Nanomechanical properties of α-synuclein amyloid fibrils: a comparative study by nanoindentation, harmonic force microscopy, and Peakforce QNM

Correlative infrared nanospectroscopic and nanomechanical imaging of block copolymer microdomains

Intermolecular interactions and nanoscale phase separation govern the properties of many molecular soft-matter systems. Here, we combine infrared vibrational scattering scanning near-field optical microscopy (IR s-SNOM) with force-distance spectroscopy for simultaneous characterization of both nanoscale optical and nanomechanical molecular properties through hybrid imaging. The resulting multichannel images and correlative analysis of chemical composition, spectral IR line shape, modulus, adhesion, deformation, and dissipation acquired for a thin film of a nanophase separated block copolymer (PS-b-PMMA) reveal complex structural variations, in particular at domain interfaces, not resolved in any individual signal channel alone. These variations suggest that regions of multicomponent chemical composition, such as the interfacial mixing regions between microdomains, are correlated with high spatial heterogeneity in nanoscale material properties.

Nanomechanics of Cells and Biomaterials Studied by Atomic Force Microscopy

The behavior and mechanical properties of cells are strongly dependent on the biochemical and biomechanical properties of their microenvironment. Thus, understanding the mechanical properties of cells, extracellular matrices, and biomaterials is key to understanding cell function and to develop new materials with tailored mechanical properties for tissue engineering and regenerative medicine applications. Atomic force microscopy (AFM) has emerged as an indispensable technique for measuring the mechanical properties of biomaterials and cells with high spatial resolution and force sensitivity within physiologically relevant environments and timescales in the kPa to GPa elastic modulus range. The growing interest in this field of bionanomechanics has been accompanied by an expanding array of models to describe the complexity of indentation of hierarchical biological samples. Furthermore, the integration of AFM with optical microscopy techniques has further opened the door to a wide range of mechanotransduction studies. In recent years, new multidimensional and multiharmonic AFM approaches for mapping mechanical properties have been developed, which allow the rapid determination of, for example, cell elasticity. This Progress Report provides an introduction and practical guide to making AFM-based nanomechanical measurements of cells and surfaces for tissue engineering applications.

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.

Polyaniline-nanodiamond fibers resulting from the self-assembly of nano-fibrils: a nanomechanical study

Based on atomic force microscopy (AFM), torsional harmonics atomic force microscopy (TH-AFM, also referred to with the commercial name HarmoniX™) allows one to perform a quantitative characterization of the mechanical properties of soft samples on the nanometer scale. In this work, such a technique has been employed to study the mechanical properties of self-assembled micrometric fibers of polyaniline (PANI) doped with nanodiamond (ND) particles and to investigate the role of ND in the assembly. In particular, besides PANI-ND fibers, other features, i.e., nano-fibrils and blobs, have also been observed on the sample, the mechanical properties of which have been determined and compared after correcting for the effect of the substrate and of the cylindrical geometry of nano-fibrils. Their similar mechanical properties suggest that PANI-ND micro-fibers are constituted by self-assembly of nano-fibrils. Finally, the combination of nanomechanical characterization with energy dispersive X-ray (EDX) and Raman analyses allowed us to determine that softer blobs are residuals of amorphous PANI not polymerized in nano-fibrils.

Structure, function and toxicity of alpha-synuclein: the Bermuda triangle in synucleinopathies

Parkinson's disease belongs to a group of currently incurable neurodegenerative disorders characterized by the misfolding and accumulation of alpha-synuclein aggregates that are commonly known as synucleinopathies. Clinically, synucleinopathies are heterogeneous, reflecting the somewhat selective neuronal vulnerability characteristic of each disease. The precise molecular underpinnings of synucleinopathies remain unclear, but the process of aggregation of alpha-synuclein appears as a central event. However, there is still no consensus with respect to the toxic forms of alpha-synuclein, hampering our ability to use the protein as a target for therapeutic intervention. To decipher the molecular bases of synucleinopathies, it is essential to understand the complex triangle formed between the structure, function and toxicity of alpha-synuclein. Recently, important steps have been undertaken to elucidate the role of the protein in both physiological and pathological conditions. Here, we provide an overview of recent findings in the field of alpha-synuclein research, and put forward a new perspective over paradigms that persist in the field. Establishing whether alpha-synuclein has a causative role in all synucleinopathies will enable the identification of targets for the development of novel therapeutic strategies for this devastating group of disorders. Alpha-synuclein is the speculated cornerstone of several neurodegenerative disorders known as Synucleinopathies. Nevertheless, the mechanisms underlying the pathogenic effects of this protein remain unknown. Here, we review the recent findings in the three corners of alpha-synuclein biology - structure, function and toxicity - and discuss the enigmatic roads that have accompanied alpha-synuclein from the beginning. This article is part of a special issue on Parkinson disease.

