First Vesicular Self-Assembly of an Apocarotenoid Bixin in Aqueous Liquids and Its Antibacterial Activity

Bixin 1 is the major constituent of the reddish carotenoids present in the seed-coat of Bixa orellana. The use of the extract of the seed-coat of Bixa orellana in food, cosmetics and garments is well known. The nano-sized long 24 C chain molecule has nine conjugated double bonds having extended conjugation with the '-COOH' and '-COOMe' groups present at the two ends of the molecule. Herein, we report the first self-assembly of bixin in several aqueous liquids. The molecule undergoes spontaneous self-assembly in several liquids yielding vesicular self-assembly. Characterizations of the self-assemblies of bixin were carried out by various microscopic techniques, X-ray diffraction and FTIR studies. The critical vesicular concentrations (CVCs) of the compound carried out in DMSO-water in three different solvent ratios as 2: 1 (v/v), 1: 1 (v/v) and 1: 4 (v/v) were determined to be 100 μM, 90 μM and 60 μM respectively indicating lower CVC values at higher proportion of water. Utilization of the vesicular self-assemblies of bixin have been demonstrated in the entrapment and release of fluorophores including the anticancer drugs doxorubicin and curcumin. Self-assembled bixin and curcumin loaded self-assembled bixin showed significant antibacterial activity with both Gram positive as well as Gram negative bacteria.

Amyloid Fibril Formation on Neuronal Cells in the Coexistence of Aβ40 and Aβ42

The abnormal aggregation and subsequent deposition of amyloid β-protein (Aβ) in the brain are considered central to the pathogenesis of Alzheimer's disease. The two major species of Aβ are Aβ40 and Aβ42, present at an approximate ratio of 9 : 1. Accumulating evidence suggests that neuronal membranes are an important platform of amyloidogenesis by Aβ. However, information on the aggregational behaviors of coexistent Aβ40 and Aβ42 on membranes is lacking. In this study, the aggregation and resultant cytotoxicity of coexistent Aβ40 and Aβ42 at a physiologically relevant ratio were investigated by fluorescence techniques. We found that the degree of coexistence of both Aβs in aggregates increased as the assembly proceeded, and reached a maximum in fibrils. Cross-seeding experiments supported the hypothesis that Aβ40 and Aβ42 interact with each other in the fibrillar states when formed on membranes. However, the cytotoxicity of the mixed fibrils was weaker than that of Aβ42 fibrils, suggesting the possibility that Aβ40 attenuates the toxicity of Aβ42 by forming mixed fibrils. In contrast, the degree of coexistence was significantly lower in aqueous phase aggregation, highlighting different aggregation mechanisms between in membranes and in the aqueous phase.

Protocol for quantifying LC3B FRET biosensor activity in living cells using a broad-to-sensitive data analysis pipeline

Here, we present a protocol to comprehensively quantify autophagy initiation using the readout of the microtubule associated protein 1 light chain 3 beta (LC3B) Förster's resonance energy transfer (FRET) biosensor. We describe steps for cell seeding, transfection, FRET/FLIM (fluorescence lifetime imaging microscopy) imaging, and image analysis. This protocol can be useful in any physiology- or disease-related paradigm where the LC3B biosensor can be expressed to determine whether autophagy has been initiated or is stalled. The analysis pipeline presented here can be applied to any other genetically encoded FRET sensor imaged using FRET/FLIM. For complete details on the use and execution of this protocol, please refer to Gökerküçük et al.1.

Modulation of Heterotypic and Homotypic Interactions to Visualize the Evolution of Organic Aggregates in a Fluorescence Turn-on Manner

The abnormal evolution of membrane-less organelles into amyloid fibrils is a causative factor in many neurodegenerative diseases. Fundamental research on evolving organic aggregates is thus instructive for understanding the root causes of these diseases. In-situ monitoring of evolving molecular aggregates with built-in fluorescence properties is a reliable approach to reflect their subtle structural variation. To increase the sensitivity of real-time monitoring, we presented organic aggregates assembled by TPAN-2MeO, which is a triphenyl acrylonitrile derivative. TPAN-2MeO showed a morphological evolution with distinct turn-on emission. Upon rapid nanoaggregation, it formed non-emissive spherical aggregates in the kinetically metastable state. Experimental and simulation results revealed that the weak homotypic interactions between the TPAN-2MeO molecules liberated their molecular motion for efficient non-radiative decay, and the strong heterotypic interactions between TPAN-2MeO and water stabilized the molecular geometry favorable for the non-fluorescent state. After ultrasonication, the decreased heterotypic interactions and increased homotypic interactions acted synergistically to allow access to the emissive thermodynamic equilibrium state with a decent photoluminescence quantum yield (PLQY). The spherical aggregates were eventually transformed into micrometer-sized blocklike particles. Under mechanical stirring, the co-assembly of TPAN-2MeO and Pluronic F-127 formed uniform fluorescent platelets, inducing a significant enhancement in PLQY. These results decipher the stimuli-triggered structural variation of organic aggregates with concurrent sensitive fluorescence response and pave the way for a deep understanding of the evolutionary events of biogenic aggregates.

