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

Effect of cross-linking density on the rheological behavior of ultra-soft chitosan microgels at the oil-water interface

In this paper, microgels with uniform particle size were prepared by physically cross-linking the hydrophobically modified chitosan (h-CS) with sodium phytate (SP). The effects of cross-linking density on the interfacial adsorption kinetics, viscoelasticity, stress relaxation, and micorheological properties of the hydrophobically modified chitosan microgels (h-CSMs) at the oil-water interface were extensively investigated by the dilatational rheology, compressional rheology, and particle tracing microrheology. The results were correlated with the particle size, morphology, and elasticity of the microgels characterized by dynamic light scattering and atomic force microscopy. It was found that with the increase of cross-linking density, the h-CSMs changed from a polymer-like state to ultra-soft fussy spheres with higher elastic modulus. The compression isotherms demonstrated multi-stage increase caused by the interaction between the shells and that between the cores of the microgels successively. As the increase of cross-linking density, the h-CSMs diffused slower to the oil-water interface, but demonstrating faster permeation adsorption and rearrangement at the oil-water interface, finally forming interfacial layers of higher viscoelastic modulus due to the core-core interaction. Both the initial tension relaxation and the microgel rearrangement after interface expansion became faster as the microgel elasticity increased. The interfacial microrheology demonstrated dynamic caging effect caused by neighboring microgels. This article provides a more comprehensive understanding of the behaviors of polysaccharide microgels at the oil-water interface.

Mechanobiological insight into brain diseases based on mechanosensitive channels: Common mechanisms and clinical potential

BACKGROUND

As physical signals, mechanical cues regulate the neural cells in the brain. The mechanosensitive channels (MSCs) perceive the mechanical cues and transduce them by permeating specific ions or molecules across the plasma membrane, and finally trigger a series of intracellular bioelectrical and biochemical signals. Emerging evidence supports that wide-distributed, high-expressed MSCs like Piezo1 play important roles in several neurophysiological processes and neurological disorders.

AIMS

To systematically conclude the functions of MSCs in the brain and provide a novel mechanobiological perspective for brain diseases.

METHOD

We summarized the mechanical cues and MSCs detected in the brain and the research progress on the functional roles of MSCs in physiological conditions. We then concluded the pathological activation and downstream pathways triggered by MSCs in two categories of brain diseases, neurodegenerative diseases and place-occupying damages. Finally, we outlined the methods for manipulating MSCs and discussed their medical potential with some crucial outstanding issues.

RESULTS

The MSCs present underlying common mechanisms in different brain diseases by acting as the "transportation hubs" to transduce the distinct signal patterns: the upstream mechanical cues and the downstream intracellular pathways. Manipulating the MSCs is feasible to alter the complicated downstream processes, providing them promising targets for clinical treatment.

CONCLUSIONS

Recent research on MSCs provides a novel insight into brain diseases. The common mechanisms mediated by MSCs inspire a wide range of therapeutic potentials targeted on MSCs in different brain diseases.

Biophysical Properties of the Fibril Structure of the Toxic Conformer of Amyloid-β42: Characterization by Atomic Force Microscopy in Liquid and Molecular Docking

Alzheimer's disease is associated with the aggregation of the misfolded neuronal peptide, amyloid-β42 (Aβ42). Evidence has suggested that several reasons are responsible for the toxicity caused by the aggregation of Aβ42, including the conformational restriction of Aβ42. In this study, one of the toxic conformers of Aβ42, which contains a Glu-to-Pro substitution (E22P-Aβ42), was explored using atomic force microscopy and molecular docking to study the aggregation dynamics. We proposed a systematic model of fibril formation to better understand the molecular basis of conformational transitions in the Aβ42 species. Our results demonstrated the formation of amorphous aggregates in E22P-Aβ42 that are stem-based, network-like structures, while the formation of mature fibrils occurred in the less toxic conformer of Aβ42, E22-Aβ42, that are sphere-like flexible structures. A comparison was made between the biophysical properties of E22P-Aβ42 and E22-Aβ42 that revealed that E22P-Aβ42 had greater stiffness, dihedral angle, number of β sheets involved, and elasticity, compared with E22-Aβ42. These findings will have considerable implications toward our understanding of the structural basis of the toxicity caused by conformational diversity in Aβ42 species.

