Domain formation induced by the adsorption of charged proteins on mixed lipid membranes

Protein (Lysozyme) Concentration-Dependent Structure, Morphology, and Hysteresis Behavior of a Three-Component (Lysozyme-DMPA-Cholesterol) Protein-Lipid Langmuir Monolayer

Protein (lysozyme)-lipid (DMPA and cholesterol) three-component mixed films (LDC) with varied lysozyme concentration (i.e., LDC_Lx) are investigated at the air-water interface. Elastic modulus-surface pressure (Cs-1-Π) curves derived from Π-A isotherms show that mechanical behavior is strongly dependent on the monolayer composition, and for the same reason, the hysteresis behavior modifies. It is evidenced that the LDC_L0.3 monolayer (lysozyme: 0.3 mg/mL) has significant hysteresis, which is reversible in nature, while the other mixed monolayers do not show such hysteresis behavior. Morphology at the air-water interface via Brewster angle microscopy (BAM) and at the air-solid interface via atomic force microscopy (AFM) shows that the presence of protein in the LDC_Lx monolayer modifies the lateral distribution of molecules, thereby forming a stripe-like pattern at the air-water interface (in optical length scale) with barrier compression or root-like structure on the solid surface at higher Π (in micron length scale), which is not observed in the case of lipid films. Moreover, lysozyme-added LDC_Lx films show an increase in thickness with compression, which is not observed for lipid films, as evidenced from the electron density profiles (EDPs). The morphology modification and thickness variation of LDC_Lx films with compression are most probably due to the reorientation of lysozyme molecules. This structural modification in LDC_Lx films with Π, however, seems to be reversible under expansion, as can be evidenced from the similar in situ morphology observation and similar thickness of the films deposited during both first and second compression. A variation in the strength of interaction forces among film-forming molecules depending on the monolayer composition basically affects the lateral distribution and organizational orientation with surface pressure, thus ultimately influencing macroscopically the monolayer properties such as elastic, hysteresis, morphological, and structural on water and solid surfaces.

"Rich arginine and strong positive charge" antimicrobial protein protamine: From its action on cell membranes to inhibition of bacterial vital functions

Protamine, an antimicrobial protein derived from salmon sperm with a molecular weight of approximately 5 kDa, is composed of 60-70 % arginine and is a highly charged protein. Here, we investigated the mechanism of antimicrobial action of protamine against Cutibacterium acnes (C. acnes) focusing on its rich arginine content and strong positive charge. Especially, we focused on the attribution of dual mechanisms of antimicrobial protein, including membrane disruption or interaction with intracellular components. We first determined the dose-dependent antibacterial activity of protamine against C. acnes. In order to explore the interaction between bacterial membrane and protamine, we analyzed cell morphology, zeta potential, membrane permeability, and the composition of membrane fatty acid. In addition, the localization of protamine in bacteria was observed using fluorescent-labeled protamine. For investigation of the intracellular targets of protamine, bacterial translation was examined using a cell-free translation system. Based on our results, the mechanism of the antimicrobial action of protamine against C. acnes is as follows: 1) electrostatic interactions with the bacterial cell membrane; 2) self-internalization into the bacterial cell by changing the composition of the bacterial membrane; and 3) inhibition of bacterial growth by blocking translation inside the bacteria. However, owing to its strong electric charge, protamine can also interact with DNA, RNA, and other proteins inside the bacteria, and may inhibit various bacterial life processes beyond the translation process.

Phosphatidylglycerol Acts as a Switch for Cholesterol-Dependent Membrane Binding of ApoE Signal Peptide

The apolipoprotein E (ApoE) signal peptide is a short stretch of N-terminal amino acids that direct the ApoE protein to the endoplasmic reticulum after synthesis. Previous studies have shown that this peptide can bind to lipid membranes in a cholesterol-dependent manner; however, the mechanism of this interaction is yet to be clarified. In this study, we aimed to investigate how the composition of neighboring lipids affects the membrane-binding of the ApoE signal peptide. We found that a negatively charged lipid, such as phosphatidylglycerol, can act as a switch that reduces the binding efficiency of the peptide to cholesterol-rich membranes. Interestingly, phosphatidylethanolamine does not activate the cholesterol-dependent binding of the ApoE signal peptide yet acts synergistically to enhance the cholesterol sensitivity in phosphatidylglycerol-containing membranes. To the best of our knowledge, this is the first report of modulation of the affinity of a peptide for a membrane by a neighboring lipid rather than by the lipid-binding domain of the peptide. Our findings revealed a novel role of lipid diversity in modulating the membrane binding of the ApoE signal peptide and its potential implications in the unidirectional trafficking of a newly synthesized protein from the ribosomes to the endoplasmic reticulum.

Protein-Rich Rafts in Hybrid Polymer/Lipid Giant Unilamellar Vesicles

Considerable attention has been dedicated to lipid rafts due to their importance in numerous cell functions such as membrane trafficking, polarization, and signaling. Next to studies in living cells, artificial micrometer-sized vesicles with a minimal set of components are established as a major tool to understand the phase separation dynamics and their intimate interplay with membrane proteins. In parallel, mixtures of phospholipids and certain amphiphilic polymers simultaneously offer an interface for proteins and mimic this segregation behavior, presenting a tangible synthetic alternative for fundamental studies and bottom-up design of cellular mimics. However, the simultaneous insertion of complex and sensitive membrane proteins is experimentally challenging and thus far has been largely limited to natural lipids. Here, we present the co-reconstitution of the proton pump bo3 oxidase and the proton consumer ATP synthase in hybrid polymer/lipid giant unilamellar vesicles (GUVs) via fusion/electroformation. Variations of the current method allow for tailored reconstitution protocols and control of the vesicle size. In particular, mixing of protein-free and protein-functionalized nanosized vesicles in the electroformation film results in larger GUVs, while separate reconstitution of the respiratory enzymes enables higher ATP synthesis rates. Furthermore, protein labeling provides a synthetic mechanism for phase separation and protein sequestration, mimicking lipid- and protein-mediated domain formation in nature. The latter means opens further possibilities for re-enacting phenomena like supercomplex assembly or symmetry breaking and enriches the toolbox of bottom-up synthetic biology.

