Revealing molecular-level surface structure of amyloid fibrils in liquid by means of frequency modulation atomic force microscopy

Probing the Nature of Chemical Bonds by Atomic Force Microscopy

The nature of the chemical bond is important in all natural sciences, ranging from biology to chemistry, physics and materials science. The atomic force microscope (AFM) allows to put a single chemical bond on the test bench, probing its strength and angular dependence. We review experimental AFM data, covering precise studies of van-der-Waals-, covalent-, ionic-, metallic- and hydrogen bonds as well as bonds between artificial and natural atoms. Further, we discuss some of the density functional theory calculations that are related to the experimental studies of the chemical bonds. A description of frequency modulation AFM, the most precise AFM method, discusses some of the experimental challenges in measuring bonding forces. In frequency modulation AFM, forces between the tip of an oscillating cantilever change its frequency. Initially, cantilevers were made mainly from silicon. Most of the high precision measurements of bonding strengths by AFM became possible with a technology transfer from the quartz watch technology to AFM by using quartz-based cantilevers ("qPlus force sensors"), briefly described here.

Subnanometer-scale imaging of nanobio-interfaces by frequency modulation atomic force microscopy

Recently, there have been significant advancements in dynamic-mode atomic force microscopy (AFM) for biological applications. With frequency modulation AFM (FM-AFM), subnanometer-scale surface structures of biomolecules such as secondary structures of proteins, phosphate groups of DNAs, and lipid-ion complexes have been directly visualized. In addition, three-dimensional AFM (3D-AFM) has been developed by combining a high-resolution AFM technique with a 3D tip scanning method. This method enabled visualization of 3D distributions of water (i.e. hydration structures) with subnanometer-scale resolution on various biological molecules such as lipids, proteins, and DNAs. Furthermore, 3D-AFM also allows visualization of subnanometer-scale 3D distributions of flexible surface structures such as thermally fluctuating lipid headgroups. Such a direct local information at nano-bio interfaces can play a critical role in determining the atomic- or molecular-scale model to explain interfacial structures and functions. Here, we present an overview of these recent advancements in the dynamic-mode AFM techniques and their biological applications.

Improvements in fundamental performance of in-liquid frequency modulation atomic force microscopy

In-liquid frequency modulation atomic force microscopy (FM-AFM) has been used for visualizing subnanometer-scale surface structures of minerals, organic thin films and biological systems. In addition, three-dimensional atomic force microscopy (3D-AFM) has been developed by combining it with a three-dimensional (3D) tip scanning method. This method enabled the visualization of 3D distributions of water (i.e. hydration structures) and flexible molecular chains at subnanometer-scale resolution. While these applications highlighted the unique capabilities of FM-AFM, its force resolution, speed and stability are not necessarily at a satisfactory level for practical applications. Recently, there have been significant advancements in these fundamental performances. The force resolution was dramatically improved by using a small cantilever, which enabled the imaging of a 3D hydration structure even in pure water and made it possible to directly compare experimental results with simulated ones. In addition, the improved force resolution allowed the enhancement of imaging speed without compromising spatial resolution. To achieve this goal, efforts have been made for improving bandwidth, resonance frequency and/or latency of various components, including a high-speed phase-locked loop (PLL) circuit. With these improvements, now atomic-resolution in-liquid FM-AFM imaging can be performed at ∼1 s/frame. Furthermore, a Si-coating method was found to improve stability and reproducibility of atomic-resolution imaging owing to formation of a stable hydration structure on a tip apex. These improvements have opened up new possibilities of atomic-scale studies on solid-liquid interfacial phenomena by in-liquid FM-AFM.

Three-dimensional atomic force microscopy mapping at the solid-liquid interface with fast and flexible data acquisition

We present the implementation of a three-dimensional mapping routine for probing solid-liquid interfaces using frequency modulation atomic force microscopy. Our implementation enables fast and flexible data acquisition of up to 20 channels simultaneously. The acquired data can be directly synchronized with commercial atomic force microscope controllers, making our routine easily extendable for related techniques that require additional data channels, e.g., Kelvin probe force microscopy. Moreover, the closest approach of the tip to the sample is limited by a user-defined threshold, providing the possibility to prevent potential damage to the tip. The performance of our setup is demonstrated by visualizing the hydration structure above the calcite (10.4) surface in water.