Synthesis of Fluorescent Cyclic Peptides via Gold(I)-Catalyzed Macrocyclization

Rapid and efficient cyclization methods that form structurally novel peptidic macrocycles are of high importance for medicinal chemistry. Herein, we report the first gold(I)-catalyzed macrocyclization of peptide-EBXs (ethynylbenziodoxolones) via C2-Trp C-H activation. This reaction was carried out in the presence of protecting group free peptide sequences and is enabled by a simple commercial gold catalyst (AuCl·Me2S). The method displayed a rapid reaction rate (within 10 min), wide functional group tolerance (27 unprotected peptides were cyclized), and up to 86% isolated yield. The obtained highly conjugated cyclic peptide linker, formed through C-H alkynylation, can be directly applied to live-cell imaging as a fluorescent probe without further attachment of fluorophores.

Inherent Adaptivity of Alzheimer Peptides to Crowded Environments

Amyloid β (Aβ) is the major constituent in senile plaques of Alzheimer's disease in which peptides initially undergo structural conversions to form elongated fibrils. The impact of crowding on the fibrillation pathways of Aβ40 and Aβ42 , the most common peptide isoforms are studied. PEG and Ficoll are used as model crowders to mimic a macromolecular enriched surrounding. The fibrillar growth is monitored with the help of ThT-fluorescence assays in order to extract two rates describing primary and secondary processes of nucleation and growth. Techniques as fluorescence correlation spectroscopy and analytical ultracentrifugation are used to discuss oligomeric states; fibril morphologies are investigated using negative-staining transmission electron microscopy. While excluded volume effects imposed by macromolecular crowding are expected to always increase rates of intermolecular interactions and structural conversion, a vast variety of effects are found depending on the peptide, the crowder, or ionic strength of the solution. While investigations of the obtained rates with respect to a reactant-occluded model are capable to display specific surface interactions with the crowder, the employment of crystallization-like models reveal the crowder-induced entropic gain withΔ Δ G fib crow = - 116 ± 21 k $\Delta \Delta G_{\text{fib}}^{\text{crow}}=-116\pm 21\; k$ J mol-1 per volume fraction of the crowder.

Early Aggregation of Amyloid-β(1-42) Studied by Fluorescence Correlation Spectroscopy

Alzheimer's disease (AD) is a progressive neurodegenerative disease affecting cognitive and memory abilities and is believed to be linked to the formation and accumulation of neurotoxic aggregates of the Amyloid-β peptide (Aβ). In particular, it is the formation of soluble pre-fibrillar oligomers within the early stage of Aβ aggregation which is thought to represent a key step in the development of AD, thus underlining the interest in characterizing the aggregation process and the nature of these aggregates. In this context, fluorescence correlation spectroscopy (FCS) has emerged as a valuable alternative for the study of these systems in solution. Indeed, the use of FCS to study terminally labelled Aβ provides a means to detect changes in the size and concentration of initially monomeric Aβ samples by monitoring these fluorescently labelled species freely diffusing in solution with single-molecule resolution. Herein, we show how to employ FCS to study the early aggregation process of Aβ(1-42) and how this can be used to estimate the critical concentration for oligomer formation and to characterize the aggregates formed.

Optical Nanosensor for Intracellular and Intracranial Detection of Amyloid-Beta

Amyloid-beta (Aβ) deposition occurs in the early stages of Alzheimer's disease (AD), but the early detection of Aβ is a persistent challenge. Herein, we engineered a near-infrared optical nanosensor capable of detecting Aβ intracellularly in live cells and intracranially in vivo. The sensor is composed of single-walled carbon nanotubes functionalized with Aβ wherein Aβ-Aβ interactions drive the response. We found that the Aβ nanosensors selectively responded to Aβ via solvatochromic modulation of the near-infrared emission of the nanotube. The sensor tracked Aβ accumulation in live cells and, upon intracranial administration in a genetic model of AD, signaled distinct responses in aged mice. This technology enables the interrogation of molecular mechanisms underlying Aβ neurotoxicity in the development of AD in living systems.

