Mutual modulation between membrane-embedded receptor clustering and ligand binding in lipid membranes

Solvent effects in anion recognition

Anion recognition is pertinent to a range of environmental, medicinal and industrial applications. Recent progress in the field has relied on advances in synthetic host design to afford a broad range of potent recognition motifs and novel supramolecular structures capable of effective binding both in solution and at derived molecular films. However, performance in aqueous media remains a critical challenge. Understanding the effects of bulk and local solvent on anion recognition by host scaffolds is imperative if effective and selective detection in real-world media is to be viable. This Review seeks to provide a framework within which these effects can be considered both experimentally and theoretically. We highlight proposed models for solvation effects on anion binding and discuss approaches to retain strong anion binding in highly competitive (polar) solvents. The synthetic design principles for exploiting the aforementioned solvent effects are explored.

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.

In Situ DNA Self-Assembly on the Cell Surface Drives Unidirectional Clustering of Membrane Proteins for the Modulation of Cell Behaviors

Cell membrane proteins play a pivotal role in regulating intracellular signal transductions and cell behaviors. Many membrane proteins form clusters in order to initiate downstream signaling pathways for the modulation of cell behaviors. Developing rational methods to program the in situ clustering of designated membrane proteins on the cell surface to form large assemblies remains challenging. Here we use the membrane-anchored DNA hybridization chain reaction (HCR) to induce DNA self-assembly on the live cell surface and drive the unidirectional clustering of membrane proteins for the modulation of cell behaviors. Reactive DNA strands are specifically anchored onto the membrane proteins of interest by using DNA aptamers. Upon activation, the chain reaction between the protein-anchored DNA strands drives the assembly of membrane proteins forming one-dimensional clusters. We demonstrate both homogeneous and heterogeneous clustering of membrane proteins on multiple cell types that exhibit a potent capability for modulating cell behaviors including migration, proliferation, and survival.

Significance of Receptor Mobility in Multivalent Binding on Lipid Membranes

Numerous key biological processes rely on the concept of multivalency, where ligands achieve stable binding only upon engaging multiple receptors. These processes, like viral entry or immune synapse formation, occur on the diffusive cellular membrane. One crucial, yet underexplored aspect of multivalent binding is the mobility of coupled receptors. Here, we discuss the consequences of mobility in multivalent processes from four perspectives: (I) The facilitation of receptor recruitment by the multivalent ligand due to their diffusivity prior to binding. (II) The effects of receptor preassembly, which allows their local accumulation. (III) The consequences of changes in mobility upon the formation of receptor/ligand complex. (IV) The changes in the diffusivity of lipid environment surrounding engaged receptors. We demonstrate how understanding mobility is essential for fully unravelling the principles of multivalent membrane processes, leading to further development in studies on receptor interactions, and guide the design of new generations of multivalent ligands.

Supramolecular chemistry in lipid bilayer membranes

Lipid bilayer membranes form compartments requisite for life. Interfacing supramolecular systems, including receptors, catalysts, signal transducers and ion transporters, enables the function of the membrane to be controlled in artificial and living cellular compartments. In this perspective, we take stock of the current state of the art of this rapidly expanding field, and discuss prospects for the future in both fundamental science and applications in biology and medicine.

How the biomimetic assembly of membrane receptors into multivalent domains is regulated by a small ligand

In living cells, communication requires the action of membrane receptors that are activated following very small environmental changes. A binary all-or-nothing behavior follows, making the organism extremely efficient at responding to specific stimuli. Using a minimal system composed of lipid vesicles, chemical models of a membrane receptor and their ligands, we show that bio-mimetic ON/OFF assembly of high avidity, multivalent domains is triggered by small temperature changes. Moreover, the intensity of the ON signal at the onset of the switch is modulated by the presence of small, weakly binding divalent ligands, reminiscent of the action of primary messengers in biological systems. Based on the analysis of spectroscopic data, we develop a mathematical model that rigorously describes the temperature-dependent switching of the membrane receptor assembly and ligand binding. From this we derive an equation that predicts the intensity of the modulation of the ON signal by the ligand-messenger as a function of the pairwise binding parameters, the number of binding sites that it features and the concentration. The behavior of our system, and the model derived, highlight the usefulness of weakly binding ligands in the regulation of membrane receptors and the pitfalls inherent to their binding promiscuity, such as non-specific binding to the membrane. Our model, and the equations derived from it, offer a valuable tool for the study of membrane receptors in both biological and biomimetic settings. The latter can be exploited to program membrane receptor avidity on sensing vesicles, create hierarchical protocell tissues or develop highly specific drug delivery vehicles.

