Investigations of bivalent antibody binding on fluid-supported phospholipid membranes: the effect of hapten density

Detection of Tumor-Associated Autoantibodies in the Sera of Pancreatic Cancer Patients Using Engineered MUC1 Glycopeptide Nanoparticle Probes

Pancreatic cancer is one of the deadliest cancers worldwide, mainly due to late diagnosis. Therefore, there is an urgent need for novel diagnostic approaches to identify the disease as early as possible. We have developed a diagnostic assay for pancreatic cancer based on the detection of naturally occurring tumor associated autoantibodies against Mucin-1 (MUC1) using engineered glycopeptides on nanoparticle probes. We used a structure-guided approach to develop unnatural glycopeptides as model antigens for tumor-associated MUC1. We designed a collection of 13 glycopeptides to bind either SM3 or 5E5, two monoclonal antibodies with distinct epitopes known to recognize tumor associated MUC1. Glycopeptide binding to SM3 or 5E5 was confirmed by surface plasmon resonance and rationalized by molecular dynamics simulations. These model antigens were conjugated to gold nanoparticles and used in a dot-blot assay to detect autoantibodies in serum samples from pancreatic cancer patients and healthy volunteers. Nanoparticle probes with glycopeptides displaying the SM3 epitope did not have diagnostic potential. Instead, nanoparticle probes displaying glycopeptides with high affinity for 5E5 could discriminate between cancer patients and healthy controls. Remarkably, the best-discriminating probes show significantly better true and false positive rates than the current clinical biomarkers CA19-9 and carcinoembryonic antigen (CEA).

Serum immunoglobulin and the threshold of Fc receptor-mediated immune activation

Antibodies can mediate immune recruitment or clearance of immune complexes through the interaction of their Fc domain with cellular Fc receptors. Clustering of antibodies is a key step in generating sufficient avidity for efficacious receptor recognition. However, Fc receptors may be saturated with prevailing, endogenous serum immunoglobulin and this raises the threshold by which cellular receptors can be productively engaged. Here, we review the factors controlling serum IgG levels in both healthy and disease states, and discuss how the presence of endogenous IgG is encoded into the functional activation thresholds for low- and high-affinity Fc receptors. We discuss the circumstances where antibody engineering can help overcome these physiological limitations of therapeutic antibodies. Finally, we discuss how the pharmacological control of Fc receptor saturation by endogenous IgG is emerging as a feasible mechanism for the enhancement of antibody therapeutics.

Engineered molecular sensors for quantifying cell surface crowding

Cells mediate interactions with the extracellular environment through a crowded assembly of transmembrane proteins, glycoproteins and glycolipids on their plasma membrane. The extent to which surface crowding modulates the biophysical interactions of ligands, receptors, and other macromolecules is poorly understood due to the lack of methods to quantify surface crowding on native cell membranes. In this work, we demonstrate that physical crowding on reconstituted membranes and live cell surfaces attenuates the effective binding affinity of macromolecules such as IgG antibodies in a surface crowding-dependent manner. We combine experiment and simulation to design a crowding sensor based on this principle that provides a quantitative readout of cell surface crowding. Our measurements reveal that surface crowding decreases IgG antibody binding by 2 to 20 fold in live cells compared to a bare membrane surface. Our sensors show that sialic acid, a negatively charged monosaccharide, contributes disproportionately to red blood cell surface crowding via electrostatic repulsion, despite occupying only ~1% of the total cell membrane by mass. We also observe significant differences in surface crowding for different cell types and find that expression of single oncogenes can both increase and decrease crowding, suggesting that surface crowding may be an indicator of both cell type and state. Our high-throughput, single-cell measurement of cell surface crowding may be combined with functional assays to enable further biophysical dissection of the cell surfaceome.

Recapitulating the Lateral Organization of Membrane Receptors at the Nanoscale

Many cell membrane functions emerge from the lateral presentation of membrane receptors. The link between the nanoscale organization of the receptors and ligand binding remains, however, mostly unclear. In this work, we applied surface molecular imprinting and utilized the phase behavior of lipid bilayers to create platforms that recapitulate the lateral organization of membrane receptors at the nanoscale. We used liposomes decorated with amphiphilic boronic acids that commonly serve as synthetic saccharide receptors and generated three lateral modes of receptor presentation─random distribution, nanoclustering, and receptor crowding─and studied their interaction with saccharides. In comparison to liposomes with randomly dispersed receptors, surface-imprinted liposomes resulted in more than a 5-fold increase in avidity. Quantifying the binding affinity and cooperativity proved that the boost was mediated by the formation of the nanoclusters rather than a local increase in the receptor concentration. In contrast, receptor crowding, despite the presence of increased local receptor concentrations, prevented multivalent oligosaccharide binding due to steric effects. The findings demonstrate the significance of nanometric aspects of receptor presentation and generation of multivalent ligands including artificial lectins for the sensitive and specific detection of glycans.

Micropatterning of functional lipid bilayer assays for quantitative bioanalysis

Interactions of the cell with its environment are mediated by the cell membrane and membrane-localized molecules. Supported lipid bilayers have enabled the recapitulation of the basic properties of cell membranes and have been broadly used to further our understanding of cellular behavior. Coupled with micropatterning techniques, lipid bilayer platforms have allowed for high throughput assays capable of performing quantitative analysis at a high spatiotemporal resolution. Here, an overview of the current methods of the lipid membrane patterning is presented. The fabrication and pattern characteristics are briefly described to present an idea of the quality and notable features of the methods, their utilizations for quantitative bioanalysis, as well as to highlight possible directions for the advanced micropatterning lipid membrane assays.

