Mechanical mapping of single membrane proteins at submolecular resolution

Side-view optical microscopy-assisted atomic force microscopy for thickness-dependent nanobiomechanics

The mechanical properties of biomaterials play an important role in regulating life processes, and thus accurately delineating the mechanical properties of biomaterials is critical to understand their functionality. Particularly, atomic force microscopy (AFM) has become a powerful and standard tool for characterizing and analyzing the nanomechanical properties of biomaterials, and providing a capability to visualize the thickness of the specimen during AFM-based force spectroscopy experiments benefits the biomedical applications of AFM. Here, we present a study of side-view optical microscopy-assisted AFM based on the integration of AFM and a detachable side-view optical microscopy module, which is able to image in real time the AFM indentation process from the side-view perspective and consequently facilitates the utilization of AFM-based indentation assay to precisely detect the mechanical properties of a specimen by taking its thickness into account. The effectiveness of side-view optical microscopy-assisted AFM was confirmed on four different types of biomaterial systems, including microfabricated structures, hydrogels, living cells, and cell spheroids, and the experimental results significantly show that the mechanical properties of samples at the micro/nanoscale are closely related to their thickness, vividly illustrating side-view optical microscopy-assisted AFM as a promising approach for accurate nanomechanics of biomaterial systems. The study provides additional possibilities for measuring the thickness-dependent nanomechanical properties of biomaterials by AFM, which will enable AFM-based force spectroscopy technology to address more biological issues with enhanced precision and will benefit the field of mechanobiology.

Photosynthetic Protein-Based Retinal Ganglion Cell Receptive Fields for Detecting Edges and Brightness Illusions

Bacteriorhodopsin, isolated from a halophilic bacterium, is a photosynthetic protein with a structure and function similar to those of the visual pigment rhodopsin. A voltaic cell with bacteriorhodopsin sandwiched between two transparent electrodes exhibits a time-differential response akin to that observed in retinal ganglion cells. It is intriguing as a means to emulate excitation and inhibition in the neural response. Here, we present a neuromorphic device emulating the retinal ganglion cell receptive field fabricated by patterning bacteriorhodopsin onto two transparent electrodes and encapsulating them with an electrolyte solution. This protein-based artificial ganglion cell receptive field is characterized as a bandpass filter that simultaneously replicates excitatory and inhibitory responses within a single element, successfully detecting image edges and phenomena of brightness illusions. The device naturally emulates the highly interacting ganglion cell receptive fields by exploiting the inherent properties of proteins without the need for electronic components, bias power supply, or an external operating circuit.

Reduction of alcohol-induced mitochondrial damage with ginsenoside Rg1 studied by atomic force microscopy

The quantification of mitochondrial morphology and mechanical properties is useful for the diagnosis and treatment of mitochondrial and alcoholic liver disease. In this study, the effects of ginsenoside Rg1 (G-Rg1) on the morphology and mechanical properties of mitochondria that had suffered alcohol-induced damage were investigated under near-physiological conditions. Additionally, the morphological and mechanical properties of mitochondria were quantified through atomic force microscopy. Atomic force microscopy revealed that alcohol-induced significant morphological changes in mitochondria. Compared with that of the mitochondria of normal hepatocytes, the average surface area of the damaged mitochondria was found to have increased significantly under the influence of alcohol. Furthermore, the mitochondrial area tended to be normal under the action of G-Rg1, whilst other parameters (length, width and perimeter) were significantly different from those of the mitochondria with the alcohol-induced damage. Simultaneously, alcohol significantly reduced the adhesion and elastic modulus of mitochondria, whilst the adhesion and elastic modulus of mitochondria in the G-Rg1 treatment group were closer to the values of normal mitochondria. This study overall showed that G-Rg1 could effectively alleviate the swelling and anomalous mechanical properties of mitochondria induced by alcohol.

Attenuation of alcohol-induced hepatocyte damage by ginsenoside Rg1 evaluated using atomic force microscopy

Alcoholic liver disease is an important cause of death worldwide. Hepatocyte apoptosis is commonly observed in alcoholic liver disease. In this study, we investigated the effect of ginsenoside Rg1 (G-Rg1), an organic component of ginseng, on the alcohol-induced morphological and biophysical properties of hepatocytes. Human hepatocytes (HL-7702) were treated in vitro with alcohol and G-Rg1. The cell morphology was observed using scanning electron microscopy. Cell height, roughness, adhesion, and elastic modulus were detected using atomic force microscopy. We found that alcohol significantly induced hepatocyte apoptosis, whereas G-Rg1 attenuated the alcohol-induced hepatocyte damage. Scanning electron microscopy revealed that alcohol-induced significant morphological changes in hepatocytes, including decreased cell contraction, roundness, and pseudopods, whereas G-Rg1 inhibited these negative changes. Atomic force microscopy revealed that alcohol increased the cell height and decreased the adhesion and elastic modulus of hepatocytes. Following treatment with G-Rg1, the cell height, adhesion, and elastic modulus of alcohol-injured hepatocytes were all similar to those of normal cells. Thus, G-Rg1 can attenuate the alcohol-induced damage to hepatocytes by modulating the morphology and biomechanics of the cells. RESEARCH HIGHLIGHTS: In this study, the morphological characteristics of hepatocytes were observed using SEM. The changes in hepatocyte three-dimensional images and biomechanical action caused by alcohol and G-Rg1 were examined at the nanoscale using AFM under near-physiological conditions. Alcohol-induced hepatocytes showed abnormal morphology and biophysical properties. G-Rg1 attenuated the alcohol-induced damage to hepatocytes by modulating the morphology and biomechanics of the cells.

