On the Protein Fibrillation Pathway: Oligomer Intermediates Detection Using ATR-FTIR Spectroscopy

Oligomeric intermediates on the pathway of amyloid fibrillation are suspected as the main cytotoxins responsible for amyloid-related pathogenicity. As they appear to be a part of the lag phase of amyloid fibrillation when analyzed using standard methods such as Thioflavin T (ThT) fluorescence, a more sensitive method is needed for their detection. Here we apply Fourier transform infrared spectroscopy (FTIR) in attenuated total reflectance (ATR) mode for fast and cheap analysis of destabilized hen-egg-white lysozyme solution and detection of oligomer intermediates of amyloid fibrillation. Standard methods of protein aggregation analysis— Thioflavin T (ThT) fluorescence, atomic force microscopy (AFM), and 8-anilinonaphthalene-1-sulphonic acid (ANS) fluorescence were applied and compared to FTIR spectroscopy data. Results show the great potential of FTIR for both, qualitative and quantitative monitoring of oligomer formation based on the secondary structure changes. While oligomer intermediates do not induce significant changes in ThT fluorescence, their secondary structure changes were very prominent. Normalization of specific Amide I region peak intensities by using Amide II peak intensity as an internal standard provides an opportunity to use FTIR spectroscopy for both qualitative and quantitative analysis of biological samples and detection of potentially toxic oligomers, as well as for screening of efficiency of fibrillation procedures.     

Pathway Dependence of the Formation and Development of Prefibrillar Aggregates in Insulin B Chain

Amyloid fibrils have been an important subject as they are involved in the development of many amyloidoses and neurodegenerative diseases. The formation of amyloid fibrils is typically initiated by nucleation, whereas its exact mechanisms are largely unknown. With this situation, we have previously identified prefibrillar aggregates in the formation of insulin B chain amyloid fibrils, which have provided an insight into the mechanisms of protein assembly involved in nucleation. Here, we have investigated the formation of insulin B chain amyloid fibrils under different pH conditions to better understand amyloid nucleation mediated by prefibrillar aggregates. The B chain showed strong propensity to form amyloid fibrils over a wide pH range, and prefibrillar aggregates were formed under all examined conditions. In particular, different structures of amyloid fibrils were found at pH 5.2 and pH 8.7, making it possible to compare different pathways. Detailed investigations at pH 5.2 in comparison with those at pH 8.7 have suggested that the evolution of protofibril-like aggregates is a common mechanism. In addition, different processes of evolution of the prefibrillar aggregates have also been identified, suggesting that the nucleation processes diversify depending on the polymorphism of amyloid fibrils.     

A Competition of Secondary and Primary Nucleation Controls Amyloid Fibril Formation of the Parathyroid Hormone

Functional amyloids belong to an increasing class of non-toxic biologic material, in contrast to the prominent disease-related amyloids. Herein, this work reports on the fibril formation of the parathyroid hormone PTH₈₄ as a representative candidate following the same generic principles of primary and secondary nucleation. Employing Thioflavin T monitored kinetics analyses and negative-staining transmission electron microscopy, an intricate, concentration dependent behavior of time dependent generation and morphologies of PTH₈₄ fibrils are found. While at low peptide concentrations, fibril formation is driven by surface catalyzed secondary nucleation, an increased amount of peptides cause a negative feedback on fibril elongation and secondary nucleation. Moreover, the source of primary nuclei is found to regulate the overall macroscopic fibrillation. As a consequence, the concentration dependent competition of primary versus secondary nucleation pathways is found to dominate the mechanism of fibril generation. This work is able to hypothesize an underlying monomer-oligomer equilibrium providing high-order species for primary nucleation and, additionally, negatively affecting the available monomer pool.     

Dual binding modes of Congo red to amyloid protofibril surface observed in molecular dynamics simulations

Congo red has been used to identify amyloid fibrils in tissues for more than 80 years and is also a weak inhibitor to both amyloid-beta fibril formation and toxicity. However, the specificity of the binding and its inhibition mechanism remain unclear. Using all-atom molecular dynamics simulations with the explicit solvent model, we have identified and characterized two specific binding modes of Congo red molecules to a protofibril formed by an amyloidogenic fragment (GNNQQNY) of the yeast prion protein Sup35. The observation of dual-mode was consistent with the experimentally observed dual-mode binding to Abeta fibrils by a series of compounds similar to Congo red. In the primary mode, Congo red bound to a regular groove formed by the first three residues (GNN) of the beta-strands along the beta-sheet extension direction. Comparative simulations demonstrated that Thioflavin T also bound to the grooves on KLVFFAE protofibril surface. Because of the ubiquitous long grooves on the amyloid fibril surface, we propose that this binding interaction could be a general recognition mode of amyloid fibrils by Congo red, Thioflavin T, and other long flat molecules. In the secondary mode, Congo red bound parallel to the beta-strands on the edge or in the middle of a beta-sheet. The primary binding mode of Congo red and GNNQQNY protofibril was more stable than the secondary mode by -5.7 kcal/mol as estimated by the MM-GBSA method. Detailed analysis suggests that the hydrophobic interactions play important roles for burial of the hydrophobic part of the Congo red molecules. Two potential inhibition mechanisms of disrupting beta-sheet stacking were inferred from the primary mode, which could be exploited for the development of non-peptidic amyloid-specific inhibitors.     

