Identification of hybrid amyloid strains assembled from amyloid-βand human islet amyloid polypeptide

Cross-fibrillation of amyloid-β(Aβ) peptides and human islet amyloid polypeptides (hIAPP) has revealed a close correlation between Alzheimer's disease and type 2 diabetes (T2D). Importantly, different amyloid strains are likely to lead to the clinical pathological heterogeneity of degenerative diseases due to toxicity. However, given the complicated cross-interactions between different amyloid peptides, it is still challenging to identify the polymorphism of the hybrid amyloid strains and reveal mechanistic insights into aggregation, but highly anticipated due to their significance. In this study, we investigated the cross-fibrillation of Aβpeptides and different hIAPP species (monomers, oligomers, and fibrils) using combined experimental and simulation approaches. Cross-seeding and propagation of different amyloid peptides monitored by experimental techniques proved that the three species of hIAPP aggregates have successively enhanced Aβfibrillation, especially for hIAPP fibrils. Moreover, the polymorphism of these morphologically similar hybrid amyloid strains could be distinguished by testing their mechanical properties using quantitative nanomechanical mapping, where the assemblies of Aβ-hIAPP fibrils exhibited the high Young's modulus. Furthermore, the enhanced internal molecular interactions andβ-sheet structural transformation were proved by exploring the conformational ensembles of Aβ-hIAPP heterodimer and Aβ-hIAPP decamer using molecular dynamic simulations. Our findings pave the way for identifying different hybrid amyloid strains by quantitative nanomechanical mapping and molecular dynamic simulations, which is important not only for the precise classification of neurodegenerative disease subtypes but also for future molecular diagnosis and therapeutic treatment of multiple interrelated degenerative diseases.

The giant staphylococcal protein Embp facilitates colonization of surfaces through Velcro-like attachment to fibrillated fibronectin

Staphylococcus epidermidis causes some of the most hard-to-treat clinical infections by forming biofilms: Multicellular communities of bacteria encased in a protective matrix, supporting immune evasion and tolerance against antibiotics. Biofilms occur most commonly on medical implants, and a key event in implant colonization is the robust adherence to the surface, facilitated by interactions between bacterial surface proteins and host matrix components. S. epidermidis is equipped with a giant adhesive protein, extracellular matrix-binding protein (Embp), which facilitates bacterial interactions with surface-deposited, but not soluble fibronectin. The structural basis behind this selective binding process has remained obscure. Using a suite of single-cell and single-molecule analysis techniques, we show that S. epidermidis is capable of such distinction because Embp binds specifically to fibrillated fibronectin on surfaces, while ignoring globular fibronectin in solution. S. epidermidis adherence is critically dependent on multivalent interactions involving 50 fibronectin-binding repeats of Embp. This unusual, Velcro-like interaction proved critical for colonization of surfaces under high flow, making this newly identified attachment mechanism particularly relevant for colonization of intravascular devices, such as prosthetic heart valves or vascular grafts. Other biofilm-forming pathogens, such as Staphylococcus aureus, express homologs of Embp and likely deploy the same mechanism for surface colonization. Our results may open for a novel direction in efforts to combat devastating, biofilm-associated infections, as the development of implant materials that steer the conformation of adsorbed proteins is a much more manageable task than avoiding protein adsorption altogether.

A usually harmless bacterium called Staphylococcus epidermidis lives on human skin. Sometimes it makes its way into the bloodstream through a cut or surgical procedure, but it rarely causes blood infections. It can, however, cause severe infections when it attaches to the surface of a medical implant like a pacemaker or an artificial replacement joint. It does this by forming a colony of bacteria on the implant’s surface called a biofilm, which protects the bacteria from destruction by the immune system or antibiotics.

Understanding how Staphylococcus epidermidis implant infections start is critical to preventing them. This information may help scientists develop infection-resistant implants or new treatments for implant infections. Scientists suspect that Staphylococcus epidermidis attaches to implants by binding to a human protein called fibronectin, which coats medical implants in the human body. Another protein on the surface of the bacteria, called Embp, facilitates the connection. But why the bacteria attach to fibronectin on implants, and not fibronectin molecules in the bloodstream, is unclear.

Now, Khan, Aslan et al. show that Embp forms a Velcro-like bond with fibronectin on the surface of implants. In the experiments, Khan and Aslan et al. used powerful microscopes to create 3-dimensional images of the interactions between Embp and fibronectin. The experiments showed that Embp's attachment site is hidden on the globe-shaped form of fibronectin circulating in the blood. But when fibronectin covers an implant surface, it forms a fibrous network, and Embp can attach to it with up to 50 Velcro-like individual connections. These many weak connections form a strong bond that withstands the force of blood pumping past.

The experiments show that the fibrous coating of fibronectin on implants makes them a hotspot for Staphylococcus epidermidis infections. Finding ways to block Embp from attaching to fibronectin on implants, or altering the form fibronectin takes on implants, may help prevent these infections. Many bacteria that form biofilms have an Embp-like protein. As a result, these discoveries may also help scientists develop prevention or treatment strategies for other bacterial biofilm infections.