Nanomechanical Signatures of Extracellular Vesicles from Hematologic Cancer Patients Unraveled by Atomic Force Microscopy for Liquid Biopsy

Cells release extracellular vesicles (EVs) as the carriers for intercellular communications to regulate life activities. Particularly, it is increasingly apparent that mechanical forces play an essential role in biological systems. The nanomechanical properties of EVs and their dynamics in cancer development are still not fully understood. Herein, with the use of atomic force microscopy (AFM), the nanomechanical signatures of EVs from the liquid biopsies of hematologic cancer patients were unraveled. Single native EVs were probed by AFM under aqueous conditions. The elastic and viscous properties of EVs were measured and visualized to correlate EV mechanics with EV geometry. Experimental results remarkably reveal the significant differences in EV mechanics among multiple myeloma patients, lymphoma patients, and healthy volunteers. The study unveils the unique nanomechanical signatures of EVs in hematologic cancers, which will benefit the studies of liquid biopsies for cancer diagnosis and prognosis with translational significance.

Intramolecular covalent bonds in Gram-positive bacterial surface proteins

Gram-positive bacteria experience considerable mechanical perturbation when adhering to host surfaces during colonization and infection. They have evolved various adhesion proteins that are mechanically robust to ensure strong surface adhesion. Recently, it was discovered that these adhesion proteins contain rare, extra intramolecular covalent bonds that stabilize protein structures and participate in surface bonding. These intramolecular covalent bonds include isopeptides, thioesters, and ester bonds, which often form spontaneously without the need for additional enzymes. With the development of single-molecule force spectroscopy techniques, the detailed mechanical roles of these intramolecular covalent bonds have been revealed. In this review, we summarize the recent advances in this area of research, focusing on the link between the mechanical stability and function of these covalent bonds in Gram-positive bacterial surface proteins. We also highlight the potential impact of these discoveries on the development of novel antibiotics and chemical biology tools.

Super-resolution mid-infrared spectro-microscopy of biological applications through tapping mode and peak force tapping mode atomic force microscope

Small biomolecules at the subcellular level are building blocks for the manifestation of complex biological activities. However, non-intrusive in situ investigation of biological systems has been long daunted by the low spatial resolution and poor sensitivity of conventional light microscopies. Traditional infrared (IR) spectro-microscopy can enable label-free visualization of chemical bonds without extrinsic labeling but is still bound by Abbe's diffraction limit. This review article introduces a way to bypass the optical diffraction limit and improve the sensitivity for mid-IR methods - using tip-enhanced light nearfield in atomic force microscopy (AFM) operated in tapping and peak force tapping modes. Working principles of well-established scattering-type scanning near-field optical microscopy (s-SNOM) and two relatively new techniques, namely, photo-induced force microscopy (PiFM) and peak force infrared (PFIR) microscopy, will be briefly presented. With ∼ 10-20 nm spatial resolution and monolayer sensitivity, their recent applications in revealing nanoscale chemical heterogeneities in a wide range of biological systems, including biomolecules, cells, tissues, and biomaterials, will be reviewed and discussed. We also envision several future improvements of AFM-based tapping and peak force tapping mode nano-IR methods that permit them to better serve as a versatile platform for uncovering biological mechanisms at the fundamental level.

Use of Atomic Force Microscopy to Characterize LPS Perturbations

Lipopolysaccharide (LPS) on Gram-negative bacterial outer membranes is the first target for antimicrobial agents, due to their spatial proximity to outer environments of microorganisms. To understand the molecular nature and their interaction with antimicrobial agents, establishing a model LPS structure is of key importance. Here, we describe procedures for following LPS layer attachment to a solid surface and provide protocols for measuring bacterial membrane morphology after adding antibiotics. Using atomic force microscopy (AFM), we show methods to characterize the effects of antibiotic polymyxin B to the LPS layers at the nanoscale.

DNA Studies: Latest Spectroscopic and Structural Approaches

This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.

Evaluation of the optimal dosage of BMP-9 through the comparison of bone regeneration induced by BMP-9 versus BMP-2 using an injectable microparticle embedded thermosensitive polymeric carrier in a rat cranial defect model

Bone morphogenetic proteins (BMPs) are well known as enhancers and facilitators of osteogenesis during bone regeneration. The use of recombinant BMP-2 (rhBMP-2) in bone defect healing has drawbacks, which has driven the scouting for alternatives, such as recombinant BMP-9 (rhBMP-9), to provide comparable new bone formation. However, the dosage of rhBMP-9 is quintessential for the facilitation of adequate bone defect healing. Therefore, this study has been designed to evaluate the optimal dosage of BMP-9 by comparing the bone defect healing induced by rhBMP-9 over rhBMP-2. The chitosan (CS) microparticles (MPs), coated with BMPs, were embedded in a thermoresponsive methylcellulose (MC) and calcium alginate (Alg) based injectable delivery system containing a dosage of either 0.5 μg or 1.5 μg of the respective rhBMP per bone defect. A 5 mm critical-sized cranial defect rat model has been used in this study, and bone tissues were harvested at eight weeks post-surgery. The standard tools for comparing the new bone regeneration included micro computerized tomography (micro-CT) and histological analysis. A novel perspective of analyzing the new bone quality and crystallinity was employed by using Raman spectroscopy, along with its elastic modulus quantified through Atomic Force Microscopy (AFM). Results showed that the rhBMP-9 administered at a dosage of 1.5 μg per bone defect, using this delivery system, can adequately facilitate the bone void filling with ample new bone mineralization and crystallinity as compared to rhBMP-2, thus approving the hypothesis for a viable rhBMP-2 alternative.

Peak force tapping atomic force microscopy for advancing cell and molecular biology

The advent of atomic force microscopy (AFM) provides an exciting tool to detect molecular and cellular behaviors under aqueous conditions. AFM is able to not only visualize the surface topography of the specimens, but also can quantify the mechanical properties of the specimens by force spectroscopy assay. Nevertheless, integrating AFM topographic imaging with force spectroscopy assay has long been limited due to the low spatiotemporal resolution. In recent years, the appearance of a new AFM imaging mode called peak force tapping (PFT) has shattered this limit. PFT allows AFM to simultaneously acquire the topography and mechanical properties of biological samples with unprecedented spatiotemporal resolution. The practical applications of PFT in the field of life sciences in the past decade have demonstrated the excellent capabilities of PFT in characterizing the fine structures and mechanics of living biological systems in their native states, offering novel possibilities to reveal the underlying mechanisms guiding physiological/pathological activities. In this paper, the recent progress in cell and molecular biology that has been made with the utilization of PFT is summarized, and future perspectives for further progression and biomedical applications of PFT are provided.

