AFM-based force-clamp monitors lipid bilayer failure kinetics

Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems

During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into a nanoscopic laboratory to directly observe and chemically characterize molecular and cell biological systems under physiological conditions. Here, we review key technological improvements that have established AFM as an analytical tool to observe and quantify native biological systems from the micro- to the nanoscale. Native biological systems include living tissues, cells, and cellular components such as single or complexed proteins, nucleic acids, lipids, or sugars. We showcase the procedures to customize nanoscopic chemical laboratories by functionalizing AFM tips and outline the advantages and limitations in applying different AFM modes to chemically image, sense, and manipulate biosystems at (sub)nanometer spatial and millisecond temporal resolution. We further discuss theoretical approaches to extract the kinetic and thermodynamic parameters of specific biomolecular interactions detected by AFM for single bonds and extend the discussion to multiple bonds. Finally, we highlight the potential of combining AFM with optical microscopy and spectroscopy to address the full complexity of biological systems and to tackle fundamental challenges in life sciences.

Lipid bilayers: Phase behavior and nanomechanics

Lipid membranes are involved in many physiological processes like recognition, signaling, fusion or remodeling of the cell membrane or some of its internal compartments. Within the cell, they are the ultimate barrier, while maintaining the fluidity or flexibility required for a myriad of processes, including membrane protein assembly. The physical properties of in vitro model membranes as model cell membranes have been extensively studied with a variety of techniques, from classical thermodynamics to advanced modern microscopies. Here we review the nanomechanics of solid-supported lipid membranes with a focus in their phase behavior. Relevant information obtained by quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM) as complementary techniques in the nano/mesoscale interface is presented. Membrane morphological and mechanical characterization will be discussed in the framework of its phase behavior, phase transitions and coexistence, in simple and complex models, and upon the presence of cholesterol.

Altering model cell membranes by means of localized magnetic heating

Isolated iron oxide magnetic nanoparticles (MNPs), 12 nm in diameter, coated with oleic acid molecules as capping agents have been deposited by the Langmuir-Blodgett (LB) method onto a model cell membrane incorporating 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and Cholesterol (Chol) in the 1:1 ratio, which was also fabricated by the LB technique. Atomic Force Microscopy (AFM) experiments showed that the application of an alternating magnetic field results in the embedding of the MNPs through the phospholipidic layer. These experimental results reveal that the heating of individual MNPs may induce a local increase in the fluidity of the film with a large control of the spatial and temporal specificity.

Compression, Rupture, and Puncture of Model Membranes at the Molecular Scale

Elastic properties of biological membranes are involved in a large number of membrane functionalities and activities. Conventionally characterized in terms of Young's modulus, bending stiffness and stretching modulus, membrane mechanics can be assessed at high lateral resolution by means of atomic force microscopy (AFM). Here we show that the mechanical response of biomimetic model systems such as supported lipid bilayers (SLBs) is highly affected by the size of the AFM tip employed as a membrane indenter. Our study is focused on phase-separated fluid-gel lipid membranes at room temperature. In a small tip radius regime (≈ 2 nm) and in the case of fluid phase membranes, we show that the tip can penetrate through the membrane minimizing molecular vertical compression and in absence of molecular membrane rupture. In this case, AFM indentation experiments cannot assess the vertical membrane Young's modulus. In agreement with the data reported in the literature, in the case of larger indenters (>2 nm) SLBs can be compressed leading to an evaluation of Young's modulus and membrane maximal withstanding force before rupture. We show that such force increases with the indenter in agreement with the existing theoretical frame. Finally, we demonstrate that the latter has no influence on the number of molecules involved in the rupture process that is observed to be constant and rather dependent on the indenter chemical composition.

How the phage T4 injection machinery works including energetics, forces, and dynamic pathway

The virus bacteriophage T4, from the family Myoviridae, employs an intriguing contractile injection machine to inject its genome into the bacterium Escherichia coli Although the atomic structure of phage T4 is largely understood, the dynamics of its injection machinery remains unknown. This study contributes a system-level model describing the nonlinear dynamics of the phage T4 injection machinery interacting with a host cell. The model employs a continuum representation of the contractile sheath using elastic constants inferred from atomistic molecular-dynamics (MD) simulations. Importantly, the sheath model is coupled to component models representing the remaining structures of the virus and the host cell. The resulting system-level model captures virus-cell interactions as well as competing energetic mechanisms that release and dissipate energy during the injection process. Simulations reveal the dynamical pathway of the injection process as a "contraction wave" that propagates along the sheath, the energy that powers the injection machinery, the forces responsible for piercing the host cell membrane, and the energy dissipation that controls the timescale of the injection process. These results from the model compare favorably with the available (but limited) experimental measurements.