Reshapable Osteogenic Biomaterials Combining Flexible Melt Electrowritten Organic Fibers with Inorganic Bioceramics

Ever-growing various applications, especially for tissue regeneration, cause a pressing need for novel methods to functionalize melt electrowritten (MEW) microfibrous scaffolds with unique nanomaterials. Here, two novel strategies are proposed to modify MEW polycaprolactone (PCL) grids with ZnO nanoparticles (ZP) or ZnO nanoflakes (ZF) to enhance osteogenic differentiation. The calcium mineralization levels of MC3T3 osteoblasts cultured on PCL/ZP 0.1 scaffolds are ∼3.91-fold higher than those cultured on nonmodified PCL scaffolds, respectively. Due to the nanotopography mimicking bone anatomy, the PCL/ZF scaffolds (∼2.60 times higher in ALP activity compared to PCL/ZP 1 and ∼2.17 times higher in mineralization compared to PCL/ZP 0.1) achieved superior results. Moreover, the flexible feature inherited from PCL grids makes it possible for them to act as a reshapable osteogenic bioscaffold. This study provides new strategies for synthesizing nanomaterials on microscale surfaces, opening up a new route for functionalizing MEW scaffolds to fulfill the growing demand of tissue engineering.

A unifying framework for amyloid-mediated membrane damage: The lipid-chaperone hypothesis

Over the past thirty years, researchers have highlighted the role played by a class of proteins or polypeptides that forms pathogenic amyloid aggregates in vivo, including i) the amyloid Aβ peptide, which is known to form senile plaques in Alzheimer's disease; ii) α-synuclein, responsible for Lewy body formation in Parkinson's disease and iii) IAPP, which is the protein component of type 2 diabetes-associated islet amyloids. These proteins, known as intrinsically disordered proteins (IDPs), are present as highly dynamic conformational ensembles. IDPs can partially (mis) fold into (dys) functional conformations and accumulate as amyloid aggregates upon interaction with other cytosolic partners such as proteins or lipid membranes. In addition, an increasing number of reports link the toxicity of amyloid proteins to their harmful effects on membrane integrity. Still, the molecular mechanism underlying the amyloidogenic proteins transfer from the aqueous environment to the hydrocarbon core of the membrane is poorly understood. This review starts with a historical overview of the toxicity models of amyloidogenic proteins to contextualize the more recent lipid-chaperone hypothesis. Then, we report the early molecular-level events in the aggregation and ion-channel pore formation of Aβ, IAPP, and α-synuclein interacting with model membranes, emphasizing the complexity of these processes due to their different spatial-temporal resolutions. Next, we underline the need for a combined experimental and computational approach, focusing on the strengths and weaknesses of the most commonly used techniques. Finally, the last two chapters highlight the crucial role of lipid-protein complexes as molecular switches among ion-channel-like formation, detergent-like, and fibril formation mechanisms and their implication in fighting amyloidogenic diseases.

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

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

Quantitative mapping of magnetic properties at the nanoscale with bimodal AFM

We demonstrate that a force microscope operated in a bimodal configuration enables the mapping of magnetic interactions with high quantitative accuracy and high-spatial resolution (∼30 nm). Bimodal AFM operation doubles the number of observables with respect to conventional magnetic force microscopy methods which enables to determine quantitatively in a single processing step several magnetic properties. The theory of bimodal AFM provides analytical expressions for different magnetic force models, in particular those characterized by power-law and exponential distance dependences. Bimodal AFM provides a self-evaluation protocol to test the accuracy of the measurements. The agreement obtained between the experiments and theory for two different magnetic samples support the application of bimodal AFM to map quantitatively long-range magnetic interactions.

Activation of the Two-Component System LisRK Promotes Cell Adhesion and High Ampicillin Tolerance in Listeria monocytogenes

Listeria monocytogenes is a foodborne pathogen which can survive in harsh environmental conditions. It responds to external stimuli through an array of two-component systems (TCS) that sense external cues. Several TCS, including LisRK, have been linked to Listeria’s ability to grow at slightly elevated antibiotic levels. The aim of this study was to determine if the TCS LisRK is also involved in acquiring the high antibiotic tolerance that is characteristic of persister cells. LisRK activates a response that leads to remodeling of the cell envelope, and we therefore hypothesized that activation of LisRK could also increase in the cells’ adhesiveness and initiate the first step in biofilm formation. We used a ΔlisR mutant to study antibiotic tolerance in the presence and absence of LisRK, and a GFP reporter strain to visualize the activation of LisRK in L. monocytogenes LO28 at a single-cell level. LisRK was activated in most cells in stationary phase cultures. Antimicrobial susceptibility tests showed that LisRK was required for the generation of ampicillin tolerance under these conditions. The wildtype strain tolerated exposure to ampicillin at 1,000 × inhibitory levels for 24 h, and the fraction of surviving cells was 20,000-fold higher in the wildtype strain compared to the ΔlisR mutant. The same protection was not offered to other antibiotics (vancomycin, gentamicin, tetracycline), and the mechanism for antibiotic tolerance is thus highly specific. Furthermore, quantification of bacterial attachment rates and attachment force also revealed that the absence of a functional LisRK rendered the cells less adhesive. Hence, LisRK TCS promotes multiple protective mechanisms simultaneously.

Nanomechanical mapping of soft materials with the atomic force microscope: methods, theory and applications

Fast, high-resolution, non-destructive and quantitative characterization methods are needed to develop materials with tailored properties at the nanoscale or to understand the relationship between mechanical properties and cell physiology. This review introduces the state-of-the-art force microscope-based methods to map at high-spatial resolution the elastic and viscoelastic properties of soft materials. The experimental methods are explained in terms of the theories that enable the transformation of observables into material properties. Several applications in materials science, molecular biology and mechanobiology illustrate the scope, impact and potential of nanomechanical mapping methods.

