Lifting the Concentration Limit of Mass Photometry by PEG Nanopatterning

Mass photometry (MP) is a rapidly growing optical technique for label-free mass measurement of single biomolecules in solution. The underlying measurement principle provides numerous advantages over ensemble-based methods but has been limited to low analyte concentrations due to the need to uniquely and accurately quantify the binding of individual molecules to the measurement surface, which results in diffraction-limited spots. Here, we combine nanoparticle lithography with surface PEGylation to substantially lower surface binding, resulting in a 2 orders of magnitude improvement in the upper concentration limit associated with mass photometry. We demonstrate the facile tunability of degree of passivation, enabling measurements at increased analyte concentrations. These advances provide access to protein-protein interactions in the high nanomolar to low micromolar range, substantially expanding the application space of mass photometry.

Instrumentational implementation for parallelized nanopore electrochemical measurements

Nanopore electrochemistry, as one of the promising tools for single molecule sensing, has proved its capability in DNA sequencing and protein analysis. To achieve a high resolution for obtaining molecular information, the nanopore electrochemical technique not only urgently requires an appropriate nanopore sensing interface with atomic resolution but also requires advanced instrumentation and its related data processing methods. In order to reveal the fundamental biological process and process the point-of-care diagnosis, it is necessary to use a nanopore sensing instrument with a high amperometric and temporal resolution as well as high throughput. The development of the instrumentation requires multi-disciplinary collaboration involving preparing a sensitive nanopore interface, low-noise circuit design, and intelligent data analysis. In this review, we have summarized the recent improvements in the nanopore sensing interface as well as discussed the higher throughput achieved by nanopore arrays and intelligent nanopore data analysis methods. The parallelized nanopore instrumentation could be popularized to all ranges of single-molecule applications.

Enhanced Stability of Lipid Structures by Dip-Pen Nanolithography on Block-Type MPC Copolymer

Biomimetic lipid membranes on solid supports have been used in a plethora of applications, including as biosensors, in research on membrane proteins or as interfaces in cell experiments. For many of these applications, structured lipid membranes, e.g., in the form of arrays with features of different functionality, are highly desired. The stability of these features on a given substrate during storage and in incubation steps is key, while at the same time the substrate ideally should also exhibit antifouling properties. Here, we describe the highly beneficial properties of a 2-methacryloyloxyethyl phosphorylcholine (MPC) copolymer for the stability of supported lipid membrane structures generated by dip-pen nanolithography with phospholipids (L-DPN). The MPC copolymer substrates allow for more stable and higher membrane stack structures in comparison to other hydrophilic substrates, like glass or silicon oxide surfaces. The structures remain highly stable under immersion in liquid and subsequent incubation and washing steps. This allows multiplexed functionalization of lipid arrays with antibodies via microchannel cantilever spotting (µCS), without the need of orthogonal binding tags for each antibody type. The combined properties of the MPC copolymer substrate demonstrate a great potential for lipid-based biomedical sensing and diagnostic platforms.

Biomimetic Phospholipid Membrane Organization on Graphene and Graphene Oxide Surfaces: A Molecular Dynamics Simulation Study

Supported phospholipid membrane patches stabilized on graphene surfaces have shown potential in sensor device functionalization, including biosensors and biocatalysis. Lipid dip-pen nanolithography (L-DPN) is a method useful in generating supported membrane structures that maintain lipid functionality, such as exhibiting specific interactions with protein molecules. Here, we have integrated L-DPN, atomic force microscopy, and coarse-grained molecular dynamics simulation methods to characterize the molecular properties of supported lipid membranes (SLMs) on graphene and graphene oxide supports. We observed substantial differences in the topologies of the stabilized lipid structures depending on the nature of the surface (polar graphene oxide vs nonpolar graphene). Furthermore, the addition of water to SLM systems resulted in large-scale reorganization of the lipid structures, with measurable effects on lipid lateral mobility within the supported membranes. We also observed reduced lipid ordering within the supported structures relative to free-standing lipid bilayers, attributed to the strong hydrophobic interactions between the lipids and support. Together, our results provide insight into the molecular effects of graphene and graphene oxide surfaces on lipid bilayer membranes. This will be important in the design of these surfaces for applications such as biosensor devices.

Sticking and sliding of lipid bilayers on deformable substrates

We examine here the properties of lipid bilayers coupled to deformable substrates. We show that by changing the extent of the substrate hydrophilicity, we can control the membrane-substrate coupling and the response of the bilayer to strain deformation. Our results demonstrate that lipid bilayers coupled to flexible substrates can easily accommodate large strains, form stable protrusions and open reversibly pores. These properties, which differ significantly from those of free standing membranes, can extend the applications of the current lipid technologies. Moreover, such systems better capture the mechanical architecture of the cell interface and can provide insights into the capacity of cells to reshape and respond to mechanical perturbations.