Insights into the structure and nanomechanics of a quatsome membrane by force spectroscopy measurements and molecular simulations

Quatsomes (QS) are unilamellar nanovesicles constituted by quaternary ammonium surfactants and sterols in defined molar ratios. Unlike conventional liposomes, QS are stable upon long storage such as for several years, they show outstanding vesicle-to-vesicle homogeneity regarding size and lamellarity, and they have the structural and physicochemical requirements to be a potential platform for site-specific delivery of hydrophilic and lipophilic molecules. Knowing in detail the structure and mechanical properties of the QS membrane is of great importance for the design of deformable and flexible nanovesicle alternatives, highly pursued in nanomedicine applications such as the transdermal administration route. In this work, we report the first study on the detailed structure of the cholesterol : CTAB QS membrane at the nanoscale, using atomic force microscopy (AFM) and spectroscopy (AFM-FS) in a controlled liquid environment (ionic medium and temperature) to assess the topography of supported QS membranes (SQMs) and to evaluate the local membrane mechanics. We further perform molecular dynamics (MD) simulations to provide an atomistic interpretation of the obtained results. Our results are direct evidence of the bilayer nature of the QS membrane, with characteristics of a fluid-like membrane, compact and homogeneous in composition, and with structural and mechanical properties that depend on the surrounding environment. We show how ions alter the lateral packing, modifying the membrane mechanics. We observe that according to the ionic environment and temperature, different domains may coexist in the QS membranes, ascribed to variations in molecular tilt angles. Our results indicate that QS membrane properties may be easily tuned by altering the lateral interactions with either different environmental ions or counterions.

Pulling lipid tubes from supported bilayers unveils the underlying substrate contribution to the membrane mechanics

Cell processes like endocytosis, membrane resealing, signaling and transcription involve conformational changes which depend on the chemical composition and the physicochemical properties of the lipid membrane. The better understanding of the mechanical role of lipids in cell membrane force-triggered and sensing mechanisms has recently become the focus of attention. Different membrane models and experimental methodologies are commonly explored. While general approaches involve controlled vesicle deformation using micropipettes or optical tweezers, due to the local and dynamic nature of the membrane, high spatial resolution atomic force microscopy (AFM) has been widely used to study the mechanical compression and indentation of supported lipid bilayers (SLBs). However, the substrate contribution remains unkown. Here, we demonstrate how pulling lipid tubes with an AFM out of model SLBs can be used to assess the nanomechanics of SLBs through the evaluation of the tube growing force (Ftube), allowing for very local evaluation with high spatial and force resolution of the lipid membrane tension. We first validate this approach to determine the contribution of different phospholipids, by varying the membrane composition, in both one-component and phase-segregated membranes. Finally, we successfully assess the contribution of the underlying substrate to the membrane mechanics, demonstrating that SLB models may represent an intermediate scenario between a free membrane (blebs) and a cytoskeleton supported membrane.

Multilamellar nanovesicles show distinct mechanical properties depending on their degree of lamellarity

Small multilamellar vesicles may have benefits over unilamellar vesicles for drug delivery, such as an increased volume for hydrophobic drugs. In addition, their altered mechanical properties might be beneficial for cellular uptake. Here, we show how atomic force microscopy (AFM) can be used to detect and characterize multilamellar vesicles. We quantify the size of each break event occurring during AFM nanoindentations, which shows good agreement with the thickness of supported lipid bilayers. Analyzing the size and number of these events for individual vesicles allows us to distinguish between vesicles consisting of 1 up to 5 bilayers. We validate these results by comparison with correlative cryo-electron microscopy (cryo-EM) data at the vesicle population level. Finally, we quantify the vesicle geometry and mechanical properties, and show that with additional bilayers adherent vesicles are more spherical and stiffer. Surprisingly, at ∼20% stiffening for each additional bilayer, the vesicle stiffness scales only weakly with lamellarity. Our results show the potential of AFM for studying liposomal nanoparticles and suggest that small multilamellar vesicles may have beneficial mechanical properties for cellular uptake.

