Sound-mediated nucleation and growth of amyloid fibrils

Mechanical energy, specifically in the form of ultrasound, can induce pressure variations and temperature fluctuations when applied to an aqueous media. These conditions can both positively and negatively affect protein complexes, consequently altering their stability, folding patterns, and self-assembling behavior. Despite much scientific progress, our current understanding of the effects of ultrasound on the self-assembly of amyloidogenic proteins remains limited. In the present study, we demonstrate that when the amplitude of the delivered ultrasonic energy is sufficiently low, it can induce refolding of specific motifs in protein monomers, which is sufficient for primary nucleation; this has been revealed by MD. These ultrasound-induced structural changes are initiated by pressure perturbations and are accelerated by a temperature factor. Furthermore, the prolonged action of low-amplitude ultrasound enables the elongation of amyloid protein nanofibrils directly from natively folded monomeric lysozyme protein, in a controlled manner, until it reaches a critical length. Using solution X-ray scattering, we determined that nanofibrillar assemblies, formed either under the action of sound or from natively fibrillated lysozyme, share identical structural characteristics. Thus, these results provide insights into the effects of ultrasound on fibrillar protein self-assembly and lay the foundation for the potential use of sound energy in protein chemistry.

Significance Statement

Understanding how and why proteins form amyloid fibrils is crucial for research into various diseases, including neurodegeneration. Ultrasound is routinely used in research settings as a tool for generating amyloid seeds (nucleation sites) from mature fibrils, which accelerate the rate of fibril growth. However, ultrasound can have various effects on aqueous media including temperature, extreme shear, and free radicals. Here we show that when the ultrasound parameters are precisely adjusted, they can be utilized as a tool for amyloid growth directly from the natively folded monomers. Thus, it is possible to induce minor changes in the folding of proteins, which trigger nucleation and accelerate amyloid growth. This knowledge lays the foundation for the potential use of sound in protein chemistry.

Decoupling cell size homeostasis in diatoms from the geometrical constraints of the silica cell wall

Unicellular organisms are known to exert tight control over their cell size. In the case of diatoms, abundant eukaryotic microalgae, two opposing notions are widely accepted. On the one hand, the rigid silica cell wall that forms inside the parental cell is thought to enforce geometrical reduction of the cell size. On the other hand, numerous exceptions cast doubt on the generality of this model. Here, we monitored clonal cultures of the diatom Stephanopyxis turris for up to 2 yr, recording the sizes of thousands of cells, in order to follow the distribution of cell sizes in the population. Our results show that S. turris cultures above a certain size threshold undergo a gradual size reduction, in accordance with the postulated geometrical driving force. However, once the cell size reaches a lower threshold, it fluctuates around a constant size using the inherent elasticity of cell wall elements. These results reconcile the disparate observations on cell size regulation in diatoms by showing two distinct behaviors, reduction and homeostasis. The geometrical size reduction is the dominant driving force for large cells, but smaller cells have the flexibility to re-adjust the size of their new cell walls.

Proteolytic Vesicles Derived from Salmonella enterica Serovar Typhimurium-Infected Macrophages: Enhancing MMP-9-Mediated Invasion and EV Accumulation

Proteolysis of the extracellular matrix (ECM) by matrix metalloproteinases (MMPs) plays a crucial role in the immune response to bacterial infections. Here we report the secretion of MMPs associated with proteolytic extracellular vesicles (EVs) released by macrophages in response to Salmonella enterica serovar Typhimurium infection. Specifically, we used global proteomics, in vitro, and in vivo approaches to investigate the composition and function of these proteolytic EVs. Using a model of S. Typhimurium infection in murine macrophages, we isolated and characterized a population of small EVs. Bulk proteomics analysis revealed significant changes in protein cargo of naïve and S. Typhimurium-infected macrophage-derived EVs, including the upregulation of MMP-9. The increased levels of MMP-9 observed in immune cells exposed to S. Typhimurium were found to be regulated by the toll-like receptor 4 (TLR-4)-mediated response to bacterial lipopolysaccharide. Macrophage-derived EV-associated MMP-9 enhanced the macrophage invasion through Matrigel as selective inhibition of MMP-9 reduced macrophage invasion. Systemic administration of fluorescently labeled EVs into immunocompromised mice demonstrated that EV-associated MMP activity facilitated increased accumulation of EVs in spleen and liver tissues. This study suggests that macrophages secrete proteolytic EVs to enhance invasion and ECM remodeling during bacterial infections, shedding light on an essential aspect of the immune response.

LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways

Lissencephaly-1 (LIS1) is associated with neurodevelopmental diseases and is known to regulate the molecular motor cytoplasmic dynein activity. Here we show that LIS1 is essential for the viability of mouse embryonic stem cells (mESCs), and it governs the physical properties of these cells. LIS1 dosage substantially affects gene expression, and we uncovered an unexpected interaction of LIS1 with RNA and RNA-binding proteins, most prominently the Argonaute complex. We demonstrate that LIS1 overexpression partially rescued the extracellular matrix (ECM) expression and mechanosensitive genes conferring stiffness to Argonaute null mESCs. Collectively, our data transforms the current perspective on the roles of LIS1 in post-transcriptional regulation underlying development and mechanosensitive processes.

