onto phospholipid monolayers. Indeed, PM-IRRAS spectra indicated that the myristoyl group allows a proper orientation and organization as well as faster and stronger binding of myristoylated recoverin to lipid monolayers compared to nonmyristoylated recoverin. Simulations of the spectra have allowed us to postulate that nonmyristoylated recoverin changes conformation and becomes hydrated at large extents of adsorption as well as to estimate the orientation of myristoylated recoverin with respect to the monolayer plane. In addition, adsorption measurements and electrophoresis of trypsin-treated myristoylated recoverin in the presence of zinc or calcium demonstrated that recoverin has a different conformation but a similar extent of monolayer binding in the presence of such ions.