Non-contact microfluidic mechanical property measurements of single apoptotic bodies

BACKGROUND

Cells exchange information by secreting micro- and nanosized extracellular vesicles (EVs), ranging from exosomes (30-100 nm) to apoptotic bodies (ABs, 1-5 μm). There is still much to understand about fundamental EV biological, physical, and chemical properties before clinical applications can be developed. EV mechanical properties have only been measured with atomic force microscopy (AFM) with its problematic adhesion and hard substrate effects. To understand EV mechanical behavior in less extreme mechanical conditions relevant to blood flow and many soft tissue environments, a non-contact measurement technique is needed.

METHODS

We measured the mechanical properties of single microscale ABs derived from human blood plasma using non-contact microfluidics. EVs were gently stretched in extensional flow, similar to a traditional tensile test, and a linear mechanical model was applied to estimate mechanical stiffnesses from the observed stretching.

RESULTS

The effective shear elastic modulus of ABs in non-contact flow conditions is approximately 5.6 ± 0.5 Pa, 7 orders of magnitude lower than previously reported AFM-measured biological exosome stiffnesses and 200 times smaller than suspended cells.

CONCLUSIONS

Apoptotic bodies are very soft in fluid environments and exhibit lower effective stiffnesses than suspended cells. By measuring ABs in a natural fluid environment and low-force regime without hard probes and surfaces, we achieved closer agreement with linear mechanical theory and therefore more accurate stiffness measurements.

GENERAL SIGNIFICANCE

AFM manufacturers and users should consider implementing new mechanical models to interpret AFM force indentation curves so that accurate extracellular vesicle mechanical properties can be extracted.

Diversity of physical properties of bacterial extracellular membrane vesicles revealed through atomic force microscopy phase imaging

Bacteria release nanometer-scale extracellular membrane vesicles (MVs) to mediate a variety of biological processes. We analyzed individual MVs under physiological conditions by phase imaging of high-speed atomic force microscopy to assess the physiological heterogeneity of MVs isolated from bacterial cultures. Phase imaging makes it possible to map the physical properties of an individual, fragile MV in an isolated MV population containing a broad variety of vesicle diameters, from 20 to 150 nm. We also developed a method for quantitatively comparing the physical properties of MVs among samples. This allowed for the comparison of the physical properties of MVs isolated from different bacterial species. We compared bacterial MVs isolated from four bacterial species and artificially synthesized liposomes. We demonstrate that each bacterial species generates physically heterogeneous types of MVs, unlike the physical homogeneity displayed by liposomes. These results indicate that the physical heterogeneity of bacterial MVs is mainly caused by compositional differences mediated through biological phenomena and could be unique to each species. We provide a new methodology using phase imaging that would pave the way for single-vesicle analysis of extracellular vesicles of a broad size range.

Carbon dots-fed Shewanella oneidensis MR-1 for bioelectricity enhancement

Bioelectricity generation, by Shewanella oneidensis (S. oneidensis) MR-1, has become particularly alluring, thanks to its extraordinary prospects for energy production, pollution treatment, and biosynthesis. Attempts to improve its technological output by modification of S. oneidensis MR-1 remains complicated, expensive and inefficient. Herein, we report on the augmentation of S. oneidensis MR-1 with carbon dots (CDs). The CDs-fed cells show accelerated extracellular electron transfer and metabolic rate, with increased intracellular charge, higher adenosine triphosphate level, quicker substrate consumption and more abundant extracellular secretion. Meanwhile, the CDs promote cellular adhesion, electronegativity, and biofilm formation. In bioelectrical systems the CDs-fed cells increase the maximum current value, 7.34 fold, and power output, 6.46 fold. The enhancement efficacy is found to be strongly dependent on the surface charge of the CDs. This work demonstrates a simple, cost-effective and efficient route to improve bioelectricity generation of S. oneidensis MR-1, holding promise in all relevant technologies.

Bacterial fuel cells have generated attention with the prospect of green energy production; current research is focused on optimising the system to improve efficiency. Here, the authors report on the feeding of carbon dots to S. oneidensis MR-1 to enhance metabolic activity and bioelectric generation.

Nanoscale adhesion forces of glucosyltransferase B and C genes regulated Streptococcal mutans probed by AFM

Glucosyltransferases (Gtfs), represented by GtfB and GtfC, are important virulence factors of Streptococcus mutans and the major etiologic pathogens of tooth decay. However, the individual roles of gtfB and gtfC in the initial attachment of S. mutans are not known. We used atomic force microscopy to explore the contribution of gtfB and gtfC, as well as enamel-surface roughness, on the initial attachment of S. mutans. Adhesion forces of four S. mutans strains (wild-type, ΔgtfB, ΔgtfC, and ΔgtfBC), onto etched enamel surfaces, were determined. Force curves showed that, with increasing etching time from 0 to 10 s, the forces of all strains increased accordingly with acid-exposure time, the adhesion forces of wild-type strains were significantly greater than those of mutant strains (p < .05), and the forces of the three mutants were similar (p < .05). When the etching time was increased from 10 to 30 s, difference in force between 20 and 30 s was not observed, and adhesion forces among ΔgtfB, ΔgtfC, and wild-type strains were not significantly different when the etching time was >20 s (p > .05). These data suggest that the roughness and morphology of enamel surfaces may have a significant influence upon the initial attachment of bacteria, and that gtfB and gtfC are essential for the adhesion activity of bacteria. Furthermore, gtfB seems to be more important than gtfC for bacterial-biofilm formation, and gtfB inactivation is an effective strategy to inhibit the virulence of cariogenic biofilms.