Calcium-induced reversible assembly of phosphorylated amphiphile within lipid bilayer membranes

Inspired by calcium-induced reversible assembly and disassembly of membrane proteins found in nature, here we developed a phosphorylated amphiphile (PA) that contains an oligo(phenylene-ethynylene) unit as a hydrophobic unit and a phosphate ester group as a hydrophilic calcium-binding unit. We demonstrated that PA can assemble and disassemble in a reversible manner in response to the sequential addition of calcium chloride and ethylene-diaminetetraacetic acid within the lipid bilayer membranes for the first time as a synthetic molecule.

Template effects of vesicles in dynamic covalent chemistry

Vesicle lipid bilayers have been employed as templates to modulate the product distribution in a dynamic covalent library of Michael adducts formed by mixing a Michael acceptor with thiols. In methanol solution, all possible Michael adducts were obtained in similar amounts. Addition of vesicles to the dynamic covalent library led to the formation of a single major product. The equilibrium constants for formation of the Michael adducts are similar for all of the thiols used in this experiment, and the effect of the vesicles on the composition of the library is attributed to the differential partitioning of the library members between the lipid bilayer and the aqueous solution. The results provide a quantitative approach for exploiting dynamic covalent chemistry within lipid bilayers.

Multivalent nanosystems: targeting monocytes/macrophages

Among all the cellular partners involved in inflammatory processes, monocytes and macrophages are the master regulators of inflammation. They are found in almost all the tissues and are nearly the only cells capable of performing each step of inflammation. Consequently, they stand as major relevant therapeutic targets to treat inflammatory disorders and diseases. The physiological phagocytic activity of macrophages prompts them to detect, to recognize, and eventually to engulf any nanosystem cruising in their neighborhood. Interestingly, nanosystems can be rationally engineered to afford multivalent, and multifunctional if needed, entities with multiplexed and/or reinforced biological activities. Indeed, engineered nanosystems bearing moieties specifically targeting macrophages, and loaded with or bound to drugs are promising candidates to modulate, or even eradicate, deleterious macrophages in vivo. In this review we highlight recent articles and concepts of multivalent nanosystems targeting monocytes and macrophages to treat inflammatory disorders.

Exploring Molecular-Biomembrane Interactions with Surface Plasmon Resonance and Dual Polarization Interferometry Technology: Expanding the Spotlight onto Biomembrane Structure

The molecular analysis of biomolecular-membrane interactions is central to understanding most cellular systems but has emerged as a complex technical challenge given the complexities of membrane structure and composition across all living cells. We present a review of the application of surface plasmon resonance and dual polarization interferometry-based biosensors to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. We first describe the optical principals and instrumentation of surface plasmon resonance, including both linear and extraordinary transmission modes and dual polarization interferometry. We then describe the wide range of model membrane systems that have been developed for deposition on the chips surfaces that include planar, polymer cushioned, tethered bilayers, and liposomes. This is followed by a description of the different chemical immobilization or physisorption techniques. The application of this broad range of engineered membrane surfaces to biomolecular-membrane interactions is then overviewed and how the information obtained using these techniques enhance our molecular understanding of membrane-mediated peptide and protein function. We first discuss experiments where SPR alone has been used to characterize membrane binding and describe how these studies yielded novel insight into the molecular events associated with membrane interactions and how they provided a significant impetus to more recent studies that focus on coincident membrane structure changes during binding of peptides and proteins. We then discuss the emerging limitations of not monitoring the effects on membrane structure and how SPR data can be combined with DPI to provide significant new information on how a membrane responds to the binding of peptides and proteins.

The impact of metal complex lipids on viscosity and curvature of hybrid liposomes

A morphology transformation of hybrid liposomes was shown to occur from spherical vesicles to tubular micelles when increasing the ratio of the metal complex lipid present. Phase transition temperatures increased while viscosities decreased, indicating that the hybrids exhibit stronger interaction between heads but weaker interaction between alkyl chains than occurs in pristine liposomes.

