Charge of a transmembrane peptide alters its interaction with lipid membranes

Transmembrane (TM) proteins interact closely with the surrounding membrane lipids. Lipids in the vicinity of TM proteins were reported to have hindered mobility, which has been associated with lipids being caught up in the rough surface of the TM domains. These reports, however, neglect one important factor that largely influences the membrane behavior - electrostatics of the TM peptides that are usually positively charged at their cytosolic end. Here, we study on the example of a neutral and a positively charged WALP peptide, how the charge of a TM peptide influences the membrane. We investigate both its dynamics and mechanics by: (i) time dependent fluorescent shift in combination with classical and FRET generalized polarization to evaluate the mobility of lipids at short and long-range distance from the peptide, (ii) atomic force microscopy to observe the mechanical stability of the peptide-containing membranes, and (iii) molecular dynamics simulations to analyze the peptide-lipid interactions. We show that both TM peptides lower lipid mobility in their closest surroundings. The peptides cause lateral heterogeneity in lipid mobility, which in turn prevents free lipid rearrangement and lowers the membrane ability to seal ruptures after mechanical indentations. Introduction of a positive charge to the peptide largely enhances these effects, affecting the whole membrane. We thus highlight that unspecific peptide-lipid interactions, especially the electrostatics, should not be overlooked as they have a great impact on the mechanics and dynamics of the whole membrane.

The Adsorption of P2X2 Receptors Interacting with IgG Antibodies Revealed by Combined AFM Imaging and Mechanical Simulation

The adsorption of proteins onto surfaces significantly impacts biomaterials, medical devices, and biological processes. This study aims to provide insights into the irreversible adsorption process of multiprotein complexes, particularly focusing on the interaction between anti-His6 IgG antibodies and the His6-tagged P2X2 receptor. Traditional approaches to understanding protein adsorption have centered around kinetic and thermodynamic models, often examining individual proteins and surface coverage, typically through Molecular Dynamics (MD) simulations. In this research, we introduce a computational approach employing Autodesk Maya 3D software for the investigation of multiprotein complexes' adsorption behavior. Utilizing Atomic Force Microscopy (AFM) imaging and Maya 3D-based mechanical simulations, our study yields real-time structural and kinetic observations. Our combined experimental and computational findings reveal that the P2X2 receptor-IgG antibody complex likely undergoes absorption in an 'extended' configuration. Whereas the P2X2 receptor is less adsorbed once is complexed to the IgG antibody compared to its individual state, the opposite is observed for the antibody. This insight enhances our understanding of the role of protein-protein interactions in the process of protein adsorption.

Nanoscale Prognosis of Colorectal Cancer Metastasis from AFM Image Processing of Histological Sections

Early ascertainment of metastatic tumour phases is crucial to improve cancer survival, formulate an accurate prognostic report of disease advancement, and, most importantly, quantify the metastatic progression and malignancy state of primary cancer cells with a universal numerical indexing system. This work proposes an early improvement to metastatic cancer detection with 97.7 nm spatial resolution by indexing the metastatic cancer phases from the analysis of atomic force microscopy images of human colorectal cancer histological sections. The procedure applies variograms of residuals of Gaussian filtering and theta statistics of colorectal cancer tissue image settings. This methodology elucidates the early metastatic progression at the nanoscale level by setting metastatic indexes and critical thresholds based on relatively large histological sections and categorising the malignancy state of a few suspicious cells not identified with optical image analysis. In addition, we sought to detect early tiny morphological differentiations indicating potential cell transition from epithelial cell phenotypes of low metastatic potential to those of high metastatic potential. This metastatic differentiation, which is also identified in higher moments of variograms, sets different hierarchical levels for metastatic progression dynamics.