Practical Guide to Single-Protein AFM Nanomechanical Spectroscopy Mapping: Insights and Pitfalls As Unraveled by All-Atom MD Simulations on Immunoglobulin G

Atomic force microscopy is an invaluable characterization tool in almost every biophysics laboratory. However, obtaining atomic/sub-nanometer resolution on single proteins has thus far remained elusive-a feat long achieved on hard substrates. In this regard, nanomechanical spectroscopy mapping may provide a viable approach to overcome this limitation. By complementing topography with mechanical properties measured locally, one may thus enhance spatial resolution at the single-protein level. In this work, we perform all-atom molecular dynamics simulations of the indentation process on a single immunoglobulin G (IgG) adsorbed on a graphene slab. Our simulations reveal three different stages as a function of strain: a noncontact regime-where the mechanical response is linked to the presence of the water environment- followed by an elastic response and a final plastic deformation regime. In the noncontact regime, we are able to identify hydrophobic/hydrophilic patches over the protein. This regime provides the most local mechanical information that allows one to discern different regions with similar height/topography and leads to the best spatial resolution. In the elastic regime, we conclude that the Young modulus is a well-defined property only within mechanically decoupled domains. This is caused by the fact that the elastic deformation is associated with a global reorganization of the domain. Differences in the mechanical response are large enough to clearly resolve domains within a single protein, such as the three subunits forming the IgG. Two events, unfolding or protein slipping, are observed in the plastic regime. Our simulations allow us to characterize these two processes and to provide a strategy to identify them in the force curves. Finally, we elaborate on possible challenges that could hamper the interpretation of such experiments/simulations and how to overcome them. All in all, our simulations provide a detailed picture of nanomechanical spectroscopy mapping on single proteins, showing its potential and the challenges that need to be overcome to unlock its full potential.

Liquid-Phase Peak Force Infrared Microscopy for Chemical Nanoimaging and Spectroscopy

Peak force infrared (PFIR) microscopy is an emerging atomic force microscopy that bypasses Abbe's diffraction limit in achieving chemical nanoimaging and spectroscopy. The PFIR microscopy mechanically detects the infrared photothermal responses in the dynamic tip-sample contact of peak force tapping mode and has been applied for a variety of samples, ranging from soft matters, photovoltaic heterojunctions, to polaritonic materials under the air conditions. In this article, we develop and demonstrate the PFIR microscopy in the liquid phase for soft matters and biological samples. With the capability of controlling fluid compositions on demand, the liquid-phase peak force infrared (LiPFIR) microscopy enables in situ tracking of the polymer surface reorganization in fluids and detecting the product of click chemical reaction in the aqueous phase. Both broadband spectroscopy and infrared imaging with ∼10 nm spatial resolution are benchmarked in the fluid phase, together with complementary mechanical information. We also demonstrate the LiPFIR microscopy on revealing the chemical composition of a budding site of yeast cell wall particles in water as an application on biological structures. The label-free, nondestructive chemical nanoimaging and spectroscopic capabilities of the LiPFIR microscopy will facilitate the investigations of soft matters and their transformations at the solid/liquid interface.

Effects of Dissolved Gases on the Amyloid Fibril Morphology

The onset or progression of numerous neurodegenerative diseases occurs due to aggregation of proteins that ultimately form fibrils. The assembly and morphology of fibrils are susceptible to environmental factors. In this work, we used atomic force microscopy (AFM) to investigate the effects of dissolved nitrogen and oxygen molecules on the morphology of fibrils formed by a hydrophobic amyloid peptide implicated in amyotrophic lateral sclerosis, 15 repeats of glycine-alanine, on a highly oriented pyrolytic graphite substrate. We started with preformed fibril solutions that were then diluted with buffers of different gas conditions, resulting in the aggregation of the fibrils into different morphologies that were revealed by AFM after adsorption on the substrate. Straight fibrils were observed in both degassed and ambient buffers, but a stronger lateral association was seen in degassed buffers. Smaller and softer fibrils were observed in O₂-supersaturated buffers, and plaque-like fibril aggregates of considerably large size were evident in N₂-supersaturated buffers. In overnight incubation experiments, we observed changes in both the morphology and height of the fibril aggregates, and their evolution varied with different gas conditions. These findings indicate that the gas type and concentration affect the aggregation of amyloid fibrils and may facilitate the development of biomaterial applications and treatments for amyloid-related diseases.

Atomic force microscopy: Emerging illuminated and operando techniques for solar fuel research

Integrated photoelectrochemical devices rely on the synergy between components to efficiently generate sustainable fuels from sunlight. The micro- and/or nanoscale characteristics of the components and their interfaces often control critical processes of the device, such as charge-carrier generation, electron and ion transport, surface potentials, and electrocatalysis. Understanding the spatial properties and structure-property relationships of these components can provide insight into designing scalable and efficient solar fuel components and systems. These processes can be probed ex situ or in situ with nanometer-scale spatial resolution using emerging scanning-probe techniques based on atomic force microscopy (AFM). In this Perspective, we summarize recent developments of AFM-based techniques relevant to solar fuel research. We review recent progress in AFM for (1) steady-state and dynamic light-induced surface photovoltage measurements; (2) nanoelectrical conductive measurements to resolve charge-carrier heterogeneity and junction energetics; (3) operando investigations of morphological changes, as well as surface electrochemical potentials, currents, and photovoltages in liquids. Opportunities for research include: (1) control of ambient conditions for performing AFM measurements; (2) in situ visualization of corrosion and morphological evolution of electrodes; (3) operando AFM techniques to allow nanoscale mapping of local catalytic activities and photo-induced currents and potentials.