Multifunctional fluorescent probe for effective visualization, inhibition, and detoxification of β-amyloid aggregation via covalent binding

A multifunctional reactive fluorescent probe DTB was constructed for biosensing, aggregation inhibition, and toxicity alleviation of β-amyloid. The synergistic effect of hydrophobic interaction and covalent interaction makes DTB have more stable binding and better selectivity to Aβ. The detoxification effect of DTB on Aβ aggregates was also verified in live nerve cells and microglia cells. Furthermore, DTB exhibits an excellent staining of Aβ plaques.

Direct evaluation of self-quenching behavior of fluorophores at high concentrations using an evanescent field

The quantum yield of a fluorophore is reduced when two or more identical fluorophores are in close proximity to each other. The study of protein folding or particle aggregation is can be done based on this above-mentioned phenomenon—called self-quenching. However, it is challenging to characterize the self-quenching of a fluorophore at high concentrations because of the inner filter effect, which involves depletion of excitation light and re-absorption of emission light. Herein, a novel method to directly evaluate the self-quenching behavior of fluorophores was developed. The evanescent field from an objective-type total internal reflection fluorescence (TIRF) microscope was used to reduce the path length of the excitation and emission light to ~100 nm, thereby supressing the inner filter effect. Fluorescence intensities of sulforhodamine B, fluorescein isothiocyanate (FITC), and calcein solutions with concentrations ranging from 1 μM to 50 mM were directly measured to evaluate the concentration required for 1000-fold degree of self-quenching and to examine the different mechanisms through which the fluorophores undergo self-quenching.

Tracking Internal and Global Diffusive Dynamics During Protein Aggregation by High-Resolution Neutron Spectroscopy

Proteins can misfold and form either amorphous or organized aggregates with different morphologies and features. Aggregates of amyloid nature are pathological hallmarks in so-called protein conformational diseases, including Alzheimer's and Parkinson's. Evidence prevails that the transient early phases of the reaction determine the aggregate morphology and toxicity. As a consequence, real-time monitoring of protein aggregation is of utmost importance. Here, we employed time-resolved neutron backscattering spectroscopy to follow center-of-mass self-diffusion and nano- to picosecond internal dynamics of lysozyme during aggregation into a specific β-sheet rich superstructure, called particulates, formed at the isoelectric point of the protein. Particulate formation is found to be a one-step process, and protein internal dynamics, to remain unchanged during the entire aggregation process. The time-resolved neutron backscattering spectroscopy approach developed here, in combination with standard kinetics assays, provides a unifying framework in which dynamics and conformational transitions can be related to the different aggregation pathways.

Amyloid-β oligomerization monitored by single-molecule stepwise photobleaching

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Method enables investigation of amyloid-β oligomer stoichiometry without requiring extrinsic fluorescent probes.

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Uses single-molecule stepwise photobleaching in vitro.

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Unveils heterogeneity within populations of oligomers.

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Assays oligomer-induced dysregulation of intracellular Ca²⁺ homeostasis in living cells.

A major hallmark of Alzheimer’s disease is the misfolding and aggregation of the amyloid- β peptide (Aβ). While early research pointed towards large fibrillar- and plaque-like aggregates as being the most toxic species, recent evidence now implicates small soluble Aβ oligomers as being orders of magnitude more harmful. Techniques capable of characterizing oligomer stoichiometry and assembly are thus critical for a deeper understanding of the earliest stages of neurodegeneration and for rationally testing next-generation oligomer inhibitors. While the fluorescence response of extrinsic fluorescent probes such as Thioflavin-T have become workhorse tools for characterizing large Aβ aggregates in solution, it is widely accepted that these methods suffer from many important drawbacks, including an insensitivity to oligomeric species. Here, we integrate several biophysics techniques to gain new insight into oligomer formation at the single-molecule level. We showcase single-molecule stepwise photobleaching of fluorescent dye molecules as a powerful method to bypass many of the traditional limitations, and provide a step-by-step guide to implementing the technique in vitro. By collecting fluorescence emission from single Aβ(1–42) peptides labelled at the N-terminal position with HiLyte Fluor 555 via wide-field total internal reflection fluorescence (TIRF) imaging, we demonstrate how to characterize the number of peptides per single immobile oligomer and reveal heterogeneity within sample populations. Importantly, fluorescence emerging from Aβ oligomers cannot be easily investigated using diffraction-limited optical microscopy tools. To assay oligomer activity, we also demonstrate the implementation of another biophysical method involving the ratiometric imaging of Fura-2-AM loaded cells which quantifies the rate of oligomer-induced dysregulation of intracellular Ca²⁺ homeostasis. We anticipate that the integrated single-molecule biophysics approaches highlighted here will develop further and in principle may be extended to the investigation of other protein aggregation systems under controlled experimental conditions.