Amyloid-like fibrils formed from intrinsically disordered caseins: physicochemical and nanomechanical properties

Amyloid-like fibrils are studied because of their significance in understanding pathogenesis and creating functional materials. Amyloid-like fibrils have been studied by heating globular proteins at acidic conditions. In the present study, intrinsically disordered α-, β-, and κ-caseins were studied to form amyloid-like fibrils at pH 2.0 and 90 °C. No fibrils were observed for α-caseins, and acid hydrolysis was found to be the rate-limiting step of fibrillation of β- and κ-caseins. An increase of β-sheet structure was observed after fibrillation. Nanomechanic analysis of long amyloid-like fibrils using peak-force quantitative nanomechanical atomic force microscopy showed the lowest and highest Young's modulus for β-casein (2.35 ± 0.29 GPa) and κ-casein (4.14 ± 0.66 GPa), respectively. The dispersion with β-casein fibrils had a viscosity more than 10 and 5 times higher than those of κ-casein and β-lactoglobulin, respectively, at 0.1 s(-1) at comparable concentrations. The current findings may assist not only the understanding of amyloid fibril formation but also the development of novel functional materials from disordered proteins.

Multidimensional characterisation of biomechanical structures by combining Atomic Force Microscopy and Focused Ion Beam: A study of the rat whisker

Understanding the heterogeneity of biological structures, particularly at the micro/nano scale can offer insights valuable for multidisciplinary research in tissue engineering and biomimicry designs. Here we propose to combine nanocharacterisation tools, particularly Focused Ion Beam (FIB) and Atomic Force Microscopy (AFM) for three dimensional mapping of mechanical modulus and chemical signatures. The prototype platform is applied to image and investigate the fundamental mechanics of the rat face whiskers, a high-acuity sensor used to gain detailed information about the world. Grazing angle FIB milling was first applied to expose the interior cross section of the rat whisker sample, followed by a "lift-out" method to retrieve and position the target sample for further analyses. AFM force spectroscopy measurements revealed a non-uniform pattern of elastic modulus across the cross section, with a range from 0.8GPa to 13.5GPa. The highest elastic modulus was found at the outer cuticle region of the whisker, and values gradually decreased towards the interior cortex and medulla regions. Elemental mapping with EDS confirmed that the interior of the rat whisker is dominated by C, O, N, S, Cl and K, with a significant change of elemental distribution close to the exterior cuticle region. Based on these data, a novel comprehensive three dimensional (3D) elastic modulus model was constructed, and stress distributions under realistic conditions were investigated with Finite Element Analysis (FEA). The simulations could well account for the passive whisker deflections, with calculated resonant frequency as well as force-deflection for the whiskers being in good agreement with reported experimental data. Limitations and further applications are discussed for the proposed FIB/AFM approach, which holds good promise as a unique platform to gain insights on various heterogeneous biomaterials and biomechanical systems.

In vitro culture and directed osteogenic differentiation of human pluripotent stem cells on peptides-decorated two-dimensional microenvironment

Human pluripotent stem cells (hPSCs) are a promising cell source with pluripotency and capacity to differentiate into all human somatic cell types. Designing simple and safe biomaterials with an innate ability to induce osteoblastic lineage from hPSCs is desirable to realize their clinical adoption in bone regenerative medicine. To address the issue, here we developed a fully defined synthetic peptides-decorated two-dimensional (2D) microenvironment via polydopamine (pDA) chemistry and subsequent carboxymethyl chitosan (CMC) grafting to enhance the culture and osteogenic potential of hPSCs in vitro. The hPSCs including human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) were successfully cultured on the peptides-decorated surface without Matrigel and ECM protein coating and underwent promoted osteogenic differentiation in vitro, determined from the alkaline phosphate (ALP) activity, gene expression, and protein production as well as calcium deposit amount. It was found that directed osteogenic differentiation of hPSCs was achieved through a peptides-decorated niche. This chemically defined and safe 2D microenvironment, which facilitates proliferation and osteo-differentiation of hPSCs, not only helps to accelerate the translational perspectives of hPSCs but also provides tissue-specific functions such as directing stem cell differentiation commitment, having great potential in bone tissue engineering and opening new avenues for bone regenerative medicine.

Membrane interactions and fibrillization of α-synuclein play an essential role in membrane disruption

We studied α-synuclein (αS) aggregation in giant vesicles, and observed dramatic membrane disintegration, as well as lipid incorporation into micrometer-sized suprafibrillar aggregates. In the presence of dye-filled vesicles, dye leakage and fibrillization happen concurrently. However, growing fibrils do not impair the integrity of phospholipid vesicles that have a low affinity for αS. Seeding αS aggregation accelerates dye leakage, indicating that oligomeric species are not required to explain the observed effect. The evolving picture suggests that fibrils that appear in solution bind membranes and recruit membrane-bound monomers, resulting in lipid extraction, membrane destabilization and the formation of lipid-containing suprafibrillar aggregates.

Influence of the β-sheet content on the mechanical properties of aggregates during amyloid fibrillization

Amyloid fibrils associated with neurodegenerative diseases, such as Parkinson's and Alzheimer's, consist of insoluble aggregates of α-synuclein and Aβ-42 proteins with a high β-sheet content. The aggregation of both proteins occurs by misfolding of the monomers and proceeds through the formation of intermediate oligomeric and protofibrillar species to give the final fibrillar cross-β-sheet structure. The morphological and mechanical properties of oligomers, protofibrils, and fibrils formed during the fibrillization process were investigated by thioflavin T fluorescence and circular dichroism in combination with AFM peak force quantitative nanomechanical technique. The results reveal an increase in the Young's modulus during the transformation from oligomers to mature fibrils, thus inferring that the difference in their mechanical properties is due to an internal structural change from a random coil to a structure with increased β-sheet content.