Inter-Leaflet Phospholipid Exchange Impacts the Ligand Density Available for Protein Binding at Supported Lipid Bilayers

Phospholipid bilayers formed at solid-liquid interfaces have garnered interest as mimics of cell membranes to model association reactions of proteins with lipid bilayer-tethered ligands. Despite the importance of understanding how ligand density in a lipid bilayer impacts the protein-ligand association response, relating the ligand-modified lipid fraction to the absolute density of solution-accessible ligands in a lipid bilayer remains a challenge in interfacial quantitative analysis. In this work, confocal Raman microscopy is employed to quantify the association of anti-biotin IgG with a small fraction of biotinylated lipids dispersed in either gel-phase or liquid-crystalline supported lipid bilayers deposited on the interior surfaces of wide-pore silica surfaces. We examine the question of whether inter-leaflet lipid translocation contributes to the population of solution-accessible biotin ligands on the distal leaflet of a supported lipid bilayer by comparing their protein accumulation response with ligands dispersed in lipid monolayers on nitrile-derivatized silica surfaces. The binding of the antibody to biotin ligands dispersed in gel-phase bilayers exhibited an equivalent biotin coverage response as the accumulation of IgG onto gel-phase monolayers, indicating that gel-phase bilayer symmetry was preserved. This result contrasts with the ∼60% greater anti-biotin capture observed at fluid-phase bilayers compared to fluid-phase monolayers prepared at equivalent biotin fractions. This enhanced protein capture is attributed to biotin-capped lipids being transferred from the surface-associated proximal leaflet of the bilayer to the solution-exposed distal leaflet by the inter-leaflet exchange or lipid flip-flop, a facile process in fluid-phase supported lipid bilayers. The results suggest caution in interpreting the results of quantitative studies of protein binding to lipid-tethered ligands dispersed in fluid-phase phospholipid bilayers.

Electrochemical Biosensors Based on Membrane-Bound Enzymes in Biomimetic Configurations

In nature, many enzymes are attached or inserted into the cell membrane, having hydrophobic subunits or lipid chains for this purpose. Their reconstitution on electrodes maintaining their natural structural characteristics allows for optimizing their electrocatalytic properties and stability. Different biomimetic strategies have been developed for modifying electrodes surfaces to accommodate membrane-bound enzymes, including the formation of self-assembled monolayers of hydrophobic compounds, lipid bilayers, or liposomes deposition. An overview of the different strategies used for the formation of biomimetic membranes, the reconstitution of membrane enzymes on electrodes, and their applications as biosensors is presented.

Mesoscale computational protocols for the design of highly cooperative bivalent macromolecules

The last decade has witnessed a swiftly increasing interest in the design and production of novel multivalent molecules as powerful alternatives for conventional antibodies in the fight against cancer and infectious diseases. However, while it is widely accepted that large-scale flexibility (10–100 nm) and free/constrained dynamics (100 ns -μs) control the activity of such novel molecules, computational strategies at the mesoscale still lag behind experiments in optimizing the design of crucial features, such as the binding cooperativity (a.k.a. avidity). In this study, we introduced different coarse-grained models of a polymer-linked, two-nanobody composite molecule, with the aim of laying down the physical bases of a thorough computational drug design protocol at the mesoscale. We show that the calculation of suitable potentials of mean force allows one to apprehend the nature, range and strength of the thermodynamic forces that govern the motion of free and wall-tethered molecules. Furthermore, we develop a simple computational strategy to quantify the encounter/dissociation dynamics between the free end of a wall-tethered molecule and the surface, at the roots of binding cooperativity. This procedure allows one to pinpoint the role of internal flexibility and weak non-specific interactions on the kinetic constants of the nanobody-wall encounter and dissociation. Finally, we quantify the role and weight of rare events, which are expected to play a major role in real-life situations, such as in the immune synapse, where the binding kinetics is likely dominated by fluctuations.

Quantitative Study of the Interaction of Multivalent Ligand-Modified Nanoparticles with Breast Cancer Cells with Tunable Receptor Density

Multivalent nanoparticles that target a cell surface receptor that is overexpressed by cancer cells are a promising delivery system for cancer therapy. However, the impact of the receptor density and nanoparticle ligand valency on the cell uptake has not been studied in a system where both variables can be systematically tuned over a wide range. To address this lacuna, we report cell-uptake studies on a genetically engineered breast cancer cell line with tunable ErbB2 expression by a polypeptide micelle with tunable ligand valency. We examined the uptake of ErbB2-targeting micelles at 5 ligand densities and 11 receptor densities. We identified a matching pattern between receptors and ligands in which a receptor-to-ligand density ratio of 0.7-4.5 and a minimum of ∼1.6 bonds are required to initiate receptor-mediated endocytosis. Lower and upper limits of receptor density in the cell-uptake profile suggested a standard by which to categorize breast cancer patients as ErbB2-low, ErbB2-medium, and ErbB2-high, with each group expected to respond differently to multivalent therapeutic nanoparticles. At ErbB2-medium and ErbB2-high levels, increasing the ligand valency to 40-valent ErbB2-targeting peptides for a 20 nm radius nanoparticle accelerated the cell uptake, suggesting that the use of nanoparticles with high ligand valency for drug delivery will greatly benefit patients in these two groups. This study advances our understanding of how to rationally optimize nanotechnology for targeted drug delivery.