Amyloid-β Peptide-Lipid Bilayer Interaction Investigated by Supercritical Angle Fluorescence

The understanding of the interaction between the membrane of neurons and amyloid-β peptides is of crucial importance to shed light on the mechanism of toxicity in Alzheimer's disease. This paper describes how supercritical angle fluorescence spectroscopy was applied to monitor in real-time the interaction between a supported lipid bilayer (SLB) and the peptide. Different forms of amyloid-β (40 and 42 amino acids composition) were tested, and the interfacial fluorescence was measured to get information about the lipid integrity and mobility. The results show a concentration-dependent damaging process of the lipid bilayer. Prolonged interaction with the peptide up to 48 h lead to an extraction and clustering of lipid molecules from the surface and a potential disruption of the bilayer, correlated with the formation of peptide aggregates. The natural diffusion of the lipid was slightly hindered by the interaction with amyloid-β(1-42) and closely related to the oligomerization of the peptide. The adsorption and desorption of Amyloid-β was also characterized in terms of affinity. Amyloid-β(1-42) exhibited a slightly higher affinity than amyloid-β(1-40). The former was also more prone to aggregate and to adsorb on the bilayer as oligomer.

Silver Nanoparticle Surface Enabled Self-Assembly of Organic Dye Molecules

Fluorescence titration of methylene blue, rhodamine B and rhodamine 6G (R6G) by silver nanoparticle (AgNP) all resulted in an initial steep quenching curve followed with a sharp turn and a much flatter quenching curve. At the turn, there are about 200,000 dye molecules per a single AgNP, signifying self-assembly of approximately 36-layers of dye molecules on the surface of the AgNP to form a micelle-like structure. These fluorescence-quenching curves fit to a mathematical model with an exponential term due to molecular self-assembly on AgNP surface, or we termed it "self-assembly shielding effect", and a Stern-Volmer term (nanoparticle surface enhanced quenching). Such a "super-quenching" by AgNP can only be attributed to "pre-concentration" of the dye molecules on the nanoparticle surface that yields the formation of micelle-like self-assembly, resulting in great fluorescence quenching. Overall, the fluorescence quenching titration reveals three different types of interactions of dye molecules on AgNP surface: 1) self-assembly (methylene blue, rhodamine B and R6G), 2) absorption/tight interaction (tryptamine and fluorescein), and 3) loose interaction (eosin Y). We attribute the formation of micelle-like self-assembly of these three dye molecules on AgNP to their positive charge, possession of nitrogen atoms, and with relatively large and flat aromatic moieties.

Single-Molecule Fluorescence Detection of the Epidermal Growth Factor Receptor in Membrane Discs

The epidermal growth factor receptor (EGFR) is critical to normal cellular signaling pathways. Moreover, it has been implicated in a range of pathologies, including cancer. As a result, it is the primary target of many anticancer drugs. One limitation to the design and development of these drugs has been the lack of molecular-level information about the interactions and conformational dynamics of EGFR. To overcome this limitation, this work reports the construction and characterization of functional, fluorescently labeled, and full-length EGFR in model membrane nanolipoprotein particles (NLPs) for in vitro fluorescence studies. To demonstrate the utility of the system, we investigate ATP-EGFR interactions. We observe that ATP binds at the catalytic site providing a means to measure a range of distances between the catalytic site and the C-terminus via Förster resonance energy transfer (FRET). These ATP-based experiments suggest a range of conformations of the C-terminus that may be a function of the phosphorylation state for EGFR. This work is a proof-of-principle demonstration of single-molecule studies as a noncrystallographic assay for EGFR interactions in real-time and under near-physiological conditions. The diverse nature of EGFR interactions means that new tools at the molecular level have the potential to significantly enhance our understanding of receptor pathology and are of utmost importance for cancer-related drug discovery.