Functionalization of α-synuclein fibrils

The propensity of peptides and proteins to form self-assembled structures has very promising applications in the development of novel nanomaterials. Under certain conditions, amyloid protein α-synuclein forms well-ordered structures - fibrils, which have proven to be valuable building blocks for bionanotechnological approaches. Herein we demonstrate the functionalization of fibrils formed by a mutant α-synuclein that contains an additional cysteine residue. The fibrils have been biotinylated via thiol groups and subsequently joined with neutravidin-conjugated gold nanoparticles. Atomic force microscopy and transmission electron microscopy confirmed the expected structure - nanoladders. The ability of fibrils (and of the additional components) to assemble into such complex structures offers new opportunities for fabricating novel hybrid materials or devices.

Poly[3,4-ethylene dioxythiophene (EDOT) -co- 1,3,5-tri[2-(3,4-ethylene dioxythienyl)]-benzene (EPh)] copolymers (PEDOT-co-EPh): optical, electrochemical and mechanical properties

PEDOT-co-EPh copolymers with systematic variations in composition were prepared by electrochemical polymerization from mixed monomer solutions in acetonitrile. The EPh monomer is a trifunctional crosslinking agent with three EDOTs around a central benzene ring. With increasing EPh content, the color of the copolymers changed from blue to yellow to red due to decreased absorption in the near infrared (IR) spectrum and increased absorption in the visible spectrum. The surface morphology changed from rough and nanofibrillar to more smooth with rounded bumps. The electrical transport properties dramatically decreased with increasing EPh content, resulting in coatings that either substantially lowered the impedance of the electrode (at the lowest EPh content), leave the impedance nearly unchanged (near 1% EPh), or significantly increase the impedance (at 1% and above). The mechanical properties of the films were substantially improved with EPh content, with the 0.5% EPh films showing an estimated 5x improvement in modulus measured by AFM nanoindentation. The PEDOT-co-EPh copolymer films were all shown to be non-cytotoxic toward and promote the neurite outgrowth of PC12 cells. Given these results, we expect that the films of most interest for neural interface applications will be those with improved mechanical properties that maintain the improved charge transport performance (with 1% EPh and below).

Nanoscale electrical and mechanical characteristics of conductive polyaniline network in polymer composite films

The presence and characteristics of a connected network of polyaniline (PANI) within a composite coating based on polyester acrylate (PEA) has been investigated. The bulk electrical conductivity of the composite was measured by impedance spectroscopy. It was found that the composite films containing PANI have an electrical conductivity level in the range of semiconductors (order of 10(-3) S cm(-1)), which suggests the presence of a connected network of the conductive phase. The nanoscopic distribution of such a network within the cured film was characterized by PeakForce tunneling atomic force microscopy (AFM). This method simultaneously provides local information about surface topography and nanomechanical properties, together with electrical conductivity arising from conductive paths connecting the metallic substrate to the surface of the coating. The data demonstrates that a PEA-rich layer exists at the composite-air interface, which hinders the conductive phase to be fully detected at the surface layer. However, by exposing the internal structure of the composites using a microtome, a much higher population of a conductive network of PANI, with higher elastic modulus than the PEA matrix, was observed and characterized. Local current-voltage (I-V) spectroscopy was utilized to investigate the conduction mechanism within the nanocomposite films, and revealed non-Ohmic characteristics of the conductive network.

Localizing chemical groups while imaging single native proteins by high-resolution atomic force microscopy

Simultaneous high-resolution imaging and localization of chemical interaction sites on single native proteins is a pertinent biophysical, biochemical, and nanotechnological challenge. Such structural mapping and characterization of binding sites is of importance in understanding how proteins interact with their environment and in manipulating such interactions in a plethora of biotechnological applications. Thus far, this challenge remains to be tackled. Here, we introduce force-distance curve-based atomic force microscopy (FD-based AFM) for the high-resolution imaging of SAS-6, a protein that self-assembles into cartwheel-like structures. Using functionalized AFM tips bearing Ni(2+)-N-nitrilotriacetate groups, we locate specific interaction sites on SAS-6 at nanometer resolution and quantify the binding strength of the Ni(2+)-NTA groups to histidine residues. The FD-based AFM approach can readily be applied to image any other native protein and to locate and structurally map histidine residues. Moreover, the surface chemistry used to functionalize the AFM tip can be modified to map other chemical interaction sites.

High intrinsic mechanical flexibility of mouse prion nanofibrils revealed by measurements of axial and radial Young's moduli

Self-templated protein aggregation and intracerebral deposition of aggregates, sometimes in the form of amyloid fibrils, is a hallmark of mammalian prion diseases. What distinguishes amyloid fibrils formed by prions from those formed by other proteins is not clear. On the basis of previous studies on yeast prions that correlated high intrinsic fragmentation rates of fibrils with prion propagation efficiency, it has been hypothesized that the nanomechanical properties of prion amyloid such as strength and elastic modulus may be the distinguishing feature. Here, we reveal that fibrils formed by mammalian prions are relatively soft and clearly in a different class of rigidities when compared to nanofibrils formed by nonprions. We found that amyloid fibrils made of both wild-type and mutant mouse recombinant PrP(23-231) have remarkably low axial elastic moduli of 0.1-1.4 GPa. We demonstrate that even the proteinase K resistant core of these fibrils has similarly low intrinsic rigidities. Using a new mode of atomic force microscopy called AM-FM mode, we estimated the radial modulus of PrP fibrils at ∼0.6 GPa, consistent with the axial moduli derived by using an ensemble method. Our results have far-reaching implications for the understanding of protein-based infectivity and the design of amyloid biomaterials.