Mechanical Properties of Sub-Microbubbles with a Nanoparticle-Decorated Polymer Shell

Nanoparticle-decorated polymer-coated sub-microbubbles (NP-P-coated SMBs), as proved, have shown promising application prospects in ultrasound imaging, magnetic resonance imaging, drug delivery, and so forth. However, the quantitative evaluation of the stability and mechanical properties of single NP-P-coated SMB is absent. Here, we first reported the stiffness and Young's modulus of single NP-P-coated SMB obtained by the PeakForce mode of atomic force microscopy. Such NP-P-coated SMBs could maintain perfect spherical shapes and have a thinner shell thickness (about 10 nm), as determined by characterization using a transmission electron microscope. Young's modulus of NP-P-coated SMBs is about 4.6 ± 1.2 GPa, and their stiffness is about 15.0 ± 3.1 N/m. Both modulus and stiffness are obtained from the linear region in the force-deformation curve and are nearly independent of their sizes. These results should be very useful to evaluate their stability, which plays a key role in maintaining the shell drug loading and acoustic capabilities.

Ultra-Sensitive and Label-Free Probing of Binding Affinity Using Recognition Imaging

Reliable quantification of binding affinity is important in biotechnology and pharmacology and increasingly coupled with a demand for ultrasensitivity, nanoscale resolution, and minute sample amounts. Standard techniques are not able to meet these criteria. This study provides a new platform based on atomic force microscopy (AFM)-derived recognition imaging to determine affinity by visualizing single molecular bindings on nanosize dendrons. Using DNA hybridization as a demonstrator, an AFM sensor adorned with a cognate binding strand senses and localizes target DNAs at nanometer resolution. To overcome the limitations of speed and resolution, the AFM cantilever is sinusoidally oscillated close to resonance conditions at small amplitudes. The equilibrium dissociation constant of capturing DNA duplexes was obtained, yielding 2.4 × 10^-10 M. Our label-free single-molecular biochemical analysis approach evidences the utility of recognition imaging and analysis in quantifying biomolecular interactions of just a few hundred molecules.

AFM-Based Force Spectroscopy Guided by Recognition Imaging: A New Mode for Mapping and Studying Interaction Sites at Low Lateral Density

Ligand binding to receptors is one of the most important regulatory elements in biology as it is the initiating step in signaling pathways and cascades. Thus, precisely localizing binding sites and measuring interaction forces between cognate receptor-ligand pairs leads to new insights into the molecular recognition involved in these processes. Here we present a detailed protocol about applying a technique, which combines atomic force microscopy (AFM)-based recognition imaging and force spectroscopy for studying the interaction between (membrane) receptors and ligands on the single molecule level. This method allows for the selection of a single receptor molecule reconstituted into a supported lipid membrane at low density, with the subsequent quantification of the receptor-ligand unbinding force. Based on AFM tapping mode, a cantilever tip carrying a ligand molecule is oscillated across a membrane. Topography and recognition images of reconstituted receptors are recorded simultaneously by analyzing the downward and upward parts of the oscillation, respectively. Functional receptor molecules are selected from the recognition image with nanometer resolution before the AFM is switched to the force spectroscopy mode, using positional feedback control. The combined mode allows for dynamic force probing on different pre-selected molecules. This strategy results in higher throughput when compared with force mapping. Applied to two different receptor-ligand pairs, we validated the presented new mode.

Investigation of Bacterial Curli Production and Adhesion Using AFM

Escherichia coli cells containing the amyloid curli protein CsgA bind to abiotic surfaces and the extracellular matrix protein fibronectin. Here we describe procedures for following bacterial attachment to glass surfaces and provide protocols for coupling bacterial cells to AFM tips. Using single microbial cell force spectroscopy in physiological environment, we show methods to probe mechanical parameters and the dissociation of curliated E. coli cells from fibronectin surfaces by quantifying Young's modulus, unbinding forces, and de-adhesion works.

Sensing the Ultrastructure of Bacterial Surfaces and Their Molecular Binding Forces Using AFM

In this protocol, we provide a detailed step-by-step bacterial surface imaging and molecular analysis procedure. With SPM (scanning probe microscopy)-based dynamic force microscopy (DFM) imaging, we achieved a so far unprecedented resolution of ~1 nm on the outer surface layer of Tannerella forsythia and monitored the production of curli fibers on Escherichia coli in physiological conditions. Moreover, using these immobilization methods, single-molecule force spectroscopy experiments were conducted on living bacterial cells.

Compressive Force Spectroscopy: From Living Cells to Single Proteins

One of the most successful applications of atomic force microscopy (AFM) in biology involves monitoring the effect of force on single biological molecules, often referred to as force spectroscopy. Such studies generally entail the application of pulling forces of different magnitudes and velocities upon individual molecules to resolve individualistic unfolding/separation pathways and the quantification of the force-dependent rate constants. However, a less recognized variation of this method, the application of compressive force, actually pre-dates many of these "tensile" force spectroscopic studies. Further, beyond being limited to the study of single molecules, these compressive force spectroscopic investigations have spanned samples as large as living cells to smaller, multi-molecular complexes such as viruses down to single protein molecules. Correspondingly, these studies have enabled the detailed characterization of individual cell states, subtle differences between seemingly identical viral structures, as well as the quantification of rate constants of functionally important, structural transitions in single proteins. Here, we briefly review some of the recent achievements that have been obtained with compressive force spectroscopy using AFM and highlight exciting areas of its future development.

Elastic strain and twist analysis of protein structural data and allostery of the transmembrane channel KcsA

The abundance of available static protein structural data makes the more effective analysis and interpretation of this data a valuable tool to supplement the experimental study of protein mechanics. Structural displacements can be difficult to analyze and interpret. Previously, we showed that strains provide a more natural and interpretable representation of protein deformations, revealing mechanical coupling between spatially distinct sites of allosteric proteins. Here, we demonstrate that other transformations of displacements yield additional insights. We calculate the divergence and curl of deformations of the transmembrane channel KcsA. Additionally, we introduce quantities analogous to bend, splay, and twist deformation energies of nematic liquid crystals. These transformations enable the decomposition of displacements into different modes of deformation, helping to characterize the type of deformation a protein undergoes. We apply these calculations to study the filter and gating regions of KcsA. We observe a continuous path of rotational deformations physically coupling these two regions, and, we propose, underlying the allosteric interaction between these regions. Bend, splay, and twist distinguish KcsA gate opening, filter opening, and filter-gate coupling, respectively. In general, physically meaningful representations of deformations (like strain, curl, bend, splay, and twist) can make testable predictions and yield insights into protein mechanics, augmenting experimental methods and more fully exploiting available structural data.