Comparative Study of the Solid-Liquid Interfacial Adsorption of Proteins in Their Native and Amyloid Forms

The adhesive properties of amyloid fibers are thought to play a crucial role in various negative and positive aggregation processes, the study of which might help in their understanding and control. Amyloids have been prepared from two proteins, lysozyme and β-lactoglobulin, as well as an Exendin-4 derivative miniprotein (E5). Thermal treatment was applied to form amyloids and their structure was verified by thioflavin T (ThT), 8-Anilino-1-naphthalenesulfonic acid (ANS) dye tests and electronic circular dichroism spectroscopy (ECD). Adsorption properties of the native and amyloid forms of the three proteins were investigated and compared using the mass-sensitive quartz crystal microbalance (QCM) technique. Due to the possible electrostatic and hydrophobic interactions, similar adsorbed amounts were found for the native or amyloid forms, while the structures of the adsorbed layers differed significantly. Native proteins formed smooth and dense adsorption layers. On the contrary, a viscoelastic, highly loose layer was formed in the presence of the amyloid forms, shown by increased motional resistance values determined by the QCM technique and also indicated by atomic force microscopy (AFM) and wettability measurements. The elongated structure and increased hydrophobicity of amyloids might contribute to this kind of aggregation.

The articular cartilage surface is impaired by a loss of thick collagen fibers and formation of type I collagen in early osteoarthritis

Osteoarthritis (OA) is a joint disease affecting millions of patients worldwide. During OA onset and progression, the articular cartilage is destroyed, but the underlying complex mechanisms remain unclear. Here, we uncover changes in the thickness of collagen fibers and their composition at the onset of OA. For articular cartilage explants from knee joints of OA patients, we find that type I collagen-rich fibrocartilage-like tissue was formed in macroscopically intact cartilage, distant from OA lesions. Importantly, the number of thick fibers (>100 nm) has decreased early in the disease, followed by complete absence of thick fibers in advanced OA. We have obtained these results by a combination of high-resolution atomic force microscopy imaging under near-native conditions, immunofluorescence, scanning electron microscopy and a fluorescence-based classification of the superficial chondrocyte spatial organization. Taken together, our data suggests that the loss of tissue functionality in early OA cartilage is caused by a reduction of thick type II collagen fibers, likely due to the formation of type I collagen-rich fibrocartilage, followed by the development of focal defects in later OA stages. We anticipate that such an integrative characterization will be very beneficial for an in-depth understanding of other native biological tissues and the development of sustainable biomaterials. STATEMENT OF SIGNIFICANCE: In early osteoarthritis (OA) the cartilage appears macroscopically intact. However, this study demonstrates that the collagen network already changes in early OA by collagen fiber thinning and the formation of fibrocartilage-like tissue. Both nanoscopic deficiencies already occur in macroscopically intact regions of the human knee joint and are likely connected to processes that result in a weakened extracellular matrix. This study enhances the understanding of earliest progressive cartilage degeneration in the absence of external damage. The results suggest a determination of the mean collagen fiber thickness as a new target for the detection of early OA and a regulation of type I collagen synthesis as a new path for OA treatment.

Heads or tails: Nanostructure and molecular orientations in organised erucamide surface layers

HYPOTHESIS

Despite the widespread industrial usage of erucamide as a slip additive to modify polymer surface properties, a controversy appears to have persisted regarding the nanostructure of erucamide surface layers, particularly the molecular orientation at the outermost layer. The erucamide nanostructure and molecular orientation, along with its surface coverage, hydrophobicity, and adhesive response, can be tuned by simply varying the erucamide concentration in the solution from which the spin coated layer is prepared.

EXPERIMENTS

Synchrotron X-ray reflectivity (XRR) allowed a comprehensive characterisation of the out-of-plane structural parameters (e.g. molecular packing and thickness) of the erucamide layers prepared via spin coating from nonaqueous solution on silica. Complementary Atomic Force Microscopy (AFM) imaging with high lateral resolution revealed localised in-plane structures. Contact angle measurements provided information on the wettability of erucamide-coated surfaces. Peak Force Quantitative Nanomechanical Mapping (QNM) allowed a correlation between the erucamide nanostructure with the surface nanomechanical properties (i.e. adhesive response).

FINDINGS

Our results reveal erucamide surface nanostructures on silica as patchy monolayers, isolated circular bilayers/rounded rectangle-like aggregates and overlapping plate-like multilayers as the erucamide concentration in the spin coating solution was varied. In all the cases, XRR and AFM results were consistent with the picture that the erucamide tails were oriented outwards. The QNM adhesion force mapping of all the observed morphologies also supported this molecular orientation at the outermost erucamide monolayer. The wettability study further confirmed this conclusion with the observed increase in the surface hydrophobicity and coverage upon increasing erucamide concentration, with the macroscopic water contact angle θ = 92.9° ± 2.9° at the highest erucamide concentration of 2 wt%.