Surface Modification with Control over Ligand Density for the Study of Multivalent Biological Systems

In the study of multivalent interactions at interfaces, as occur for example at cell membranes, the density of the ligands or receptors displayed at the interface plays a pivotal role, affecting both the overall binding affinities and the valencies involved in the interactions. In order to control the ligand density at the interface, several approaches have been developed, and they concern the functionalization of a wide range of materials. Here, different methods employed in the modification of surfaces with controlled densities of ligands are being reviewed. Examples of such methods encompass the formation of self-assembled monolayers (SAMs), supported lipid bilayers (SLBs) and polymeric layers on surfaces. Particular emphasis is given to the methods employed in the study of different types of multivalent biological interactions occurring at the functionalized surfaces and their working principles.

PM-IRRAS Study on the Effect of Phytantriol-Based Cubosomes on DMPC Bilayers as Model Lipid Membranes

The effect of phytantriol (PT)-based liquid-crystalline nanoparticles, cubosomes, on the lipid bilayer membranes has been investigated using the combined Langmuir-Blodgett/Langmuir-Schaefer (LB-LS) technique to form an h-1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) monolayer at the air-water interface and transfer the lipid bilayer onto the Au(111) substrate. Changes of the compression isotherms confirmed incorporation of cubosomes dispersed in the subphase into the h-DMPC monolayer at the air-water interface. The photon polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) measurements of the gold electrode covered by the transferred DMPC bilayer showed for the first time how the incorporation of cubosome material affects the orientation and conformation of lipid molecules in the membrane. Exposure to cubosomes affected the packing of d₅₄-DMPC bilayers and introduced disorder of chains by increasing the contribution of gauche conformation. The decrease of the tilt angle of the acyl chains of adsorbed DMPC in the whole range of potentials applied to the gold electrode confirmed that incorporation of cubosome material results in a more tightly packed bilayer. The presence of phytantriol molecules within the d₆₃-DMPC matrix was confirmed by PM-IRRAS studies of the PT-related bands. The LB and PM-IRRAS studies demonstrated in a convincing way that PT-based cubosomes change the organization of model lipid layers leading to structural changes of the membranes which have to be taken into consideration when PT-cubosomes are employed as drug carriers.

Stoichiometry controls activity of phase-separated clusters of actin signaling proteins

Biomolecular condensates concentrate macromolecules into foci without a surrounding membrane. Many condensates appear to form through multivalent interactions that drive liquid-liquid phase separation (LLPS). LLPS increases the specific activity of actin regulatory proteins toward actin assembly by the Arp2/3 complex. We show that this increase occurs because LLPS of the Nephrin-Nck-N-WASP signaling pathway on lipid bilayers increases membrane dwell time of N-WASP and Arp2/3 complex, consequently increasing actin assembly. Dwell time varies with relative stoichiometry of the signaling proteins in the phase-separated clusters, rendering N-WASP and Arp2/3 activity stoichiometry dependent. This mechanism of controlling protein activity is enabled by the stoichiometrically undefined nature of biomolecular condensates. Such regulation should be a general feature of signaling systems that assemble through multivalent interactions and drive nonequilibrium outputs.

Regulation of Transmembrane Signaling by Phase Separation

Cell surface transmembrane receptors often form nanometer- to micrometer-scale clusters to initiate signal transduction in response to environmental cues. Extracellular ligand oligomerization, domain-domain interactions, and binding to multivalent proteins all contribute to cluster formation. Here we review the current understanding of mechanisms driving cluster formation in a series of representative receptor systems: glycosylated receptors, immune receptors, cell adhesion receptors, Wnt receptors, and receptor tyrosine kinases. We suggest that these clusters share properties of systems that undergo liquid-liquid phase separation and could be investigated in this light.

Mathematical Modeling of Bioassays

The high affinity and specificity of biological receptors determine the demand for and the intensive development of analytical systems based on use of these receptors. Therefore, theoretical concepts of the mechanisms of these systems, quantitative parameters of their reactions, and relationships between their characteristics and ligand-receptor interactions have become extremely important. Many mathematical models describing different bioassay formats have been proposed. However, there is almost no information on the comparative characteristics of these models, their assumptions, and predictive insights. In this review we suggested a set of criteria to classify various bioassays and reviewed classical and contemporary publications on these bioassays with special emphasis on immunochemical analysis systems as the most common and in-demand techniques. The possibilities of analytical and numerical modeling are discussed, as well as estimations of the minimum concentrations that may be detected in bioassays and recommendations for the choice of assay conditions.

Impact of Antigen Density on the Binding Mechanism of IgG Antibodies

The density and distribution pattern of epitopes at the surface of pathogens have a profound impact on immune responses. Although multiple lines of evidence highlight the significance of antigen surface density for antibody binding, a quantitative description of its effect on recognition mechanisms is missing. Here, we analyzed binding kinetics and thermodynamics of six HIV-1 neutralizing antibodies as a function of the surface density of envelope glycoprotein gp120. Antibodies that recognize gp120 with low to moderate binding affinity displayed the most pronounced sensitivity to variation in antigen density, with qualitative and substantial quantitative changes in the energetics of the binding process as revealed by non-equilibrium and equilibrium thermodynamic analyses. In contrast, the recognition of gp120 by the antibodies with the highest affinity was considerably less influenced by variations in antigen density. These data suggest that a lower affinity of antibodies permits higher dynamics during the antigen recognition process, which may have considerable functional repercussions. These findings contribute to a better understanding of the mechanisms of antigen recognition by antibodies. They are also of importance for apprehending the impact of antigen topology on immune-defense functions of antibodies.