Super-resolution Stimulated Emission Depletion-Fluorescence Correlation Spectroscopy Reveals Nanoscale Membrane Reorganization Induced by Pore-Forming Proteins

Membrane-protein interactions play a central role in membrane mediated cellular processes ranging from signaling, budding, and fusion, to transport across the cell membrane. Of particular significance is the process of efficient protein olgomerization and transmembrane pore formation on the membrane surface; the primary virulent pathway for the action of antimicrobial peptides and pore forming toxins (PFTs). The suggested nanoscopic length scales and dynamic nature of such membrane lipid-protein interactions makes their detection extremely challenging. Using a combination of super-resolution stimulated emission depletion nanoscopy with fluorescence correlation spectroscopy (STED-FCS) we unravel the emergence of nanoscale lateral heterogeneity in supported bilayer membranes made up of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and cholesterol upon interaction with the PFT, listeriolysin O (LLO). A distinct length scale-dependent dynamical crossover (<200 nm) from a Brownian diffusive regime is observed at 33 and 50% cholesterol compositions, indicating the partitioning of lipids into domains with variable cholesterol content. At 25% cholesterol content, this dyamical crossover is observed only in bilayers incubated with LLO providing evidence for the existence of sub ∼100 nm dynamical lipid nanodomains bound to LLO pore assemblies. By introducing asymmetry in cholesterol composition across the bilayer leaflets we infer that this domain formation is driven largely due to active cholesterol sequestration and transient trapping of lipids to the membrane bound motifs present in the toxins, en route to LLO oligomerization and subsequent pore formation. Bilayers prepared with labeled lipids present in either the proximal or distal leaflet allow us to track the dynamical perturbation in a leaflet-dependent manner upon LLO incubation. From the differences in the extent and intensity of the dynamical crossover as observed with STED-FCS, these experiments reveal that the affinity for cholesterol in the membrane binding motifs of the LLO subdomains induce cholesterol and lipid reorganization to a greater extent in the distal (upper) leaflet when compared with the proximal (lower) leaflet. The observed length scale-dependent membrane reorganization that occurs due to invasion by LLO could be generalized to other cholesterol-dependent cytolysins and emphasizes the significant advantage of using super-resolution STED nanoscopy to unravel complex lipid-protein interactions in membrane and cellular biophysics.

Mixtures of supported and hybrid lipid membranes on heterogeneously modified silica nanoparticles

Simple supported lipid bilayers do not accurately reflect the complex heterogeneity of cellular membranes; however, surface modification makes it possible to tune membrane properties to better mimic biological systems. Here, 3-[2-(2-aminoethylamino)ethylamino]propyl-trimethoxysilane (DETAS), a silica modifier, facilitated formation of supported lipid bilayers on silica nanoparticles. Evidence for a stable supported bilayer came from the successful entrapment of a soluble fluorophore within an interstitial water layer. A fluorescence-quenching assay that utilized a pore-forming peptide was used to demonstrate the existence of two separate lipid leaflets. In this assay, fluorescence was quenched by dithionite in roughly equal proportions prior to and after addition of melittin. When a hydrophobic modifier, octadecyltriethoxysilane, was codeposited on the nanoparticles with DETAS, there was a decrease in the amount of supported bilayer on the nanoparticles and an increase in the quantity of hybrid membrane. This allowed for a controlled mixture of two distinct types of membranes on a single substrate, one separated by a water cushion and the other anchored directly on the surface, thereby providing a new mimic of cellular membranes.

Adhesion-induced phase behavior of two-component membranes and vesicles

The interplay of adhesion and phase separation is studied theoretically for two-component membranes that can phase separate into two fluid phases such as liquid-ordered and liquid-disordered phases. Many adhesion geometries provide two different environments for these membranes and then partition the membranes into two segments that differ in their composition. Examples are provided by adhering vesicles, by hole- or pore-spanning membranes, and by membranes supported by chemically patterned surfaces. Generalizing a lattice model for binary mixtures to these adhesion geometries, we show that the phase behavior of the adhering membranes depends, apart from composition and temperature, on two additional parameters, the area fraction of one membrane segment and the affinity contrast between the two segments. For the generic case of non-vanishing affinity contrast, the adhering membranes undergo two distinct phase transitions and the phase diagrams in the composition/temperature plane have a generic topology that consists of two two-phase coexistence regions separated by an intermediate one-phase region. As a consequence, phase separation and domain formation is predicted to occur separately in each of the two membrane segments but not in both segments simultaneously. Furthermore, adhesion is also predicted to suppress the phase separation process for certain regions of the phase diagrams. These generic features of the adhesion-induced phase behavior are accessible to experiment.

Mechanism of lipid nanodrop spreading in a case of asymmetric wetting

Using the surface enhanced ellipsometric contrast microscopy, we follow the last stage of the spreading of egg phosphatidylcholine nanodroplets on a hydrophilic substrate in a humid atmosphere, focusing on the vanishing trilayer in terraced droplets reduced to coexisting monolayer and trilayer. We find that the line interface between them exhibits two coexisting states, one mobile and one fixed. From there, it is possible to elucidate the internal structure and the spreading mechanism of the stratified liquid in a case of asymmetric wetting, i.e., where the lipid film is made of an odd number of leaflets.