How Fluorescent Tags Modify Oligomer Size Distributions of the Alzheimer Peptide

Within the complex aggregation process of amyloidogenic peptides into fibrils, early stages of aggregation play a central role and reveal fundamental properties of the underlying mechanism of aggregation. In particular, low-molecular-weight aggregates of the Alzheimer amyloid-β peptide (Aβ) have attracted increasing interest because of their role in cytotoxicity and neuronal apoptosis, typical of aggregation-related diseases. One of the main techniques used to characterize oligomeric stages is fluorescence spectroscopy. To this end, Aβ peptide chains are functionalized with fluorescent tags, often covalently bound to the disordered N-terminus region of the peptide, with the assumption that functionalization and presence of the fluorophore will not modify the process of self-assembly nor the final fibrillar structure. In this investigation, we systematically study the effects of four of the most commonly used fluorophores on the aggregation of Aβ (1–40). Time-resolved and single-molecule fluorescence spectroscopy have been chosen to monitor the oligomer populations at different fibrillation times, and transmission electron microscopy, atomic force microscopy and x-ray diffraction to investigate the structure of mature fibrils. Although the structures of the fibrils were only slightly affected by the fluorescent tags, the sizes of the detected oligomeric species varied significantly depending on the chosen fluorophore. In particular, we relate the presence of high-molecular-weight oligomers of Aβ (1–40) (as found for the fluorophores HiLyte 647 and Atto 655) to net-attractive, hydrophobic fluorophore-peptide interactions, which are weak in the case of HiLyte 488 and Atto 488. The latter leads for Aβ (1–40) to low-molecular-weight oligomers only, which is in contrast to Aβ (1–42). The disease-relevant peptide Aβ (1–42) displays high-molecular-weight oligomers even in the absence of significant attractive fluorophore-peptide interactions. Hence, our findings reveal the potentially high impact of the properties of fluorophores on transient aggregates, which needs to be included in the interpretation of experimental data of oligomers of fluorescently labeled peptides.

Cell surface proteoglycan-mediated uptake and accumulation of the Alzheimer's disease peptide Aβ(1-42)

Proteoglycans (PGs) have been found in Alzheimer's disease amyloid-β (Aβ) plaques and their glycosaminoglycan chains reportedly influence Aβ aggregation, neurotoxicity and intracellular accumulation in cell and animal models, but their exact pathophysiological role(s) remain unclear. We have studied the cellular uptake of fluorescently labelled Aβ(1-42) and Aβ(1-40) peptides in normal CHO cells (K1) and the mutant cell line (pgsA-745) which lacks all protein-attached heparan and chondroitin sulfate chains. After 24 h of incubation, CHO-K1 accumulates more Aβ(1-42) and Aβ(1-40) compared with CHO-pgsA-745, consistent with the suggested role of PGs in Aβ uptake. However, after short incubation times (≤3 h) there was no difference; moreover, the time evolution of Aβ(1-42) accumulation in CHO-K1 followed an unusual sigmoidal-like trend, indicating a possible involvement of PG-mediated peptide aggregation in Aβ endocytosis. Neither Aβ(1-42) nor Aβ(1-40) could stimulate uptake of a 10 kDa dextran (a general endocytosis marker) suggesting that Aβ-induced upregulation of endocytosis does not occur. CHO-K1 cells contained a higher number of Aβ(1-42)-positive vesicles, but the intensity difference per vesicle was only marginal suggesting that the superior accumulation of Aβ(1-42) stems from a higher number of endocytic events. FRET imaging support that intracellular Aβ(1-42) is aggregated in both cell types. We also report that CHO-pgsA-745 cells perform less endocytosis than CHO-K1 and, albeit this does not explain their difference in Aβ internalisation, we discuss a general method for data compensation. Altogether, this study contributes new insights into the mechanisms of PG-mediated Aβ uptake that may be relevant for our understanding of their role in AD pathology.