A designed protein interface that blocks fibril formation

Protein fibril formation is implicated in many diseases, and therefore much effort has been focused toward the development of inhibitors of this process. In a previous project, a monomeric protein was computationally engineered to bind itself and form a heterodimer complex following interfacial redesign. One of the protein monomers, termed monomer-B, was unintentionally destabilized and shown to form macroscopic fibrils. Interestingly, in the presence of the designed binding partner, fibril formation was blocked. Here we describe the complete characterization of the amyloid properties of monomer-B and the inhibition of fiber formation by the designed binding partner, monomer-A. Both proteins are mutants of the betal domain of streptococcal protein-G. The free monomer-B protein forms amyloid-type fibrils, as determined by transmission electron microscopy and the change in fluorescence of Thioflavin T, an amyloid-specific dye. Fibril formation kinetics are influenced by pH, protein concentration, and seeding with preformed fibrils. Under all conditions tested, monomer-A was able to inhibit the formation of monomer-B fibrils. This inhibition is specific to the engineered interaction, as incubation of monomer-B with wild-type protein-G (a structural homologue) did not result in inhibition under the same conditions. Thus, this de novo-designed heterodimeric complex is an excellent model system for the study of protein-based fibril formation and inhibition. This system provides additional insight into the development of pharmaceuticals for amyloid disorders, as well as the potential use of amyloid fibrils for self-assembling nanostructures.     

Hydrogen exchange mass spectrometry as an analytical tool for the analysis of amyloid fibrillogenesis

In this study, we have used glucagon as a model system for analyzing amyloid fibrillogenesis by hydrogen exchange MALDI mass spectrometry (HXMS). The hydrogen exchange mass spectrometry data correlated well with the traditional method based on Thioflavin T fluorescence and provided quantitative information by measuring the fibrillating molecules directly. The hydrogen exchange mass spectrometry data collected during fibrillogenesis revealed that glucagon fibrillation was a two component system showing an on/off type of interaction where only monomeric and fibrils were present without any substantial amount of intermediate species. This was evident by the extensive deuteration of the monomer and protection of the entire 29 residue glucagon peptide upon fibrillation.. The method complements the traditional procedures and has the potential to provide new information with respect to the nature of transient species, the structure of the growing fibrils and the mechanism of formation.     

Monitoring and inhibition of insulin fibrillation by a small organic fluorogen with aggregation-induced emission characteristics

Amyloid fibrillation of proteins is associated with a great variety of pathologic conditions. Development of new molecules that can monitor amyloidosis kinetics and inhibit fibril formation is of great diagnostic and therapeutic value. In this work, we have developed a biocompatible molecule that functions as an ex situ monitor and an in situ inhibitor for protein fibrillation, using insulin as a model protein. 1,2-Bis[4-(3-sulfonatopropoxyl)phenyl]-1,2-diphenylethene salt (BSPOTPE) is nonemissive when it is dissolved with native insulin in an incubation buffer but starts to fluoresce when it is mixed with preformed insulin fibril, enabling ex situ monitoring of amyloidogenesis kinetics and high-contrast fluorescence imaging of protein fibrils. Premixing BSPOTPE with insulin, on the other hand, inhibits the nucleation process and impedes the protofibril formation. Increasing the dose of BSPOTPE boosts its inhibitory potency. Theoretical modeling using molecular dynamics simulations and docking reveals that BSPOTPE is prone to binding to partially unfolded insulin through hydrophobic interaction of the phenyl rings of BSPOTPE with the exposed hydrophobic residues of insulin. Such binding is assumed to have stabilized the partially unfolded insulin and obstructed the formation of the critical oligomeric species in the protein fibrillogenesis process.     