The Nanomechanics of Lipid Multibilayer Stacks Exhibits Complex Dynamics

The nanomechanics of lipid membranes regulates a large number of cellular functions. However, the molecular mechanisms underlying the plastic rupture of individual bilayers remain elusive. This study uses force clamp spectroscopy to capture the force-dependent dynamics of membrane failure on a model diphytanoylphosphatidylcholine multilayer stack, which is devoid of surface effects. The obtained kinetic measurements demonstrate that the rupture of an individual lipid bilayer, occurring in the bilayer parallel plane, is a stochastic process that follows a log-normal distribution, compatible with a pore formation mechanism. Furthermore, the vertical individual force-clamp trajectories, occurring in the bilayer orthogonal bilayer plane, reveal that rupturing process occurs through distinct intermediate mechanical transition states that can be ascribed to the fine chemical composition of the hydrated phospholipid moiety. Altogether, these results provide a first description of unanticipated complexity in the energy landscape governing the mechanically induced bilayer rupture process.

True non-contact atomic force microscopy imaging of heterogeneous biological samples in liquids: topography and material contrast

The present work analyses how the tip-sample interaction signals critically determine the operation of an Atomic Force Microscope (AFM) set-up immersed in liquid. On heterogeneous samples, the conservative tip-sample interaction may vary significantly from point to point - in particular from attractive to repulsive - rendering correct feedback very challenging. Lipid membranes prepared on a mica substrate are analyzed as reference samples which are locally heterogeneous (material contrast). The AFM set-up is operated dynamically at low oscillation amplitude and all available experimental data signals - the normal force, as well as the amplitude and frequency - are recorded simultaneously. From the analysis of how the dissipation (oscillation amplitude) and the conservative interaction (normal force and resonance frequency) vary with the tip-sample distance we conclude that dissipation is the only appropriate feedback source for stable and correct topographic imaging. The normal force and phase then carry information about the sample composition ("chemical contrast"). Dynamic AFM allows imaging in a non-contact regime where essentially no forces are applied, rendering dynamic AFM a truly non-invasive technique.

Structure and Nanomechanics of Model Membranes by Atomic Force Microscopy and Spectroscopy: Insights into the Role of Cholesterol and Sphingolipids

Biological membranes mediate several biological processes that are directly associated with their physical properties but sometimes difficult to evaluate. Supported lipid bilayers (SLBs) are model systems widely used to characterize the structure of biological membranes. Cholesterol (Chol) plays an essential role in the modulation of membrane physical properties. It directly influences the order and mechanical stability of the lipid bilayers, and it is known to laterally segregate in rafts in the outer leaflet of the membrane together with sphingolipids (SLs). Atomic force microscope (AFM) is a powerful tool as it is capable to sense and apply forces with high accuracy, with distance and force resolution at the nanoscale, and in a controlled environment. AFM-based force spectroscopy (AFM-FS) has become a crucial technique to study the nanomechanical stability of SLBs by controlling the liquid media and the temperature variations. In this contribution, we review recent AFM and AFM-FS studies on the effect of Chol on the morphology and mechanical properties of model SLBs, including complex bilayers containing SLs. We also introduce a promising combination of AFM and X-ray (XR) techniques that allows for in situ characterization of dynamic processes, providing structural, morphological, and nanomechanical information.

Impact of galactosylceramides on the nanomechanical properties of lipid bilayer models: an AFM-force spectroscopy study

Galactosylceramides (GalCer) are glycosphingolipids bound to a monosaccharide group, responsible for inducing extensive hydrogen bonds that yield their alignment and accumulation in the outer leaflet of the biological membrane together with cholesterol (Chol) in rafts. In this work, the influence of GalCer on the nanomechanical properties of supported lipid bilayers (SLBs) based on DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) and DLPC (1,2-didodecanoyl-sn-glycero-3-phosphocoline) as model systems was assessed. Phosphatidylcholine (PC):GalCer SLBs were characterized by means of differential scanning calorimetry (DSC) and atomic force microscopy (AFM), in both imaging and force spectroscopy (AFM-FS) modes. Comparing both PC systems, we determined that the behaviour of SLB mixtures is governed by the PC phase-like state at the working temperature. While a phase segregated system is observed for DLPC:GalCer SLBs, GalCer are found to be dissolved in DPPC SLBs for GalCer contents up to 20 mol%. In both systems, the incorporation of GalCer intensifies the nanomechanical properties of SLBs. Interestingly, segregated domains of exceptionally high mechanical stability are formed in DLPC:GalCer SLBs. Finally, the role of 20 mol% Chol in GalCer organization and function in the membranes was assessed. Both PC model systems displayed phase segregation and remarkable nanomechanical stability when GalCer and Chol coexist in SLBs.