Polymersomes at the solid-liquid interface: Dynamic morphological transformation and lubrication

Polymersomes are hollow spheres self-assembled from amphiphilic block copolymers of certain molecular architecture. Whilst they have been widely studied for biomedical applications, relatively few studies have reported their interfacial properties. In particular, lubrication by polymersomes has not been previously reported. Here, interfacial properties of polymersomes self-assembled from poly(butadiene)-poly(ethylene oxide) (PBD-PEO; molecular weight 10,400 g mol^-1) have been studied at both hydrophilic and hydrophobic surfaces. Their morphology at silica and mica surfaces was imaged with quantitative nanomechanical property mapping atomic force microscopy (QNM AFM), and friction and surface forces they mediate under confinement between two surfaces were studied using colloidal probe AFM (CP-AFM). We find that the polymersomes remained intact but adopted flattened conformation once adsorbed to mica, with a relatively low coverage. However, on silica these polymersomes were unstable, rupturing to form donut shaped residues or patchy bilayers. On a silica surface hydrophobized with a 19 nm polystyrene (PS) film, the polymer vesicles formed a more stable layer with a higher surface coverage as compared to the hydrophilic surface, and the interfacial structure also evolved over time. Moreover, friction was greatly reduced on hydrophobized silica surfaces in the presence of polymersomes, suggesting their potential as effective aqueous lubricants.

Mapping Elastic Properties of Heterogeneous Materials in Liquid with Angstrom-Scale Resolution

Fast quantitative mapping of mechanical properties with nanoscale spatial resolution represents one of the major goals of force microscopy. This goal becomes more challenging when the characterization needs to be accomplished with subnanometer resolution in a native environment that involves liquid solutions. Here we demonstrate that bimodal atomic force microscopy enables the accurate measurement of the elastic modulus of surfaces in liquid with a spatial resolution of 3 Å. The Young's modulus can be determined with a relative error below 5% over a 5 orders of magnitude range (1 MPa to 100 GPa). This range includes a large variety of materials from proteins to metal-organic frameworks. Numerical simulations validate the accuracy of the method. About 30 s is needed for a Young's modulus map with subnanometer spatial resolution.

Ions Modulate Stress-Induced Nanotexture in Supported Fluid Lipid Bilayers

Most plasma membranes comprise a large number of different molecules including lipids and proteins. In the standard fluid mosaic model, the membrane function is effected by proteins whereas lipids are largely passive and serve solely in the membrane cohesion. Here we show, using supported 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayers in different saline solutions, that ions can locally induce ordering of the lipid molecules within the otherwise fluid bilayer when the latter is supported. This nanoordering exhibits a characteristic length scale of ∼20 nm, and manifests itself clearly when mechanical stress is applied to the membrane. Atomic force microscopy (AFM) measurements in aqueous solutions containing NaCl, KCl, CaCl₂, and Tris buffer show that the magnitude of the effect is strongly ion-specific, with Ca²⁺ and Tris, respectively, promoting and reducing stress-induced nanotexturing of the membrane. The AFM results are complemented by fluorescence recovery after photobleaching experiments, which reveal an inverse correlation between the tendency for molecular nanoordering and the diffusion coefficient within the bilayer. Control AFM experiments on other lipids and at different temperatures support the hypothesis that the nanotexturing is induced by reversible, localized gel-like solidification of the membrane. These results suggest that supported fluid phospholipid bilayers are not homogenous at the nanoscale, but specific ions are able to locally alter molecular organization and mobility, and spatially modulate the membrane’s properties on a length scale of ∼20 nm. To illustrate this point, AFM was used to follow the adsorption of the membrane-penetrating antimicrobial peptide Temporin L in different solutions. The results confirm that the peptides do not absorb randomly, but follow the ion-induced spatial modulation of the membrane. Our results suggest that ionic effects have a significant impact for passively modulating the local properties of biological membranes, when in contact with a support such as the cytoskeleton.

Multiparametric Atomic Force Microscopy Imaging of Biomolecular and Cellular Systems

There is a need in biochemical research for new tools that can image and manipulate biomolecular and cellular systems at the nanoscale. During the past decades, there has been tremendous progress in developing atomic force microscopy (AFM) techniques to analyze biosystems, down to the single-molecule level. Force-distance (FD) curve-based AFM in particular has enabled researchers to map and quantify biophysical properties and biomolecular interactions on a wide variety of specimens. Despite its great potential, this AFM method has long been limited by its low spatial and temporal resolutions. Recently, novel FD-based multiparametric imaging modalities have been developed, allowing us to simultaneously image the structure, elasticity and interactions of biological samples at high spatiotemporal resolution. By oscillating the AFM tip, spatially resolved FD curves are obtained at much higher frequency than before, and as a result, samples are mapped at a speed similar to that of conventional topographic imaging. In this Account, we discuss the general principle of multiparametric AFM imaging and we provide a snapshot of recent studies showing how this new technology has been applied to biological specimens, from soluble proteins to membranes and cells. We emphasize novel methodologies that we recently developed, in which multiparametric imaging is combined with probes functionalized with chemical groups, ligands, or even live cells, in order to image and quantify receptor interaction forces and free-energy landscapes in a way not possible before. Key breakthroughs include observing the mechanical and chemical properties of single proteins in purple membranes, measuring the electrostatic potential of transmembrane pore forming proteins, structurally localizing chemical groups of water-soluble proteins, mapping and nanomechanical analysis of single sensors on yeast cells, imaging the sites of assembly and extrusion of single filamentous bacteriophages in living bacteria, unravelling the adhesive properties of biofilm-forming microbial pathogens, mapping the ligand-binding free energy landscape of human membrane receptors in proteoliposomes, and finally, the nanomechanical mapping of the first binding events of viruses to animal cells. In the coming years, it is anticipated that multiparametric AFM imaging will be increasingly used by chemists from broad horizons, enabling them to shed light into the sophisticated functions of biomolecular and cellular systems.