Trace amounts of pyroglutaminated Aβ-(3-42) enhance aggregation of Aβ-(1-42) on neuronal membranes at physiological concentrations: FCS analysis of cell surface

Minor species of amyloid β-peptide (Aβ), such as Aβ-(1-43) and pyroglutaminated Aβ-(3-42) (Aβ-(3pE-42)), have been suggested to be involved in the initiation of the Aβ aggregation process, which is closely associated with the etiology of Alzheimer's disease. They can play important roles in aggregation not only in the aqueous phase but also on neuroral membranes; however, the latter behaviors remain mostly unexplored. Here, initial aggregation processes of Aβ on living cells were monitored at physiological nanomolar concentrations by fluorescence correlation spectroscopy. Membrane-bound Aβ-(1-42) and Aβ-(1-40) formed oligomers composed of ~4 Aβ molecules during 48-h incubation, whereas the peptides remained monomeric in the culture medium, indicating that the membranes facilitated Aβ aggregation. The presence of 5 mol% Aβ-(3pE-42), but not Aβ-(1-43), significantly enhanced the aggregation of Aβ-(1-42) up to ~10-mers. On the other hand, neither trace amounts of Aβ-(1-42) nor Aβ-(3pE-42) enhanced the aggregation of Aβ-(1-40). The observed small Aβ oligomers are expected to act as pathogenic seeds for amyloid fibrils responsible for neurotoxicity. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.

Fluorescence Self-Quenching from Reporter Dyes Informs on the Structural Properties of Amyloid Clusters Formed in Vitro and in Cells

The characterization of the aggregation kinetics of protein amyloids and the structural properties of the ensuing aggregates are vital in the study of the pathogenesis of many neurodegenerative diseases and the discovery of therapeutic targets. In this article, we show that the fluorescence lifetime of synthetic dyes covalently attached to amyloid proteins informs on the structural properties of amyloid clusters formed both in vitro and in cells. We demonstrate that the mechanism behind such a "lifetime sensor" of protein aggregation is based on fluorescence self-quenching and that it offers a good dynamic range to report on various stages of aggregation without significantly perturbing the process under investigation. We show that the sensor informs on the structural density of amyloid clusters in a high-throughput and quantitative manner and in these aspects the sensor outperforms super-resolution imaging techniques. We demonstrate the power and speed of the method, offering capabilities, for example, in therapeutic screenings that monitor biological self-assembly. We investigate the mechanism and advantages of the lifetime sensor in studies of the K18 protein fragment of the Alzheimer's disease related protein tau and its amyloid aggregates formed in vitro. Finally, we demonstrate the sensor in the study of aggregates of polyglutamine protein, a model used in studies related to Huntington's disease, by performing correlative fluorescence lifetime imaging microscopy and structured-illumination microscopy experiments in cells.

Selective inhibition of phosphodiesterases 4, 5 and 9 induces HSP20 phosphorylation and attenuates amyloid beta 1-42-mediated cytotoxicity

Phosphodiesterase (PDE) inhibitors are currently under evaluation as agents that may facilitate the improvement of cognitive impairment associated with Alzheimer's disease. Our aim was to determine whether inhibitors of PDEs 4, 5 and 9 could alleviate the cytotoxic effects of amyloid beta 1–42 (Aβ_1–42) via a mechanism involving the small heatshock protein HSP20. We show that inhibition of PDEs 4, 5 and 9 but not 3 induces the phosphorylation of HSP20 which, in turn, increases the colocalisation between the chaperone and Aβ_1–42 to significantly decrease the toxic effect of the peptide. We conclude that inhibition of PDE9 is most effective to combat Aβ_1–42 cytotoxicity in our cell model.

Morphology-Specific Inhibition of β-Amyloid Aggregates by 17β-Hydroxysteroid Dehydrogenase Type 10

A major hallmark of Alzheimer's disease (AD) is the formation of toxic aggregates of the β-amyloid peptide (Aβ). Given that Aβ peptides are known to localise within mitochondria and interact with 17β-HSD10, a mitochondrial protein expressed at high levels in AD brains, we investigated the inhibitory potential of 17β-HSD10 against Aβ aggregation under a range of physiological conditions. Fluorescence self-quenching (FSQ) of Aβ(1-42) labelled with HiLyte Fluor 555 was used to evaluate the inhibitory effect under conditions established to grow distinct Aβ morphologies. 17β-HSD10 preferentially inhibits the formation of globular and fibrillar-like structures but has no effect on the growth of amorphous plaque-like aggregates at endosomal pH 6. This work provides insights into the dependence of the Aβ-17β-HSD10 interaction with the morphology of Aβ aggregates and how this impacts enzymatic function.