Direct observation of surface charge and stiffness of human metaphase chromosomes

Metaphase chromosomes in which both polynucleotides and proteins are condensed with hierarchies are closely related to life phenomena such as cell division, cancer development, and cellular senescence. Nevertheless, their nature is rarely revealed, owing to their structural complexity and technical limitations in analytical methods. In this study, we used surface potential and nanomechanics mapping technology based on atomic force microscopy to measure the surface charge and intrinsic stiffness of metaphase chromosomes. We found that extra materials covering the chromosomes after the extraction process were positively charged. With the covering materials, the chromosomes were positively charged (ca. 44.9 ± 16.48 mV) and showed uniform stiffness (ca. 6.23 ± 1.98 MPa). In contrast, after getting rid of the extra materials through treatment with RNase and protease, the chromosomes were strongly negatively charged (ca. -197.4 ± 77.87 mV) and showed relatively non-uniform and augmented stiffness (ca. 36.87 ± 17.56 MPa). The results suggested undulating but compact coordination of condensed chromosomes. Additionally, excessive treatment with RNase and protease could destroy the chromosomal structure, providing an exceptional opportunity for multiscale stiffness mapping of polynucleotides, nucleosomes, chromatin fibers, and chromosomes in a single image. Our approach offers a new horizon in terms of an analytical technique for studying chromosome-related diseases.

C9orf72-Derived Proline:Arginine Poly-Dipeptides Modulate Cytoskeleton and Mechanical Stress Response

Proline:arginine (PR) poly-dipeptides from the GGGGCC repeat expansion in C9orf72 have cytotoxicity and bind intermediate filaments (IFs). However, it remains unknown how PR poly-dipeptides affect cytoskeletal organization and focal adhesion (FA) formation. Here, we show that changes to the cytoskeleton and FA by PR poly-dipeptides result in the alteration of cell stiffness and mechanical stress response. PR poly-dipeptides increased the junctions and branches of the IF network and increased cell stiffness. They also changed the distribution of actin filaments and increased the size of FA and intracellular calcium concentration. PR poly-dipeptides or an inhibitor of IF organization prevented cell detachment. Furthermore, PR poly-dipeptides induced upregulation of mechanical stress response factors and led to a maladaptive response to cyclic stretch. These results suggest that the effects of PR poly-dipeptides on mechanical properties and mechanical stress response may serve as a pathogenesis of C9orf72-related neurodegeneration.

Biosensing, Characterization of Biosensors, and Improved Drug Delivery Approaches Using Atomic Force Microscopy: A Review

Since its invention, atomic force microscopy (AFM) has come forth as a powerful member of the “scanning probe microscopy” (SPM) family and an unparallel platform for high-resolution imaging and characterization for inorganic and organic samples, especially biomolecules, biosensors, proteins, DNA, and live cells. AFM characterizes any sample by measuring interaction force between the AFM cantilever tip (the probe) and the sample surface, and it is advantageous over other SPM and electron micron microscopy techniques as it can visualize and characterize samples in liquid, ambient air, and vacuum. Therefore, it permits visualization of three-dimensional surface profiles of biological specimens in the near-physiological environment without sacrificing their native structures and functions and without using laborious sample preparation protocols such as freeze-drying, staining, metal coating, staining, or labeling. Biosensors are devices comprising a biological or biologically extracted material (assimilated in a physicochemical transducer) that are utilized to yield electronic signal proportional to the specific analyte concentration. These devices utilize particular biochemical reactions moderated by isolated tissues, enzymes, organelles, and immune system for detecting chemical compounds via thermal, optical, or electrical signals. Other than performing high-resolution imaging and nanomechanical characterization (e.g., determining Young’s modulus, adhesion, and deformation) of biosensors, AFM cantilever (with a ligand functionalized tip) can be transformed into a biosensor (microcantilever-based biosensors) to probe interactions with a particular receptors of choice on live cells at a single-molecule level (using AFM-based single-molecule force spectroscopy techniques) and determine interaction forces and binding kinetics of ligand receptor interactions. Targeted drug delivery systems or vehicles composed of nanoparticles are crucial in novel therapeutics. These systems leverage the idea of targeted delivery of the drug to the desired locations to reduce side effects. AFM is becoming an extremely useful tool in figuring out the topographical and nanomechanical properties of these nanoparticles and other drug delivery carriers. AFM also helps determine binding probabilities and interaction forces of these drug delivery carriers with the targeted receptors and choose the better agent for drug delivery vehicle by introducing competitive binding. In this review, we summarize contributions made by us and other researchers so far that showcase AFM as biosensors, to characterize other sensors, to improve drug delivery approaches, and to discuss future possibilities.