Probing the interactions of the HIV-1 matrix protein-derived polybasic region with lipid bilayers: insights from AFM imaging and force spectroscopy

The human immunodeficiency virus type 1 (HIV-1) matrix protein contains a highly basic region, MA-HBR, crucial for various stages of viral replication. To elucidate the interactions between the polybasic peptide MA-HBR and lipid bilayers, we employed liquid-based atomic force microscopy (AFM) imaging and force spectroscopy on lipid bilayers of differing compositions. In 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers, AFM imaging revealed the formation of annulus-shaped protrusions upon exposure to the polybasic peptide, accompanied by distinctive mechanical responses characterized by enhanced bilayer puncture forces. Importantly, our AFM-based force spectroscopy measurements unveiled that MA-HBR induces interleaflet decoupling within the cohesive bilayer organization. This is evidenced by a force discontinuity observed within the bilayer's elastic deformation regime. In POPC/cholesterol bilayers, MA-HBR caused similar yet smaller annular protrusions, demonstrating an intriguing interplay with cholesterol-rich membranes. In contrast, in bilayers containing anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS) lipids, MA-HBR induced unique annular protrusions, granular nanoparticles, and nanotubules, showcasing its distinctive effects in anionic lipid-enriched environments. Notably, our force spectroscopy data revealed that anionic POPS lipids weakened interleaflet adhesion within the bilayer, resulting in interleaflet decoupling, which potentially contributes to the specific bilayer perturbations induced by MA-HBR. Collectively, our findings highlight the remarkable variations in how the polybasic peptide, MA-HBR, interacts with lipid bilayers of differing compositions, shedding light on its role in host membrane restructuring during HIV-1 infection.

Physical Concept to Explain the Regulation of Lipid Membrane Phase Separation under Isothermal Conditions

Lateral phase separation within lipid bilayer membranes has attracted considerable attention in the fields of biophysics and cell biology. Living cells organize laterally segregated compartments, such as raft domains in an ordered phase, and regulate their dynamic structures under isothermal conditions to promote cellular functions. Model membrane systems with minimum components are powerful tools for investigating the basic phenomena of membrane phase separation. With the use of such model systems, several physicochemical characteristics of phase separation have been revealed. This review focuses on the isothermal triggering of membrane phase separation from a physical point of view. We consider the free energy of the membrane that describes lateral phase separation and explain the experimental results of model membranes to regulate domain formation under isothermal conditions. Three possible regulation factors are discussed: electrostatic interactions, chemical reactions and membrane tension. These findings may contribute to a better understanding of membrane lateral organization within living cells that function under isothermal conditions and could be useful for the development of artificial cell engineering.

Antibiotics and Carbohydrate-Containing Drugs Targeting Bacterial Cell Envelopes: An Overview

Certain bacteria constitute a threat to humans due to their ability to escape host defenses as they easily develop drug resistance. Bacteria are classified into gram-positive and gram-negative according to the composition of the cell membrane structure. Gram-negative bacteria have an additional outer membrane (OM) that is not present in their gram-positive counterpart; the latter instead hold a thicker peptidoglycan (PG) layer. This review covers the main structural and functional properties of cell wall polysaccharides (CWPs) and PG. Drugs targeting CWPs are discussed, both noncarbohydrate-related (β-lactams, fosfomycin, and lipopeptides) and carbohydrate-related (glycopeptides and lipoglycopeptides). Bacterial resistance to these drugs continues to evolve, which calls for novel antibacterial approaches to be developed. The use of carbohydrate-based vaccines as a valid strategy to prevent bacterial infections is also addressed.

Heterogeneity in Lateral Distribution of Polycations at the Surface of Lipid Membrane: From the Experimental Data to the Theoretical Model

Natural and synthetic polycations of different kinds attract substantial attention due to an increasing number of their applications in the biomedical industry and in pharmacology. The key characteristic determining the effectiveness of the majority of these applications is the number of macromolecules adsorbed on the surface of biological cells or their lipid models. Their study is complicated by a possible heterogeneity of polymer layer adsorbed on the membrane. Experimental methods reflecting the structure of the layer include the electrokinetic measurements in liposome suspension and the boundary potential of planar bilayer lipid membranes (BLM) and lipid monolayers with a mixed composition of lipids and the ionic media. In the review, we systematically analyze the methods of experimental registration and theoretical description of the laterally heterogeneous structures in the polymer layer published in the literature and in our previous studies. In particular, we consider a model based on classical theory of the electrical double layer, used to analyze the available data of the electrokinetic measurements in liposome suspension with polylysines of varying molecular mass. This model suggests a few parameters related to the heterogeneity of the polymer layer and allows determining the conditions for its appearance at the membrane surface. A further development of this theoretical approach is discussed.

Recent developments in membrane curvature sensing and induction by proteins

BACKGROUND

Membrane-bound intracellular organelles have characteristic shapes attributed to different local membrane curvatures, and these attributes are conserved across species. Over the past decade, it has been confirmed that specific proteins control the large curvatures of the membrane, whereas many others due to their specific structural features can sense the curvatures and bind to the specific geometrical cues. Elucidating the interplay between sensing and induction is indispensable to understand the mechanisms behind various biological processes such as vesicular trafficking and budding.