Large electric field-enhanced-hardness effect in a SiO2 film

Silicon dioxide films are extensively used in nano and micro–electromechanical systems. Here we studied the influence of an external electric field on the mechanical properties of a SiO₂ film by using nanoindentation technique of atomic force microscopy (AFM) and friction force microscopy (FFM). A giant augmentation of the relative elastic modulus was observed by increasing the localized electric field. A slight decrease in friction coefficients was also clearly observed by using FFM with the increase of applied tip voltage. The reduction of the friction coefficients is consistent with the great enhancement of sample hardness by considering the indentation–induced deformation during the friction measurements.

Lewy bodies under atomic force microscope

Lewy bodies are the hallmark of Parkinson disease and their sophisticated analysis will undoubtedly elucidate the pathogenic process. They have been studied by using different microscopic tools. The authors have used atomic force microscopy (AFM) to study the ultramicrotom cut postmortem brain tissue of Parkinson disease patients. Under the same preparation conditions, they have found aggregated fibrillary nanostructures in Lewy bodies, as well as a loss of connections between neurons located in other parts of the substantia nigra. Although these results are preliminary and descriptive in nature, this paper reports the application of a novel and intriguing technique. Further studies including the study of cortical LB and Lewy neurites will be needed to determine the full potential of AFM in the study of the pathogenesis of cell death in Parkinson disease and other synucleinopathies.

Consolidation trend design based on Young's modulus of clarithromycin single crystals

The key aim of this study was to determine single mechanical properties of clarithromycin polymorphic forms in order to select some of them as more suitable for the tableting process. For this purpose, AFM single-point nanoindentation was used. The Young's moduli of clarithromycin polymorphs were substantially different, which was consistent with the structural variations in their packing motifs. The presence of the adjacent layers, which can easily slide over each other due to the low energy barrier (the lowest Young's modulus was 0.25 GPa) resulted in better bulk compressibility (the highest Heckel coefficient) of clarithromycin Form I. We also addressed the importance of tip geometry screening because the stress during the force mode often results in tip apex fracture. Even the initial manufacture of the diamond-coated tips can result in defects such as double-apex tips.

Nanostructured composite layers of mussel adhesive protein and ceria nanoparticles

Mussel adhesive proteins are known for their high affinity to a range of different surfaces, and they therefore appear as ideal candidates for producing thin inorganic-organic composite films with high robustness. In this work we explore the possibility of making cohesive films utilizing layer-by-layer deposition of the highly positively charged mussel adhesive protein, Mefp-1, and negatively charged ceria nanoparticles. This particular material combination was chosen due to recent findings that such films provide good corrosion protection. Quartz crystal microbalance with dissipation monitoring (QCM-D) was used for following the film formation process in situ on silica surfaces. A close to linear growth of the film with number of deposited layers was found for up to 18 deposition steps, the highest number of depositions investigated in this work. The Mefp-1 concentration during film deposition affected the film properties, where a higher protein concentration resulted in a stiffer film. It was also found that the added mass could be amplified by using a Mefp-1 solution containing small aggregates. The surface nanomechanical properties of dried multilayer films were investigated using peak force QNM (quantitative nanomechanical mapping) in air. Homogeneous surface coverage was found under all conditions explored, and the Young's modulus of the outer region of the coating increased when a higher Mefp-1 concentration was used during film deposition. The nature of the outermost surface layer was found to significantly affect the surface nanomechanical properties. The abrasion resistance of the coating was measured by using controlled-force contact mode AFM.

Direct AFM force mapping of surface nanoscale organization and protein adsorption on an aluminum substrate

We investigate the nanoscale organization of a superficially hydroxylated Al substrate and its effect on subsequent protein adsorption using atomic force microscopy (AFM). For this purpose we used a mode which allows a direct mapping of a variety of surface properties (adhesion, elasticity, dissipation, etc.) to be probed simultaneously with topographical images. The hydroxylation treatment leads to a drastic modification of the surface morphology, owing to the formation of AlOOH compounds. In air, AFM images revealed the formation of regular nanorod-like structures randomly distributed, inducing the appearance of nanoporous domains on the surface. In buffer solution, prior to the adsorption of proteins, the surface nanoscale organization is preserved, mainly due to the chemical stability of AlOOH compounds under these conditions. The adsorption of proteins on the obtained nanostructured surface was performed using either a globular (β-lactoglobulin) or a fibrillar (collagen) protein and by modulating the adsorbed amount through the incubation time or the concentration of proteins in solution. At low amounts, collagen adsorbs on the whole surface without preferential localization. The surface topography remains similar to the bare surface, while significant changes were evidenced on adhesion and elasticity maps. This is due to the fact that the surface became adhesive and less stiff, owing to the presence of a soft and hydrated protein layer. By contrast, β-lactoglobulin tends to diffuse into the nanoporous domains, leading to their filling up, and the surface is blurred with a thick and dense protein layer upon increasing the amount of adsorbed molecules. Our findings demonstrate the interest in using AFM for surface mapping to investigate the mechanism of protein adsorption at the nanoscale on materials with high surface roughness.