Lipidoid-polymer hybrid nanoparticles loaded with TNF siRNA suppress inflammation after intra-articular administration in a murine experimental arthritis model

Rheumatoid arthritis (RA) is a common autoimmune disease, which is characterized by painful chronic inflammation in the joints, and novel safe and efficacious treatments are urgently needed. RNA interference (RNAi) therapy based on small interfering RNA (siRNA) is a promising approach for silencing specific genes involved in inflammation. However, delivery of siRNA to the target site, i.e. the cytosol of immune cells, is a challenge. Here, we designed lipid-polymer hybrid nanoparticles (LPNs) composed of lipidoid and poly(DL-lactic-co-glycolic acid) loaded with a therapeutic cargo siRNA directed against the proinflammatory cytokine tumor necrosis factor (TNF), which plays a key role in the progression of RA. We compared their efficacy and safety with reference lipidoid-based stable nucleic acid lipid particles (SNALPs) in vitro and in vivo. Cryogenic transmission electron microscopy, atomic force microscopy and small-angle X-ray scattering revealed that the mode of loading of siRNA in lamellar structures differs between the two formulations. Thus, siRNA was tightly packed in LPNs, while LPNs displayed lower adhesion than SNALPs. The LPNs mediated a higher TNF silencing effect in vitro than SNALPs in the RAW 264.7 macrophage cell line activated with lipopolysaccharide. For both types of delivery systems, macropinocytosis was involved in cellular uptake. In addition, clathrin-mediated endocytosis contributed to uptake of SNALPs. LPNs loaded with TNF siRNA mediated sequence-specific suppression of inflammation in a murine experimental arthritis model upon intra-articular administration. Hence, the present study demonstrates that LPN-mediated TNF knockdown constitutes a promising approach for arthritis therapy of TNF-mediated chronic inflammatory conditions.

Atomic force microscopy for single molecule characterisation of protein aggregation

The development of atomic force microscopy (AFM) has opened up a wide range of novel opportunities in nanoscience and new modalities of observation in complex biological systems. AFM imaging has been widely employed to resolve the complex and heterogeneous conformational states involved in protein aggregation at the single molecule scale and shed light onto the molecular basis of a variety of human pathologies, including neurodegenerative disorders. The study of individual macromolecules at nanoscale, however, remains challenging, especially when fully quantitative information is required. In this review, we first discuss the principles of AFM with a special emphasis on the fundamental factors defining its sensitivity and accuracy. We then review the fundamental parameters and approaches to work at the limit of AFM resolution in order to perform single molecule statistical analysis of biomolecules and nanoscale protein aggregates. This single molecule statistical approach has proved to be powerful to unravel the molecular and hierarchical assembly of the misfolded species present transiently during protein aggregation, to visualise their dynamics at the nanoscale, as well to study the structural properties of amyloid-inspired functional nanomaterials.

In Situ Observation of Amyloid Nucleation and Fibrillation by FastScan Atomic Force Microscopy

Amyloidogenic proteins are key components in various amyloid diseases. The aggregation process and the local structural changes of the toxic species from toxic oligomers to protofibrils and subsequently to mature fibrils are crucial for understanding the molecular mechanism of the amyloidgenic process and also for developing a treatment strategy. Exploration on amyloid aggregation dynamics in situ under real liquid condition is feasible for reflection of the whole process with biological correlations. Herein we report the in situ dynamic study and structure exploration of Amylin_1-37 aggregation by FastScan atomic force microscopy. Amylin_1-37 nucleation process was observed in which smaller oligomers or monomers were assimilated by the surrounding big oligomers. Amylin_1-37 protofibril aggregation was positively correlated with monomer concentration, whereas no direct relationship was observed between fibril elongation and monomer concentration. Growing end and passivated end were found during Amylin_1-37 fibrillation. In the assembly process, the growing end kept its structure, and its stiffness was lower than the aggregate body, whereas the passivated end might experience rearrangements of β-structures, which eventually enabled fibril growth from this end. This work is beneficial to the insights of amyloid fibrillation and may shed light on the development of drugs targeting the specific phase of amyloid aggregation.

Structural and Mechanical Characterization of Viruses with AFM

Microscopes are used to characterize small objects with the help of probes that interact with the specimen, such as photons and electrons in optical and electron microscopies, respectively. In atomic force microscopy (AFM) the probe is a nanometric tip located at the end of a micro cantilever which palpates the specimen under study as a blind person manages a walking stick. In this way AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables not only the manipulation of single protein cages, but also the characterization of every physicochemical property able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. In this chapter we start revising some recipes for adsorbing protein shells on surfaces. Then we describe several AFM approaches to study individual protein cages, ranging from imaging to spectroscopic methodologies devoted for extracting physical information, such as mechanical and electrostatic properties. We also explain how a convenient combination of AFM and fluorescence methodologies entails monitoring genome release from individual viral shells during mechanical unpacking.