SCOPE OF REVIEW

We provide an overview of major classes of membrane proteins and the mechanisms of curvature sensing and induction. We then discuss the importance of membrane elastic characteristics to induce the membrane shapes similar to intracellular organelles. Finally, we survey recently available assays developed for studying the curvature sensing and induction by many proteins.

MAJOR CONCLUSIONS

Recent theoretical/computational modeling along with experimental studies have uncovered fascinating connections between lipid membrane and protein interactions. However, the phenomena of protein localization and synchronization to generate spatiotemporal dynamics in membrane morphology are yet to be fully understood.

GENERAL SIGNIFICANCE

The understanding of protein-membrane interactions is essential to shed light on various biological processes. This further enables the technological applications of many natural proteins/peptides in therapeutic treatments. The studies of membrane dynamic shapes help to understand the fundamental functions of membranes, while the medicinal roles of various macromolecules (such as proteins, peptides, etc.) are being increasingly investigated.

Inhomogeneity of polylysine adsorption layers on lipid membranes revealed by theoretical analysis of electrokinetic data and molecular dynamics simulations

The adsorption of large polycations on a charged lipid membrane is qualitatively different from the small inorganic cations, which almost uniformly populate the membrane surface. We assume that the polycationic adsorption layer might be laterally inhomogeneous starting from a certain polymer length, and this effect can be more visible for membranes with low anionic lipid content. To study systems with inhomogeneous adsorption layers, we carried out electrokinetic measurements of mobility of liposomes containing anionic and neutral phospholipids in the presence of polylysine molecules. Some of these systems were simulated by all-atom molecular dynamics. Here we proposed a theoretical approach accounting for the formation of separated regions at the membrane surface, which differ in charge density and surface potential. Our model allowed us to determine the adsorption layer's geometric parameters such as surface coverage and surface-bound monomer fraction of polymer, which correlate with the molecular dynamics (MD) simulations. We demonstrated that the configuration polylysine adopts on the membrane surface (tall or planar) depends on the polymer/membrane charge ratio. Both theory and MD indicate a decrease in the anionic lipid content, alongside with a decrease in the bound monomer fraction and corresponding increase in the extension length of the adsorbed polymers.

Debye-Hückel Free Energy of an Electric Double Layer with Discrete Charges Located at a Dielectric Interface

Poisson-Boltzmann theory provides an established framework to calculate properties and free energies of an electric double layer, especially for simple geometries and interfaces that carry continuous charge densities. At sufficiently small length scales, however, the discreteness of the surface charges cannot be neglected. We consider a planar dielectric interface that separates a salt-containing aqueous phase from a medium of low dielectric constant and carries discrete surface charges of fixed density. Within the linear Debye-Hückel limit of Poisson-Boltzmann theory, we calculate the surface potential inside a Wigner-Seitz cell that is produced by all surface charges outside the cell using a Fourier-Bessel series and a Hankel transformation. From the surface potential, we obtain the Debye-Hückel free energy of the electric double layer, which we compare with the corresponding expression in the continuum limit. Differences arise for sufficiently small charge densities, where we show that the dominating interaction is dipolar, arising from the dipoles formed by the surface charges and associated counterions. This interaction propagates through the medium of a low dielectric constant and alters the continuum power of two dependence of the free energy on the surface charge density to a power of 2.5 law.

Surface-Binding to Cardiolipin Nanodomains Triggers Cytochrome c Pro-apoptotic Peroxidase Activity via Localized Dynamics

The peroxidation of cardiolipins by reactive oxygen species, which is regulated and enhanced by cytochrome c (cyt c), is a critical signaling event in mitochondrial apoptosis. We probe the molecular underpinnings of this mitochondrial death signal through structural and functional studies of horse heart cyt c binding to mixed-lipid membranes containing cardiolipin with mono- and polyunsaturated acyl chains. Lipidomics reveal the selective oxidation of polyunsaturated fatty acid (PUFA) cardiolipin (CL), while multidimensional solid-state NMR probes the structure and dynamics of the membrane and the peripherally bound protein. The hydrophilic milieu at the membrane interface stabilizes a native-like fold, but also leads to localized flexibility at the membrane-interacting protein face. PUFA CL acts as both a preferred substrate and a dynamic regulator by affecting the dynamics of the cyt c N70-I85 Ω loop, which covers the heme cavity.

Regulation of phase boundaries and phase-segregated patterns in model membranes

Demixing of components has long been described in model membranes. It is a consequence of non-ideal lateral interactions between membrane components, and it causes the presence of segregated phases, forming patches (domains) of different properties, thus introducing heterogeneity into the membrane. In the present review we first describe the processes through which domains are generated, how they grow, and why they are rounded, striped or fractal-like, as well as why they get distributed forming defined patterns. Next, we focus on the effect of an additive on a lipid mixture, which usually induces shifts in demixing points, thus stabilizing or destabilizing the phase-segregated state. Results found for different model membranes are summarized, detailing the ways in which phase segregation and the generated patterns may be modulated. We focus on which are, from our viewpoint, the most relevant regulating factors affecting the surface texture observed in model membranes. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.

Bacterial Membranes: Structure, Domains, and Function

The bacterial cytoplasmic membrane is composed of roughly equal proportions of lipids and proteins. The main lipid components are phospholipids, which vary in acyl chain length, saturation, and branching and carry head groups that vary in size and charge. Phospholipid variants determine membrane properties such as fluidity and charge that in turn modulate interactions with membrane-associated proteins. We summarize recent advances in understanding bacterial membrane structure and function, focusing particularly on the possible existence and significance of specialized membrane domains. We review the role of membrane curvature as a spatial cue for recruitment and regulation of proteins involved in morphogenic functions, especially elongation and division. Finally, we examine the role of the membrane, especially regulation of synthesis and fluid properties, in the life cycle of cell wall-deficient L-form bacteria.