Toxicity of selected airborne nitrophenols on eukaryotic cell membrane models

Nitroaromatics belong to the group of toxic components of aerosol particles and atmospheric hydrometeors that enter the atmosphere through biomass burning and fuel combustion. In the present work, we report on the cytotoxic effects of a 2-, 3- and 4-nitrophenol mixture on a model eukaryotic-like cell membrane and compared it with in vitro cellular models BEAS-2B (immortalized bronchial epithelial cells) and A549 (cancerous alveolar epithelial cells). A selected model biomembrane comprised of DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine), DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) and POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) was studied. The electrochemical-based method, combined with atomic force microscopy (AFM) and phase-contrast microscopy imaging, allowed to get insights into the mechanism of cellular function disruption caused by airborne nitrophenols. The efficacy of the method is supported by the data obtained from in vitro experiments performed on cell models. The nitrophenol mixture exhibited cytotoxic effects at concentrations above 100 μg mL^-1, as demonstrated by phase-contrast microscopy in real lung cell lines. Electrochemical impedance spectroscopy (EIS) revealed the formation of membrane defects at a nitrophenol concentration of 200 μg mL^-1. AFM imaging confirmed the model membrane disintegration and phospholipids rearrangement in the presence of nitrophenols. These observations indicate that particle-bound nitrophenols induce substantial changes in cell membranes and make them more permeable to aerosol, resulting in major cellular damage in the lungs when inhaled. The study provides initial evidence of cellular membrane damage induced by three important nitrated phenols present in the environment.

Plant cell wall hydrolysis process reveals structure-activity relationships

BACKGROUND

Recent interest in Populus as a source of renewable energy, combined with its numerous available pretreatment methods, has enabled further research on structural modification and hydrolysis. To improve the biodegradation efficiency of biomass, a better understanding of the relationship between its macroscopic structures and enzymatic process is important.

RESULTS

This study investigated mutant cell wall structures compared with wild type on a molecular level. Furthermore, a novel insight into the structural dynamics occurring on mutant biomass was assessed in situ and in real time by functional Atomic Force Microscopy (AFM) imaging. High-resolution AFM images confirmed that genetic pretreatment effectively inhibited the production of irregular lignin. The average roughness values of the wild type are 78, 60, and 30 nm which are much higher than that of the mutant cell wall, approximately 10 nm. It is shown that the action of endoglucanases would expose pure crystalline cellulose with more cracks for easier hydrolysis by cellobiohydrolase I (CBHI). Throughout the entire CBHI hydrolytic process, when the average roughness exceeded 3 nm, the hydrolysis mode consisted of a peeling action.

CONCLUSION

Functional AFM imaging is helpful for biomass structural characterization. In addition, the visualization of the enzymatic hydrolysis process will be useful to explore the cell wall structure-activity relationships.

Atomic Force Microscope Guided SERS Spectra Observation for Au@Ag-4MBA@PVP Plasmonic Nanoparticles

Recently polymer encapsulated surface-enhanced-Raman-scattering (SERS) probes with internal noble metal core-shell structure has found growing applications in biomedical applications. Here we studied the SERS spectra of Au@Ag-4MBA@PVP (4MBA: 4-mercaptobenzoic acid; PVP: polyvinylpyrrolidone) plasmonic nanoparticles produced from a chemical reduction method. By linking the atomic force microscope (AFM) with the homebuilt confocal Raman spectrometer thus to use AFM images as guidance, we realized the measurement of the SERS spectra from separated nanoparticles. We investigated the cases for single nanoparticles and for dimer structures and report several observed results including SERS spectra linearly scaled with laser power, abrupt boosting and abnormal shape changing of SERS spectra for dimer structures. Based on the finite element method simulation, we explained the observed ratio of SERS signals between the dimer structure and the single nanoparticle, and attributed the observed abnormal spectra to the photothermal effect of these plasmonic nanoparticles. Our study provides valuable guidance for choosing appropriate laser power when applying similar SERS probes to image biological cells.