High-resolution nanomechanical analysis of suspended electrospun silk fibers with the torsional harmonic atomic force microscope

Atomic force microscopes have become indispensable tools for mechanical characterization of nanoscale and submicron structures. However, materials with complex geometries, such as electrospun fiber networks used for tissue scaffolds, still pose challenges due to the influence of tension and bending modulus on the response of the suspended structures. Here we report mechanical measurements on electrospun silk fibers with various treatments that allow discriminating among the different mechanisms that determine the mechanical behavior of these complex structures. In particular we were able to identify the role of tension and boundary conditions (pinned versus clamped) in determining the mechanical response of electrospun silk fibers. Our findings show that high-resolution mechanical imaging with torsional harmonic atomic force microscopy provides a reliable method to investigate the mechanics of materials with complex geometries.

Imaging living cells surface and quantifying its properties at high resolution using AFM in QI™ mode

Since the last 10 years, AFM has become a powerful tool to study biological samples. However, the classical modes offered (imaging or tapping mode) often damage sample that are too soft or loosely immobilized. If imaging and mechanical properties are required, it requests long recording time as two different experiments must be conducted independently. In this study we compare the new QI™ mode against contact imaging mode and force volume mode, and we point out its benefit in the new challenges in biology on six different models: Escherichia coli, Candida albicans, Aspergillus fumigatus, Chinese hamster ovary cells and their isolated nuclei, and human colorectal tumor cells.

Concurrent quantitative conductivity and mechanical properties measurements of organic photovoltaic materials using AFM

Organic photovoltaic (OPV) materials are inherently inhomogeneous at the nanometer scale. Nanoscale inhomogeneity of OPV materials affects performance of photovoltaic devices. Thus, understanding of spatial variations in composition as well as electrical properties of OPV materials is of paramount importance for moving PV technology forward. In this paper, we describe a protocol for quantitative measurements of electrical and mechanical properties of OPV materials with sub-100 nm resolution. Currently, materials properties measurements performed using commercially available AFM-based techniques (PeakForce, conductive AFM) generally provide only qualitative information. The values for resistance as well as Young's modulus measured using our method on the prototypical ITO/PEDOT:PSS/P3HT:PC(61)BM system correspond well with literature data. The P3HT:PC(61)BM blend separates onto PC(61)BM-rich and P3HT-rich domains. Mechanical properties of PC(61)BM-rich and P3HT-rich domains are different, which allows for domain attribution on the surface of the film. Importantly, combining mechanical and electrical data allows for correlation of the domain structure on the surface of the film with electrical properties variation measured through the thickness of the film.

The model of amyloid aggregation of Escherichia coli RNA polymerase σ70 subunit based on AFM data and in vitro assays

To propose a model for recently described amyloid aggregation of E.coli RNA polymerase σ(70) subunit, we have investigated the role of its N-terminal region. For this purpose, three mutant variants of protein with deletions Δ1-73, Δ1-100 and Δ74-100 were constructed and studied in a series of in vitro assays and using atomic force microscopy (AFM). Specifically, all RNA polymerase holoenzymes, reconstituted with the use of mutant σ subunits, have shown reduced affinity for promoter-containing DNA and reduced activity in run-off transcription experiments (compared to that of WT species), thus substantiating the modern concept on the modulatory role of N-terminus in formation of open complex and transcription initiation. The ability of mutant proteins to form amyloid-like structures has been investigated using AFM, which revealed the increased propensity of mutant proteins to form rodlike aggregates with the effect being more pronounced for the mutant with the deletion Δ1-73 (10 fold increase). σ(70) subunit aggregation ability has shown complex dependence on the ionic surrounding, which we explain by Debye screening effect and the change of the internal state of the protein. Basing on the obtained data, we propose the model of amyloid fibril formation by σ(70) subunit, implying the involvement of N-terminal region according to the domain swapping mechanism.

Interactions of Thellungiella salsuginea dehydrins TsDHN-1 and TsDHN-2 with membranes at cold and ambient temperatures-surface morphology and single-molecule force measurements show phase separation, and reveal tertiary and quaternary associations

Dehydrins (group 2 late embryogenesis abundant proteins) are intrinsically-disordered proteins that are expressed in plants experiencing extreme environmental conditions such as drought or low temperature. Their roles include stabilizing cellular proteins and membranes, and sequestering metal ions. Here, we investigate the membrane interactions of the acidic dehydrin TsDHN-1 and the basic dehydrin TsDHN-2 derived from the crucifer Thellungiella salsuginea that thrives in the Canadian sub-Arctic. We show using compression studies with a Langmuir-Blodgett trough that both dehydrins can stabilize lipid monolayers with a lipid composition mimicking the composition of the plant outer mitochondrial membrane, which had previously been shown to induce ordered secondary structures (disorder-to-order transitions) in the proteins. Ellipsometry of the monolayers during compression showed an increase in monolayer thickness upon introducing TsDHN-1 (acidic) at 4°C and TsDHN-2 (basic) at room temperature. Atomic force microscopy of supported lipid bilayers showed temperature-dependent phase transitions and domain formation induced by the proteins. These results support the conjecture that acidic dehydrins interact with and potentially stabilize plant outer mitochondrial membranes in conditions of cold stress. Single-molecule force spectroscopy of both proteins pulled from supported lipid bilayers indicated the induced formation of tertiary conformations in both proteins, and potentially a dimeric association for TsDHN-2.