Mitochondrial-derived vesicles retain membrane potential and contain a functional ATP synthase

Vesicular transport is a means of communication. While cells can communicate with each other via secretion of extracellular vesicles, less is known regarding organelle-to organelle communication, particularly in the case of mitochondria. Mitochondria are responsible for the production of energy and for essential metabolic pathways in the cell, as well as fundamental processes such as apoptosis and aging. Here, we show that functional mitochondria isolated from Saccharomyces cerevisiae release vesicles, independent of the fission machinery. We isolate these mitochondrial-derived vesicles (MDVs) and find that they are relatively uniform in size, of about 100 nm, and carry selective protein cargo enriched for ATP synthase subunits. Remarkably, we further find that these MDVs harbor a functional ATP synthase complex. We demonstrate that these vesicles have a membrane potential, produce ATP, and seem to fuse with naive mitochondria. Our findings reveal a possible delivery mechanism of ATP-producing vesicles, which can potentially regenerate ATP-deficient mitochondria and may participate in organelle-to-organelle communication.

Polymer Gel with Tunable Conductive Properties: A Material for Thermal Energy Harvesting

The spontaneous gelation of poly(4-vinyl pyridine)/pyridine solution produces materials with conductive properties that are suitable for various energy conversion technologies. The gel is a thermoelectric material with a conductivity of 2.2-5.0 × 10^-6 S m^-1 and dielectric constant ε = 11.3. On the molecular scale, the gel contains various types of hydrogen bonding, which are formed via self-protonation of the pyridine side chains. Our measurements and calculations revealed that the gelation process produces bias-dependent polymer complexes: quasi-symmetric, strongly hydrogen-bonded species, and weakly bound protonated structures. Under an applied DC bias, the gelled complexes differ in their capacitance/conductive characteristics. In this work, we exploited the bias-responsive characteristics of poly(4-vinyl pyridine) gelled complexes to develop a prototype of a thermal energy harvesting device. The measured device efficiency is S = ΔV/ΔT = 0.18 mV/K within the temperature range of 296-360 K. Investigation of the mechanism underlying the conversion of thermal energy into electric charge showed that the heat-controlled proton diffusion (the Soret effect) produces thermogalvanic redox reactions of hydrogen ions on the anode. The charge can be stored in an external capacitor for heat energy harvesting. These results advance our understanding of the molecular mechanisms underlying thermal energy conversion in the poly(4-vinyl pyridine)/pyridine gel. A device prototype, enabling thermal energy harvesting, successfully demonstrates a simple path toward the development of inexpensive, low-energy thermoelectric generators.

Micro and nano-scale compartments guide the structural transition of silk protein monomers into silk fibers

Silk is a unique, remarkably strong biomaterial made of simple protein building blocks. To date, no synthetic method has come close to reproducing the properties of natural silk, due to the complexity and insufficient understanding of the mechanism of the silk fiber formation. Here, we use a combination of bulk analytical techniques and nanoscale analytical methods, including nano-infrared spectroscopy coupled with atomic force microscopy, to probe the structural characteristics directly, transitions, and evolution of the associated mechanical properties of silk protein species corresponding to the supramolecular phase states inside the silkworm's silk gland. We found that the key step in silk-fiber production is the formation of nanoscale compartments that guide the structural transition of proteins from their native fold into crystalline β-sheets. Remarkably, this process is reversible. Such reversibility enables the remodeling of the final mechanical characteristics of silk materials. These results open a new route for tailoring silk processing for a wide range of new material formats by controlling the structural transitions and self-assembly of the silk protein's supramolecular phases.

Imaging of Extracellular Vesicles Derived from Plasmodium falciparum-Infected Red Blood Cells Using Atomic Force Microscopy

Malaria is one the most devastating infectious diseases in the world: of the five malaria-associated parasites, Plasmodium falciparum and P. vivax are the most pathogenic and widespread, respectively. P. falciparum invades human red blood cells (RBCs), releasing extracellular vesicles (Pf-EV) carrying DNA, RNA and protein cargo components involved in host-pathogen communications in the course of the disease. Different strategies have been used to analyze Pf-EV biophysically and chemically. Atomic force microscopy (AFM) stands out as a powerful tool for rendering high quality images of extracellular vesicles. In this technique, a sharp tip attached to a cantilever reconstructs the topographic surface of the extracellular vesicles and probes their nano-mechanical properties based on force-distance curves. Here, we describe a method to separate Pf-EV using differential ultracentrifugation, followed by nanoparticle tracking analysis (NTA) to quantify and estimate the size distribution. Finally, the AFM imaging procedure on Pf-EV adsorbed on a Mg²⁺-modified mica surface is detailed.