Colorimetric and fluorometric monitoring of the helix composition of collagen-like peptides at the nM level

We have demonstrated that the incorporation of a dye-labeled collagen-like peptide in the homotrimeric versus heterotrimeric context results in visible color changes and distinct fluorescence. The unique fluorescence self-quenching assay can unambiguously determine the helix composition of heterotrimers at the nM level, far extending our capability to characterize a collagen triple helix.

[Physico-chemical methods for studing β-amyloid aggregation]

Alzheimer's disease is the most prevalent neurodegenerative pathology. According to the amyloid cascade hypothesis, a key event of the Alzheimer's disease pathogenesis is a transition of the β-amyloid peptide (Аβ) from the monomeric form to the aggregated state. The mechanism of Аβ aggregation is intensively studied in vitro, by means of synthetic peptides and various physico-chemical methods allowing evaluation of size, molecular structure, and morphology of the formed aggregates. The paper reviews both the well-known and recently introduced physico-chemical methods for analysis of Аβ aggregation, including microscopу, optical and fluorescent methods, method of electron paramagnetic resonance, electrochemical and electrophoretic methods, gel-filtration, and mass spectrometric methods. Merits and drawbacks of the methods are discussed. The unique possibility to simultaneously observe Аβ monomers as well oligomers and large aggregates by means of atomic force microscopy or fluorescence correlation spectroscopy is emphasized. The high detection sensitivity of the latter method, monitoring the aggregation process in Аβ solutions at low peptide concentrations is underlined. Among mass spectrometric methods, the ion mobility mass spectrometry is marked out as a method enabling to obtain information about both the spectrum of Аβ oligomers and their structure. It is pointed out that the use of several methods giving the complementary data about Аβ aggregates is the best experimental approach to studying the process of b-amyloid peptide aggregation in vitro.

Surface plasmon resonance biosensors for simultaneous monitoring of amyloid-beta oligomers and fibrils and screening of select modulators

Oligomeric amyloid-beta (Aβ) peptides are considered as the most toxic species in Alzheimer's disease (AD). Monitoring of the Aβ aggregation profiles is critical for elucidating the oligomer toxicity and may serve as a therapeutic target for AD. By immobilizing the capture antibodies of A11 and OC that are specific to the oligomers and fibrils, respectively, in separate fluidic channels, a novel surface plasmon resonance (SPR) biosensor was designed for monitoring the oligomeric and fibrillar species of Aβ(1-42) simultaneously. The influence of curcumin, Cu(2+) and methylene blue on the amount of toxic oligomers and fibrils was evaluated. The half maximal inhibitory concentration (IC50) of curcumin and methylene blue was determined. The formation of Aβ fibrils was also validated by the thioflavin T (ThT) fluorescence assay. The results demonstrate the utility of SPR as an analytical tool for rapid and comprehensive monitoring of Aβ aggregation and screening of Aβ modulators.

Binding dynamics of a monomeric SSB protein to DNA: a single-molecule multi-process approach

Single-stranded DNA binding proteins (SSBs) are ubiquitous across all organisms and are characterized by the presence of an OB (oligonucleotide/oligosaccharide/oligopeptide) binding motif to recognize single-stranded DNA (ssDNA). Despite their critical role in genome maintenance, our knowledge about SSB function is limited to proteins containing multiple OB-domains and little is known about single OB-folds interacting with ssDNA. Sulfolobus solfataricus SSB (SsoSSB) contains a single OB-fold and being the simplest representative of the SSB-family may serve as a model to understand fundamental aspects of SSB:DNA interactions. Here, we introduce a novel approach based on the competition between Förster resonance energy transfer (FRET), protein-induced fluorescence enhancement (PIFE) and quenching to dissect SsoSSB binding dynamics at single-monomer resolution. We demonstrate that SsoSSB follows a monomer-by-monomer binding mechanism that involves a positive-cooperativity component between adjacent monomers. We found that SsoSSB dynamic behaviour is closer to that of Replication Protein A than to Escherichia coli SSB; a feature that might be inherited from the structural analogies of their DNA-binding domains. We hypothesize that SsoSSB has developed a balance between high-density binding and a highly dynamic interaction with ssDNA to ensure efficient protection of the genome but still allow access to ssDNA during vital cellular processes.