In vitro single-cell dissection revealing the interior structure of cable bacteria

Filamentous Desulfobulbaceae bacteria were recently discovered as long-range transporters of electrons from sulfide to oxygen in marine sediments. The long-range electron transfer through these cable bacteria has created considerable interests, but it has also raised many questions, such as what structural basis will be required to enable micrometer-sized cells to build into centimeter-long continuous filaments? Here we dissected cable bacteria cells in vitro by atomic force microscopy and further explored the interior, which is normally hidden behind the outer membrane. Using nanoscale topographical and mechanical maps, different types of bacterial cell-cell junctions and strings along the cable length were identified. More important, these strings were found to be continuous along the bacterial cells passing through the cell-cell junctions. This indicates that the strings serve an important function in maintaining integrity of individual cable bacteria cells as a united filament. Furthermore, ridges in the outer membrane are found to envelop the individual strings at cell-cell junctions, and they are proposed to strengthen the junctions. Finally, we propose a model for the division and growth of the cable bacteria, which illustrate the possible structural requirements for the formation of centimeter-length filaments in the recently discovered cable bacteria.

Multiscale Frictional Properties of Cotton Fibers: A Review

This review discusses the important concept of cotton fiber friction at both the macro- and nanoscale. First, the technological importance of fiber friction and its role in fiber breakage during fiber processing is discussed. Next, previous studies on frictional properties of cotton fibers are reviewed and different experimental procedures to measure friction between fibers or against another surface are evaluated. Friction models developed to explain friction process during various experimental procedures are considered and their limitations are discussed. Since interpretation of friction processes at the macroscale can be challenging (mainly due to difficulties in analyzing the multiple asperities in contact), a separate section is devoted to surveying studies on the emerging field of single-asperity friction experiments with atomic force microscope (AFM). Special attention is given to studies on nanoscale frictional characteristics of rough viscoelastic surfaces (e.g., plant cuticular biopolymers and cotton fibers). Due to the close relationship between friction and adhesion hysteresis at the nanoscale, adhesion studies with AFM on viscoelastic surfaces are also reviewed. Lastly, recommendations are made for future research in the field of frictional properties of cotton fibers.

Size-Dependent Affinity of Glycine and Its Short Oligomers to Pyrite Surface: A Model for Prebiotic Accumulation of Amino Acid Oligomers on a Mineral Surface

The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, and penta-Gly, with a natural pyrite surface was directly measured using the force mode of an atomic force microscope (AFM). In recent years, selective activation of abiotically formed amino acids on mineral surfaces, especially that of pyrite, has been proposed as an important step in many origins of life scenarios. To investigate such notions, we used AFM-based force measurements to probe possible non-covalent interactions between pyrite and amino acids, starting from the simplest amino acid, Gly. Although Gly itself interacted with the pyrite surface only weakly, progressively larger unbinding forces and binding frequencies were obtained using oligomers from di-Gly to penta-Gly. In addition to an expected increase of the configurational entropy and size-dependent van der Waals force, the increasing number of polar peptide bonds, among others, may be responsible for this observation. The effect of chain length was also investigated by performing similar experiments using l-lysine vs. poly-l-lysine (PLL), and l-glutamic acid vs. poly-l-glutamic acid. The results suggest that longer oligomers/polymers of amino acids can be preferentially adsorbed on pyrite surfaces.

Graphene Oxide Hybridized nHAC/PLGA Scaffolds Facilitate the Proliferation of MC3T3-E1 Cells

Biodegradable porous biomaterial scaffolds play a critical role in bone regeneration. In this study, the porous nano-hydroxyapatite/collagen/poly(lactic-co-glycolic acid)/graphene oxide (nHAC/PLGA/GO) composite scaffolds containing different amount of GO were fabricated by freeze-drying method. The results show that the synthesized scaffolds possess a three-dimensional porous structure. GO slightly improves the hydrophilicity of the scaffolds and reinforces their mechanical strength. Young's modulus of the 1.5 wt% GO incorporated scaffold is greatly increased compared to the control sample. The in vitro experiments show that the nHAC/PLGA/GO (1.5 wt%) scaffolds significantly cell adhesion and proliferation of osteoblast cells (MC3T3-E1). This present study indicates that the nHAC/PLGA/GO scaffolds have excellent cytocompatibility and bone regeneration ability, thus it has high potential to be used as scaffolds in the field of bone tissue engineering.

Pan-genome analysis of the genus Finegoldia identifies two distinct clades, strain-specific heterogeneity, and putative virulence factors

Finegoldia magna, a Gram-positive anaerobic coccus, is an opportunistic pathogen, associated with medical device-related infections. F. magna is the only described species of the genus Finegoldia. We report the analysis of 17 genomes of Finegoldia isolates. Phylogenomic analyses showed that the Finegoldia population can be divided into two distinct clades, with an average nucleotide identity of 90.7%. One clade contains strains of F. magna, whereas the other clade includes more heterogeneous strains, hereafter tentatively named "Finegoldia nericia". The latter species appears to be more abundant in the human microbiome. Surface structure differences between strains of F. magna and "F. nericia" were detected by microscopy. Strain-specific heterogeneity is high and previously identified host-interacting factors are present only in subsets of "F. nericia" and F. magna strains. However, all genomes encode multiple host factor-binding proteins such as albumin-, collagen-, and immunoglobulin-binding proteins, and two to four copies of CAMP (Christie-Atkins-Munch-Petersen) factors; in accordance, most strains show a positive CAMP reaction for co-hemolysis. Our work sheds new light of the genus Finegoldia and its ability to bind host components. Future research should explore if the genomic differences identified here affect the potential of different Finegoldia species and strains to cause opportunistic infections.