Challenges in Experimental Methods

Experimental studies of amyloids encounter many challenges. There are many methods available for studying proteins, which can be applied to amyloids: from basic staining techniques, allowing visualization of fibers, to complex methods, e.g., AFM-IR used to their detailed biochemical and structural characterization in nanoscale. Which method is appropriate depends on the goal of an experiment: verification of aggregational properties of a peptide, distinguishing oligomers from mature fibers, or kinetic studies. Insolubility, rapid aggregation, and the need of using a high-purity peptide may be a limiting factor in studies involving amyloids. Moreover, the results obtained by various experimental methods often differ significantly, which may lead to misclassification of amyloid peptides. Due to ambiguity of experimental results, laborious and time-consuming analysis, bioinformatical methods become more widely used for amyloids.

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

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

Comparative study of photoinduced surface-relief-gratings on azo polymer and azo molecular glass films

Photoinduced surface-relief-gratings (SRGs) on azo polymer and azo molecular glass films, caused by trans–cis isomerization of azo chromophores, have attracted wide interest for their intriguing nature and many possible applications in recent years. Understanding the mechanical properties of SRGs at the nanoscale is critically important for elucidating their formation mechanism and exploring their applications. In this work, a representative azo polymer (BP-AZ-CA) and a typical azo molecular glass (IAC-4) were comparatively studied for the first time concerning their properties related to SRG formation through a variety of methods. The results indicate that when inscribing SRGs on the films, IAC-4 shows a much higher efficiency for forming SRGs relative to that of BP-AZ-CA. The overall average moduli of SRGs measured by nanomechanical mapping techniques are obviously smaller compared with the moduli of the corresponding films of both materials. The moduli at different regions of SRGs are periodically varied along the grating vector direction for both BP-AZ-CA and IAC-4 gratings. The moduli at the trough regions of SRGs are always larger than those of the crests, while the moduli at the hillsides are the smallest. Distinct from BP-AZ-CA, even the moduli at the trough regions of IAC-4 SRG are smaller compared with that of the original film, and the ratio between the trough and crest moduli is significantly larger for IAC-4. These results provide deep understanding of the SRG formation mechanism and reveal the clear distinction between these two types of glassy materials for their SRG-forming behavior, which are important for future applications.

A representative azo polymer (BP-AZ-CA) and a typical azo molecular glass (IAC-4) were studied for their surface-relief-grating formation behavior to provide a deep understanding of the clear distinction between these two types of glassy material.

Amyloids and their untapped potential as hydrogelators

Amyloid fibrils are cross-β-sheet-rich fibrous aggregates. They were originally identified as disease-associated protein/peptide deposits. The cross-β motif was consequently labelled as an alien and pathogenic fold. Subsequent research revealed that the fibrillar aggregates were benign, and the cytotoxicity in the amyloid diseases was attributed to the pre-fibrillar structures. Research in the past two decades has identified the native functional amyloids in organisms ranging from bacteria to human. The amyloid-like fibrils, therefore, are not necessarily pathogenic, and the cross-β motif is very much native. This premise makes way for the amyloids to be used as biocompatible materials. Many naturally occurring amyloidogenic proteins/peptides or their fragments have been reported in the literature to form hydrogels. Hydrogels constitute one of the most interesting classes of soft materials that find application in diverse fields such as environmental, electronic, and biomedical engineering. Applications of hydrogels in medicine are particularly extensive. Among various classes of peptides that form hydrogels, the potential of amyloids is largely untapped. In this review, we have attempted to compile the literature on amyloid hydrogels and discuss their potential applications.

Mechanical Characterization for Cellular Mechanobiology: Current Trends and Future Prospects

Accurate mechanical characterization of adherent cells and their substrates is important for understanding the influence of mechanical properties on cells themselves. Recent mechanobiology studies outline the importance of mechanical parameters, such as stress relaxation and strain stiffening on the behavior of cells. Numerous techniques exist for probing mechanical properties and it is vital to understand the benefits of each technique and how they relate to each other. This mini review aims to guide the reader through the toolbox of mechanical characterization techniques by presenting well-established and emerging methods currently used to assess mechanical properties of substrates and cells.

Mechanical and Tribological Performances Enhanced by Self-Assembled Structures

Taking inspiration from natural materials, composite materials can be reinforced by creating matrix architectures that can better accommodate and control internal stresses. Despite the recent success in the synthesis of artificial assemblies for local reinforcement through the introduction of oriented fibers and plates into host multilayered composites, there is a lack of fundamental understanding of the factors that determine mechanical properties. Moreover, designing building blocks and interfaces that facilitate higher resistance and energy dissipation is highly challenging. When the intrinsic material is fixed, the mechanical and tribological properties can be further adjusted. In this study, europium oxide nanosheets are arranged in interlocked-junction superstructures that resist sliding at junction points, thereby enhancing the mechanical properties of the nanosheet assemblies compared to those of the conventional face-to-face superstructures formed by parallel nanosheets. Furthermore, the crystalline origin of building blocks is revealed by demonstrating that faulty crystal nanosheets adopting an amorphous structure are different from single-crystal nanosheets, with the former exhibiting superior mechanical reinforcement and improved abrasive resistance.