Multivalence cooperativity leading to "all-or-nothing" assembly: the case of nucleation-growth in supramolecular polymers

All-or-nothing molecular assembly events, essential for the efficient regulation of living systems at the molecular level, are emerging properties of complex chemical systems that are largely attributed to the cooperativity of weak interactions. The link between the self-assembly and the interactions responsible for the assembly is however often poorly defined. In this work we demonstrate how the chelate effect (multivalence cooperativity) can play a central role in the regulation of the all-or-nothing assembly of structures (supramolecular polymers here), even if the building blocks are not multivalent. We have studied the formation of double-stranded supramolecular polymers formed from Co-metalloporphyrin and bi-pyridine building blocks. Their cooperative nucleation-elongation assembly can be summarized as a thermodynamic cycle, where the monomer weakly oligomerizes linearly or weakly dimerizes laterally. But thanks to the chelate effect, the lateral dimer readily oligomerizes linearly and the oligomer readily dimerizes laterally, leading to long double stranded polymers. A model based on this simple thermodynamic cycle can be applied to the assembly of polymers with any number of strands, and allows for the determination of the length of the polymer and the all-or-nothing switching concentration from the pairwise binding constants. The model, which is consistent with the behaviour of supramolecular polymers such as microtubules and gelators, clearly shows that all-or-nothing assembly is triggered by a change in the mode of assembly, from non-multivalent to multivalent, when a critical concentration is reached. We believe this model is applicable to many molecular assembly processes, ranging from the formation of cell-cell focal adhesion points to crystallization.

Affinity Enhancement by Ligand Clustering Effect Inspired by Peptide Dendrimers-Shank PDZ Proteins Interactions

High-affinity binders are desirable tools to probe the function that specific protein−protein interactions play in cell. In the process of seeking a general strategy to design high-affinity binders, we found a clue from the βPIX (p21-activated kinase interacting exchange factor)−Shank PDZ interaction in synaptic assembly: three PDZ-binding sites are clustered by a parallel coiled-coil trimer but bind to Shank PDZ protein with 1:1 stoichiometry (1 trimer/1 PDZ). Inspired by this architecture, we proposed that peptide dendrimer, mimicking the ligand clustering in βPIX, will also show enhanced binding affinity, yet with 1:1 stoichiometry. This postulation has been proven here, as we synthesized a set of monomeric, dimeric and trimeric peptides and measured their binding affinity and stoichiometry with Shank PDZ domains by isothermal titration calorimetry, native mass spectrometry and surface plasmon resonance. This affinity enhancement, best explained by proximity effect, will be useful to guide the design of high-affinity blockers for protein−protein interactions.

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.

Biotinylated Cyclophane: Synthesis, Cyclophane-Avidin Conjugates, and Their Enhanced Guest-Binding Affinity

Cationic and anionic cyclophanes bearing a biotin moiety were synthesized as a water-soluble host (1a and 1b, respectively). Both hosts 1a and 1b were found to strongly bind avidin with binding constants of 1.3 × 10(8) M(-1), as confirmed by surface plasmon resonance measurements. The present conjugate of 1a with avidin (1a-avidin) showed an enhanced guest binding affinity toward fluorescence guests such as TNS and 2,6-ANS. The K values of 1a-avidin conjugate with TNS and 2,6-ANS were ~19-fold larger than those of monocyclic cyclophane 1a with the identical guests. Favorable hydrophobic and electrostatic interactions between 1a-avidin and TNS were suggested by computer-aided molecular modeling calculations. Moreover, addition of excess biotin to the complexes of 1a-avidin with the guests resulted in dissociation of 1a-avidin to avidin and 1a having less guest-binding affinity. Conversely, such enhancements in the guest-binding affinity were not obviously observed for the conjugate of anionic 1b with avidin (1b-avidin) due to electrostatic repulsion between anionic 1b and anionic guests.