Atomic Force Microscopy of Protein Shells: Virus Capsids and Beyond

In Atomic Force Microscopy (AFM) the probe is a nanometric tip located at the end of a microcantilever which palpates the specimen under study as a blind person uses a white cane. In this way AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables the manipulation of single protein cages, and the characterization a variety physicochemical properties able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. In this chapter we start revising some recipes for adsorbing protein shells on surfaces. Then we describe several AFM approaches to study individual protein cages, ranging from imaging to spectroscopic methodologies devoted to extracting physical information, such as mechanical and electrostatic properties.

Interface effect on the cohesive energy of nanostructured materials and substrate-supported nanofilms

The cohesive energy is a key quantity to determine the mechanical, physical, chemical, and electronic properties of materials.

Broad modulus range nanomechanical mapping by magnetic-drive soft probes

Stiffness matching between the probe and deformed portion of the sample in piezo-drive peak force modulation atomic force microscopy (AFM) limits the modulus measurement range of single probes. Here we develop a magnetic drive peak force modulation AFM to broaden the dynamic range of the probe with direct cantilever excitation. This approach not only successfully drives the softest commercial probe (6 pN nm^-1) for mapping extremely soft samples in liquid but also provides an indentation force of hundreds of nanonewtons for stiff samples with a soft probe. Features of direct measurements of the indentation force and depth can unify the elastic modulus range up to four orders of magnitude, from 1 kPa to 10 MPa (in liquid) and 1 MPa to 20 GPa (in air or liquid) using a single probe. This approach can be particularly useful for analysing heterogeneous samples with large elastic modulus variations in multi-environments.

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.

Facile Fabrication of a Flexible LiNbO3 Piezoelectric Sensor through Hot Pressing for Biomechanical Monitoring

Wearable pressure sensors have attracted increasing attention for biomechanical monitoring due to their portability and flexibility. Although great advances have been made, there are no facile methods to produce sensors with good performance. Here, we present a simple method for manufacturing flexible and self-powered piezoelectric sensors based on LiNbO₃ (LN) particles. The LN particles are dispersed in polypropylene (PP) doped with multiwalled carbon nanotubes (MWCNTs) by hot pressing (200 °C) to form a flexible LN/MWCNT/PP piezoelectric composite film (PCF) sensor. This cost-effective sensor has high sensitivity (8 Pa), fast response time (ca. 40 ms), and long-term stability (>3000 cycles). Measurements of pressure changes from peripheral arteries demonstrate the applicability of the LN/MWCNT/PP PCF sensor to biomechanical monitoring as well as its potential for biomechanics-related clinical diagnosis and forecasting.

Study of morphological and mechanical features of multinuclear and mononuclear SW480 cells by atomic force microscopy

This article studies the morphological and mechanical features of multinuclear and mononuclear SW480 colon cancer cells by atomic force microscopy to understand their drug-resistance. The SW480 cells were incubated with the fullerenol concentrations of 1 mg/ml and 2 mg/ml. Morphological and mechanical features including the height, length, width, roughness, adhesion force and Young's modulus of three multinuclear cell groups and three mononuclear cell groups were imaged and analyzed. It was observed that the features of multinuclear cancer cells and mononuclear cancer cells were significantly different after the treatment with fullerenol. The experiment results indicated that the mononuclear SW480 cells were more sensitive to fullerenol than the multinuclear SW480 cells, and the multinuclear SW480 cells exhibited a stronger drug-resistance than the mononuclear SW480 cells. This work provides a guideline for the treatments of multinuclear and mononuclear cancer cells with drugs.

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

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

Atomic force microscopy of virus shells

Microscopes are used to characterize small specimens with the help of probes, such as photons and electrons in optical and electron microscopies, respectively. In atomic force microscopy (AFM) the probe is a nanometric tip located at the end of a microcantilever which palpates the specimen under study as a blind person manages a white cane to explore the surrounding. In this way, AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables the manipulation of single protein cages, and the characterization of every physico-chemical property able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. Here we describe several AFM approaches to study individual protein cages, including imaging and spectroscopic methodologies for extracting mechanical and electrostatic properties. In addition, AFM allows discovering and testing the self-healing capabilities of protein cages because occasionally they may recover fractures induced by the AFM tip. Beyond the protein shells, AFM also is able of exploring the genome inside, obtaining, for instance, the condensation state of dsDNA and measuring its diffusion when the protein cage breaks.

Time-resolved nanomechanics of a single cell under the depolymerization of the cytoskeleton

Single cell stiffness measurements consider cells as passive and elastic materials which react instantaneously to an external force. This approximation is at odds with the complex structure of the cell which includes solid and liquid components. Here we develop a force microscopy method to measure the time and frequency dependencies of the elastic modulus, the viscosity coefficient, the loss modulus and the relaxation time of a single live cell. These parameters have different time and frequency dependencies. At low modulation frequencies (0.2-4 Hz), the elastic modulus remains unchanged; the loss modulus increases while the viscosity and the relaxation time decrease. We have followed the evolution of a fibroblast cell subjected to the depolymerization of its F-actin cytoskeleton. The elastic modulus, the loss modulus and the viscous coefficient decrease with the exposure time to the depolymerization drug while the relaxation time increases. The latter effect reflects that the changes in the elastic response happen at a higher rate than those affecting the viscous flow. The observed behavior is compatible with a cell mechanical response described by the poroelastic model.