Characterization of Gd loaded chitosan-TPP nanohydrogels by a multi-technique approach combining dynamic light scattering (DLS), asymetrical flow-field-flow-fractionation (AF4) and atomic force microscopy (AFM) and design of positive contrast agents for molecular resonance imaging (MRI)

Chitosan CS-tripolyphosphate TPP/hyaluronic acid HA nanohydrogels loaded with gadolinium chelates (GdDOTA ⊂ CS-TPP/HA NGs) synthesized by ionic gelation were designed for lymph node (LN) MRI. In order to be efficiently drained to LNs, nanogels (NGs) needed to exhibit a diameter ϕ < 100 nm. For that, formulation parameters were tuned, using (i) CS of two different molecular weights (51 and 37 kDa) and (ii) variable CS/TPP ratio (2 < CS/TPP < 8). Characterization of NG size distribution by dynamic light scattering (DLS) and asymetrical flow-field-flow-fractionation (AF4) showed discrepancies since DLS diameters were consistently above 200 nm while AF4 showed individual nano-objects with ϕ < 100 nm. Such a difference could be correlated to the presence of aggregates inherent to ionic gelation. This point was clarified by atomic force microscopy (AFM) in liquid mode which highlighted the main presence of individual nano-objects in nanosuspensions. Thus, combination of DLS, AF4 and AFM provided a more precise characterization of GdDOTA ⊂ CS-TPP/HA nanohydrogels which, in turn, allowed to select formulations leading to NGs of suitable mean sizes showing good MRI efficiency and negligible toxicity.

Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy

The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed.

Scaling law to determine peak forces in tapping-mode AFM experiments on finite elastic soft matter systems

Analytical equations to estimate the peak force will facilitate the interpretation and the planning of amplitude-modulation force microscopy (tapping mode) experiments. A closed-form analytical equation to estimate the tip-sample peak forces while imaging soft materials in liquid environment and within an elastic deformation regime has been deduced. We have combined a multivariate regression method with input from the virial-dissipation equations and Tatara's bidimensional deformation contact mechanics model. The equation enables to estimate the peak force based on the tapping mode observables, probe characteristics and the material properties of the sample. The accuracy of the equation has been verified by comparing it to numerical simulations for the archetypical operating conditions to image soft matter with high spatial resolution in tapping-mode AFM.

Sub-nanometer Resolution Imaging with Amplitude-modulation Atomic Force Microscopy in Liquid

Atomic force microscopy (AFM) has become a well-established technique for nanoscale imaging of samples in air and in liquid. Recent studies have shown that when operated in amplitude-modulation (tapping) mode, atomic or molecular-level resolution images can be achieved over a wide range of soft and hard samples in liquid. In these situations, small oscillation amplitudes (SAM-AFM) enhance the resolution by exploiting the solvated liquid at the surface of the sample. Although the technique has been successfully applied across fields as diverse as materials science, biology and biophysics and surface chemistry, obtaining high-resolution images in liquid can still remain challenging for novice users. This is partly due to the large number of variables to control and optimize such as the choice of cantilever, the sample preparation, and the correct manipulation of the imaging parameters. Here, we present a protocol for achieving high-resolution images of hard and soft samples in fluid using SAM-AFM on a commercial instrument. Our goal is to provide a step-by-step practical guide to achieving high-resolution images, including the cleaning and preparation of the apparatus and the sample, the choice of cantilever and optimization of the imaging parameters. For each step, we explain the scientific rationale behind our choices to facilitate the adaptation of the methodology to every user's specific system.

Optical and force nanoscopy in microbiology

Microbial cells have developed sophisticated multicomponent structures and machineries to govern basic cellular processes, such as chromosome segregation, gene expression, cell division, mechanosensing, cell adhesion and biofilm formation. Because of the small cell sizes, subcellular structures have long been difficult to visualize using diffraction-limited light microscopy. During the last three decades, optical and force nanoscopy techniques have been developed to probe intracellular and extracellular structures with unprecedented resolutions, enabling researchers to study their organization, dynamics and interactions in individual cells, at the single-molecule level, from the inside out, and all the way up to cell-cell interactions in microbial communities. In this Review, we discuss the principles, advantages and limitations of the main optical and force nanoscopy techniques available in microbiology, and we highlight some outstanding questions that these new tools may help to answer.

Dependence of the volume of an antibody on the force applied in a force microscopy experiment in liquid

The volume of a protein can be estimated from its molecular weight. This approach has also been applied in force microscopy experiments. Two factors contribute to the determination of the volume from a force microscope image, the applied force and the tip radius. Those factors act in opposite directions. Here, we demonstrate that in the optimum conditions to image a protein, the apparent volume deduced from an AFM image overestimates the real protein volume. The lateral broadening due to the tip finite size, makes the simulated volume to exceed the real protein volume value, while the force applied by the tip tends to decrease the measured volume. The measured volume could coincide with the real volume for either a point-size tip at zero force or when the compression exerted by the tip compensates its dilation effects. The interplay between the above factors make unsuitable to apply the molecular weight method to determine the volume of a protein from AFM data.