Double-Tip Artefact Removal from Atomic Force Microscopy Images

The Atomic Force Microscope (AFM) allows the measurement of interactions at interfaces with nanoscale resolution. Imperfections in the shape of the tip often lead to the presence of imaging artefacts such as the blurring and repetition of objects within images. Generally, these artefacts can only be avoided by discarding data and replacing the probe. Under certain circumstances (e.g., rare, high value samples, or extensive chemical/physical tip modification) such an approach is not feasible. Here, we apply a novel deblurring technique, using a Bayesian framework, to yield a reliable estimation of the real surface topography without any prior knowledge of the tip geometry (blind reconstruction). A key contribution is to leverage the significant recently successful body of work in natural image deblurring to solve this problem. We focus specifically on the 'double-tip' effect, where two asperities 1 are present on the tip, each contributing to the image formation mechanism. Finally, we demonstrate that the proposed technique successfully removes the 'double-tip' effect from high resolution AFM images which demonstrate this artefact whilst preserving feature resolution.

Flattened-Top Domical Water Drops Formed through Self-Organization of Hydrophobin Membranes: A Structural and Mechanistic Study Using Atomic Force Microscopy

The Trichoderma reesei hydrophobin, HFBI, is a unique structural protein. This protein forms membranes by self-organization at air/water or water/solid interfaces. When HFBI forms a membrane at an air/water interface, the top of the water droplet is flattened. The mechanism underlying this phenomenon has not been explored. In this study, this unique phenomenon has been investigated. Self-organized HFBI membranes form a hexagonal structured membrane on the surface of water droplets; the structure was confirmed by atomic force microscopy (AFM) measurement. Assembled hexagons can form a planar sheet or a tube. Self-organized HFBI membranes on water droplets form a sheet with an array of hexagonal structures or a honeycomb structure. This membrane, with its arrayed hexagonal structures, has very high buckling strength. We hypothesized that the high buckling strength is the reason that water droplets containing HFBI form flattened domes. To test this hypothesis, the strength of the self-organized HFBI membranes was analyzed using AFM. The buckling strength of HFBI membranes was measured to be 66.9 mN/m. In contrast, the surface tension of water droplets containing dissolved HFBI is 42 mN/m. Thus, the buckling strength of a self-organized HFBI membrane is higher than the surface tension of water containing dissolved HFBI. This mechanistic study clarifies why the water droplets formed by self-organized HFBI membranes have a flattened top.

Atomic Force Microscopy Characterization of Protein Fibrils Formed by the Amyloidogenic Region of the Bacterial Protein MinE on Mica and a Supported Lipid Bilayer

Amyloid fibrils play a crucial role in many human diseases and are found to function in a range of physiological processes from bacteria to human. They have also been gaining importance in nanotechnology applications. Understanding the mechanisms behind amyloid formation can help develop strategies towards the prevention of fibrillation processes or create new technological applications. It is thus essential to observe the structures of amyloids and their self-assembly processes at the nanometer-scale resolution under physiological conditions. In this work, we used highly force-sensitive frequency-modulation atomic force microscopy (FM-AFM) to characterize the fibril structures formed by the N-terminal domain of a bacterial division protein MinE in solution. The approach enables us to investigate the fibril morphology and protofibril organization over time progression and in response to changes in ionic strength, molecular crowding, and upon association with different substrate surfaces. In addition to comparison of the fibril structure and behavior of MinE1-31 under varying conditions, the study also broadens our understanding of the versatile behavior of amyloid-substrate surface interactions.