Molecular Dynamics of POPC Phospholipid Bilayers through the Gel to Fluid Phase Transition: An Incoherent Quasi-Elastic Neutron Scattering Study

The microscopic dynamics for the gel and liquid-crystalline phase of highly aligned D2O-hydrated bilayers of 1-palmitoyl-oleoyl-sn-glycero-phosphocholine (POPC) were investigated in the temperature range from 248 to 273 K by using incoherent quasi-elastic neutrons scattering (QENS). We develop a model for describing the molecular motions of the liquid phase occurring in the 0.3 to 350 ps time range. Accordingly, the complex dynamics of hydrogen are described in terms of simple dynamical processes involving different parts of the phospholipid chain. The analysis of the data evidences the existence of three different motions: the fast motion of hydrogen vibrating around the carbon atoms, the intermediate motion of carbon atoms in the acyl chains, and the slower translational motion of the entire phospholipid molecule. The influence of the temperature on these dynamical processes is investigated. In particular, by going from gel to liquid-crystalline phase, we reveal an increase of the segmental motion mainly affecting the terminal part of the acyl chains and a change of the diffusional dynamics from a localized rattling-like motion to a confined diffusion.

Structure of lipid multilayers via drop casting of aqueous liposome dispersions

Understanding the structure of solid supported lipid multilayers is crucial to their application as a platform for novel materials. Conventionally, they are prepared from drop casting or spin coating of lipids dissolved in organic solvents, and lipid multilayers prepared from aqueous media and their structural characterisation have not been reported previously, due to their extremely low lipid solubility (i.e.∼10(-9) M) in water. Herein, using X-ray reflectivity (XRR) facilitated by a "bending mica" method, we have studied the structural characteristics of dioleoylphosphatidylcholine (DOPC) multilayers prepared via drop casting aqueous small unilamellar and multilamellar vesicle or liposome (i.e. SUV and MLV) dispersions on different surfaces, including mica, positively charged polyethylenimine (PEI) coated mica, and stearic trimethylammonium iodide (STAI) coated mica which exposes a monolayer of hydrocarbon tails. We suggest that DOPC liposomes served both as a delivery matrix where an appreciable lipid concentration in water (∼25 mg mL(-1) or 14 mM) was feasible, and as a structural precursor where the lamellar structure was readily retained on the rupture of the vesicles at the solid surface upon solvent evaporation to facilitate rapid multilayer formation. We find that multilayers on mica from MLVs exhibited polymorphism, whereas the SUV multilayers were well ordered and showed stronger stability against water. The influence of substrate chemistry (i.e. polymer coating, charge and hydrophobicity) on the multilayer structure is discussed in terms of lipid-substrate molecular interactions determining the bilayer packing proximal to the solid-liquid interface, which then had a templating effect on the structure of the bilayers distal from the interface, resulting in the overall different multilayer structural characteristics on different substrates. Such a fundamental understanding of the correlation between the physical parameters that characterise liposomes and substrate chemistry, and the structure of lipid multilayers underpins the potential development of a simple method via an aqueous liposome dispersion route for the inclusion of hydrophilic functional additives (e.g. drugs or nanoparticles) into lipid multilayer based hybrid materials, where tailored structural characteristics are an important consideration.

Experimental and computational study of membrane affinity for selected energetic compounds

The affinity of various energetic compounds for a biological membrane was investigated using experimental and computational techniques. We measured octanol-water (log(Kow)) and liposome-water (log(Klipw)) partition coefficients for the following chemicals: trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 2,6-dinitrotoluene (2,6-DNT), 2,4-dinitroanisole (DNAN), 2methoxy-5-nitrophenol (2M5NP), 2,4,6-trinitrobenzene (TNB), and 2,4-dinitrophenol (2,4-DNP). In order to determine log(Klipw) experimentally, we used artificial solid supported lipid liposomes produced under trade mark TRANSIL. Log(Kow) value were predicted with several program packages including the COSMOthermX software. Log(Klipw) were estimated with COSMOmic as implemented in the COSMOthermX program package. In order to verify accuracy of our experimentally obtained results, we performed basic statistical analysis of data taken from the literature. We concluded that compounds considered in this study possess a moderate ability to penetrate into membranes. Comparison of both coefficients has shown that in general, the log(Kow) values are slightly smaller than log(Klipw).

Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces

In this paper we introduce a fully flexible coarse-grained model of immunoglobulin G (IgG) antibodies parametrized directly on cryo-EM data and simulate the binding dynamics of many IgGs to antigens adsorbed on a surface at increasing densities. Moreover, we work out a theoretical model that allows to explain all the features observed in the simulations. Our combined computational and theoretical framework is in excellent agreement with surface-plasmon resonance data and allows us to establish a number of important results. (i) Internal flexibility is key to maximize bivalent binding, flexible IgGs being able to explore the surface with their second arm in search for an available hapten. This is made clear by the strongly reduced ability to bind with both arms displayed by artificial IgGs designed to rigidly keep a prescribed shape. (ii) The large size of IgGs is instrumental to keep neighboring molecules at a certain distance (surface repulsion), which essentially makes antigens within reach of the second Fab always unoccupied on average. (iii) One needs to account independently for the thermodynamic and geometric factors that regulate the binding equilibrium. The key geometrical parameters, besides excluded-volume repulsion, describe the screening of free haptens by neighboring bound antibodies. We prove that the thermodynamic parameters govern the low-antigen-concentration regime, while the surface screening and repulsion only affect the binding at high hapten densities. Importantly, we prove that screening effects are concealed in relative measures, such as the fraction of bivalently bound antibodies. Overall, our model provides a valuable, accurate theoretical paradigm beyond existing frameworks to interpret experimental profiles of antibodies binding to multi-valent surfaces of different sorts in many contexts.