Atomic force microscopy characterization of palmitoylceramide and cholesterol effects on phospholipid bilayers: a topographic and nanomechanical study

Supported planar bilayers (SPBs) on mica substrates have been studied at 23 °C under atomic force microscopy (AFM)-based surface topography and force spectroscopy with two main objectives: (i) to characterize palmitoylceramide (pCer)-induced gel (Lβ) domains in binary mixtures with either its sphingolipid relative palmitoylsphingomyelin (pSM) or the glycerophospholipid dipalmitoylphosphorylcholine (DPPC) and (ii) to evaluate effects of incorporating cholesterol (Chol) into the previous mixtures in terms of Cer and Chol cooperation for the generation of lamellar gel (Lβ) phases of ternary composition. Binary phospholipid/pCer mixtures at XpCer < 0.33 promote the generation of laterally segregated micron-sized pCer-rich domains. Their analysis at different phospholipid/pCer ratios, by means of domain thickness, roughness, and mechanical resistance to tip piercing, reveals unvarying AFM-derived features over increasing pCer concentrations. These results suggest that the domains grow in size with increasing pCer concentrations while keeping a constant phospholipid/pCer stoichiometry. Moreover, the data show important differences between pCer interactions with pSM or DPPC. Gel domains generated in pSM/pCer bilayers are thinner than the pSM-rich surrounding phase, while the opposite is observed in DPPC/pCer mixtures. Furthermore, a higher breakthrough force is observed for pSM/pCer as compared to DPPC/pCer domains, which can be associated with the preferential pCer interaction with its sphingolipid relative pSM. Cholesterol incorporation into both binary mixtures at a high Chol and pCer ratio abolishes any phospholipid/pCer binary domains. Bilayers with properties different from any of the pure or binary samples are observed instead. The data support no displacement of Chol by pCer or vice versa under these conditions, but rather a preferential interaction between the two hydrophobic lipids.

Role of the fast kinetics of pyroglutamate-modified amyloid-β oligomers in membrane binding and membrane permeability

Membrane permeability to ions and small molecules is believed to be a critical step in the pathology of Alzheimer’s disease (AD). Interactions of oligomers formed by amyloid-β (Aβ) peptides with the plasma cell membrane are believed to play a fundamental role in the processes leading to membrane permeability. Among the family of Aβs, pyroglutamate (pE)-modified Aβ peptides constitute the most abundant oligomeric species in the brains of AD patients. Although membrane permeability mechanisms have been studied for full-length Aβ_1–40/42 peptides, these have not been sufficiently characterized for the more abundant Aβ_pE3–42 fragment. Here we have compared the adsorbed and membrane-inserted oligomeric species of Aβ_pE3–42 and Aβ_1–42 peptides. We find lower concentrations and larger dimensions for both species of membrane-associated Aβ_pE3–42 oligomers. The larger dimensions are attributed to the faster self-assembly kinetics of Aβ_pE3–42, and the lower concentrations are attributed to weaker interactions with zwitterionic lipid headgroups. While adsorbed oligomers produced little or no significant membrane structural damage, increased membrane permeabilization to ionic species is understood in terms of enlarged membrane-inserted oligomers. Membrane-inserted Aβ_pE3–42 oligomers were also found to modify the mechanical properties of the membrane. Taken together, our results suggest that membrane-inserted oligomers are the primary species responsible for membrane permeability.