Quantitative mapping of the elastic modulus of soft materials with HarmoniX and PeakForce QNM AFM modes

The modulus of elasticity of soft materials on the nanoscale is of interest when studying thin films, nanocomposites, and biomaterials. Two novel modes of atomic force microscopy (AFM) have been introduced recently: HarmoniX and PeakForce QNM. Both modes produce distribution maps of the elastic modulus over the sample surface. Here we investigate the question of how quantitative these maps are when studying soft materials. Three different polymers with a macroscopic Young's modulus of 0.6-0.7 GPa (polyurethanes) and 2.7 GPa (polystyrene) are analyzed using these new modes. The moduli obtained are compared to the data measured with the other commonly used techniques, dynamic mechanical analyzer (DMA), regular AFM, and nanoindenter. We show that the elastic modulus is overestimated in both the HarmoniX and PeakForce QNM modes when using regular sharp probes because of excessively overstressed material in the samples. We further demonstrate that both AFM modes can work in the linear stress-strain regime when using a relatively dull indentation probe (starting from ~210 nm). The analysis of the elasticity models to be used shows that the JKR model should be used for the samples considered here instead of the DMT model, which is currently implemented in HarmoniX and PeakForce QNM modes. Using the JKR model and ~240 nm AFM probe in the PeakForce QNM mode, we demonstrate that a quantitative mapping of the elastic modulus of polymeric materials is possible. A spatial resolution of ~50 nm and a minimum 2 to 3 nm indentation depth are achieved.

Nanomechanical characterization of chemical interaction between gold nanoparticles and chemical functional groups

We report on how to quantify the binding affinity between a nanoparticle and chemical functional group using various experimental methods such as cantilever assay, PeakForce quantitative nanomechanical property mapping, and lateral force microscopy. For the immobilization of Au nanoparticles (AuNPs) onto a microscale silicon substrate, we have considered two different chemical functional molecules of amine and catecholamine (here, dopamine was used). It is found that catecholamine-modified surface is more effective for the functionalization of AuNPs onto the surface than the amine-modified surface, which has been shown from our various experiments. The dimensionless parameter (i.e., ratio of binding affinity) introduced in this work from such experiments is useful in quantitatively depicting such binding affinity, indicating that the binding affinity and stability between AuNPs and catecholamine is approximately 1.5 times stronger than that between amine and AuNPs. Our study sheds light on the experiment-based quantitative characterization of the binding affinity between nanomaterial and chemical groups, which will eventually provide an insight into how to effectively design the functional material using chemical groups.

Structural and nanomechanical properties of paperboard coatings studied by peak force tapping atomic force microscopy

Paper coating formulations containing starch, latex, and clay were applied to paperboard and have been investigated by scanning electron microscopy and Peak Force tapping atomic force microscopy. A special focus has been on the measurement of the variation of the surface topography and surface material properties with a nanometer scaled spatial resolution. The effects of coating composition and drying conditions were investigated. It is concluded that the air-coating interface of the coating is dominated by close-packed latex particles embedded in a starch matrix and that the spatial distribution of the different components in the coating can be identified due to their variation in material properties. Drying the coating at an elevated temperature compared to room temperature changes the surface morphology and the surface material properties due to partial film formation of latex. However, it is evident that the chosen elevated drying temperature and exposure time is insufficient to ensure complete film formation of the latex which in an end application will be needed.

Mechanical characterization of polymeric thin films by atomic force microscopy based techniques

Polymeric thin films have been awakening continuous and growing interest for application in nanotechnology. For such applications, the assessment of their (nano)mechanical properties is a key issue, since they may dramatically vary between the bulk and the thin film state, even for the same polymer. Therefore, techniques are required for the in situ characterization of mechanical properties of thin films that must be nondestructive or only minimally destructive. Also, they must also be able to probe nanometer-thick ultrathin films and layers and capable of imaging the mechanical properties of the sample with nanometer lateral resolution, since, for instance, at these scales blends or copolymers are not uniform, their phases being separated. Atomic force microscopy (AFM) has been proposed as a tool for the development of a number of techniques that match such requirements. In this review, we describe the state of the art of the main AFM-based methods for qualitative and quantitative single-point measurements and imaging of mechanical properties of polymeric thin films, illustrating their specific merits and limitations.