The role of convolutional neural networks in scanning probe microscopy: a review

Progress in computing capabilities has enhanced science in many ways. In recent years, various branches of machine learning have been the key facilitators in forging new paths, ranging from categorizing big data to instrumental control, from materials design through image analysis. Deep learning has the ability to identify abstract characteristics embedded within a data set, subsequently using that association to categorize, identify, and isolate subsets of the data. Scanning probe microscopy measures multimodal surface properties, combining morphology with electronic, mechanical, and other characteristics. In this review, we focus on a subset of deep learning algorithms, that is, convolutional neural networks, and how it is transforming the acquisition and analysis of scanning probe data.

Protein nanofibril design via manipulation of hydrogen bonds

The process of amyloid nanofibril formation has broad implications including the generation of the strongest natural materials, namely silk fibers, and their major contribution to the progression of many degenerative diseases. The key question that remains unanswered is whether the amyloidogenic nature, which includes the characteristic H-bonded β-sheet structure and physical characteristics of protein assemblies, can be modified via controlled intervention of the molecular interactions. Here we show that tailored changes in molecular interactions, specifically in the H-bonded network, do not affect the nature of amyloidogenic fibrillation, and even have minimal effect on the initial nucleation events of self-assembly. However, they do trigger changes in networks at a higher hierarchical level, namely enhanced 2D packaging which is rationalized by the 3D hierarchy of β-sheet assembly, leading to variations in fibril morphology, structural composition and, remarkably, nanomechanical properties. These results pave the way to a better understanding of the role of molecular interactions in sculpting the structural and physical properties of protein supramolecular constructs.

The pursuit of stability in halide perovskites: the monovalent cation and the key for surface and bulk self-healing

We find significant differences between degradation and healing at the surface or in the bulk for each of the different APbBr₃ single crystals (A = CH₃NH₃⁺, methylammonium (MA); HC(NH₂)₂⁺, formamidinium (FA); and cesium, Cs⁺). Using 1- and 2-photon microscopy and photobleaching we conclude that kinetics dominate the surface and thermodynamics the bulk stability. Fluorescence-lifetime imaging microscopy, as well as results from several other methods, relate the (damaged) state of the halide perovskite (HaP) after photobleaching to its modified optical and electronic properties. The A cation type strongly influences both the kinetics and the thermodynamics of recovery and degradation: FA heals best the bulk material with faster self-healing; Cs⁺ protects the surface best, being the least volatile of the A cations and possibly through O-passivation; MA passivates defects via methylamine from photo-dissociation, which binds to Pb²⁺. DFT simulations provide insight into the passivating role of MA, and also indicate the importance of the Br₃^- defect as well as predicts its stability. The occurrence and rate of self-healing are suggested to explain the low effective defect density in the HaPs and through this, their excellent performance. These results rationalize the use of mixed A-cation materials for optimizing both solar cell stability and overall performance of HaP-based devices, and provide a basis for designing new HaP variants.

Surface Pyroelectricity in Cubic SrTiO3

Symmetry-imposed restrictions on the number of available pyroelectric and piezoelectric materials remain a major limitation as 22 out of 32 crystallographic material classes exhibit neither pyroelectricity nor piezoelectricity. Yet, by breaking the lattice symmetry it is possible to circumvent this limitation. Here, using a unique technique for measuring transient currents upon rapid heating, direct experimental evidence is provided that despite the fact that bulk SrTiO₃ is not pyroelectric, the (100) surface of TiO₂ -terminated SrTiO₃ is intrinsically pyroelectric at room temperature. The pyroelectric layer is found to be ≈1 nm thick and, surprisingly, its polarization is comparable with that of strongly polar materials such as BaTiO₃ . The pyroelectric effect can be tuned ON/OFF by the formation or removal of a nanometric SiO₂ layer. Using density functional theory, the pyroelectricity is found to be a result of polar surface relaxation, which can be suppressed by varying the lattice symmetry breaking using a SiO₂ capping layer. The observation of pyroelectricity emerging at the SrTiO₃ surface also implies that it is intrinsically piezoelectric. These findings may pave the way for observing and tailoring piezo- and pyroelectricity in any material through appropriate breaking of symmetry at surfaces and artificial nanostructures such as heterointerfaces and superlattices.

Trapped Aqueous Films Lubricate Highly Hydrophobic Surfaces

Friction at hydrophobic surfaces in aqueous media is ubiquitous ( e.g., prosthetic implants, contact lenses, microfluidic devices, biological tissue) but is not well understood. Here, we measure directly, using a surface force balance, both normal stresses and sliding friction in an aqueous environment between a hydrophilic surface (single-crystal mica) and the stable, molecularly smooth, highly hydrophobic surface of a spin-cast fluoropolymer film. Normal force versus surface separation profiles indicate a high negative charge density at the water-immersed fluoropolymer surface, consistent with previous studies. Sliding of the compressed surfaces under water or in physiological-level salt solution (0.1 M NaCl) reveals strikingly low boundary friction (friction coefficient μ ≈ 0.003-0.009) up to contact pressures of at least 50 atm. This is attributed largely to hydrated counterions (protons and Na⁺ ions) trapped in thin interfacial films between the compressed, sliding surfaces. Our results reveal how frictional dissipation may occur at hydrophobic surfaces in water and how modification of such surfaces may suppress this dissipation.