Morphological and nanomechanical behavior of supported lipid bilayers on addition of cationic surfactants

The addition of surfactants to lipid bilayers is important for the modulation of lipid bilayer properties (e.g., in protein reconstitution and development of nonviral gene delivery vehicles) and to provide insight on the properties of natural biomembranes. In this work, the thermal behavior, organization, and nanomechanical stability of model cationic lipid-surfactant bilayers have been investigated. Two different cationic surfactants, hexadecyltrimethylammonium bromide (CTAB) and a novel derivative of the amino acid serine (Ser16TFAc), have been added (up to 50 mol %) to both liposomes and supported lipid bilayers (SLBs) composed by the zwitterionic phospholipid DPPC. The thermal phase behavior of mixed liposomes has been probed by differential scanning calorimetry (DSC), and the morphology and nanomechanical properties of mixed SLBs by atomic force microscopy-based force spectroscopy (AFM-FS). Although DSC thermograms show different results for the two mixed liposomes, when both are deposited on mica substrates similar trends on the morphology and the mechanical response of the lipid-surfactant bilayers are observed. DSC thermograms indicate microdomain formation in both systems, but while CTAB decreases the degree of organization on the liposome bilayer, Ser16TFAc ultimately induces the opposite effect. Regarding the AFM-FS studies, they show that microphase segregation occurs for these systems and that the effect is dependent on the surfactant content. In both SLB systems, different microdomains characterized by their height and breakthrough force Fb are formed. The molecular organization and composition is critically discussed in the light of our experimental results and literature data on similar lipid-surfactant systems.

Force dependency of biochemical reactions measured by single-molecule force-clamp spectroscopy

Here we describe a protocol for using force-clamp spectroscopy to precisely quantify the effect of force on biochemical reactions. A calibrated force is used to control the exposure of reactive sites in a single polyprotein substrate composed of repeated domains. The use of polyproteins allows the identification of successful single-molecule recordings from unambiguous mechanical unfolding fingerprints. Biochemical reactions are then measured directly by detecting the length changes of the substrate held at a constant force. We present the layout of a force-clamp spectrometer along with protocols to design and conduct experiments. These experiments measure reaction kinetics as a function of applied force. We show sample data of the force dependency of two different reactions, protein unfolding and disulfide reduction. These data, which can be acquired in just a few days, reveal mechanistic details of the reactions that currently cannot be resolved by any other technique.

Atomic force microscopy: a versatile tool to probe the physical and chemical properties of supported membranes at the nanoscale

Atomic force microscopy (AFM) was developed in the 1980s following the invention of its precursor, scanning tunneling microscopy (STM), earlier in the decade. Several modes of operation have evolved, demonstrating the extreme versatility of this method for measuring the physicochemical properties of samples at the nanoscopic scale. AFM has proved an invaluable technique for visualizing the topographic characteristics of phospholipid monolayers and bilayers, such as roughness, height or laterally segregated domains. Implemented modes such as phase imaging have also provided criteria for discriminating the viscoelastic properties of different supported lipid bilayer (SLB) regions. In this review, we focus on the AFM force spectroscopy (FS) mode, which enables determination of the nanomechanical properties of membrane models. The interpretation of force curves is presented, together with newly emerging techniques that provide complementary information on physicochemical properties that may contribute to our understanding of the structure and function of biomembranes. Since AFM is an imaging technique, some basic indications on how real-time AFM imaging is evolving are also presented at the end of this paper.

Influence of cholesterol on the phase transition of lipid bilayers: a temperature-controlled force spectroscopy study

Cholesterol (Chol) plays the essential function of regulating the physical properties of the cell membrane by controlling the lipid organization and phase behavior and, thus, managing the membrane fluidity and its mechanical strength. Here, we explore the model system DPPC:Chol by means of temperature-controlled atomic force microscopy (AFM) imaging and AFM-based force spectroscopy (AFM-FS) to assess the influence of Chol on the membrane ordering and stability. We analyze the system in a representative range of compositions up to 50 mol % Chol studying the phase evolution upon temperature increase (from room temperature to temperatures high above the T(m) of the DPPC bilayer) and the corresponding (nano)mechanical stability. By this means, we correlate the mechanical behavior and composition with the lateral order of each phase present in the bilayers. We prove that low Chol contents lead to a phase-segregated system, whereas high contents of Chol can give a homogeneous bilayer. In both cases, Chol enhances the mechanical stability of the membrane, and an extraordinarily stable system is observed for equimolar fractions (50 mol % Chol). In addition, even when no thermal transition is detected by the traditional bulk analysis techniques for liposomes with high Chol content (40 and 50 mol %), we demonstrate that temperature-controlled AFM-FS is capable of identifying a thermal transition for the supported lipid bilayers. Finally, our results validate the AFM-FS technique as an ideal platform to differentiate phase coexistence and transitions in lipid bilayers and bridge the gap between the results obtained by traditional methods for bulk analysis, the theoretical predictions, and the behavior of these systems at the nanoscale.