Antibodies are the main working horses of the human immune system. Remarkably, no matter the size or the shape of the pathological intruders, these extremely flexible three-lobe molecules are able to form a complex, thus eliciting an immune response. What makes antibodies so effective? To answer this and other questions, we have developed a simplified computational scheme to simulate the dynamics of many antibodies interacting with each other and with antigens. Coarse-grained models are a great opportunity, as they give access to a true multi-scale approach to biologically relevant problems. In this work, our innovative method allowed us to simulate the binding process of many antibodies to surface-adsorbed antigens. This led us to elucidate and quantify many important physical aspects of their biological function in agreement with experiments, such as the role of their flexibility and crowding effects at the hapten-covered surface, which were shown to finely regulate the avidity.

Supported Lipid Bilayers for the Generation of Dynamic Cell-Material Interfaces

Supported lipid bilayers (SLB) offer unique possibilities for studying cellular membranes and have been used as a synthetic architecture to interact with cells. Here, the state-of-the-art in SLB-based technology is presented. The fabrication, analysis, characteristics and modification of SLBs are described in great detail. Numerous strategies to form SLBs on different substrates, and the means to patteren them, are described. The use of SLBs as model membranes for the study of membrane organization and membrane processes in vitro is highlighted. In addition, the use of SLBs as a substratum for cell analysis is presented, with discrimination between cell-cell and cell-extracellular matrix (ECM) mimicry. The study is concluded with a discussion of the potential for in vivo applications of SLBs.

Measuring Binding Kinetics of Antibody-Conjugated Gold Nanoparticles with Intact Cells

Antibody-conjugated nanomaterials have attracted much attention because of their applications in nanomedicine and nanotheranostics, and amplification of detection signals. For many of these applications, the nanoconjugates must bind with a cell membrane receptor (antigen) specifically before entering the cells and reaching the final target, which is thus important but not well understood. Here, a plasmonic imaging study of the binding kinetics of antibody-conjugated gold nanoparticles with antigen-expressing cells is presented, and the results are compared with that of the nanoparticle-free antibody. It is found that the nanoconjugates can significantly affect the binding kinetics compared with free antibody molecules, depending on the density of the antibody conjugated on the nanoparticles, and expressing level of the antigen on the cell membrane. The results are analyzed in terms of a transition from monovalent binding model to a bivalent binding model when the conjugation density and expressing level increase. These findings help optimize the design of functional nanomaterials for drug delivery and correct interpretation of data obtained with nanoparticle signal amplification.

Unquenchable Surface Potential Dramatically Enhances Cu(2+) Binding to Phosphatidylserine Lipids

Herein, the apparent equilibrium dissociation constant, K(Dapp), between Cu(2+) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS), a negatively charged phospholipid, was measured as a function of PS concentrations in supported lipid bilayers (SLBs). The results indicated that K(Dapp) for Cu(2+) binding to PS-containing SLBs was enhanced by a factor of 17,000 from 110 nM to 6.4 pM as the PS density in the membrane was increased from 1.0 to 20 mol %. Although Cu(2+) bound bivalently to POPS at higher PS concentrations, this was not the dominant factor in increasing the binding affinity. Rather, the higher concentration of Cu(2+) within the double layer above the membrane was largely responsible for the tightening. Unlike the binding of other divalent metal ions such as Ca(2+) and Mg(2+) to PS, Cu(2+) binding does not alter the net negative charge on the membrane as the Cu(PS)2 complex forms. As such, the Cu(2+) concentration within the double layer region was greatly amplified relative to its concentration in bulk solution as the PS density was increased. This created a far larger enhancement to the apparent binding affinity than is observed by standard multivalent effects. These findings should help provide an understanding on the extent of Cu(2+)-PS binding in cell membranes, which may be relevant to biological processes such as amyloid-β peptide toxicity and lipid oxidation.

Lipid compositions modulate fluidity and stability of bilayers: characterization by surface pressure and sum frequency generation spectroscopy

Cell membranes are crucial to many biological processes. Because of their complexity, however, lipid bilayers are often used as model systems. Lipid structures influence the physical properties of bilayers, but their interplay, especially in multiple-component lipid bilayers, has not been fully explored. Here, we used the Langmuir-Blodgett method to make mono- and bilayers of 1,2-dihexadecanoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DPPG), 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG), and 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-L-serine (POPS) as well as their 1:1 binary mixtures. We studied the fluidity, stability, and rigidity of these structures using sum frequency generation (SFG) spectroscopy combined with analyses of surface pressure-area isotherms, compression modulus, and stability. Our results show that single-component bilayers, both saturated and unsaturated, may not be ideal membrane mimics because of their low fluidity and/or stability. However, the binary saturated and unsaturated DPPG/POPG and DPPG/POPS systems show not only high stability and fluidity but also high resistance to changes in surface pressure, especially in the range of 25-35 mN/m, the range typical of cell membranes. Because the ratio of saturated to unsaturated lipids is highly regulated in cells, our results underline the possibility of modulating biological properties using lipid compositions. Also, our use of flat optical windows as solid substrates in SFG experiments should make the SFG method more compatible with other techniques, enabling more comprehensive future surface characterizations of bilayers.

Lipid bilayer composition can influence the orientation of proteorhodopsin in artificial membranes

Artificial membrane systems allow researchers to study the structure and function of membrane proteins in a matrix that approximates their natural environment and to integrate these proteins in ex vivo devices such as electronic biosensors, thin-film protein arrays, or biofuel cells. Given that most membrane proteins have vectorial functions, both functional studies and applications require effective control over protein orientation within a lipid bilayer. In this work, we explored the role of the bilayer surface charge in determining transmembrane protein orientation and functionality during formation of proteoliposomes. We reconstituted a model vectorial ion pump, proteorhodopsin, in liposomes of opposite charges and varying charge densities and determined the resultant protein orientation. Antibody-binding assay and proteolysis of proteoliposomes showed physical evidence of preferential orientation, and functional assays verified the vectorial nature of ion transport in this system. Our results indicate that the manipulation of lipid composition can indeed control orientation of an asymmetrically charged membrane protein, proteorhodopsin, in liposomes.