Calibration of T-shaped atomic force microscope cantilevers using the thermal noise method

The tip-sample interaction force measurements in atomic force microscopy (AFM) provide information about materials' properties with nanoscale resolution. The T-shaped cantilevers used in Torsional-Harmonic AFM allow measuring the rapidly changing tip-sample interaction forces using the torsional (twisting) deflections of the cantilever due to the off-axis placement of the sharp tip. However, it has been difficult to calibrate these cantilevers using the commonly used thermal noise-based calibration method as the mechanical coupling between flexural and torsional deflections makes it challenging to determine the deflection sensitivities from force-distance curves. Here, we present thermal noise-based calibration of these T-shaped AFM cantilevers by simultaneously analyzing flexural and torsional thermal noise spectra, along with deflection signals during a force-distance curve measurement. The calibration steps remain identical to the conventional thermal noise method, but a computer performs additional calculations to account for mode coupling. We demonstrate the robustness of the calibration method by determining the sensitivity of calibration results to the laser spot position on the cantilever, to the orientation of the cantilever in the cantilever holder, and by repeated measurements. We validated the quantitative force measurements against the known unfolding force of a protein, the I91 domain of titin, which resulted in consistent unfolding force values among six independently calibrated cantilevers.

Can AFM be used to measure absolute values of Young's modulus of nanocomposite materials down to the nanoscale?

At present, a technique potentially capable of measuring values of Young's modulus at the nanoscale is atomic force microscopy (AFM) working in the indentation mode. However, the question if AFM indentation data can be translated into absolute values of the modulus is not well-studied as yet, in particular, for the most interesting case of stiff nanocomposite materials. Here we investigate this question. A special sample of nanocomposite material, shale rock, was used, which is relatively homogeneous at the multi-micron scale. Two AFM modes, force-volume and PeakForce QNM were used in this study. The nanoindentation technique was used as a control benchmark for the measurement of effective Young's modulus of the shale sample. The indentation rate was carefully controlled. To ensure the self-consistency of the mechanical model used to analyze AFM data, the model was modified to take into account the presence of the surface roughness. We found excellent agreement between the average values of effective Young's modulus calculated within AFM and the nanoindenter benchmark method. At the same time, the softest and hardest areas of the sample were seen only with AFM.

Atomic Force Microscopy: The Characterisation of Amyloid Protein Structure in Pathology

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Proteins are versatile macromolecules that perform a variety of functions and participate in virtually all cellular processes. The functionality of a protein greatly depends on its structure and alterations may result in the development of diseases. Most well-known of these are protein misfolding disorders, which include Alzheimer’s and Parkinson’s diseases as well as type 2 diabetes mellitus, where soluble proteins transition into insoluble amyloid fibrils. Atomic Force Microscopy (AFM) is capable of providing a topographical map of the protein and/or its aggregates, as well as probing the nanomechanical properties of a sample. Moreover, AFM requires relatively simple sample preparation, which presents the possibility of combining this technique with other research modalities, such as confocal laser scanning microscopy, Raman spectroscopy and stimulated emission depletion microscopy. In this review, the basic principles of AFM are discussed, followed by a brief overview of how it has been applied in biological research. Finally, we focus specifically on its use as a characterisation method to study protein structure at the nanoscale in pathophysiological conditions, considering both molecules implicated in disease pathogenesis and the plasma protein fibrinogen. In conclusion, AFM is a userfriendly tool that supplies multi-parametric data, rendering it a most valuable technique.

Binary Structure of Amyloid Beta Oligomers Revealed by Dual Recognition Mapping

Amyloid beta (Aβ) oligomers are widely considered to be the causative agent of Alzheimer's disease (AD), a progressive neurodegenerative disorder. Determining the structure of oligomers is, therefore, important for understanding the disease and developing therapeutic agents; however, elucidating the structure has been proven difficult due to heterogeneity, noncrystallinity, and variability. Herein, we investigated homo- and hetero-oligomers of Aβ40 and Aβ42 using atomic force microscopy (AFM) and revealed characteristics of the molecular structure. By examining the surface of individual oligomers with sequential N- and C-terminus specific antibody-tethered tips, we simultaneously mapped the N- and C-terminus distributions and the elastic modulus. Interestingly, both the N- and C-termini of Aβ peptides were recognized on the oligomer surface, and the termini detected pixel regions exhibited a lower elastic modulus than silent pixel regions. These two types of regions were randomly distributed on the oligomer surface.