Amyloid inspired self-assembled peptide nanofibers

Amyloid peptides are important components in many degenerative diseases as well as in maintaining cellular metabolism. Their unique stable structure provides new insights in developing new materials. Designing bioinspired self-assembling peptides is essential to generate new forms of hierarchical nanostructures. Here we present oppositely charged amyloid inspired peptides (AIPs), which rapidly self-assemble into nanofibers at pH 7 upon mixing in water caused by noncovalent interactions. Mechanical properties of the gels formed by self-assembled AIP nanofibers were analyzed with oscillatory rheology. AIP gels exhibited strong mechanical characteristics superior to gels formed by self-assembly of previously reported synthetic short peptides. Rheological studies of gels composed of oppositely charged mixed AIP molecules (AIP-1 + 2) revealed superior mechanical stability compared to individual peptide networks (AIP-1 and AIP-2) formed by neutralization of net charges through pH change. Adhesion and elasticity properties of AIP mixed nanofibers and charge neutralized AIP-1, AIP-2 nanofibers were analyzed by high resolution force-distance mapping using atomic force microscopy (AFM). Nanomechanical characterization of self-assembled AIP-1 + 2, AIP-1, and AIP-2 nanofibers also confirmed macroscopic rheology results, and mechanical stability of AIP mixed nanofibers was higher compared to individual AIP-1 and AIP-2 nanofibers self-assembled at acidic and basic pH, respectively. Experimental results were supported with molecular dynamics simulations by considering potential noncovalent interactions between the amino acid residues and possible aggregate forms. In addition, HUVEC cells were cultured on AIP mixed nanofibers at pH 7 and biocompatibility and collagen mimetic scaffold properties of the nanofibrous system were observed. Encapsulation of a zwitterionic dye (rhodamine B) within AIP nanofiber network was accomplished at physiological conditions to demonstrate that this network can be utilized for inclusion of soluble factors as a scaffold for cell culture studies.

D-alanylation of lipoteichoic acids confers resistance to cationic peptides in group B streptococcus by increasing the cell wall density

Cationic antimicrobial peptides (CAMPs) serve as the first line of defense of the innate immune system against invading microbial pathogens. Gram-positive bacteria can resist CAMPs by modifying their anionic teichoic acids (TAs) with D-alanine, but the exact mechanism of resistance is not fully understood. Here, we utilized various functional and biophysical approaches to investigate the interactions of the human pathogen Group B Streptococcus (GBS) with a series of CAMPs having different properties. The data reveal that: (i) D-alanylation of lipoteichoic acids (LTAs) enhance GBS resistance only to a subset of CAMPs and there is a direct correlation between resistance and CAMPs length and charge density; (ii) resistance due to reduced anionic charge of LTAs is not attributed to decreased amounts of bound peptides to the bacteria; and (iii) D-alanylation most probably alters the conformation of LTAs which results in increasing the cell wall density, as seen by Transmission Electron Microscopy, and reduces the penetration of CAMPs through the cell wall. Furthermore, Atomic Force Microscopy reveals increased surface rigidity of the cell wall of the wild-type GBS strain to more than 20-fold that of the dltA mutant. We propose that D-alanylation of LTAs confers protection against linear CAMPs mainly by decreasing the flexibility and permeability of the cell wall, rather than by reducing the electrostatic interactions of the peptide with the cell surface. Overall, our findings uncover an important protective role of the cell wall against CAMPs and extend our understanding of mechanisms of bacterial resistance.

Leaf traits in parental and hybrid species of Sorbus (Rosaceae)

PREMISE OF THE STUDY

Knowledge of functional leaf traits can provide important insights into the processes structuring plant communities. In the genus Sorbus, the generation of taxonomic novelty through reticulate evolution that gives rise to new microspecies is believed to be driven primarily by a series of interspecific hybridizations among closely related taxa. We tested hypotheses for dispersion of intermediacy across the leaf traits in Sorbus hybrids and for trait linkages with leaf area and specific leaf area.

METHODS

Here, we measured and compared the whole complex of growth, vascular, and ecophysiological leaf traits among parental (Sorbus aria, Sorbus aucuparia, Sorbus chamaemespilus) and natural hybrid (Sorbus montisalpae, Sorbus zuzanae) species growing under field conditions. A recently developed atomic force microscopy technique, PeakForce quantitative nanomechanical mapping, was used to characterize the topography of cell wall surfaces of tracheary elements and to map the reduced Young's modulus of elasticity.

KEY RESULTS

Intermediacy was associated predominantly with leaf growth traits, whereas vascular and ecophysiological traits were mainly parental-like and transgressive phenotypes. Larger-leaf species tended to have lower modulus of elasticity values for midrib tracheary element cell walls. Leaves with a biomass investment related to a higher specific leaf area had a lower density. Leaf area- and length-normalized theoretical hydraulic conductivity was related to leaf thickness.

CONCLUSIONS

For the whole complex of examined leaf traits, hybrid microspecies were mosaics of parental-like, intermediate, and transgressive phenotypes. The high proportion of transgressive character expressions found in Sorbus hybrids implies that generation of extreme traits through transgressive segregation played a key role in the speciation process.

Measurement of intrinsic properties of amyloid fibrils by the peak force QNM method

We report the investigation of the mechanical properties of different types of amyloid fibrils by the peak force quantitative nanomechanical (PF-QNM) technique. We demonstrate that this technique correctly measures the Young's modulus independent of the polymorphic state and the cross-sectional structural details of the fibrils, and we show that values for amyloid fibrils assembled from heptapeptides, α-synuclein, Aβ(1-42), insulin, β-lactoglobulin, lysozyme, ovalbumin, Tau protein and bovine serum albumin all fall in the range of 2-4 GPa.