Spatial Rearrangement and Mobility Heterogeneity of an Anionic Lipid Monolayer Induced by the Anchoring of Cationic Semiflexible Polymer Chains

We use Monte Carlo simulations to investigate the interactions between cationic semiflexible polymer chains and a model fluid lipid monolayer composed of charge-neutral phosphatidyl-choline (PC), tetravalent anionic phosphatidylinositol 4,5-bisphosphate (PIP₂), and univalent anionic phosphatidylserine (PS) lipids. In particular, we explore how chain rigidity and polymer concentration influence the spatial rearrangement and mobility heterogeneity of the monolayer under the conditions where the cationic polymers anchor on the monolayer. We find that the anchored cationic polymers only sequester the tetravalent PIP₂ lipids at low polymer concentrations, where the interaction strength between the polymers and the monolayer exhibits a non-monotonic dependence on the degree of chain rigidity. Specifically, maximal anchoring occurs at low polymer concentrations, when the polymer chains have an intermediate degree of rigidity, for which the PIP₂ clustering becomes most enhanced and the mobility of the polymer/PIP₂ complexes becomes most reduced. On the other hand, at sufficiently high polymer concentrations, the anchoring strength decreases monotonically as the chains stiffen-a result that arises from the pronounced competitions among polymer chains. In this case, the flexible polymers can confine all PIP₂ lipids and further sequester the univalent PS lipids, whereas the stiffer polymers tend to partially dissociate from the monolayer and only sequester smaller PIP₂ clusters with greater mobilities. We further illustrate that the mobility gradient of the single PIP₂ lipids in the sequestered clusters is sensitively modulated by the cooperative effects between anchored segments of the polymers with different rigidities. Our work thus demonstrates that the rigidity and concentration of anchored polymers are both important parameters for tuning the regulation of anionic lipids.

N-terminal-mediated oligomerization of DnaA drives the occupancy-dependent rejuvenation of the protein on the membrane

Initiation of DNA replication in bacteria requires recharging of DnaA with ATP. We demonstrate in the present study that this process involves the N-terminal domain-mediated oligomerization of the protein on the membrane, which can be modelled as a surface density-driven phase transition switch.

DnaA, the initiator of chromosome replication in most known eubacteria species, is activated once per cell division cycle. Its overall activity cycle is driven by ATP hydrolysis and ADP–ATP exchange. The latter can be promoted by binding to specific sequences on the chromosome and/or to acidic phospholipids in the membrane. We have previously shown that the transition into an active form (rejuvenation) is strongly co-operative with respect to DnaA membrane occupancy. Only at low membrane occupancy is DnaA reactivation efficiently catalysed by the acidic phospholipids. The present study was aimed at unravelling the molecular mechanism underlying the occupancy-dependent DnaA rejuvenation. We found that truncation of the DnaA N-terminal completely abolishes the co-operative transformation between the high and low occupancy states (I and II respectively) without affecting the membrane binding. The environmentally sensitive fluorophore specifically attached to the N-terminal cysteines of DnaA reported on occupancy-correlated changes in its vicinity. Cross-linking of DnaA with a short homobifunctional reagent revealed that state II of the protein on the membrane corresponds to a distinct oligomeric form of DnaA. The kinetic transition of DnaA on the membrane surface is described in the present study by a generalized 2D condensation phase transition model, confirming the existence of two states of DnaA on the membrane and pointing to the possibility that membrane protein density serves as an on-off switch in vivo. We conclude that the DnaA conformation attained at low surface density drives its N-terminal-mediated oligomerization, which is presumably a pre-requisite for facilitated nt exchange.

Platelet and red blood cell interactions and their role in rheumatoid arthritis

Cytokines, lymphocytes, platelets and several biomolecules have long been implicated in the pathology of rheumatoid arthritis (RA), and the influences of antibody production and tagging, and cytokine, chemokine and enzyme production at specific rheumatoid joints were thought to be exclusive to the advancement of disease parameters. Another role player in RA is red blood cells (RBCs) which, of late, have been found to be involved in RA pathobiology, as there is a positive correlation between RBC counts and joint pathology, as well as with inflammatory biomarkers in the disease. There is also an association between RBC distribution width and the incidence of myocardial infarction amongst RA patients, and there is a change in the lipid distribution within RBC membranes. Of late, certain RBC-associated factors with previously obscure roles and cell-derived particles thought to be inconsequential to the other constituents of plasma were found to be active biomolecular players. Several of these have been discovered to be present in or originating from RBCs. Their influences have been shown to involve in membrane dynamics that cause structural and functional changes in both platelets and RBCs. RBC-derived microparticles are emerging entities found to play direct roles in immunomodulation via interactions with other plasma cells. These correlations highlight the direct influences of RBCs on exacerbating RA pathology. This review will attempt to shed more light on how RBCs, in the true inflammatory milieu of RA, are playing an even greater role than previously assumed.

Tracking individual membrane proteins and their biochemistry: The power of direct observation

The advent of single molecule fluorescence microscopy has allowed experimental molecular biophysics and biochemistry to transcend traditional ensemble measurements, where the behavior of individual proteins could not be precisely sampled. The recent explosion in popularity of new super-resolution and super-localization techniques coupled with technical advances in optical designs and fast highly sensitive cameras with single photon sensitivity and millisecond time resolution have made it possible to track key motions, reactions, and interactions of individual proteins with high temporal resolution and spatial resolution well beyond the diffraction limit. Within the purview of membrane proteins and ligand gated ion channels (LGICs), these outstanding advances in single molecule microscopy allow for the direct observation of discrete biochemical states and their fluctuation dynamics. Such observations are fundamentally important for understanding molecular-level mechanisms governing these systems. Examples reviewed here include the effects of allostery on the stoichiometry of ligand binding in the presence of fluorescent ligands; the observation of subdomain partitioning of membrane proteins due to microenvironment effects; and the use of single particle tracking experiments to elucidate characteristics of membrane protein diffusion and the direct measurement of thermodynamic properties, which govern the free energy landscape of protein dimerization. The review of such characteristic topics represents a snapshot of efforts to push the boundaries of fluorescence microscopy of membrane proteins to the absolute limit. This article is part of the Special Issue entitled 'Fluorescent Tools in Neuropharmacology'.