The Role of Structural Polymorphism in Driving the Mechanical Performance of the Alzheimer's Beta Amyloid Fibrils

Alzheimer's Disease (AD) is related with the abnormal aggregation of amyloid β-peptides Aβ₁₋₄₀ and Aβ₁₋₄₂, the latter having a polymorphic character which gives rise to U- or S-shaped fibrils. Elucidating the role played by the nanoscale-material architecture on the amyloid fibril stability is a crucial breakthrough to better understand the pathological nature of amyloid structures and to support the rational design of bio-inspired materials. The computational study here presented highlights the superior mechanical behavior of the S-architecture, characterized by a Young's modulus markedly higher than the U-shaped architecture. The S-architecture showed a higher mechanical resistance to the enforced deformation along the fibril axis, consequence of a better interchain hydrogen bonds' distribution. In conclusion, this study, focusing the attention on the pivotal multiscale relationship between molecular phenomena and material properties, suggests the S-shaped Aβ₁₋₄₂ species as a target of election in computational screen/design/optimization of effective aggregation modulators.

Tks5 and Dynamin-2 enhance actin bundle rigidity in invadosomes to promote myoblast fusion

Skeletal muscle development requires the cell-cell fusion of differentiated myoblasts to form muscle fibers. The actin cytoskeleton is known to be the main driving force for myoblast fusion; however, how actin is organized to direct intercellular fusion remains unclear. Here we show that an actin- and dynamin-2-enriched protrusive structure, the invadosome, is required for the fusion process of myogenesis. Upon differentiation, myoblasts acquire the ability to form invadosomes through isoform switching of a critical invadosome scaffold protein, Tks5. Tks5 directly interacts with and recruits dynamin-2 to the invadosome and regulates its assembly around actin filaments to strengthen the stiffness of dynamin-actin bundles and invadosomes. These findings provide a mechanistic framework for the acquisition of myogenic fusion machinery during myogenesis and reveal a novel structural function for Tks5 and dynamin-2 in organizing actin filaments in the invadosome to drive membrane fusion.

Measurement of nanomechanical properties of DNA molecules by PeakForce atomic force microscopy based on DNA origami

Characterization of the stiffness of thin DNA strands remains difficult. By constructing bilayer DNA molecules, we investigated their mechanical properties using AFM. Increased DNA thickness through DNA origami greatly reduced the substrate effect when measuring Young's modulus, thus providing a more accurate picture of the inherent nanomechanical properties of DNA.

Mechanical and thermodynamic properties of Aβ42, Aβ40, and α-synuclein fibrils: a coarse-grained method to complement experimental studies

We perform molecular dynamics simulation on several relevant biological fibrils associated with neurodegenerative diseases such as Aβ₄₀, Aβ₄₂, and α-synuclein systems to obtain a molecular understanding and interpretation of nanomechanical characterization experiments. The computational method is versatile and addresses a new subarea within the mechanical characterization of heterogeneous soft materials. We investigate both the elastic and thermodynamic properties of the biological fibrils in order to substantiate experimental nanomechanical characterization techniques that are quickly developing and reaching dynamic imaging with video rate capabilities. The computational method qualitatively reproduces results of experiments with biological fibrils, validating its use in extrapolation to macroscopic material properties. Our computational techniques can be used for the co-design of new experiments aiming to unveil nanomechanical properties of biological fibrils from a point of view of molecular understanding. Our approach allows a comparison of diverse elastic properties based on different deformations , i.e., tensile (Y _L), shear (S), and indentation (Y _T) deformation. From our analysis, we find a significant elastic anisotropy between axial and transverse directions (i.e., Y _T > Y _L) for all systems. Interestingly, our results indicate a higher mechanostability of Aβ₄₂ fibrils compared to Aβ₄₀, suggesting a significant correlation between mechanical stability and aggregation propensity (rate) in amyloid systems. That is, the higher the mechanical stability the faster the fibril formation. Finally, we find that α-synuclein fibrils are thermally less stable than β-amyloid fibrils. We anticipate that our molecular-level analysis of the mechanical response under different deformation conditions for the range of fibrils considered here will provide significant insights for the experimental observations.