Atomic force microscopy under controlled conditions reveals structure of C-terminal region of α-synuclein in amyloid fibrils

Atomic force microscopy (AFM) is widely used to measure morphological and mechanical properties of biological materials at the nanoscale. AFM is able to visualize and measure these properties in different environmental conditions. However, these conditions can influence the results considerably, rendering their interpretation a matter of some subtlety. We demonstrate this by imaging ~10 nm diameter α-synuclein amyloid fibrils, focusing specifically on the structure of the C-terminal part of the protein monomers incorporated into fibrils. Despite these influences leading to variations in fibril heights, we have shown that by maintaining careful control of AFM settings we can quantitatively compare the morphological parameters of fibrils imaged in air or in buffer conditions. From this comparison we were able to deduce the semiflexible character of this C-terminal region. Fibril height differences measured in air and liquid indicate that the C-terminal region collapses onto the fibril core upon drying. The fibril heights decrease upon increasing ion concentration in solution, suggesting that the C-terminal tails collapse into more compact structures as a result of charge screening. Finally, PeakForce QNM measurements show an apparent heterogeneity of C-terminal packing along the fibril length.

Imaging nanometer-sized α-synuclein aggregates by superresolution fluorescence localization microscopy

The morphological features of α-synuclein (AS) amyloid aggregation in vitro and in cells were elucidated at the nanoscale by far-field subdiffraction fluorescence localization microscopy. Labeling AS with rhodamine spiroamide probes allowed us to image AS fibrillar structures by fluorescence stochastic nanoscopy with an enhanced resolution at least 10-fold higher than that achieved with conventional, diffraction-limited techniques. The implementation of dual-color detection, combined with atomic force microscopy, revealed the propagation of individual fibrils in vitro. In cells, labeled protein appeared as amyloid aggregates of spheroidal morphology and subdiffraction sizes compatible with in vitro supramolecular intermediates perceived independently by atomic force microscopy and cryo-electron tomography. We estimated the number of monomeric protein units present in these minute structures. This approach is ideally suited for the investigation of the molecular mechanisms of amyloid formation both in vitro and in the cellular milieu.

Spatially resolved frequency-dependent elasticity measured with pulsed force microscopy and nanoindentation

Recently several atomic force microscopy (AFM)-based surface property mapping techniques like pulsed force microscopy (PFM), harmonic force microscopy or Peakforce QNM® have been introduced to measure the nano- and micro-mechanical properties of materials. These modes all work at different operating frequencies. However, complex materials are known to display viscoelastic behavior, a combination of solid and fluid-like responses, depending on the frequency at which the sample is probed. In this report, we show that the frequency-dependent mechanical behavior of complex materials, such as polymer blends that are frequently used as calibration samples, is clearly measurable with AFM. Although this frequency-dependent mechanical behavior is an established observation, we demonstrate that the new high frequency mapping techniques enable AFM-based rheology with nanoscale spatial resolution over a much broader frequency range compared to previous AFM-based studies. We further highlight that it is essential to account for the frequency-dependent variation in mechanical properties when using these thin polymer samples as calibration materials for elasticity measurements by high-frequency surface property mapping techniques. These results have significant implications for the accurate interpretation of the nanomechanical properties of polymers or complex biological samples. The calibration sample is composed of a blend of soft and hard polymers, consisting of low-density polyethylene (LDPE) islands in a polystyrene (PS) surrounding, with a stiffness of 0.2 GPa and 2 GPa respectively. The spring constant of the AFM cantilever was selected to match the stiffness of LDPE. From 260 Hz to 1100 Hz the sample was imaged with the PFM method. At low frequencies (0.5-35 Hz), single-point nanoindentation was performed. In addition to the material's stiffness, the relative heights of the LDPE islands (with respect to the PS) were determined as a function of the frequency. At the lower operation frequencies for PFM, the islands exhibited lower heights than when measured with tapping mode at 120 kHz. Both spring constants and heights at the different frequencies clearly show a frequency-dependent behavior.

Supramolecular non-amyloid intermediates in the early stages of α-synuclein aggregation

The aggregation of α-synuclein is associated with progression of Parkinson's disease. We have identified submicrometer supramolecular structures that mediate the early stages of the overall mechanism. The sequence of structural transformations between metastable intermediates were captured and characterized by atomic force microscopy guided by a fluorescent probe sensitive to preamyloid species. A novel ~0.3-0.6 μm molecular assembly, denoted the acuna, nucleates, expands, and liberates fibers with distinctive segmentation and a filamentous fuzzy fringe. These fuzzy fibers serve as precursors of mature amyloid fibrils. Cryo-electron tomography resolved the acuna inner structure as a scaffold of highly condensed colloidal masses interlinked by thin beaded threads, which were perceived as fuzziness by atomic force microscopy. On the basis of the combined data, we propose a sequential mechanism comprising molecular, colloidal, and fibrillar stages linked by reactions with disparate temperature dependencies and distinct supramolecular forms. We anticipate novel diagnostic and therapeutic approaches to Parkinson's and related neurodegenerative diseases based on these new insights into the aggregation mechanism of α-synuclein and intermediates, some of which may act to cause and/or reinforce neurotoxicity.