Tuning the mobility coupling of quaternized polyvinylpyridine and anionic phospholipids in supported lipid bilayers

Binding of biomacromolecules to anionic lipids in the plasma membrane is a common motif in many cell signaling pathways. Previous work has shown that macromolecules with cationic sequences can form nanodomains with sequestered anionic lipids, which alters the lateral distribution and mobility of the membrane lipids. Such sequestration is believed to result from the formation of a lipid-macromolecule complex. To date, however, the molecular structure and dynamics of the lipid-polymer interface are poorly understood. We have investigated the behavior of polycationic quaternized polyvinylpyridine (QPVP) on supported lipid bilayers doped with phosphatidylserine (PS) or phosphatidylinositol phosphate (PIP) lipids using time-resolved fluorescence microscopy, including pulsed interleaved excitation fluorescence cross-correlation spectroscopy (PIE-FCCS). PIE-FCCS is a dual-color fluorescence spectroscopy that translates fluctuations in fluorescence signal into a measurement of diffusion and colocalization. By labeling the polymer and lipids, we investigated the adsorption-induced translational mobility of lipids and systematically studied the influence of lipid charge density and solution ionic strength. Our results show that alteration of anionic lipid lateral mobility is dependent on the net charge of the lipid headgroup and is modulated by the ionic strength of the solution, indicating that electrostatic interactions drive the decrease in lateral mobility of anionic lipids by adsorbed QPVP. At physiological salt concentration we observe that the lipid lateral mobility is weakly influenced by QPVP and that there is no evidence of stable lipid-polymer complexes.

Separation of the Stern and diffuse layer in coarse-grained models: the cases of phosphatidyl serine, phosphatidic acid, and PIP2 monolayers

We present here a method to separate the Stern and diffuse layer in general systems into two regions that can be analyzed separately. The Stern layer can be described in terms of Bjerrum pairing and the diffuse layer in terms of Poisson-Boltzmann theory (monovalent) or strong coupling theory plus a slowly decaying tail (divalent). We consider three anionic phospholipids: phosphatidyl serine, phosphatidic acid, and phosphatidylinositol(4,5)bisphosphate (PIP2), which we describe within a minimal coarse-grained model as a function of ionic concentration. The case of mixed lipid systems is also considered, which shows a high level of binding cooperativity as a function of PIP2 localization. Implications for existing experimental systems of lipid heterogeneities are also discussed.

Charge-induced phase separation in lipid membranes

Phase separation in lipid bilayers that include negatively charged lipids is examined experimentally. We observed phase-separated structures and determined the membrane miscibility temperatures in several binary and ternary lipid mixtures of unsaturated neutral lipid, dioleoylphosphatidylcholine (DOPC), saturated neutral lipid, dipalmitoylphosphatidylcholine (DPPC), unsaturated charged lipid, dioleoylphosphatidylglycerol (DOPG((-))), saturated charged lipid, dipalmitoylphosphatidylglycerol (DPPG((-))), and cholesterol. In binary mixtures of saturated and unsaturated charged lipids, the combination of the charged head with the saturation of the hydrocarbon tail is a dominant factor in the stability of membrane phase separation. DPPG((-)) enhances phase separation, while DOPG((-)) suppresses it. Furthermore, the addition of DPPG((-)) to a binary mixture of DPPC/cholesterol induces phase separation between DPPG((-))-rich and cholesterol-rich phases. This indicates that cholesterol localization depends strongly on the electric charge on the hydrophilic head group rather than on the ordering of the hydrocarbon tails. Finally, when DPPG((-)) was added to a neutral ternary system of DOPC/DPPC/cholesterol (a conventional model of membrane rafts), a three-phase coexistence was produced. We conclude by discussing some qualitative features of the phase behaviour in charged membranes using a free energy approach.

Compositional redistribution and dynamic heterogeneity in mixed lipid membrane induced by polyelectrolyte adsorption: effects of chain rigidity

Monte Carlo simulation is employed to investigate the interaction between a polyelectrolyte and a fluid mixed membrane containing neutral (phosphatidyl-choline, PC), monovalent anionic (phosphatidylserine, PS), and multivalent anionic (phosphatidylinositol, PIP2) lipids. The effects of the intrinsic polyelectrolyte rigidity and solution ionic strength on the lateral rearrangement and dynamics of different anionic lipid species are systematically studied. Our results show that, the increase of polyelectrolyte chain rigidity reduces the loss of polyelectrolyte conformational entropy and the energy gains in electrostatic interaction, but raises the demixing entropy loss of the segregated anionic lipids. Therefore, the polyelectrolyte/membrane adsorption strength exhibits a non-monotonic dependence on the polyelectrolyte rigid parameter k ang, and there exists a certain optimal k ang for which the adsorption strength is maximal. Because the less loss of chain conformational entropy dominates the increase of the demixing entropy loss of the segregated anionic lipids and the decreases of the electrostatic energy gains, the semiflexible polyelectrolyte adsorbs onto the membrane more firmly than the flexible one. Whereas, for the adsorption of rigid polyelectrolyte, larger anionic lipid demixing entropy loss and less energy gain in the electrostatic interaction dominate over the decrease of the polyelectrolyte conformation entropy loss, leading to the desorption of the chain from the membrane. By decreasing the ionic concentration of the salt solution, the certain optimal k ang shifts to larger values. The cooperative effects of the adsorbing polyelectrolyte beads determine the concentration gradients and hierarchical mobility of the bound anionic lipids, as well as the polyelectrolyte dynamics.