Small liposomes accelerate the fibrillation of amyloid β (1-40)

The deposition of amyloid β (Aβ) peptides is a pathological hallmark of Alzheimer disease. Aβ peptides were previously considered to interact specifically with ganglioside-containing membranes. Several studies have suggested that Aβ peptides also bind to phosphatidylcholine membranes, which lead to deformation of membranes and fibrillation of Aβ. Moreover, the role of membrane curvature, one type of deformation produced by binding of proteins to a membrane, in the binding and fibrillation of Aβ remains unclear. To clearly understand the relationship between the binding, consequent membrane deformation, and fibrillation of Aβ, we examined the amyloid fibrillation of Aβ-(1-40) in the presence of liposomes of various sizes. Membrane curvature increased with a decrease in the size of the liposomes. We used liposomes made of 1,2-dioleoyl-sn-glycero-3-phosphocholine to eliminate electrostatic effects. The results obtained showed that liposomes of smaller sizes (≤50 nm) significantly accelerated the nucleation step, thereby shortening the lag time of fibrillation. On the other hand, liposomes of larger sizes decreased the amount of fibrils but did not notably affect the lag time. The morphologies of fibrils, which were monitored by total internal reflection fluorescence microscopy, atomic force microscopy, and transmission electron microscopy, revealed that the length of Aβ-(1-40) fibrils became shorter and the amount of amorphous aggregates became larger as liposomes increased in size. These results suggest that the curvature of membranes coupled with an increase in water-accessible hydrophobic regions is important for binding and concentrating Aβ monomers, leading to amyloid nucleation. Furthermore, amyloid fibrillation on membranes may compete with non-productive binding to produce amorphous aggregates.

Pericellular matrix plays an active role in retention and cellular uptake of large-sized nanoparticles

As the outmost coating of cells, the pericellular matrix (PCM) involved in various cellular functions has been exploited previously to be able to accumulate 120 nm Au nanoparticles (NPs), adjust their diffusion coefficient similar to that of membrane receptors, and enhance their uptake efficiency. In this study, the interactions between PCM and NPs with different sizes and materials were systematically investigated. We found that PCM can selectively enhance the retention and cellular uptake of NPs with diameters from 50 to 180 nm, but has no enhancement effect for 20 nm NPs. Identical behaviors of PCM was observed for both Au NPs and polystyrene NPs, indicating that this unique phenomenon is more related to the dimensions of the NPs. The study of single-particle tracking of 50-180 nm NPs on the surface of thick PCM cells revealed that PCM actively adjusts the diffusion coefficient of NPs to ∼0.1 μm(2)/s regardless of their sizes. By blocking the receptor-mediated endocytosis (RME) pathway with four different inhibitors, this active role of PCM can be effectively suppressed, further confirming that the trapping and retention of NPs by PCM is an inherent biological function. These findings provided new insights for better understanding of the RME pathway and may have promising NP-based applications for controlled drug delivery and therapy in biomedicine.

Preparation of semisynthetic lipoproteins with fluorescent cholesterol anchor and their introduction to the cell membrane with minimal disruption of the membrane

The exogenous introduction of fluorescent lipoproteins into cell membranes is a method for visualizing the cellular traffic of membrane associated proteins, and also for altering the cell surface in a controlled manner. In order to achieve the cell membrane anchoring of proteins and their subsequent fluorescence based detection, a cholesterol derivative was designed. The headgroup of the novel cholesterol anchor contains a fluorescent reporter and a thiol reactive maleimide for protein conjugation. Protein conjugation was demonstrated by the addition of a green fluorescent maleimido anchor to the C-terminus of a Cys extended red fluorescent protein, mCherry. The resulting dual fluorescent cholesteryl lipoprotein was successfully separated from the micellar associates of the surplus fluorescent lipid anchor without denaturing the protein, and the lipoprotein containing only the covalently linked, stoichiometric fluorescent lipid was efficiently delivered to the plasma membrane of live cells. It was demonstrated that the membrane fluorescence could be directly assigned to the protein-anchor conjugate, because no excess of fluorescent lipid species were present during the imaging experiment and the protein and anchor fluorescence colocalized in the cell membrane. Molecular dynamics simulations and subsequent trajectory analysis suggest also the spontaneous and stable membrane association of the cholesterol anchor. Thus, the method could be beneficially applied for studying membrane associated proteins and for preparing mimetics of glycosylphosphatidylinositol (GPI)-anchored proteins to target cholesterol-rich membrane microdomains.