AFM Characterization of the Internal Mammary Artery as a Novel Target for Arterial Stiffening

Using the atomic force microscopy- (AFM-) PeakForce quantitative nanomechanical mapping (QNM) technique, we have previously shown that the adventitia of the human internal mammary artery (IMA), tested under dehydrated conditions, is altered in patients with a high degree of arterial stiffening. In this study, we explored the nanoscale elastic modulus of the tunica media of the IMA in hydrated and dehydrated conditions from the patients with low and high arterial stiffening, as assessed in vivo by carotid-femoral pulse wave velocity (PWV). In both hydrated and dehydrated conditions, the medial layer was significantly stiffer in the high PWV group. The elastic modulus of the hydrated and dehydrated tunica media was significantly correlated with PWV. In the hydrated condition, the expression activity of certain small leucine-rich repeat proteoglycans (SLRPs), which are associated with arterial stiffening, were found to be negatively correlated to the medial elastic modulus. We also compared the data with our previous work on the IMA adventitia. We found that the hydrated media and dehydrated adventitia are both suitable for reflecting the development of arterial stiffening and SLRP expression. This comprehensive study of the nanomechanical properties integrated with the proteomic analysis in the IMAs demonstrates the possibility of linking structural properties and function in small biological samples with novel AFM methods. The IMA is a suitable target for predicting arterial stiffening.

Atomic force microscopy measurements probing the mechanical properties of single collagen fibrils under the influence of UV light in situ

Collagen plays a decisive role as a functional substrate in tissue engineering. In particular, the rigidity of the collagen influences the behaviour of the attached cells. Thus, modification and controlled adjustment of collagen's characteristics are essential. To this end, controlled exposure to ultraviolet (UV) light is a promising process because it can be temporally and spatially well defined. In this study, we investigated the effect of UV exposure on surface supported single collagen fibrils in situ. This procedure allowed for a direct comparison between the untreated and modified states of type I collagen. Atomic force microscopy was used to map the mechanical properties. Exposure to UV light was used to influence the mechanical properties of the fibrils in varied liquid environments (deionized water and phosphate-buffered saline (PBS)). The results led to the assumption that combined UV/thermal treatment in deionized water continuously lowers the elastic modulus. In contrast, experiments performed in PBS-based solutions in combination with UV-B and UV-C light or thermal treatment up to 45 °C suggested an increase in the modulus within the first 30-40 min that subsequently decreased again. Thus, the wavelength, exposure, temperature, and chemical environment are relevant parameters that need to be controlled when modifying collagen using UV light.

Correlation between the hierarchical structures and nanomechanical properties of amyloid fibrils

Amyloid fibrils have recently been highlighted due to their excellent mechanical properties, which not only play a role in their biological functions but also imply their applications in biomimetic material design. Despite recent efforts to unveil how the excellent mechanical properties of amyloid fibrils originate, it has remained elusive how the anisotropic nanomechanical properties of hierarchically structured amyloid fibrils are determined. Here, we characterize the anisotropic nanomechanical properties of hierarchically structured amyloid fibrils using atomic force microscopy experiments and atomistic simulations. It is shown that the hierarchical structure of amyloid fibrils plays a crucial role in determining their radial elastic property but does not make any effect on their bending elastic property. This is attributed to the role of intermolecular force acting between the filaments (constituting the fibril) on the radial elastic modulus of amyloid fibrils. Our finding illustrates how the hierarchical structure of amyloid fibrils encodes their anisotropic nanomechanical properties. Our study provides key design principles of amyloid fibrils, which endow valuable insight into the underlying mechanisms of amyloid mechanics.

Identification of nanoparticles and nanosystems in biological matrices with scanning probe microscopy

Identification of nanoparticles and nanosystems into cells and biological matrices is a hot research topic in nanobiotechnologies. Because of their capability to map physical properties (mechanical, electric, magnetic, chemical, or optical), several scanning probe microscopy based techniques have been proposed for the subsurface detection of nanomaterials in biological systems. In particular, atomic force microscopy (AFM) can be used to reveal stiff nanoparticles in cells and other soft biomaterials by probing the sample mechanical properties through the acquisition of local indentation curves or through the combination of ultrasound-based methods, like contact resonance AFM (CR-AFM) or scanning near field ultrasound holography. Magnetic force microscopy can detect magnetic nanoparticles and other magnetic (bio)materials in nonmagnetic biological samples, while electric force microscopy, conductive AFM, and Kelvin probe force microscopy can reveal buried nanomaterials on the basis of the differences between their electric properties and those of the surrounding matrices. Finally, scanning near field optical microscopy and tip-enhanced Raman spectroscopy can visualize buried nanostructures on the basis of their optical and chemical properties. Despite at a still early stage, these methods are promising for detection of nanomaterials in biological systems as they could be truly noninvasive, would not require destructive and time-consuming specific sample preparation, could be performed in vitro, on alive samples and in water or physiological environment, and by continuously imaging the same sample could be used to dynamically monitor the diffusion paths and interaction mechanisms of nanomaterials into cells and biological systems. This article is categorized under: Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Mechanical Deformation Mechanisms and Properties of Prion Fibrils Probed by Atomistic Simulations