Liposomes physically coated with peptides: preparation and characterization

Physically coating liposomes with peptides of desirable functions is an economic, versatile, and less time-consuming approach to prepare drug delivery vehicles. In this work, we designed three peptides-Ac-WWKKKGGNNN-NH2 (W2K3), Ac-WWRRRGGNNN-NH2(W2R3), Ac-WWGGGGGNNN-NH2(W2G3)-and studied their coating ability on negatively charged liposomes. It was found that the coating was mainly driven by the electrostatic interaction between the peptides' cationic side groups and the acidic lipids, which also mediated the "anchoring " of Trp residuals in the interfacial region of lipid bilayers. At the same conditions, the amount of the coated W2R3 was more than that of W2K3, but the stability of the liposome coated with W2R3 was deteriorated. This was caused by the delocalized charge of the guanidinium group of arginine. The coating of the peptide rendered the liposome pH-responsive behavior but did not prominently change the phase transition temperature. The liposome coated with peptides displayed appropriate pH/temperature dual responsive characteristics and was able to release the content in a controlled manner.

The actin homologue MreB organizes the bacterial cell membrane

The eukaryotic cortical actin cytoskeleton creates specific lipid domains, including lipid rafts, which determine the distribution of many membrane proteins. Here we show that the bacterial actin homologue MreB displays a comparable activity. MreB forms membrane-associated filaments that coordinate bacterial cell wall synthesis. We noticed that the MreB cytoskeleton influences fluorescent staining of the cytoplasmic membrane. Detailed analyses combining an array of mutants, using specific lipid staining techniques and spectroscopic methods, revealed that MreB filaments create specific membrane regions with increased fluidity (RIFs). Interference with these fluid lipid domains (RIFs) perturbs overall lipid homeostasis and affects membrane protein localization. The influence of MreB on membrane organization and fluidity may explain why the active movement of MreB stimulates membrane protein diffusion. These novel MreB activities add additional complexity to bacterial cell membrane organization and have implications for many membrane-associated processes.

The formation of lipid domains in eukaryotic cells is controlled by the cortical actin cytoskeleton. Here, the authors show that the bacterial actin homologue MreB has a comparable activity, influencing the formation of regions of increased fluidity that determine the distribution of membrane proteins.

Minimal effect of lipid charge on membrane miscibility phase behavior in three ternary systems

Giant unilamellar vesicles composed of a ternary mixture of phospholipids and cholesterol exhibit coexisting liquid phases over a range of temperatures and compositions. A significant fraction of lipids in biological membranes are charged. Here, we present phase diagrams of vesicles composed of phosphatidylcholine (PC) lipids, which are zwitterionic; phosphatidylglycerol (PG) lipids, which are anionic; and cholesterol (Chol). Specifically, we use DiPhyPG-DPPC-Chol and DiPhyPC-DPPG-Chol. We show that miscibility in membranes containing charged PG lipids occurs over similarly high temperatures and broad lipid compositions as in corresponding membranes containing only uncharged lipids, and that the presence of salt has a minimal effect. We verified our results in two ways. First, we used mass spectrometry to ensure that charged PC/PG/Chol vesicles formed by gentle hydration have the same composition as the lipid stocks from which they are made. Second, we repeated the experiments by substituting phosphatidylserine for PG as the charged lipid and observed similar phenomena. Our results consistently support the view that monovalent charged lipids have only a minimal effect on lipid miscibility phase behavior in our system.

Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model

Characterizing atomic details of membrane binding of peripheral membrane proteins by molecular dynamics (MD) has been significantly hindered by the slow dynamics of membrane reorganization associated with the phenomena. To expedite lateral diffusion of lipid molecules without sacrificing the atomic details of such interactions, we have developed a novel membrane representation, to our knowledge, termed the highly mobile membrane-mimetic (HMMM) model to study binding and insertion of various molecular species into the membrane. The HMMM model takes advantage of an organic solvent layer to represent the hydrophobic core of the membrane and short-tailed phospholipids for the headgroup region. We demonstrate that using these components, bilayer structures are formed spontaneously and rapidly, regardless of the initial position and orientation of the lipids. In the HMMM membrane, lipid molecules exhibit one to two orders of magnitude enhancement in lateral diffusion. At the same time, the membrane atomic density profile of the headgroup region produced by the HMMM model is essentially identical to those obtained for full-membrane models, indicating the faithful representation of the membrane surface by the model. We demonstrate the efficiency of the model in capturing spontaneous binding and insertion of peripheral proteins by using the membrane anchor (γ-carboxyglutamic-acid-rich domain; GLA domain) of human coagulation factor VII as a test model. Achieving full insertion of the GLA domain consistently in 10 independent unbiased simulations within short simulation times clearly indicates the robustness of the HMMM model in capturing membrane association of peripheral proteins very efficiently and reproducibly. The HMMM model will provide significant improvements to the current all-atom models by accelerating lipid dynamics to examine protein-membrane interactions more efficiently.