Phospholipid bilayer formation on a variety of nanoporous oxide and organic xerogel films

Lipid bilayers supported by nanoporous xerogel materials are being explored as models for cell membranes. In order to better understand and characterize the nature of the surface-bilayer interactions, several oxide and organic nanoporous xerogel films (alumina, titania, iron oxide, phloroglucinol-formaldehyde, resorcinol-formaldehyde and cellulose acetate) have been investigated as a scaffold for vesicle-fused 1,2-dioleoyl-glycero-3-phosphocholine (DOPC) lipid bilayer formation and mobility. The surface topography of the different substrates was analyzed using contact and tapping-mode atomic force microscopy and the surface energy of the substrates was determined using contact angle goniometry. Lipid bilayer formation has been observed with fluorescence microscopy and lateral lipid diffusion coefficients have been determined using fluorescence recovery after photobleaching. Titania xerogel films were found to be a robust and convenient support for formation of a two-phase DOPC/1,2-distearoyl-glycero-3-phosphocholine bilayer and domains were observed with this system. It was found that the cellulose acetate xerogel film support produced the slowest lipid lateral diffusion.

Neural Stem Cell Spreading on Lipid Based Artificial Cell Surfaces, Characterized by Combined X-ray and Neutron Reflectometry

We developed a bioadhesive coating based on a synthetic peptide-conjugate (AK-cyclo[RGDfC]) which contains multiples of the arginyl-glycyl-aspartic acid (RGD) amino acid sequence. Biotinylated AK-cyclo[RGDfC] is bound to a supported lipid bilayer via a streptavidin interlayer. Layering, hydration and packing of the coating is quantified by X-ray and neutron reflectometry experiments. AK-cyclo[RGDfC] binds to the streptavidin interlayer in a stretched-out on edge configuration. The highly packed configuration with only 12% water content maximizes the number of accessible adhesion sites. Enhanced cell spreading of neural stem cells was observed for AK-cyclo[RGDfC] functionalized bilayers. Due to the large variety of surfaces which can be coated by physisorption of lipid bilayers, this approach is of general interest for the fabrication of biocompatible surfaces.

Templating membrane assembly, structure, and dynamics using engineered interfaces

The physical and chemical properties of biological membranes are intimately linked to their bounding aqueous interfaces. Supported phospholipid bilayers, obtained by surface-assisted rupture, fusion, and spreading of vesicular microphases, offer a unique opportunity, because engineering the substrate allows manipulation of one of the two bilayer interfaces as well. Here, we review a collection of recent efforts, which illustrates deliberate substrate-membrane coupling using structured surfaces exhibiting chemical and topographic patterns. Vesicle fusion on chemically patterned substrates results in co-existing lipid phases, which reflect the underlying pattern of surface energy and wettability. These co-existing bilayer/monolayer morphologies are useful both for fundamental biophysical studies (e.g., studies of membrane asymmetry) as well as for applied work, such as synthesizing large-scale arrays of bilayers or living cells. The use of patterned, static surfaces provides new models to design complex membrane topographies and curvatures. Dynamic switchable-topography surfaces and sacrificial trehalose based-substrates reveal abilities to dynamically introduce membrane curvature and change the nature of the membrane-substrate interface. Taken together, these studies illustrate the importance of controlling interfaces in devising model membrane platforms for fundamental biophysical studies and bioanalytical devices.

Protein adsorption and desorption on lipid bilayers

The protein surface usually exhibits one or a few charged spots. If a lipid bilayer contains a significant amount of lipids with oppositely charged head groups, protein adsorption on a bilayer may be energetically favourable due to the protein-lipid electrostatic interaction. The specifics of this case are that the lipids are highly mobile and the protein adsorption is accompanied by the redistribution of lipids between the areas covered and not covered by protein. We present a kinetic model illustrating that this effect is especially interesting if the fraction of the surface covered by charged lipids is relatively low. In this situation, with increasing protein coverage, the protein desorption rate constant rapidly increases while the adsorption rate constant drops, so that there is critical fraction of the area covered by protein. Adsorption above this fraction is hindered both kinetically and thermodynamically.

Formation and dynamics of supported phospholipid membranes on a periodic nanotextured substrate

We have studied and modeled the morphology and dynamics of fluid planar lipid bilayer membranes supported on a textured silicon substrate. The substrate is fabricated to have channels on its surface that are a few hundred nanometers across, with a channel depth of a few hundred nanometers perpendicular to the plane of observation. Using atomic force microscopy and quantitative fluorescence microscopy, we have shown that the bilayer assemblies conform to the underlying nanostructured substrate. As far as dynamics is concerned, when observed over length scales exceeding the dimensions of the nanostructured features, the macroscopic diffusion is anisotropic. However, the macroscopic anisotropy is well simulated using models of diffusion on the nanostructured surface that consider the lipids to diffuse homogeneously and isotropically on the supporting substrate. Consistent with previous observations on less well characterized or less periodic nanostructures, we find that the nanostructured substrate produces an effective anisotropy in macroscopic diffusion of the conformal membrane. More importantly, we demonstrate how quantitative analysis of dynamics probed by larger-scale fluorescence imaging can yield information on nanoscale thin-film morphology.