Prion fibrils, which are a hallmark for neurodegenerative diseases, have recently been found to exhibit the structural diversity that governs disease pathology. Despite our recent finding concerning the role of the disease-specific structure of prion fibrils in determining their elastic properties, the mechanical deformation mechanisms and fracture properties of prion fibrils depending on their structures have not been fully characterized. In this work, we have studied the tensile deformation mechanisms of prion and non-prion amyloid fibrils by using steered molecular dynamics simulations. Our simulation results show that the elastic modulus of prion fibril, which is formed based on left-handed β-helical structure, is larger than that of non-prion fibril constructed based on right-handed β-helix. However, the mechanical toughness of prion fibril is found to be less than that of non-prion fibril, which indicates that infectious prion fibril is more fragile than non-infectious (non-prion) fibril. Our study sheds light on the role of the helical structure of amyloid fibrils, which is related to prion infectivity, in determining their mechanical deformation mechanisms and properties.

AFM-Based Single Molecule Techniques: Unraveling the Amyloid Pathogenic Species

Background

A wide class of human diseases and neurodegenerative disorders, such as Alzheimer’s disease, is due to the failure of a specific peptide or protein to keep its native functional conformational state and to undergo a conformational change into a misfolded state, triggering the formation of fibrillar cross-β sheet amyloid aggregates. During the fibrillization, several coexisting species are formed, giving rise to a highly heterogeneous mixture. Despite its fundamental role in biological function and malfunction, the mechanism of protein self-assembly and the fundamental origins of the connection between aggregation, cellular toxicity and the biochemistry of neurodegeneration remains challenging to elucidate in molecular detail. In particular, the nature of the specific state of proteins that is most prone to cause cytotoxicity is not established.

Methods:

In the present review, we present the latest advances obtained by Atomic Force Microscopy (AFM) based techniques to unravel the biophysical properties of amyloid aggregates at the nanoscale. Unraveling amyloid single species biophysical properties still represents a formidable experimental challenge, mainly because of their nanoscale dimensions and heterogeneous nature. Bulk techniques, such as circular dichroism or infrared spectroscopy, are not able to characterize the heterogeneity and inner properties of amyloid aggregates at the single species level, preventing a profound investigation of the correlation between the biophysical properties and toxicity of the individual species.

Conclusion:

The information delivered by AFM based techniques could be central to study the aggregation pathway of proteins and to design molecules that could interfere with amyloid aggregation delaying the onset of misfolding diseases.

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

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

PeakForce QNM AFM study of chitin-silica hybrid films

Chitin-silica hybrid thin films, prepared through the colloidal self-assembly of chitin nanorods and siloxane oligomers, have been studied for the first time by PeakForce QNM AFM mode to explore their structure and mechanical behaviour. The change in structure and mechanical properties of chitin-silica hybrids is mainly driven by the relative quantities in chitin nanorods and silica, expressed as the chitin volume fraction ϕ_chi. The coating of the chitin polysaccharide by silica leads to an increase of the nanorods diameter and films surface roughness at small ϕ_chi values. The DMT (Derjaguin-Muller-Toporov) modulus increased both at small ϕ_chi due to a large amount of silica and at very high ϕ_chi→1 due to an incomplete tip penetration between nanorods. The local parallel orientation of nanorods observed at different ϕ_chi values resulted in a modulus increase due to an enhancement of the cohesion between nanorods.

Detection of stiff nanoparticles within cellular structures by contact resonance atomic force microscopy subsurface nanomechanical imaging

Detecting stiff nanoparticles buried in soft biological matrices by atomic force microscopy (AFM) based techniques represents a new frontier in the field of scanning probe microscopies, originally developed as surface characterization methods. Here we report the detection of stiff (magnetic) nanoparticles (NPs) internalized in cells by using contact resonance AFM (CR-AFM) employed as a potentially non-destructive subsurface characterization tool. Magnetite (Fe₃O₄) NPs were internalized in microglial cells from cerebral cortices of mouse embryos of 18 days by phagocytosis. Nanomechanical imaging of cells was performed by detecting the contact resonance frequencies (CRFs) of an AFM cantilever held in contact with the sample. Agglomerates of NPs internalized in cells were visualized on the basis of the local increase in the contact stiffness with respect to the surrounding biological matrix. A second AFM-based technique for nanomechanical imaging, i.e., HarmoniX™, as well as magnetic force microscopy and light microscopy were used to confirm the CR-AFM results. Thus, CR-AFM was demonstrated as a promising technique for subsurface imaging of nanomaterials in biological samples.