Aβ42 and Aβ40: similarities and differences

The abnormal accumulation of amyloid-β (Aβ) peptide in the brain is one of the most important hallmarks of Alzheimer's disease. Aβ is an aggregation-prone and toxic polypeptide with 39-43 residues, derived from the amyloid precursor protein proteolysis process. According to the amyloid hypothesis, abnormal accumulation of Aβ in the brain is the primary influence driving Alzheimer's disease pathologies. Among all kinds of Aβ isoforms, Aβ40 and Aβ42 are believed to be the most important ones. Although these two kinds of Aβ differ only in two amino acid residues, recent studies show that they differ significantly in their metabolism, physiological functions, toxicities, and aggregation mechanism. In this review, we mainly summarize the similarities and differences between Aβ42 and Aβ40, recent studies on selective inhibitors as well as probes will also be mentioned.

Local frustration determines molecular and macroscopic helix structures

Decorative domains force amyloid fibers to adopt spiral ribbon morphologies, as opposed to the more common twisted ribbon. We model the effect of decorating domains as a perturbation to the relative orientation of β strands in a bilayered extended β-sheet. The model consists of minimal energy assemblies of rigid building blocks containing two anisotropic interacting ellipsoids. The relative orientation of the ellipsoids dictates the morphology of the resulting assembly. Amyloid structures derived from experiment are consistent with our model, and we use magnets to demonstrate that the frustration principle is scale and system independent. In contrast to other models of amyloid, our model isolates the effect of frustration from the fundamental interactions between building blocks to reveal the frustration rather than dependence of morphology on the physical interactions. Consequently, amyloid is viewed as a discrete molecular version of the more general macroscopic frustrated bilayer that is exemplified by Bauhinia seedpods. The model supports the idea that the interactions arising from an arbitrary peptide sequence can support an amyloid structure if a bilayer can form first, which suggests that supplementary protein sequences, such as chaperones or decorative domains, could play a significant role in stabilizing such bilayers and therefore in selecting morphology during nucleation. Our model provides a foundation for exploring the effects of frustration on higher-order superstructural polymorphic assemblies that may exhibit complex functional behavior. Two outstanding examples are the systematic kinking of decorated fibers and the nested frustration of the Bauhinia seedpod.

Super-resolved FT-IR spectroscopy: Strategies, challenges, and opportunities for membrane biophysics

Direct correlation of molecular conformation with local structure is critical to studies of protein- and peptide-membrane interactions, particularly in the context of membrane-facilitated aggregation, and disruption or disordering. Infrared spectroscopy has long been a mainstay for determining molecular conformation, following folding dynamics, and characterizing reactions. While tremendous advances have been made in improving the spectral and temporal resolution of infrared spectroscopy, it has only been with the introduction of scanned-probe techniques that exploit the raster-scanning tip as either a source, scattering tool, or measurement probe that researchers have been able to obtain sub-diffraction limit IR spectra. This review will examine the history of correlated scanned-probe IR spectroscopies, from their inception to their use in studies of molecular aggregates, membrane domains, and cellular structures. The challenges and opportunities that these platforms present for examining dynamic phenomena will be discussed. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.

Atomic-resolution imaging in liquid by frequency modulation atomic force microscopy using small cantilevers with megahertz-order resonance frequencies

In this study, we have investigated the performance of liquid-environment FM-AFM with various cantilevers having different dimensions from theoretical and experimental aspects. The results show that reduction of the cantilever dimensions provides improvement in the minimum detectable force as long as the tip height is sufficiently long compared with the width of the cantilever. However, we also found two important issues to be overcome to achieve this theoretically expected performance. The stable photothermal excitation of a small cantilever requires much higher pointing stability of the exciting laser beam than that for a long cantilever. We present a way to satisfy this stringent requirement using a temperature controlled laser diode module and a polarization-maintaining optical fiber. Another issue is associated with the tip. While a small carbon tip formed by electron beam deposition (EBD) is desirable for small cantilevers, we found that an EBD tip is not suitable for atomic-scale applications due to the weak tip-sample interaction. Here we show that the tip-sample interaction can be greatly enhanced by coating the tip with Si. With these improvements, we demonstrate atomic-resolution imaging of mica in liquid using a small cantilever with a megahertz-order resonance frequency. In addition, we experimentally demonstrate the improvement in the minimum detectable force obtained by the small cantilever in measurements of oscillatory hydration forces.