Application of atomic force microscopy for characteristics of single intermolecular interactions

Atomic force microscopy (AFM) can be used to make measurements in vacuum, air, and water. The method is able to gather information about intermolecular interaction forces at the level of single molecules. This review encompasses experimental and theoretical data on the characterization of ligand-receptor interactions by AFM. The advantage of AFM in comparison with other methods developed for the characterization of single molecular interactions is its ability to estimate not only rupture forces, but also thermodynamic and kinetic parameters of the rupture of a complex. The specific features of force spectroscopy applied to ligand-receptor interactions are examined in this review from the stage of the modification of the substrate and the cantilever up to the processing and interpretation of the data. We show the specificities of the statistical analysis of the array of data based on the results of AFM measurements, and we discuss transformation of data into thermodynamic and kinetic parameters (kinetic dissociation constant, Gibbs free energy, enthalpy, and entropy). Particular attention is paid to the study of polyvalent interactions, where the definition of the constants is hampered due to the complex stoichiometry of the reactions.

Single plasmonic nanoparticle tracking studies of solid supported bilayers with ganglioside lipids

Single-particle tracking experiments were carried out with gold nanoparticle-labeled solid supported lipid bilayers (SLBs) containing increasing concentrations of ganglioside (GM(1)). The negatively charged nanoparticles electrostatically associate with a small percentage of positively charged lipids (ethyl phosphatidylcholine) in the bilayers. The samples containing no GM(1) show random diffusion in 92% of the particles examined with a diffusion constant of 4.3(±4.5) × 10(-9) cm(2)/s. In contrast, samples containing 14% GM(1) showed a mixture of particles displaying both random and confined diffusion, with the majority of particles, 62%, showing confined diffusion. Control experiments support the notion that the nanoparticles are not associating with the GM(1) moieties but instead most likely confined to regions in between the GM(1) clusters. Analysis of the root-mean-squared displacement plots for all of the data reveals decreasing trends in the confined diffusion constant and diameter of the confining region versus increasing GM(1) concentration. In addition, a linearly decreasing trend is observed for the percentage of randomly diffusing particles versus GM(1) concentration, which offers a simple, direct way to measure the percolation threshold for this system, which has not previously been measured. The percolation threshold is found to be 22% GM(1) and the confining diameter at the percolation threshold only ∼50 nm.

Myoglobin-directed assemblies of binary monolayers functionalized with iminodiacetic acid ligands at the air-water interface through metal coordination for multivalent protein binding

Myoglobin binding to the binary monolayers composed of sodium hexadecylimino diacetate and hexadecanol at the air-water interface by means of metal coordination has been investigated using infrared reflection absorption spectroscopy (IRRAS). In the absence of Cu(2+), no myoglobin binding to the binary monolayers was observed. In the presence of Cu(2+), remarkable myoglobin binding to the binary monolayers resulted from the formation of ternary complexes of iminodiacetate (IDA)-Cu(2+)-surface histidine. Myoglobin-directed assemblies of the binary monolayers facilitated multivalent protein binding through lateral rearrangements of the IDA ligands and reorientations of the alkyl chains for enhanced protein binding. Myoglobin binding to and desorption from the binary monolayers could be readily controlled through metal coordination.

Multiple repeat elements within the FAM21 tail link the WASH actin regulatory complex to the retromer

The WASH complex controls actin dynamics on endosomes, and its functional mechanism is poorly defined. The WASH complex subunit Fam21 bears many copies of a novel motif that directly interacts with the retromer cargo-selective complex. Endosomal localization of FAM21 requires both the retromer and multivalency of the repeat elements.

Wiskott–Aldrich syndrome protein (WASPs) control actin dynamics in cellular processes, including cell motility, receptor-mediated endocytosis, bacterial invasion, and vesicular trafficking. We demonstrated that WASH, a recently identified WASP family protein, colocalizes on endosomal subdomains with the cargo-selective complex (CSC) of the retromer, where it regulates retrograde sorting from endosomes in an actin-dependent manner. However, the mechanism of WASH recruitment to these retromer-enriched endosomal subdomains is unclear. Here we show that a component of the WASH regulatory complex (SHRC), FAM21, which contains 21 copies of a novel L-F-[D/E]_3-10-L-F motif, directly interacts with the retromer CSC protein VPS35. Endosomal localization of FAM21 is VPS35 dependent and relies on multivalency of FAM21 repeat elements. Using a combination of pull-down assays and isothermal calorimetry, we demonstrate that individual repeats can bind CSC, and binding affinity varies among different FAM21 repeats. A high-affinity repeat can be converted into a low-affinity one by mutation of a hydrophobic residue within the motif. These in vitro data mirror the localization of FAM21 to retromer-coated vesicles in cells. We propose that multivalency enables FAM21 to sense the density of retromer on membranes, allowing coordination of SHRC recruitment, and consequent actin polymerization, with retromer sorting domain organization/maturation.