Improved DNA straightening and attachment via optimal Mg2+ ionic bonding under electric field for AFM imaging in liquid phase

In this research, a novel method is proposed to improve DNA straightening under an applied electric field to facilitate imaging in a liquid phase by modifying the substrate with varying Mg²⁺ ion concentrations. A two-dimensional network of DNA structures was successfully stretched on Mg²⁺-modified mica substrates under a DC electric field (1 V, 1 A) and imaged in gaseous and aqueous phases by atomic force microscopy. The results revealed that an optimum concentration of Mg²⁺ ion (4.17 μmol/ml) allowed DNA straightening under an electric field, thus facilitating its imaging in the liquid phase. Furthermore, DNA adhesion under different concentrations of Mg²⁺ was measured and a maximum adhesion force of 76.19 pN was achieved. This vital work has great potential in gene knockout and targeted gene editing.

Interaction of Amyloidogenic Proteins with Membranes and Molecular Mechanism for the Development of Alzheimer's disease

Molecular mechanism of diseases like Alzheimer's disease (AD) and Parkinson's diseases (PD) is associated with misfolding of specific proteins, such as amyloid beta (Aβ) proteins in the case of AD, followed by their self-assembly into toxic oligomers along with the formation of amyloid fibrils assembled as plaques in the brain. Interaction of Aβ with membrane can lead to membrane damage; this process is considered as the major factor associated with the AD development. Additionally, membrane can facilitate the aggregation process of Aβ proteins. This important property of membranes is discussed in this review. A specific emphasis is given to the recently discovered property of cellular membranes to catalyze the initial step of Aβ aggregation process by which self-assembly of Aβ can be observed at physiologically low concentrations of Aβ proteins. At such low concentrations, no spontaneous aggregation occurs in the bulk solution. This fact was a major weakness of the protein aggregation model for AD. The catalytic property of membrane surfaces towards Aβ aggregation depends on the membrane composition. This finding suggests a number of novel ideas on the development of treatments and preventions for AD, which is briefly discussed in the review.

Imaging of Soft and Biological Samples Using AFM Ringing Mode

Ringing mode of atomic force microscopy (AFM) enables imaging the surfaces of biological samples, cells, tissue, biopolymers, etc. to obtain unique information, such as the size of molecules pulled by the AFM probe from the sample surface, heights of the sample at different load forces, etc. (up to eight different imaging channels can be recorded simultaneously, which is in addition to five channels already available in other rival modes). The imaging can be done in both air (gases) and liquid (buffers). In addition, the images obtained in ringing mode do not have several common artifacts and can be collected up to 20× faster compared to the rival imaging modes. Here we describe a step-by-step approach to collect images in ringing mode applied to biological and soft materials in general. Technical details, potential difficulties, and points of special attention are described.

Atomic Force Microscopy: A Promising Tool for Deciphering the Pathogenic Mechanisms of Fungi in Cystic Fibrosis

During the past decades, atomic force microscopy (AFM) has emerged as a powerful tool in microbiology. Although most of the works concerned bacteria, AFM also permitted major breakthroughs in the understanding of physiology and pathogenic mechanisms of some fungal species associated with cystic fibrosis. Complementary to electron microscopies, AFM offers unprecedented insights to visualize the cell wall architecture and components through three-dimensional imaging with nanometer resolution and to follow their dynamic changes during cell growth and division or following the exposure to drugs and chemicals. Besides imaging, force spectroscopy with piconewton sensitivity provides a direct means to decipher the forces governing cell-cell and cell-substrate interactions, but also to quantify specific and non-specific interactions between cell surface components at the single-molecule level. This nanotool explores new ways for a better understanding of the structures and functions of the cell surface components and therefore may be useful to elucidate the role of these components in the host-pathogen interactions as well as in the complex interplay between bacteria and fungi in the lung microbiome.

Self-assembly of two hydrophobins from marine fungi affected by interaction with surfaces

Hydrophobins are amphiphilic fungal proteins endowed with peculiar characteristics, such as a high surface activity and an interface triggered self-assembly. Several applications of these proteins have been proposed in the food, cosmetics and biomedical fields. Moreover, their use as proteinaceous coatings can be effective for materials and nanomaterials applications. The discovery of novel hydrophobins with diverse properties may be advantageous from both the scientific and industrial points of view. Stressful environmental conditions of fungal growth may induce the production of proteins with peculiar features. Two Class I hydrophobins from fungi isolated from marine environment have been recently purified. Herein, their propensity to aggregate forming nanometric fibrillar structures has been compared, using different techniques, such as circular dichroism, dynamic light scattering and Thioflavin T fluorescence assay. Furthermore, TEM and AFM images indicate that the interaction of these proteins with specific surfaces, are crucial in the formation of amyloid fibrils and in the assembly morphologies. These self-assembling proteins show promising properties as bio-coating for different materials via a green process. Biotechnol. Bioeng. 2017;114: 2173-2186. © 2017 Wiley Periodicals, Inc.