The morphology of decorated amyloid fibers is controlled by the conformation and position of the displayed protein

Self-assembled structures capable of mediating electron transfer are an attractive scientific and technological goal. Therefore, systematic variants of SH3-Cytochrome b(562) fusion proteins were designed to make amyloid fibers displaying heme-b(562) electron transfer complexes. TEM and AFM data show that fiber morphology responds systematically to placement of b(562) within the fusion proteins. UV-vis spectroscopy shows that, for the fusion proteins under test, only half the fiber-borne b(562) binds heme with high affinity. Cofactor binding also improves the AFM imaging properties and changes the fiber morphology through changes in cytochrome conformation. Systematic observations and measurements of fiber geometry suggest that longitudinal registry of subfilaments within the fiber, mediated by the interaction and conformation of the displayed proteins and their interaction with surfaces, gives rise to the observed morphologies, including defects and kinks. Of most interest is the role of small molecule modulation of fiber structure and mechanical stability. A minimum complexity model is proposed to capture and explain the fiber morphology in the light of these results. Understanding the complex interplay between these factors will enable a fiber design that supports longitudinal electron transfer.

Nanoscopic and photonic ultrastructural characterization of two distinct insulin amyloid states

Two different conformational isoforms or amyloid strains of insulin with different cytotoxic capacity have been described previously. Herein these filamentous and fibrillar amyloid states of insulin were investigated using biophysical and spectroscopic techniques in combination with luminescent conjugated oligothiophenes (LCO). This new class of fluorescent probes has a well defined molecular structure with a distinct number of thiophene units that can adopt different dihedral angles depending on its binding site to an amyloid structure. Based on data from surface charge, hydrophobicity, fluorescence spectroscopy and imaging, along with atomic force microscopy (AFM), we deduce the ultrastructure and fluorescent properties of LCO stained insulin fibrils and filaments. Combined total internal reflection fluorescence microscopy (TIRFM) and AFM revealed rigid linear fibrous assemblies of fibrils whereas filaments showed a short curvilinear morphology which assemble into cloudy deposits. All studied LCOs bound to the filaments afforded more blue-shifted excitation and emission spectra in contrast to those corresponding to the fibril indicating a different LCO binding site, which was also supported by less efficient hydrophobic probe binding. Taken together, the multi-tool approach used here indicates the power of ultrastructure identification applying AFM together with LCO fluorescence interrogation, including TIRFM, to resolve structural differences between amyloid states.

Submolecular-scale imaging of α-helices and C-terminal domains of tubulins by frequency modulation atomic force microscopy in liquid

In this study, we directly imaged subnanometer-scale structures of tubulins by performing frequency modulation atomic force microscopy (FM-AFM) in liquid. Individual α-helices at the surface of a tubulin protofilament were imaged as periodic corrugations with a spacing of 0.53 nm, which corresponds to the common pitch of an α-helix backbone (0.54 nm). The identification of individual α-helices allowed us to determine the orientation of the deposited tubulin protofilament. As a result, C-terminal domains of tubulins were identified as protrusions with a height of 0.4 nm from the surface of the tubulin. The imaging mechanism for the observed subnanometer-scale contrasts is discussed in relation to the possible structures of the C-terminal domains. Because the C-terminal domains are chemically modified to regulate the interactions between tubulins and other biomolecules (e.g., motor proteins and microtubule-associated proteins), detailed structural information on individual C-terminal domains is valuable for understanding such regulation mechanisms. The results obtained in this study demonstrate that FM-AFM is capable of visualizing the structural variation of tubulins with subnanometer resolution. This is an important first step toward using FM-AFM to analyze the functions of tubulins.

Wideband phase-locked loop circuit with real-time phase correction for frequency modulation atomic force microscopy

We have developed a wideband phase-locked loop (PLL) circuit with real-time phase correction for high-speed and accurate force measurements by frequency modulation atomic force microscopy (FM-AFM) in liquid. A high-speed operation of FM-AFM requires the use of a high frequency cantilever which, however, increases frequency-dependent phase delay caused by the signal delay within the cantilever excitation loop. Such phase delay leads to an error in the force measurements by FM-AFM especially with a low Q factor. Here, we present a method to compensate this phase delay in real time. Combined with a wideband PLL using a subtraction-based phase comparator, the method allows to perform an accurate and high-speed force measurement by FM-AFM. We demonstrate the improved performance by applying the developed PLL to three-dimensional force measurements at a mica/water interface.