Using covalent dimers of human carbonic anhydrase II to model bivalency in immunoglobulins

This paper describes the development of a new bivalent system comprising synthetic dimers of carbonic anhydrase linked chemically through thiol groups of cysteine residues introduced by site-directed mutagenesis. These compounds serve as models with which to study the interaction of bivalent proteins with ligands presented at the surface of mixed self-assembled monolayers (SAMs). Monovalent carbonic anhydrase (CA) binds to benzenesulfonamide ligands presented on the surface of the SAM with K(d)(surf) = 89 nM. The synthetic bivalent proteins--inspired by the structure of immunoglobulins--bind bivalently to the sulfonamide-functionalized SAMs with low nanomolar avidities (K(d)(avidity,surf) = 1-3 nM); this difference represents a ~50-fold enhancement of bivalent over monovalent association. The paper describes dimers of CA having (i) different lengths of the covalent linker that joined the two proteins and (ii) different points of attachment of the linker to the protein (either near the active site (C133) or distal to the active site (C185)). Comparison of the thermodynamics of their interactions with SAMs presenting arylsulfonamide groups demonstrated that varying the length of the linker between the molecules of CA had virtually no effect on the rate of association, or on the avidity of these dimers with ligand-presenting surfaces. Varying the point of attachment of the linker between monomeric CA's also had almost no effect on the avidity of the dimers, although changing the point of attachment affected the rates of binding and unbinding. These observations indicate that the avidities of these bivalent proteins, and by inference the avidities of structurally similar bivalent proteins such as IgG, are unexpectedly insensitive to the structure of the linker connecting them.

Nanoscale patterning of solid-supported membranes by integrated diffusion barriers

Ultraflat nanostructured substrates have been used as a template to create patterned solid-supported bilayer membranes with polymerizable tethered lipids acting as diffusion barriers. Patterns in the size range of 100 nm were successfully produced and characterized. The diffusion barriers were embedded directly into the phospholipid bilayer and could be used to control the fluidity of the membrane as well as to construct isolated membrane corrals. By using nanosphere lithography to structure the templates it was possible to systematically adjust the lipid diffusion coefficients in a range comparable to those observed in cellular membranes. Single colloids applied as mask in the patterning process yielded substrates for creation of isolated fluid membrane patches corralled by diffusion barriers. Numerous potential applications for this new model system can be envisioned, ranging from the study of cellular interactions or of molecular diffusion in confined geometries to biosensor arrays.

Multivalent protein binding in carbohydrate-functionalized monolayers through protein-directed rearrangement and reorientation of glycolipids at the air-water interface

Multivalent protein binding plays an important role not only in biological recognition but also in biosensor preparation. Infrared reflection absorption spectroscopy and surface plasmon resonance techniques have been used to investigate concanavalin A (Con A) binding to binary monolayers composed of 1,2-di-O-hexadecyl-sn-glycerol and derived glycolipids with the mannose moieties. The glycolipids in the binary monolayers at the air-water interface underwent both lateral rearrangement and molecular reorientation directed by Con A in the subphase favorable to access of the carbohydrate ligands to protein binding pockets for the formation of multivalent binding sites and the minimization of steric crowding of neighboring ligands for enhanced binding. The amounts of specifically bound proteins in the binary monolayers at the air-water interface were accordingly increased in comparison with those in the initially immobilized monolayers at the air-water interface. The directed rearranged binary monolayers with multivalent protein binding were preserved for the preparation of biosensors.

Microfluidic fabrication of asymmetric giant lipid vesicles

We have developed a microfluidic technology for the fabrication of compositionally asymmetric giant unilamellar vesicles (GUVs). The vesicles are assembled in two independent steps. In each step, a lipid monolayer is formed at a water-oil interface. The first monolayer is formed inside of a microfluidic device with a multiphase droplet flow configuration consisting of a continuous oil stream in which water droplets are formed. These droplets are dispensed into a vessel containing a layer of oil over a layer of water. The second lipid monolayer is formed by transferring the droplets through this second oil-water interface by centrifugation. By dissolving different lipid compositions in the different oil phases, the composition of each leaflet of the resulting lipid bilayer can be controlled. We have demonstrated membrane asymmetry by showing differential fluorescence quenching of labeled lipids in each leaflet and by demonstrating that asymmetric GUVs will bind an avidin-coated surface only when biotinylated lipids are targeted to the outer leaflet. In addition, we have demonstrated the successful asymmetric targeting of phosphatidylserine lipids to each leaflet, producing membranes with a biomimetic and physiologically relevant compositional asymmetry.

Oriented immobilization of prion protein demonstrated via precise interfacial nanostructure measurements

Nanopatterning of biomolecules on functionalized surfaces offers an excellent route for ultrasensitive protein immobilization, for interaction measurements, and for the fabrication of devices such as protein nanoarrays. An improved understanding of the physics and chemistry underlying the device properties and the recognition process is necessary for performance optimization. This is especially important for the recognition and immobilization of intrinsically disordered proteins (IDPs), like the prion protein (PrP), a partial IDP, whose folding and stability may be influenced by local environment and confinement. Atomic force microscopy allows for both highly controllable nanolithography and for sensitive and accurate direct detection, via precise topographic measurements on ultraflat surfaces, of protein interactions in a liquid environment, thus different environmental parameters affecting the biorecognition phenomenon can be investigated in situ. Using nanografting, a tip-induced lithographic technique, and an affinity immobilization strategy based on two different histidine tagged antibodies, with high nM affinity for two different regions of PrP, we successfully demonstrated the immobilization of recombinant mouse PrP onto nanostructured surfaces, in two different orientations. Clear discrimination of the two molecular orientations was shown by differential height (i.e., topographic) measurements, allowing for the estimation of binding parameters and the full characterization of the nanoscale biorecognition process. Our work opens the way to several high sensitivity diagnostic applications and, by controlling PrP orientation, allows for the investigation of unconventional interactions with partially folded proteins, and may serve as a platform for protein misfolding and refolding studies on PrP and other thermodynamically unstable, fibril forming, proteins.