Modulation of in-membrane receptor clustering upon binding of multivalent ligands

In living cells and biomimetic systems alike, multivalent ligands in solution can induce clustering of membrane receptors. The link between the receptor clustering and the ligand binding remains, however, poorly defined. Using minimalist divalent ligands, we develop a model that allows quantifying the modulation of receptor clustering by binding of ligands with any number of binding sites. The ligands, with weak binding affinity for the receptor and with binding sites held together by flexible linkers, lead to nearly quantitative clustering upon binding in a wide range of experimental conditions, showing that efficient modulation of receptor clustering does not require pre-organization or large binding affinities per binding site. Simulations show that, in the presence of ligands with five or more binding sites, an on/off clustering response follows a very small change in receptor density in the membrane, which is consistent with the highly cooperative behavior of multivalent biomolecular systems.

Direct three-dimensional visualization of membrane disruption by amyloid fibrils

Protein misfolding and aggregation cause serious degenerative conditions such as Alzheimer's, Parkinson, and prion diseases. Damage to membranes is thought to be one of the mechanisms underlying cellular toxicity of a range of amyloid assemblies. Previous studies have indicated that amyloid fibrils can cause membrane leakage and elicit cellular damage, and these effects are enhanced by fragmentation of the fibrils. Here we report direct 3D visualization of membrane damage by specific interactions of a lipid bilayer with amyloid-like fibrils formed in vitro from β(2)-microglobulin (β(2)m). Using cryoelectron tomography, we demonstrate that fragmented β(2)m amyloid fibrils interact strongly with liposomes and cause distortions to the membranes. The normally spherical liposomes form pointed teardrop-like shapes with the fibril ends seen in proximity to the pointed regions on the membranes. Moreover, the tomograms indicated that the fibrils extract lipid from the membranes at these points of distortion by removal or blebbing of the outer membrane leaflet. Tiny (15-25 nm) vesicles, presumably formed from the extracted lipids, were observed to be decorating the fibrils. The findings highlight a potential role of fibrils, and particularly fibril ends, in amyloid pathology, and report a previously undescribed class of lipid-protein interactions in membrane remodelling.

Role of nanomechanics in canonical and noncanonical pro-angiogenic ligand/VEGF receptor-2 activation

Vascular endothelial growth factor receptor-2 (VEGFR2) is an endothelial cell receptor that plays a pivotal role in physiologic and pathologic angiogenesis and is a therapeutic target for angiogenesis-dependent diseases, including cancer. By leveraging on a dedicated nanomechanical biosensor, we investigated the nanoscale mechanical phenomena intertwined with VEGFR2 surface recognition by its prototypic ligand VEGF-A and its noncanonical ligand gremlin. We found that the two ligands bind the immobilized extracellular domain of VEGFR2 (sVEGFR2) with comparable binding affinity. Nevertheless, they interact with sVEGFR2 with different binding kinetics and drive different in-plane piconewton intermolecular forces, suggesting that the binding of VEGF-A or gremlin induces different conformational changes in sVEGFR2. These behaviors can be effectively described in terms of a different "nanomechanical affinity" of the two ligands for sVEGFR2, about 16-fold higher for VEGF-A with respect to gremlin. Such nanomechanical differences affect the biological activity driven by the two angiogenic factors in endothelial cells, as evidenced by a more rapid VEGFR2 clustering and a more potent mitogenic response triggered by VEGF-A in respect to gremlin. Together, these data point to surface intermolecular interactions on cell membrane between activated receptors as a key modulator of the intracellular signaling cascade.

Theoretical models of nonlinear effects in two-component cooperative supramolecular copolymerizations

The understanding of multi-component mixtures of self-assembling molecules under thermodynamic equilibrium can only be advanced by a combined experimental and theoretical approach. In such systems, small differences in association energy between the various components can be significantly amplified at the supramolecular level via intricate nonlinear effects. Here we report a theoretical investigation of two-component, self-assembling systems in order to rationalize chiral amplification in cooperative supramolecular copolymerizations. Unlike previous models based on theories developed for covalent polymers, the models presented here take into account the equilibrium between the monomer pool and supramolecular polymers, and the cooperative growth of the latter. Using two distinct methodologies, that is, solving mass-balance equations and stochastic simulation, we show that monomer exchange accounts for numerous unexplained observations in chiral amplification in supramolecular copolymerization. In analogy with asymmetric catalysis, amplification of chirality in supramolecular polymers results in an asymmetric depletion of the enantiomerically related monomer pool.