Fundamental High-Speed Limits in Single-Molecule, Single-Cell, and Nanoscale Force Spectroscopies

Force spectroscopy is enhancing our understanding of single-biomolecule, single-cell, and nanoscale mechanics. Force spectroscopy postulates the proportionality between the interaction force and the instantaneous probe deflection. By studying the probe dynamics, we demonstrate that the total force acting on the probe has three different components: the interaction, the hydrodynamic, and the inertial. The amplitudes of those components depend on the ratio between the resonant frequency and the frequency at which the data are measured. A force-distance curve provides a faithful measurement of the interaction force between two molecules when the inertial and hydrodynamic components are negligible. Otherwise, force spectroscopy measurements will underestimate the value of unbinding forces. Neglecting the above force components requires the use of frequency ratios in the 50-500 range. These ratios will limit the use of high-speed methods in force spectroscopy. The theory is supported by numerical simulations.

Rapid recognition and functional analysis of membrane proteins on human cancer cells using atomic force microscopy

Understanding the physicochemical properties of cell surface signalling molecules is important for us to uncover the underlying mechanisms that guide the cellular behaviors. Atomic force microscopy (AFM) has become a powerful tool for detecting the molecular interactions on individual cells with nanometer resolution. In this paper, AFM peak force tapping (PFT) imaging mode was applied to rapidly locate and visually map the CD20 molecules on human lymphoma cells using biochemically sensitive tips. First, avidin-biotin system was used to test the effectiveness of using PFT imaging mode to probe the specific molecular interactions. The adhesion images obtained on avidin-coated mica using biotin-tethered tips obviously showed the recognition spots which corresponded to the avidins in the simultaneously obtained topography images. The experiments confirmed the specificity and reproducibility of the recognition results. Then, the established procedure was applied to visualize the nanoscale organization of CD20s on the surface of human lymphoma Raji cells using rituximab (a monoclonal anti-CD20 antibody)-tethered tips. The experiments showed that the recognition spots in the adhesion images corresponded to the specific CD20-rituximab interactions. The cluster sizes of CD20s on lymphoma Raji cells were quantitatively analyzed from the recognition images. Finally, under the guidance of fluorescence recognition, the established procedure was applied to cancer cells from a clinical lymphoma patient. The results showed that there were significant differences between the adhesion images obtained on cancer cells and on normal cells (red blood cell). The CD20 distributions on ten cancer cells from the patient were quantified according to the adhesion images. The experimental results demonstrate the capability of applying PFT imaging to rapidly investigate the nanoscale biophysical properties of native membrane proteins on the cell surface, which is of potential significance in developing novel biomarkers for cancer diagnosis and drug development.

Structural, mechanical, and dynamical variability of the actin cortex in living cells

In eukaryotic cells, an actin-based cortex lines the inner leaflet of the plasma membrane, endowing the cells with crucial mechanical and functional properties. Unfortunately, it has not been possible to study the structural dynamics of the actin cortex at high lateral resolution in living cells. Here, we performed atomic force microscopy time-lapse imaging and mechanical mapping of actin in the cortex of living cells at high lateral and temporal resolution. Cortical actin filaments adopted discernible arrangements, ranging from large parallel bundles with low connectivity to a tight meshwork of short filaments. Mixing of these architectures resulted in attuned cortex networks with specific connectivity, mechanical responses, and marked differences in their dynamic behavior.

How soft is a single protein? The stress-strain curve of antibody pentamers with 5 pN and 50 pm resolutions

Understanding the mechanical functionalities of complex biological systems requires the measurement of the mechanical compliance of their smallest components. Here, we develop a force microscopy method to quantify the softness of a single antibody pentamer by measuring the stress-strain curve with force and deformation resolutions, respectively, of 5 pN and 50 pm. The curve shows three distinctive regions. For ultrasmall compressive forces (5-75 pN), the protein's central region shows that the strain and stress are proportional (elastic regime). This region has an average Young's modulus of 2.5 MPa. For forces between 80 and 220 pN, the stress is roughly proportional to the strain with a Young's modulus of 9 MPa. Higher forces lead to irreversible deformations (plastic regime). Full elastic recovery could reach deformations amounting to 40% of the protein height. The existence of two different elastic regions is explained in terms of the structure of the antibody central region. The stress-strain curve explains the capability of the antibody to sustain multiple collisions without any loss of biological functionality.

PeakForce Tapping resolves individual microvilli on living cells

Microvilli are a common structure found on epithelial cells that increase the apical surface thus enhancing the transmembrane transport capacity and also serve as one of the cell's mechanosensors. These structures are composed of microfilaments and cytoplasm, covered by plasma membrane. Epithelial cell function is usually coupled to the density of microvilli and its individual size illustrated by diseases, in which microvilli degradation causes malabsorption and diarrhea. Atomic force microscopy (AFM) has been widely used to study the topography and morphology of living cells. Visualizing soft and flexible structures such as microvilli on the apical surface of a live cell has been very challenging because the native microvilli structures are displaced and deformed by the interaction with the probe. PeakForce Tapping® is an AFM imaging mode, which allows reducing tip-sample interactions in time (microseconds) and controlling force in the low pico-Newton range. Data acquisition of this mode was optimized by using a newly developed PeakForce QNM-Live Cell probe, having a short cantilever with a 17-µm-long tip that minimizes hydrodynamic effects between the cantilever and the sample surface. In this paper, we have demonstrated for the first time the visualization of the microvilli on living kidney cells with AFM using PeakForce Tapping. The structures observed display a force dependence representing either the whole microvilli or just the tips of the microvilli layer. Together, PeakForce Tapping allows force control in the low pico-Newton range and enables the visualization of very soft and flexible structures on living cells under physiological conditions.

Mutations in COL1A1 Gene Change Dentin Nanostructure

Although many studies have attempted to associate specific gene mutations with dentin phenotypic severity, it remains unknown how the mutations in COL1A1 gene influence the mechanical behavior of dentin collagen and matrix. Here, we reported one osteogenesis imperfecta (OI) pedigree caused by two new inserting mutations in exon 5 of COL1A1 (NM_000088.3:c.440_441insT;c.441_442insA), which resulted in the unstable expression of COL1A1 mRNA and half quantity of procollagen production. We investigated the morphological and mechanical features of proband's dentin using atomic force microscope (AFM), scanning electron microscope, and transmission electron microscope. Increased D-periodic spacing, variably enlarged collagen fibrils coating with fewer minerals were found in the mutated collagen. AFM analysis demonstrated rougher dentin surface and sparsely decreased Young's modulus in proband's dentin. We believe that our findings provide new insights into the genetic-/nano- mechanisms of dentin diseases, and may well explain OI dentin features with reduced mechanical strength and a lower crosslinked density.