Relationship between Young's Modulus and Film Architecture in Cellulose Nanofibril-Based Multilayered Thin Films

Young's moduli of cellulose nanofibril (CNF)-poly(allylamine hydrochloride) (PAH) multilayered thin films were measured using strain-induced elastic buckling instability for mechanical measurements (SIEBIMM) and the quantitative nanomechanical mapping technique (PF-QNM). To establish the relationship between structure and mechanical properties, three types of films with various architectures were built using the layer-by-layer method by changing the ionic strength of the dipping solution. Both methods demonstrate that the architecture of a film has a strong impact on its mechanical properties even though the film has similar cellulose content, emphasizing the role of the architecture. Films with lower porosity (Φ_air = 0.34) and a more intricate network display the highest Young's moduli (9.3 GPa), whereas others with higher and similar porosity (Φ_air = 0.46-0.48) present lower Young's moduli (4.0-5.0 GPa). PF-QNM measurements indicate a reverse ranking that is probably indicative of the surface composition of the films.

Nanoscale studies link amyloid maturity with polyglutamine diseases onset

The presence of expanded poly-glutamine (polyQ) repeats in proteins is directly linked to the pathogenesis of several neurodegenerative diseases, including Huntington’s disease. However, the molecular and structural basis underlying the increased toxicity of aggregates formed by proteins containing expanded polyQ repeats remain poorly understood, in part due to the size and morphological heterogeneity of the aggregates they form in vitro. To address this knowledge gap and technical limitations, we investigated the structural, mechanical and morphological properties of fibrillar aggregates at the single molecule and nanometer scale using the first exon of the Huntingtin protein as a model system (Exon1). Our findings demonstrate a direct correlation of the morphological and mechanical properties of Exon1 aggregates with their structural organization at the single aggregate and nanometric scale and provide novel insights into the molecular and structural basis of Huntingtin Exon1 aggregation and toxicity.

Structural and Mechanical Properties of Amyloid Beta Fibrils: A Combined Experimental and Theoretical Approach

In this combined experimental (deep ultraviolet resonance Raman (DUVRR) spectroscopy and atomic force microscopy (AFM)) and theoretical (molecular dynamics (MD) simulations and stress-strain (SS)) study, the structural and mechanical properties of amyloid beta (Aβ40) fibrils have been investigated. The DUVRR spectroscopy and AFM experiments confirmed the formation of linear, unbranched and β-sheet rich fibrils. The fibrils (Aβ40)n, formed using n monomers, were equilibrated using all-atom MD simulations. The structural properties such as β-sheet character, twist, interstrand distance, and periodicity of these fibrils were found to be in agreement with experimental measurements. Furthermore, Young's modulus (Y) = 4.2 GPa computed using SS calculations was supported by measured values of 1.79 ± 0.41 and 3.2 ± 0.8 GPa provided by two separate AFM experiments. These results revealed size dependence of structural and material properties of amyloid fibrils and show the utility of such combined experimental and theoretical studies in the design of precisely engineered biomaterials.

Identification of a Novel Parallel β-Strand Conformation within Molecular Monolayer of Amyloid Peptide

The differentiation of protein properties and biological functions arises from the variation in the primary and secondary structure. Specifically, in abnormal assemblies of protein, such as amyloid peptide, the secondary structure is closely correlated with the stable ensemble and the cytotoxicity. In this work, the early Aβ_33-42 aggregates forming the molecular monolayer at hydrophobic interface are investigated. The molecular monolayer of amyloid peptide Aβ_33-42 consisting of novel parallel β-strand-like structure is further revealed by means of a quantitative nanomechanical spectroscopy technique with force controlled in pico-Newton range, combining with molecular dynamic simulation. The identified parallel β-strand-like structure of molecular monolayer is distinct from the antiparallel β-strand structure of Aβ_33-42 amyloid fibril. This finding enriches the molecular structures of amyloid peptide aggregation, which could be closely related to the pathogenesis of amyloid disease.

AFM-based mechanical characterization of single nanofibres

Nanofibres are found in a broad variety of hierarchical biological systems as fundamental structural units, and nanofibrillar components are playing an increasing role in the development of advanced functional materials. Accurate determination of the mechanical properties of single nanofibres is thus of great interest, yet measurement of these properties is challenging due to the intricate specimen handling and the exceptional force and deformation resolution that is required. The atomic force microscope (AFM) has emerged as an effective, reliable tool in the investigation of nanofibrillar mechanics, with the three most popular approaches-AFM-based tensile testing, three-point deformation testing, and nanoindentation-proving preferable to conventional tensile testing in many (but not all) cases. Here, we review the capabilities and limitations of each of these methods and give a comprehensive overview of the recent advances in this field.