Protein and small molecule recognition properties of deep cavitands in a supported lipid membrane determined by calcination-enhanced SPR spectroscopy

This paper details the incorporation of a water-soluble deep cavitand into a membrane bilayer assembled onto a nanoglassified surface for study of molecular recognition in a membrane-mimicking setting. The cavitand retains its host properties, and real-time analysis of the host:guest properties of the membrane:cavitand complex via surface plasmon resonance and fluorescence microscopy is described. The host shows selectivity for choline-derived substrates, and no competitive incorporation of substrate is observed in the membrane bilayer. A variety of trimethylammonium-derived substrates are suitable guests, displaying varied binding affinities in a millimolar range. The membrane:cavitand:guest complexes can be subsequently used to capture NeutrAvidin protein at the membrane surface if a biotin-derived guest molecule is used. The surface coverage of NeutrAvidin is affected by the spacer used to derivatize the biotin. Increased distance from the bilayer allows a higher concentration of protein to be immobilized, suggesting a diminishing detrimental steric effect when the binding event is shifted away from the surface.

Selective tethering of ligands and proteins to a microfluidically patterned electroactive fluid lipid bilayer array

We report a new, quantitative methodology to pattern and present ligands from planar, supported, fluid lipid bilayers. By combining microfluidic lithography (microFL) with an electroactive, chemoselective interfacial reaction strategy, a number of ligands as well as protein concanavalin A were immobilized in lipid microarrays. Electroactive vesicles were generated after the spontaneous insertion of hydroquinone-tethered alkane (H(2)Q) into egg palmitoyl-oleoyl phosphatidylcholine (egg-POPC), followed by subsequent fusion to a siloxane-terminated self-assembled monolayer (SAM) on gold. An advantage of the H(2)Q system is that it can be electrochemically oxidized to the corresponding quinone (Q), followed by rapid chemoselective conjugation with oxyamine-functionalized (RONH(2)) ligands. The oxime product is also electroactive, and the reaction can be monitored and the amount of ligand bound can be quantified by electrochemistry. The bilayers were characterized by electrochemistry, fluorescence microscopy, and ellipsometry and were determined to be fluid by fluorescence recovery after photobleaching (FRAP). This strategy provides a synergistic method to pattern and present a number of ligands or biomolecules from the bilayer surface for the evaluation of enzyme or protein binding to biomembranes.

Correlation between the composition of multivalent antibody conjugates with colloidal gold nanoparticles and their affinity

Interactions between multivalent preparations of antibodies (conjugated with colloidal gold nanoparticles (GNP) as a carrier system) and a multivalent ligand were investigated. The aim of the present study was to reveal the relationship between the affinity of the conjugate and its composition (i.e., the valency). Surface plasmon resonance was applied to study the affinity and the kinetics of the interaction of multivalent conjugates and multivalent virus (on the example of the plum pox virus (PPV)). Three monoclonal antibodies against PPV were prepared. Five GNP preparations with an average particle size in the range from 5 to 60nm (according to electron microscopy measurements) were obtained. The series of preparations allowed us to synthesize GNP-antibody conjugates with different surface areas for immobilization of antibodies, and, consequently, conjugates with different valencies. It was shown that the affinity of the conjugates changes with size of colloidal carriers (i.e. with the valency of the conjugates). The affinity of the virus-antibody interaction (antibodies with affinities of 1.46.10(-8)M and 1.73.10(-8)M) is one to three orders of magnitude lower (depending on the valency of the conjugate) compared to that of the interactions of the virus with GNP conjugates (conjugates with the affinity varying from 1.69.10(-9) to 7.02.10(-12)M and from 2.39.10(-9) to 2.62.10(-11)M, respectively). An increase in the conjugate size leads to an increase in its affinity. The similar trends were observed for the potato virus X.

Molecular effects of a nanocrystalline quartz support upon planar lipid bilayers

Supported lipid bilayer membranes play a vital role in a number of applications from biosensors to fundamental studies of membrane proteins. It is widely understood that the underlying solid support in such assemblies causes large perturbations to the lipid bilayer as compared with black lipid membranes, but the exact nature of these effects on the membrane by the solid support is less understood. Here, all-atom molecular dynamics simulations of DLPC, DMPC, POPC, and DEPC on a hydroxylated nanocrystalline alpha-quartz (011) slab have revealed a pronounced thinning effect. It is shown that this thinning effect proceeds by one of two mechanisms; the first is through a curling of the terminal methyl groups at the interface of opposing leaflets, and the second is through increased interdigitation of the alkyl chains. In all cases, it is shown that the thinning effect is accompanied by a commensurate spreading of the lipid membrane across the quartz substrate. Also, with the introduction of the solid support, a marked asymmetry in a number of structural properties is reported. These asymmetries include (a) the surface areas per lipid, (b) the electron probabilities of the polar headgroups, (c) the radial distributions of the choline groups, and (d) the average orientation of water surrounding the membranes. Finally, asymmetries associated with the different interaction energies within each system studied are reported. These unequal interaction energies lead to a net force holding the membrane to the surface of the support. It was found that direct membrane-substrate interactions play only a minor role in holding the membrane to the surface and it is the interstitial water that dominates these interactions. This is due to the fact that the water throughout the interstitial region displays an average orientational preference that is more favorable (attractive to the membrane and yields a higher number of hydrogen bonds) than water in the external region of the assembly.

Total internal reflection with fluorescence correlation spectroscopy: Applications to substrate-supported planar membranes

In this paper, the conceptual basis and experimental design of total internal reflection with fluorescence correlation spectroscopy (TIR-FCS) is described. The few applications to date of TIR-FCS to supported membranes are discussed, in addition to a variety of applications not directly involving supported membranes. Methods related, but not technically equivalent, to TIR-FCS are also summarized. Future directions for TIR-FCS are outlined.