Nanomechanical properties of human skin and introduction of a novel hair indenter

The mechanical resistance of the stratum corneum, the outermost layer of skin, to deformation has been evaluated at different length scales using Atomic Force Microscopy. Nanomechanical surface mapping was first conducted using a sharp silicon tip and revealed that Young׳s modulus of the stratum corneum varied over the surface with a mean value of about 0.4GPa. Force indentation measurements showed permanent deformation of the skin surface only at high applied loads (above 4µN). The latter effect was further demonstrated using nanomechanical imaging in which the obtained depth profiles clearly illustrate the effects of increased normal force on the elastic/plastic surface deformation. Force measurements utilizing the single hair fiber probe supported the nanoindentation results of the stratum corneum being highly elastic at the nanoscale, but revealed that the lateral scale of the deformation determines the effective elastic modulus.This result resolves the fact that the reported values in the literature vary greatly and will help to understand the biophysics of the interaction of razor cut hairs that curl back during growth and interact with the skin.

Stiffness and evolution of interfacial micropancakes revealed by AFM quantitative nanomechanical imaging

Micropancakes are quasi-two-dimensional micron-sized domains on crystalline substrates (e.g. highly oriented pyrolytic graphite (HOPG)) immersed in water. They are only a few nanometers thick, and are suspected to come from the accumulation of dissolved air at the solid-water interface. However, the exact chemical nature and basic physical properties of micropancakes have been under debate ever since their first observation, primarily due to the lack of a suitable characterization technique. In this study, the stiffness of micropancakes at the interface between HOPG and ethanol-water solutions was investigated by using PeakForce Quantitative NanoMechanics (PF-QNM) mode Atomic Force Microscopy (AFM). Our measurements showed that micropancakes were stiffer than nanobubbles, and for bilayer micropancakes, the bottom layer in contact with the substrate was stiffer than the top one. Interestingly, the micropancakes became smaller and softer with an increase in the ethanol concentration in the solution, and were undetectable by AFM above a critical concentration of ethanol. But they re-appeared after the ethanol concentration in the solution was reduced. Clearly the evolution and stiffness of the micropancakes were dependent on the chemical composition in the solution, which could be attributed to the correlation of the mechanical properties of the micropancakes with the surface tension of the liquid phase. Based on the "go-and-come" behaviors of micropancakes with the ethanol concentration, we found that the micropancakes could actually tolerate the ethanol concentration much higher than 5%, a value reported in the literature. The results from this work may be helpful in alluding the chemical nature of micropancakes.

Force reconstruction from tapping mode force microscopy experiments

Fast, accurate, and robust nanomechanical measurements are intensely studied in materials science, applied physics, and molecular biology. Amplitude modulation force microscopy (tapping mode) is the most established nanoscale characterization technique of surfaces for air and liquid environments. However, its quantitative capabilities lag behind its high spatial resolution and robustness. We develop a general method to transform the observables into quantitative force measurements. The force reconstruction algorithm has been deduced on the assumption that the observables (amplitude and phase shift) are slowly varying functions of the tip-surface separation. The accuracy and applicability of the method is validated by numerical simulations and experiments. The method is valid for liquid and air environments, small and large free amplitudes, compliant and rigid materials, and conservative and non-conservative forces.

Dental Abnormalities Caused by Novel Compound Heterozygous CTSK Mutations

Cathepsin K (CTSK) is an important protease responsible for degrading type I collagen, osteopontin, and other bone matrix proteins. The mutations in the CTSK gene can cause pycnodysostosis (OMIM 265800), a rare autosomal recessive bone dysplasia. Patients with pycnodysostosis have been reported to present specific dental abnormalities; however, whether these dental abnormalities are related to dysfunctional CTSK has never been reported. Here we investigated the histologic changes of cementum and alveolar bone in a pycnodysostosis patient, caused by novel compound heterozygous mutations in the CTSK gene (c.87 G>A p.W29X and c.848 A>G p.Y283C). The most impressive manifestations in tooth were extensive periradicular high-density clumps with unclear periodontal space by orthopantomography examination and micro-computed tomography scanning analysis. Hematoxylin/eosin and toluidine blue staining and atomic force microscopy analysis showed that the cementum became significantly thickened, softened, and full of cementocytes. The disorganized bone structure was the main character of alveolar bone. The p.W29X mutation may represent the loss-of-function allele with an earlier termination codon in the precursor CTSK polypeptide. Residue Y283 is highly conserved among papain-like cysteine proteases. Three-dimensional structure modeling analysis found that the loss of the hydroxybenzene residue in the Y283C mutation would interrupt the hydrogen network and possibly affect the self-cleavage of the CTSK enzyme. Furthermore, p.Y283C mutation did not affect the mRNA and protein levels of overexpressed CTSK in COS-7 system but did reduce CTSK enzyme activity. In conclusion, the histologic and ultrastructural changes of cementum and alveolar bone might be affected by CTSK mutation via reduction of its enzyme activity (clinical trial registration: ChiCTR-TNC-10000876).

High-speed AFM images of thermal motion provide stiffness map of interfacial membrane protein moieties

The flexibilities of extracellular loops determine ligand binding and activation of membrane receptors. Arising from fluctuations in inter- and intraproteinaceous interactions, flexibility manifests in thermal motion. Here we demonstrate that quantitative flexibility values can be extracted from directly imaging the thermal motion of membrane protein moieties using high-speed atomic force microscopy (HS-AFM). Stiffness maps of the main periplasmic loops of single reconstituted water channels (AqpZ, GlpF) revealed the spatial and temporal organization of loop-stabilizing intraproteinaceous H-bonds and salt bridges.