Membrane-elasticity model of Coatless vesicle budding induced by ESCRT complexes

The formation of vesicles is essential for many biological processes, in particular for the trafficking of membrane proteins within cells. The Endosomal Sorting Complex Required for Transport (ESCRT) directs membrane budding away from the cytosol. Unlike other vesicle formation pathways, the ESCRT-mediated budding occurs without a protein coat. Here, we propose a minimal model of ESCRT-induced vesicle budding. Our model is based on recent experimental observations from direct fluorescence microscopy imaging that show ESCRT proteins colocalized only in the neck region of membrane buds. The model, cast in the framework of membrane elasticity theory, reproduces the experimentally observed vesicle morphologies with physically meaningful parameters. In this parameter range, the minimum energy configurations of the membrane are coatless buds with ESCRTs localized in the bud neck, consistent with experiment. The minimum energy configurations agree with those seen in the fluorescence images, with respect to both bud shapes and ESCRT protein localization. On the basis of our model, we identify distinct mechanistic pathways for the ESCRT-mediated budding process. The bud size is determined by membrane material parameters, explaining the narrow yet different bud size distributions in vitro and in vivo. Our membrane elasticity model thus sheds light on the energetics and possible mechanisms of ESCRT-induced membrane budding.

Finding a needle in a haystack: the role of electrostatics in target lipid recognition by PH domains

Interactions between protein domains and lipid molecules play key roles in controlling cell membrane signalling and trafficking. The pleckstrin homology (PH) domain is one of the most widespread, binding specifically to phosphatidylinositol phosphates (PIPs) in cell membranes. PH domains must locate specific PIPs in the presence of a background of approximately 20% anionic lipids within the cytoplasmic leaflet of the plasma membrane. We investigate the mechanism of such recognition via a multiscale procedure combining Brownian dynamics (BD) and molecular dynamics (MD) simulations of the GRP1 PH domain interacting with phosphatidylinositol (3,4,5)-trisphosphate (PI(3,4,5)P₃). The interaction of GRP1-PH with PI(3,4,5)P₃ in a zwitterionic bilayer is compared with the interaction in bilayers containing different levels of anionic ‘decoy’ lipids. BD simulations reveal both translational and orientational electrostatic steering of the PH domain towards the PI(3,4,5)P₃-containing anionic bilayer surface. There is a payoff between non-PIP anionic lipids attracting the PH domain to the bilayer surface in a favourable orientation and their role as ‘decoys’, disrupting the interaction of GRP1-PH with the PI(3,4,5)P₃ molecule. Significantly, approximately 20% anionic lipid in the cytoplasmic leaflet of the bilayer is nearly optimal to both enhance orientational steering and to localise GRP1-PH proximal to the surface of the membrane without sacrificing its ability to locate PI(3,4,5)P₃ within the bilayer plane. Subsequent MD simulations reveal binding to PI(3,4,5)P₃, forming protein-phosphate contacts comparable to those in X-ray structures. These studies demonstrate a computational framework which addresses lipid recognition within a cell membrane environment, offering a link between structural and cell biological characterisation.

Cell signalling pathways are crucial for many biological processes including cell proliferation and survival. Signalling is governed by a complex network of interactions within the cell, and disruption of signalling can lead to a variety of human diseases. Often, a key event in the signalling cascade is the reversible recruitment of peripheral membrane proteins to the surface of the cell membrane, where they then bind to a specific lipid in order to perform their function. However, it is not clear how these proteins locate their target lipid in the complex multi-lipid environment of the plasma membrane. Here, we have used a combination of computational techniques to simulate the association of a signalling protein with the surface of the cell membrane. We demonstrate that the mechanism of membrane binding is dependent upon the lipid composition of the lipid bilayer, and the results show that orientational and positional steering of the protein is optimised when the anionic lipid content of our model membrane matches the physiological composition observed in cells.

Prediction of protein domain with mRMR feature selection and analysis

The domains are the structural and functional units of proteins. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to develop effective methods for predicting the protein domains according to the sequences information alone, so as to facilitate the structure prediction of proteins and speed up their functional annotation. However, although many efforts have been made in this regard, prediction of protein domains from the sequence information still remains a challenging and elusive problem. Here, a new method was developed by combing the techniques of RF (random forest), mRMR (maximum relevance minimum redundancy), and IFS (incremental feature selection), as well as by incorporating the features of physicochemical and biochemical properties, sequence conservation, residual disorder, secondary structure, and solvent accessibility. The overall success rate achieved by the new method on an independent dataset was around 73%, which was about 28–40% higher than those by the existing method on the same benchmark dataset. Furthermore, it was revealed by an in-depth analysis that the features of evolution, codon diversity, electrostatic charge, and disorder played more important roles than the others in predicting protein domains, quite consistent with experimental observations. It is anticipated that the new method may become a high-throughput tool in annotating protein domains, or may, at the very least, play a complementary role to the existing domain prediction methods, and that the findings about the key features with high impacts to the domain prediction might provide useful insights or clues for further experimental investigations in this area. Finally, it has not escaped our notice that the current approach can also be utilized to study protein signal peptides, B-cell epitopes, HIV protease cleavage sites, among many other important topics in protein science and biomedicine.

Evidence for patchy lipid layers on gold nanoparticle surfaces

Gold nanoparticles bearing multiple surface ligands are becoming favored candidates as multifunctional targeting, imaging, and therapeutic vehicles for biomedicine. The question of spatial location of different ligands on nanoparticle surfaces, especially with those of diameters less than 100 nm, is an important one that is difficult to quantitatively address. Here we functionalize the surface of 20, 50, and 90 nm gold nanoparticles with two different lipids, both single and mixed, using two different surface chemical procedures. Mass spectrometry supports the presence of both lipids in the mixed-lipid systems on nanoparticles, while electron microscopy evidence shows domain sizes for one lipid apparently a quarter to a half the projected diameter for 50 and 90 nm particles; but for 20 nm particles, there is no evidence for the existence of patches of the two lipids. Larger gold nanoparticles (90 nm) can be decorated with an array of 12 nm gold nanoparticles by use of a third lipid and antibody-antigen connectors; the display of the 12 nm particles about the 90 nm particles can be controlled to some extent by the initial surface chemistry and is quantified via a new angle analysis procedure.