硫黄素T对淀粉样β-蛋白质40聚集成核动力学的双重影响

荧光染料硫黄素T常用于淀粉样纤维聚集过程的定性定量检测。虽然有研究表明,某些抑制淀粉样蛋白质聚集的小分子抑制剂会与硫黄素T相互作用,影响其测试结果。但硫黄素T如何影响淀粉样蛋白质的聚集成核动力学尚不清晰。本文以淀粉样β-蛋白质40 (Aβ40)为模型,系统研究了硫黄素T对Aβ40聚集成核的影响。研究发现：硫黄素T能够显著改变Aβ40的聚集成核动力学,且影响程度与硫黄素T的浓度密切相关。即在低浓度硫黄素T存在下,Aβ40成核速率的延迟时间先随着硫黄素T浓度的升高而缩短,后随着硫黄素T浓度的升高延迟时间反而延长。但延伸的速率却随硫黄素T浓度的升高而缓慢增大。另外,硫黄素T基本不会影响Aβ40的二级结构和纤维形态。同时,等温滴定微量热实验结果表明,硫黄素T结合Aβ40之间的主要作用力为疏水相互作用。据此,本研究提出硫黄素T对Aβ40聚集成核动力学的双重影响机理。这些结果有助于进一步了解硫黄素T与淀粉样蛋白质的作用特点,为今后硫黄素T在Aβ40聚集成核动力学实验中的使用提供参考。     

Understanding Amyloid‐β Oligomerization at the Molecular Level: The Role of the Fibril Surface

The aggregation of the amyloid β‐peptide into fibrils is a complex process that involves mechanisms such as primary and secondary nucleation, fibril elongation and fibril fragmentation. Some of these processes generate neurotoxic Aβ oligomers, which are involved in the development of Alzheimer's disease. Recent experimental studies have emphasized the role of the fibril as a catalytic surface for the production of highly toxic oligomers during secondary nucleation. By using molecular dynamics simulations, we show that it is the hydrophobic fibril region that causes the structural changes required for catalyzing the formation of β‐sheet‐rich Aβ1‐42 oligomers on the fibril surface. These results reveal, for the first time, the molecular basis of the secondary nucleation pathway.     

Concentration-Dependent Influence of Silver Nanoparticles on Amyloid Fibrillation Kinetics of Hen Egg-White Lysozyme

Understanding the influence of nanoparticles on the formation of protein amyloid fibrillation is crucial to extend their application in related biological diagnosis and nanomedicines. In this work, Raman spectroscopy was used to probe the amyloid fibrillation of hen egg-white lysozyme in the presence of silver nanoparticles (AgNPs) at different concentrations, combined with atomic force microscopy and thioflavin T (ThT) fluorescence assays. Four representative Raman indicators were utilized to monitor transformation of the protein tertiary and secondary structures at the molecular level: the Trp doublet bands at 1340 and 1360 cm^-1, the disulfide stretching vibrational peak at 507 cm^-1, the N-C$\alpha$-C stretching vibration at 933 cm^-1, and the amide Ⅰ band. All experimental results confirmed the concentration-dependent influence of AgNPs on the hen egg-white lysozyme amyloid fibrillation kinetics. In the presence of AgNPs at low concentration (17 μg/mL), electrostatic interaction of the nanoparticles stabilizes disulfide bonds, and protects the Trp residues from exposure to hydrophilic environment, thus leading to formation of amorphous aggregates rather than fibrils. However, with the action of AgNPs at high concentration (1700 μg/mL), the native disulfide bonds of hen egg-white lysozyme are broken to form Ag-S bonds owing to the competition of electrostatic interaction from a great deal of nanoparticles. As for providing functional surfaces for protein to interact with, AgNPs play a bridge role in direct transformation from $\alpha$-helices to organized $\beta$-sheets. The present investigation sheds light on the controversial effects of AgNPs on the kinetics of hen egg-white lysozyme amyloid fibrillation.     

Early detection of insulin fibrillation: a fluorescence lifetime assay to probe the pre-fibrillar regime

Using human insulin, we report for the first time, the evaluation of fluorescence lifetime of an extrinsically added fluorogenic dye, Thioflavin T (ThT), as a more sensitive and convenient method for the assessment of fibrillation in the pre-fibrillar regime.     

基于原子力显微镜研究农药对溶菌酶淀粉样纤维化过程的影响

本文利用原子力显微镜(AFM)在分子水平上研究了三氯杀螨醇、氟氯氰菊酯、三唑酮和西维因四种农药对淀粉样纤维化过程的影响。结果发现,四种农药对溶菌酶淀粉样纤维的形貌特征均没有明显的影响。但是,三氯杀螨醇和氟氯氰菊酯缩短了淀粉样纤维生长的指数生长期,对溶菌酶淀粉样纤维化过程有促进作用,而三唑酮和西维因对纤维化过程没有明显的影响。结合表面等离子体共振技术和荧光光谱技术的分析结果,可以推测三氯杀螨醇和氟氯氰菊酯与溶菌酶结合后,使蛋白质构象发生变化而促进了淀粉样纤维的形成。本文不仅从分子水平上研究农药与淀粉样纤维化过程的关系,还有望为预防淀粉样变性疾病提供理论参考。     