Water distribution at solid/liquid interfaces visualized by frequency modulation atomic force microscopy

Interfacial phenomena at solid/water interfaces play an important role in a wide range of industrial technologies and biological processes. However, it has been a great challenge to directly probe the molecular-scale behavior of water at solid/water interfaces. Recently, there have been tremendous advancements in frequency modulation atomic force microscopy (FM-AFM), enabling its operation in liquids with atomic resolution. The high spatial and force resolutions of FM-AFM have enabled the visualization of one-dimensional (1D) profiles of the hydration force, two-dimensional (2D) images of hydration layers and three-dimensional (3D) images of the water distribution at solid/water interfaces. Here I present an overview of the recent advances in FM-AFM instrumentation and its applications to the study of solid/water interfaces.

The structure of dopamine induced alpha-synuclein oligomers

Inclusions of aggregated alpha-synuclein (alpha-syn) in dopaminergic neurons are a characteristic histological marker of Parkinson's disease (PD). In vitro, alpha-syn in the presence of dopamine (DA) at physiological pH forms SDS-resistant non-amyloidogenic oligomers. We used a combination of biophysical techniques, including sedimentation velocity analysis, small angle X-ray scattering (SAXS) and circular dichroism spectroscopy to study the characteristics of alpha-syn oligomers formed in the presence of DA. Our SAXS data show that the trimers formed by the action of DA on alpha-syn consist of overlapping worm-like monomers, with no end-to-end associations. This lack of structure contrasts with the well-established, extensive beta-sheet structure of the amyloid fibril form of the protein and its pre-fibrillar oligomers. We propose on the basis of these and earlier data that oxidation of the four methionine residues at the C- and N-terminal ends of alpha-syn molecules prevents their end-to-end association and stabilises oligomers formed by cross linking with DA-quinone/DA-melanin, which are formed as a result of the redox process, thus inhibiting formation of the beta-sheet structure found in other pre-fibrillar forms of alpha-syn.

Wideband digital frequency detector with subtraction-based phase comparator for frequency modulation atomic force microscopy

We have developed a wideband digital frequency detector for high-speed frequency modulation atomic force microscopy (FM-AFM). We used a subtraction-based phase comparator (PC) in a phase-locked loop circuit instead of a commonly used multiplication-based PC, which has enhanced the detection bandwidth to 100 kHz. The quantitative analysis of the noise performance revealed that the internal noise from the developed detector is small enough to provide the theoretically limited noise performance in FM-AFM experiments in liquid. FM-AFM imaging of mica in liquid was performed with the developed detector, showing its stability and applicability to true atomic-resolution imaging in liquid.

Wideband low-noise optical beam deflection sensor with photothermal excitation for liquid-environment atomic force microscopy

I developed a wideband low-noise optical beam deflection sensor with a photothermal cantilever excitation system for liquid-environment atomic force microscopy. The developed sensor has a 10 MHz bandwidth and 4.7 fm/sq.rt.Hz deflection noise density in water. The theoretically limited noise performance (i.e., the noise level limited only by the photodiode shot noise) has been achieved in liquid for the first time. Owing to the wide bandwidth and the replaceable focus lens design, the sensor is applicable to cantilevers with various dimensions. The deflection noise densities of less than 7.8 fm/sq.rt.Hz have been achieved in water for cantilevers with lengths from 35 to 125 microm. The ideal amplitude and phase versus frequency curves without distortion are obtained with the developed photothermal excitation system. The excitation system is applicable to relatively stiff cantilevers (>20 N/m) in liquid, making it possible to obtain true atomic-resolution images in liquid. True atomic-resolution imaging of mica in water is demonstrated using the developed deflection sensor and the photothermal excitation system.