Lateral dynamics of charged lipids and peripheral proteins in spatially heterogeneous membranes: comparison of continuous and Monte Carlo approaches

Biological membranes are complex environments whose physico-chemical properties are of utmost importance for the understanding of many crucial biological processes. Much attention has been given in the literature to the description of membranes along the z-axis perpendicular to the membrane. Here, we instead consider the lateral dynamics of lipids and peripheral proteins due to their electrostatic interaction. Previously, we constructed a Monte Carlo automaton capable of simulating mutual diffusive dynamics of charged lipids and associated positively charged peptides. Here, we derive and numerically analyze a system of Poisson-Boltzmann-Nernst-Planck (PBNP) equations that provide a mean-field approximation compatible with our Monte Carlo model. The thorough comparison between the mean-field PBNP equations and Monte Carlo simulations demonstrates that both the approaches are in a good qualitative agreement in all tested scenarios. We find that the two methods quantitatively deviate when the local charge density is high, presumably because the Poisson-Boltzmann formalism is applicable in the so-called weak coupling limit, whose validity is restricted to low charge densities. Nevertheless, we conclude that the mean-field PBNP approach provides a good approximation for the considerably more detailed Monte Carlo model at only a fraction of the associated computational cost and allows simulation of the membrane lateral dynamics on the space and time scales relevant for the realistic biological problems.

Charged bilayer membranes in asymmetric ionic solutions: phase diagrams and critical behavior

We consider the phase separation in an asymmetrically charged lipid bilayer membrane consisting of neutral and negatively charged lipids that are in contact with in and out ionic solutions having different ionic strengths. The two asymmetric leaflets are coupled through electrostatic interactions. Based on a free-energy approach, the critical point and phase diagrams are calculated for different ionic strengths of the two solutions and coupling parameter. An increase of the coupling constant or asymmetry in the salt concentration between the in and out solutions yields a higher phase-separation temperature because of electrostatic interactions. As a consequence, the phase-coexistence region increases for strong screening (small Debye length). Finally, possible three-phase coexistence regions in the phase diagram are predicted.

Lateral dynamics of proteins with polybasic domain on anionic membranes: a dynamic Monte-Carlo study

Positively charged polybasic domains are essential for recruiting multiple signaling proteins, such as Ras GTPases and Src kinase, to the negatively charged cellular membranes. Much less, however, is known about the influence of electrostatic interactions on the lateral dynamics of these proteins. We developed a dynamic Monte-Carlo automaton that faithfully simulates lateral diffusion of the adsorbed positively charged oligopeptides as well as the dynamics of mono- (phosphatidylserine) and polyvalent (PIP(2)) anionic lipids within the bilayer. In agreement with earlier results, our simulations reveal lipid demixing that leads to the formation of a lipid shell associated with the peptide. The computed association times and average numbers of bound lipids demonstrate that tetravalent PIP(2) interacts with the peptide much more strongly than monovalent lipid. On the spatially homogeneous membrane, the lipid shell affects the behavior of the peptide only by weakly reducing its lateral mobility. However, spatially heterogeneous distributions of monovalent lipids are found to produce peptide drift, the velocity of which is determined by the total charge of the peptide-lipid complex. We hypothesize that this predicted phenomenon may affect the spatial distribution of proteins with polybasic domains in the context of cell-signaling events that alter the local density of monovalent anionic lipids.

Cytochrome c-lipid interactions: new insights from resonance energy transfer

Resonance energy transfer (RET) from anthrylvinyl-labeled phosphatidylcholine (AV-PC) or cardiolipin (AV-CL) to cytochrome c (cyt c) heme moiety was employed to assess the molecular-level details of protein interactions with lipid bilayers composed of PC with 2.5 (CL2.5), 5 (CL5), 10 (CL10), or 20 (CL20) mol % CL under conditions of varying ionic strength and lipid/protein molar ratio. Monte Carlo analysis of multiple data sets revealed a subtle interplay between 1), exchange of the neutral and acidic lipid in the protein-lipid interaction zone; 2), CL transition into the extended conformation; and 3), formation of the hexagonal phase. The switch between these states was found to be controlled by CL content and salt concentration. At ionic strengths ≥ 40 mM, lipid bilayers with CL fraction not exceeding 5 mol % exhibited the tendency to transform from lamellar to hexagonal phase upon cyt c adsorption, whereas at higher contents of CL, transition into the extended conformation seems to become thermodynamically favorable. At lower ionic strengths, deviations from homogeneous lipid distributions were observed only for model membranes containing 2.5 mol % CL, suggesting the existence of a certain surface potential critical for assembly of lipid lateral domains in protein-lipid systems that may subsequently undergo morphological transformations depending on ambient conditions. These characteristics of cyt c-CL interaction are of great interest, not only from the viewpoint of regulating cyt c electron transfer and apoptotic propensities, but also to elucidate the general mechanisms by which membrane functional activities can be modulated by protein-lipid interactions.

Morphological changes of supported lipid bilayers induced by lysozyme: planar domain formation vs. multilayer stacking

Total internal reflection fluorescence microscopy (TIRFM) has been utilized to explore the effect of cationic protein lysozyme (Lz) on the morphology of solid-supported lipid bilayers (SLBs) comprised of zwitterionic lipid phosphatidylcholine (PC) and its mixture with anionic lipid cardiolipin (CL). Kinetic TIRFM imaging of different systems revealed subtle interplay between lipid lateral segregation accompanied by exchange of neutral and acidic lipids in the protein-lipid interaction zone, and the formation of lipid multilayer stacks. The switch between these states was shown to be controlled by CL content. In weakly charged SLBs containing 5 mol% CL, assembling of CL molecules into planar domains upon Lz adsorption has been observed while at higher content of anionic lipid (25 mol%) in-plane domains tend to transform into multilayer stacks, thereby ensuring the most thermodynamically-favorable membrane conformation.