Au nanostructured surfaces for electrochemical and localized surface plasmon resonance-based monitoring of α-synuclein-small molecule interactions

In this proof-of-concept study, the fabrication of novel Au nanostructured indium tin oxide (Au-ITO) surfaces is described for the development of a dual-detection platform with electrochemical and localized surface plasmon resonance (LSPR)-based biosensing capabilities. Nanosphere lithography (NSL) was applied to fabricate Au-ITO surfaces. Oligomers of α-synuclein (αS) were covalently immobilized to determine the electrochemical and LSPR characteristics of the protein. Cyclic voltammetry (CV) and differential pulse voltammetry (DPV) were performed using the redox probe [Fe(CN)6](3-/4-) to detect the binding of Cu(II) ions and (-)-epigallocatechin-3-gallate (EGCG) to αS on the Au-ITO surface. Electrochemical and LSPR data were complemented by Thioflavin-T (ThT) fluorescence, surface plasmon resonance imaging (SPRi), and transmission electron microscopy (TEM) studies. EGCG was shown to induce the formation of amorphous aggregates that decreased the electrochemical signals. However, the binding of EGCG with αS increased the LSPR absorption band with a bathochromic shift of 10-15 nm. The binding of Cu(II) to αS enhanced the DPV peak current intensity. NSL fabricated Au-ITO surfaces provide a promising dual-detection platform to monitor the interaction of small molecules with proteins using electrochemistry and LSPR.

Site-specific dynamics of amyloid formation and fibrillar configuration of Aβ1–23 using an unnatural amino acid

Distinct local dynamics of Aβ_1–23 amyloid formation are characterized using an unnatural amino acid p-cyanophenylalanine as a spectroscopic probe.

Sensing and inhibition of amyloid-β based on the simple luminescent aptamer-ruthenium complex system

Aggregation of amyloid-β (Aβ) peptide has been known to be pathologically associated with Alzheimer and dementia diseases. Amyloid-β fibrils serve as an important target for the drugs development and diagnosis of neurodegenerative diseases. Herein, we report a new [Ru(dmbpy)(dcbpy)dppz)] complex (dmbpy; 4,4'-dimethyl-2,2'-bipyridine, dcbpy; 4,4'-dicorboxy-2,2'-bipyridine, dppz; dipyridophenazine) intercalated aptamer based recognition of amyloid-β. Interestingly, aforementioned Ru(II) complex shows weak luminescence intensity in the aqueous medium but it shows strong luminescence intensity in the presence of RNA aptamer. Upon addition of amyloid-β monomers, the luminescence intensity of Ru(II) complex is reduced due to the strong interaction of aptamer with amyloid-β monomer/small oligomers. Furthermore, present study implies that our system has ability to inhibit the formation of amyloid-β fibrils, which is confirmed from the AFM morphological structures in the absence and presence of aptamer. This work may contribute the rapid diagnosis and inhibition of amyloid-β aggregation in the clinical applications.

The phosphorylation of Hsp20 enhances its association with amyloid-β to increase protection against neuronal cell death

Up-regulation of Hsp20 protein levels in response to amyloid fibril formation is considered a key protective response against the onset of Alzheimer's disease (AD). Indeed, the physical interaction between Hsp20 and Aβ is known to prevent Aβ oligomerisation and protects neuronal cells from Aβ mediated toxicity, however, details of the molecular mechanism and regulatory cell signalling events behind this process have remained elusive. Using both conventional MTT end-point assays and novel real time measurement of cell impedance, we show that Hsp20 protects human neuroblastoma SH-SY5Y cells from the neurotoxic effects of Aβ. In an attempt to provide a mechanism for the neuroprotection afforded by Hsp20, we used peptide array, co-immunoprecipitation analysis and NMR techniques to map the interaction between Hsp20 and Aβ and report a binding mode where Hsp20 binds adjacent to the oligomerisation domain of Aβ, preventing aggregation. The Hsp20/Aβ interaction is enhanced by Hsp20 phosphorylation, which serves to increase association with low molecular weight Aβ species and decrease the effective concentration of Hsp20 required to disrupt the formation of amyloid oligomers. Finally, using a novel fluorescent assay for the real time evaluation of morphology-specific Aβ aggregation, we show that phospho-dependency of this effect is more pronounced for fibrils than for globular Aβ forms and that 25mers corresponding to the Hsp20 N-terminal can be used as Aβ aggregate inhibitors. Our report is the first to provide a molecular model for the Hsp20/Aβ complex and the first to suggest that modulation of the cAMP/cGMP pathways could be a novel route to enhance Hsp20-mediated attenuation of Aβ fibril neurotoxicity.