Morphology and force probing of primary murine liver sinusoidal endothelial cells

Liver sinusoidal endothelial cells (LSECs) represent unique type of endothelial cells featured by their characteristic morphology, ie, lack of a basement membrane and presence of fenestrations-transmembrane pores acting as a dynamic filter between the vascular space and the liver parenchyma. Delicate structure of LSECs membrane combined with a submicron size of fenestrations hinders their visualization in live cells. In this work, we apply atomic force microscopy contact mode to characterize fenestrations in LSECs. We reveal the structure of fenestrations in live LSECs. Moreover, we show that the high-resolution imaging of fenestrations is possible for the glutaraldehyde-fixed LSECs. Finally, thorough information about the morphology of LSECs including great contrast in visualization of sieve plates and fenestrations is provided using Force Modulation mode. We show also the ability to precisely localize the cell nuclei in fixed LSECs. It can be helpful for more precise description of nanomechanical properties of cell nuclei using atomic force microscopy. Presented methodology combining high-quality imaging of fixed cells with an additional nanomechanical information of both live and fixed LSECs provides a unique approach to study LSECs morphology and nanomechanics that could foster understanding of the role of LSECs in maintaining liver homeostasis.

DNA-Directed Self-Assembly of Highly Ordered and Dense Single-Walled Carbon Nanotube Arrays

Single-walled carbon nanotubes (SWNT or CNT) have unique and well-known high-performance material properties that can enable revolutionary increases in the performance of electronic devices and architectures. However, fabrication of large-scale SWNT-based ICs is an enormously challenging, unsolved problem, and self-assembly is likely needed for critical steps. Over the past several years, methods have been introduced to created ordered carbon nanotube structures using DNA guided self-assembly. In this chapter, we briefly review the challenges involved in using DNA to assemble SWNT nanostructures, and then give detailed methods to assemble dense, aligned SWNT arrays. In particular, we discuss the preparation of DNA wrapped single-walled nanotubes (DNA-CNTs) using commercial carbon nanotube products that are suitable for electronics applications. Then, we discuss methods to characterize DNA-CNTs using fluid mode atomic force microscopy (AFM). Finally, we give detailed procedures for assembly of DNA-CNTs into dense parallel arrays via linker induced surface assembly (LISA).

Morphological and nanomechanical changes in mechanosensitive endothelial cells induced by colloidal AFM probes

Mechanotransduction is one of the main properties of endothelial cells (ECs) phenotype. Hemodynamic forces like flow-generated endothelial shear stress play a fundamental role in ECs cytoskeletal remodeling and activate signaling cascades in ECs. AFM methods are widely used to characterize morphology as well as mechanical properties of cells. In both cases AFM probes directly interact with cell surface exerting mechanical forces on the cellular membrane, which in turn may stimulate mechanosensitive receptors present in EC. This article presents examples of how the colloidal AFM probes influence ECs during multiple scans. The results revealed that multiple scans of the ECs significantly influenced the morphology and elasticity of cells. Moreover, changes in the cell shape and mechanical properties were dependent on the scan direction (across or along the main axis of the cell). Multiple scans with a colloidal probe leaded to reorientation of the cell main axis and this effect was similar to the action of the shear stress induced by flow conditions. Furthermore, the correlation between the tip-induced modification of the cell properties and the remodeling of the cell's glycocalyx was observed. SCANNING 38:654-664, 2016. © 2016 Wiley Periodicals, Inc.

Preferential 5-Methylcytosine Oxidation in the Linker Region of Reconstituted Positioned Nucleosomes by Tet1 Protein

Tet (ten-eleven translocation) family proteins oxidize 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC), and are suggested to be involved in the active DNA demethylation pathway. In this study, we reconstituted positioned mononucleosomes using CpG-methylated 382 bp DNA containing the Widom 601 sequence and recombinant histone octamer, and subjected the nucleosome to treatment with Tet1 protein. The sites of oxidized methylcytosine were identified by bisulfite sequencing. We found that, for the oxidation reaction, Tet1 protein prefers mCs located in the linker region of the nucleosome compared with those located in the core region.