Atomic force microscopy of virus shells

Microscopes are used to characterize small objects with the help of probes that interact with the specimen, such as photons and electrons in optical and electron microscopies, respectively. In atomic force microscopy (AFM), the probe is a nanometric tip located at the end of a microcantilever which palpates the specimen under study just as a blind person manages a walking stick. In this way, AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in a liquid milieu. Beyond imaging, AFM also enables not only the manipulation of single protein cages, but also the characterization of every physicochemical property capable of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. In the present revision, we start revising some recipes for adsorbing protein shells on surfaces. Then, we describe several AFM approaches to study individual protein cages, ranging from imaging to spectroscopic methodologies devoted to extracting physical information, such as mechanical and electrostatic properties. We also explain how a convenient combination of AFM and fluorescence methodologies entails monitoring genome release from individual viral shells during mechanical unpacking.

Imaging modes of atomic force microscopy for application in molecular and cell biology

Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.

Direct mapping of chemical oxidation of individual graphene sheets through dynamic force measurements at the nanoscale

Graphene oxide is one of the most studied nanomaterials owing to its huge application potential in many fields, including biomedicine, sensing, drug delivery, optical and optoelectronic technologies. However, a detailed description of the chemical composition and the extent of oxidation in graphene oxide remains a key challenge affecting its applicability and further development of new applications. Here, we report direct monitoring of the chemical oxidation of an individual graphene flake during ultraviolet/ozone treatment through in situ atomic force microscopy based on dynamic force mapping. The results showed that graphene oxidation expanded from the graphene edges to the entire graphene surface. The interaction force mapping results correlated well with X-ray photoelectron spectroscopy data quantifying the degree of chemical oxidation. Density functional theory calculations confirmed the specific interaction forces measured between a silicon tip and graphene oxide. The developed methodology can be used as a simple protocol for evaluating the chemical functionalization of other two-dimensional materials with covalently attached functional groups.

Self-assembled peptide nanostructures for functional materials

Nature is an important inspirational source for scientists, and presents complex and elegant examples of adaptive and intelligent systems created by self-assembly. Significant effort has been devoted to understanding these sophisticated systems. The self-assembly process enables us to create supramolecular nanostructures with high order and complexity, and peptide-based self-assembling building blocks can serve as suitable platforms to construct nanostructures showing diverse features and applications. In this review, peptide-based supramolecular assemblies will be discussed in terms of their synthesis, design, characterization and application. Peptide nanostructures are categorized based on their chemical and physical properties and will be examined by rationalizing the influence of peptide design on the resulting morphology and the methods employed to characterize these high order complex systems. Moreover, the application of self-assembled peptide nanomaterials as functional materials in information technologies and environmental sciences will be reviewed by providing examples from recently published high-impact studies.

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

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

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

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

Effect of Actin Organization on the Stiffness of Living Breast Cancer Cells Revealed by Peak-Force Modulation Atomic Force Microscopy

We study the correlation between cytoskeleton organization and stiffness of three epithelial breast cancer cells lines with different degrees of malignancy: MCF-10A (healthy), MCF-7 (tumorigenic/noninvasive), and MDA-MB-231 (tumorigenic/invasive). Peak-force modulation atomic force microscopy is used for high-resolution topography and stiffness imaging of actin filaments within living cells. In healthy cells, local stiffness is maximum where filamentous actin is organized as well-aligned stress fibers, resulting in apparent Young's modulus values up to 1 order of magnitude larger than those in regions where these structures are not observed, but these organized actin fibers are barely observed in tumorigenic cells. We further investigate cytoskeleton conformation in the three cell lines by immunofluorescence confocal microscopy. The combination of both techniques determines that actin stress fibers are present at apical regions of healthy cells, while in tumorigenic cells they appear only at basal regions, where they cannot contribute to stiffness as probed by atomic force microscopy. These results substantiate that actin stress fibers provide a dominant contribution to stiffness in healthy cells, while the elasticity of tumorigenic cells appears not predominantly determined by these structures. We also discuss the effects of the high-frequency indentations inherent to peak-force atomic force microscopy for the identification of mechanical cancer biomarkers. Whereas conventional low loading rate indentations (1 Hz) result in slightly differentiated average stiffness for each cell line, in high-frequency measurements (250 Hz) healthy cells are clearly discernible from both tumorigenic cells with an enhanced stiffness ratio; however, the two cancerous cell lines produced indistinguishable results.

The Ultrastructures and Mechanical Properties of the Descement's Membrane in Fuchs Endothelial Corneal Dystrophy

Fuchs endothelial corneal dystrophy (FECD), is the most common corneal endothelial dystrophy, and contributes up to 50% of all corneal transplantations performed in developed countries. FECD develops in Descemet’s membrane (DM) and possibly alters the mechanical properties and internal structures in this basal lamina. In this work, the morphology and mechanical properties of FECD-DMs are studied by transmission electron microscopy (TEM) and quantitative dynamic atomic force microscopy (QD-AFM) at nano scale. Pathological wide-space collagens that are typical of FECD display different mechanical properties in that they are softer than the remaining tissue both for dehydrated- and fully hydrated samples. Additionally, the hydration level has major influence on the mechanical properties. These findings could help to further understand the structural changes in FECD, and possibly be useful for further characterization of the disease, the diagnosis and assessment or even pathologic analysis.