Data on step-by-step atomic force microscopy monitoring of changes occurring in single melanoma cells undergoing ToF SIMS specialized sample preparation protocol

Data included in this article are associated with the research article entitled ‘Protocol of single cells preparation for time-of-flight secondary ion mass spectrometry’ (Bobrowska et al., 2016 in press) [1]. This data file contains topography images of single melanoma cells recorded using atomic force microscopy (AFM). Single cells cultured on glass surface were subjected to the proposed sample preparation protocol applied to prepare biological samples for time-of-flight secondary ion mass spectrometry (ToF SIMS) measurements. AFM images were collected step-by-step for the single cell, after each step of the proposed preparation protocol. It consists of four main parts: (i) paraformaldehyde fixation, (ii) salt removal, (iii) dehydrating, and (iv) sample drying. In total 13 steps are required, starting from imaging of a living cell in a culture medium and ending up at images of a dried cell in the air. The protocol was applied to melanoma cells from two cell lines, namely, WM115 melanoma cells originated from primary melanoma site and WM266-4 ones being the metastasis of WM115 cells to skin.

Cellular automata modeling depicts degradation of cellulosic material by a cellulase system with single-molecule resolution

BACKGROUND

Enzymatic hydrolysis of cellulose involves the spatiotemporally correlated action of distinct polysaccharide chain cleaving activities confined to the surface of an insoluble substrate. Because cellulases differ in preference for attacking crystalline compared to amorphous cellulose, the spatial distribution of structural order across the cellulose surface imposes additional constraints on the dynamic interplay between the enzymes. Reconstruction of total system behavior from single-molecule activity parameters is a longstanding key goal in the field.

RESULTS

We have developed a stochastic, cellular automata-based modeling approach to describe degradation of cellulosic material by a cellulase system at single-molecule resolution. Substrate morphology was modeled to represent the amorphous and crystalline phases as well as the different spatial orientations of the polysaccharide chains. The enzyme system model consisted of an internally chain-cleaving endoglucanase (EG) as well as two processively acting, reducing and non-reducing chain end-cleaving cellobiohydrolases (CBHs). Substrate preference (amorphous: EG, CBH II; crystalline: CBH I) and characteristic frequencies for chain cleavage, processive movement, and dissociation were assigned from biochemical data. Once adsorbed, enzymes were allowed to reach surface-exposed substrate sites through "random-walk" lateral diffusion or processive motion. Simulations revealed that slow dissociation of processive enzymes at obstacles obstructing further movement resulted in local jamming of the cellulases, with consequent delay in the degradation of the surface area affected. Exploiting validation against evidence from atomic force microscopy imaging as a unique opportunity opened up by the modeling approach, we show that spatiotemporal characteristics of cellulose surface degradation by the system of synergizing cellulases were reproduced quantitatively at the nanometer resolution of the experimental data. This in turn gave useful prediction of the soluble sugar release rate.

CONCLUSIONS

Salient dynamic features of cellulose surface degradation by different cellulases acting in synergy were reproduced in simulations in good agreement with evidence from high-resolution visualization experiments. Due to the single-molecule resolution of the modeling approach, the utility of the presented model lies not only in predicting system behavior but also in elucidating inherently complex (e.g., stochastic) phenomena involved in enzymatic cellulose degradation. Thus, it creates synergy with experiment to advance the mechanistic understanding for improved application.

Assemblies of pore-forming toxins visualized by atomic force microscopy

A number of pore-forming toxins (PFTs) can assemble on lipid membranes through their specific interactions with lipids. The oligomeric assemblies of some PFTs have been successfully revealed either by electron microscopy (EM) and/or atomic force microscopy (AFM). Unlike EM, AFM imaging can be performed under physiological conditions, enabling the real-time visualization of PFT assembly and the transition from the prepore state, in which the toxin does not span the membrane, to the pore state. In addition to characterizing PFT oligomers, AFM has also been used to examine toxin-induced alterations in membrane organization. In this review, we summarize the contributions of AFM to the understanding of both PFT assembly and PFT-induced membrane reorganization. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.