The structure and function of cell membranes examined by atomic force microscopy and single-molecule force spectroscopy

The cell membrane is one of the most complicated biological complexes, and long-term fierce debates regarding the cell membrane persist because of technical hurdles. With the rapid development of nanotechnology and single-molecule techniques, our understanding of cell membranes has substantially increased. Atomic force microscopy (AFM) has provided several unprecedented advances (e.g., high resolution, three-dimensional and in situ measurements) in the study of cell membranes and has been used to systematically dissect the membrane structure in situ from both sides of membranes; as a result, novel models of cell membranes have recently been proposed. This review summarizes the new progress regarding membrane structure using in situ AFM and single-molecule force spectroscopy (SMFS), which may shed light on the study of the structure and functions of cell membranes.

Tumour exosomes display differential mechanical and complement activation properties dependent on malignant state: implications in endothelial leakiness

Background

Exosomes have been implicated in tumour progression and metastatic spread. Little is known of the effect of mechanical and innate immune interactions of malignant cell-derived exosomes on endothelial integrity, which may relate to increased extravasation of circulating tumour cells and, therefore, increased metastatic spread.

Methods

Exosomes isolated from non-malignant immortalized HCV-29 and isogenic malignant non-metastatic T24 and malignant metastatic FL3 bladder cells were characterized by nanoparticle tracking analysis and quantitative nanomechanical mapping atomic force microscopy (QNM AFM) to determine size and nanomechanical properties. Effect of HCV-29, T24 and FL3 exosomes on human umbilical vein endothelial cell (HUVEC) monolayer integrity was determined by transendothelial electrical resistance (TEER) measurements and transport was determined by flow cytometry. Complement activation studies in human serum of malignant and non-malignant cell-derived exosomes were performed.

Results

FL3, T24 and HCV-29 cells produced exosomes at similar concentration per cell (6.64, 6.61 and 6.46×10⁴ exosomes per cell for FL3, T24 and HCV-29 cells, respectively) and of similar size (120.2 nm for FL3, 127.6 nm for T24 and 117.9 nm for HCV-29, respectively). T24 and FL3 cell-derived exosomes exhibited a markedly reduced stiffness, 95 MPa and 280 MPa, respectively, compared with 1,527 MPa with non-malignant HCV-29 cell-derived exosomes determined by QNM AFM. FL3 and T24 exosomes induced endothelial disruption as measured by a decrease in TEER in HUVEC monolayers, whereas no effect was observed for HCV-29 derived exosomes. FL3 and T24 exosomes traffic more readily (11.6 and 21.4% of applied exosomes, respectively) across HUVEC monolayers than HCV-29 derived exosomes (7.2% of applied exosomes). Malignant cell-derived exosomes activated complement through calcium-sensitive pathways in a concentration-dependent manner.

Conclusions

Malignant (metastatic and non-metastatic) cell line exosomes display a markedly reduced stiffness and adhesion but an increased complement activation compared to non-malignant cell line exosomes, which may explain the observed increased endothelial monolayer disruption and transendothelial transport of these vesicles.

Quantitative nanoscale electrostatics of viruses

Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed ϕ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material.

Microfluidic Synthesis of Hybrid Nanoparticles with Controlled Lipid Layers: Understanding Flexibility-Regulated Cell-Nanoparticle Interaction

The functionalized lipid shell of hybrid nanoparticles plays an important role for improving their biocompatibility and in vivo stability. Yet few efforts have been made to critically examine the shell structure of nanoparticles and its effect on cell-particle interaction. Here we develop a microfluidic chip allowing for the synthesis of structurally well-defined lipid-polymer nanoparticles of the same sizes, but covered with either lipid-monolayer-shell (MPs, monolayer nanoparticles) or lipid-bilayer-shell (BPs, bilayer nanoparticles). Atomic force microscope and atomistic simulations reveal that MPs have a lower flexibility than BPs, resulting in a more efficient cellular uptake and thus anticancer effect than BPs do. This flexibility-regulated cell-particle interaction may have important implications for designing drug nanocarriers.

Growth and Dissolution of Calcite in the Presence of Adsorbed Stearic Acid

The interaction of organic molecules with the surface of calcite plays a central role in many geochemical, petrochemical, and industrial processes and in biomineralization. Adsorbed organics, typically fatty acids, can interfere with the evolution of calcite when immersed in aqueous solutions. Here we use atomic force microscopy in liquid to explore in real-time the evolution of the (1014) surface of calcite covered with various densities of stearic acid and exposed to different saline solutions. Our results show that the stearic acid molecules tend to act as "pinning points" on the calcite's surface and slow down the crystal's restructuring kinetics. Depending on the amount of material adsorbed, the organic molecules can form monolayers or bilayer islands that become embedded into the growing crystal. The growth process can also displaces the organic molecules and actively concentrate them into stacked multilayers. Our results provide molecular-level insights into the interplay between the adsorbed fatty acid molecules and the evolving calcite crystal, highlighting mechanisms that could have important implications for several biochemical and geochemical processes and for the oil industry.