Inhibition of amyloid beta protein fibrillation by polymeric nanoparticles

Copolymeric NiPAM:BAM nanoparticles of varying hydrophobicity were found to retard fibrillation of the Alzheimer's disease-associated amyloid beta protein (Abeta). We found that these nanoparticles affect mainly the nucleation step of Abeta fibrillation. The elongation step is largely unaffected by the particles, and once the Abeta is nucleated, the fibrillation process occurs with the same rate as in the absence of nanoparticles. The extension of the lag phase for fibrillation of Abeta is strongly dependent on both the amount and surface character of the nanoparticles. Surface plasmon resonance studies show that Abeta binds to the nanoparticles and provide rate and equilibrium constants for the interaction. Numerical analysis of the kinetic data for fibrillation suggests that binding of monomeric Abeta and prefibrillar oligomers to the nanoparticles prevents fibrillation. Moreover, we find that fibrillation of Abeta initiated in the absence of nanoparticles can be reversed by addition of nanoparticles up to a particular time point before mature fibrils appear.     

Unraveling the Pressure Effect on Nucleation Processes of Amyloidogenic Proteins

The influence of pressure on the nucleation rate of insulin under fibril‐forming conditions was studied and subsequently analysed using classical nucleation theory. The aim was a better understanding and quantification of the influence of pressure on protein aggregation/fibrillation reactions. The application of pressure has a drastic accelerating effect on the nucleation and growth process of insulin fibrils. We show that this effect arises from a volume decrease upon nucleus formation, due to formation of a less hydrated and more compact transition state that can be quantified extending nucleation theory by a pressure–volume term. Conversely, the absolute values of the lag time and the critical size of the nucleus cannot be satisfactorily described by the classical nucleation theory, which might be due to the presence of secondary effects, such as parallel aggregation pathways or fragmentation processes.     

Microfluidic self-assembly of insulin monomers into amyloid fibrils on a solid surface

We report the self-assembly of insulin monomers into amyloid fibrils within microchannels. To demonstrate the microfluidic amyloid formation and fibril growth on a solid surface, we seeded the internal surfaces of the microchannels with insulin monomers via N-hydroxysuccinimide ester activation and continuously flushed a fresh insulin solution through the microchannels. According to our analysis using optical and fluorescence microscopy, insulin amyloid preferentially formed in the center of the microchannels and, after reaching a certain density, spread to the side walls of the microchannels. By using ex situ atomic force microscopy, we observed the growth of amyloid fibrils inside the microchannels, which occurred at a much higher rate than that in bulk systems. After 12 h of incubation, insulin formed amyloid spherulites having "Maltese cross" extinction patterns within the microchannels according to the polarized microscopic analysis. Microfluidic amyloid formation enabled low consumption of reagents, reduction of incubation time, and simultaneous observation of amyloid formation under different conditions. This work will contribute to the rapid analysis of amyloid formation associated with many protein misfolding diseases.     

Lag phase alteration in the modified bovine serum albumin under the inducing and inhibitory effect of vitamin C

Lag phase as the initial stage of protein aggregation has an important role in fibril formation and contributes to pathogenesis of many human diseases. Harsh environments provided by some additives can change the rate and the amounts of protein abnormalities. Here we studied the lag phase as the first stage of fibrillation process of bovine serum albumin (BSA) and determined the effects of potassium sorbate (PS) a widespread industrial preservative and vitamin C as an important antioxidant on these changes. Thioflavin T binding assay, circular dichroism, intrinsic and extrinsic fluorescence spectroscopy, and atomic force microscopy techniques were used for these assessments. Our results indicated that the lag phase of BSA fibrillation was affected under different conditions. The length of lag phase in BSA protein aggregation process was short due to the generation of the advanced glycation end products (AGEs) by PS. In contrast, vitamin C by its antioxidant properties and chaperone ability dramatically prolonged BSA lag phase, preserved BSA structural changes that lead to aggregation, and dramatically decreased formation of AGEs and the amount of fibrillation.     

Inhibition of Amyloid Fibril Growth and Dissolution of Amyloid Fibrils by Curcumin–Gold Nanoparticles

Inhibition of amyloid fibrillation and clearance of amyloid fibrils/plaques are essential for the prevention and treatment of various neurodegenerative disorders involving protein aggregation. Herein, we report curcumin‐functionalized gold nanoparticles (Au‐curcumin) of hydrodynamic diameter 10–25 nm, which serve to inhibit amyloid fibrillation and disintegrate/dissolve amyloid fibrils. In nanoparticle form, curcumin is water‐soluble and can efficiently interact with amyloid protein/peptide, offering enhanced performance in inhibiting amyloid fibrillation and dissolving amyloid fibrils. Our results imply that nanoparticle‐based artificial molecular chaperones may offer a promising therapeutic approach to combat neurodegenerative disease.     

Adsorption-induced fibronectin aggregation and fibrillogenesis

Fibronectin (Fn), a high molecular weight glycoprotein, is a central element of extracellular matrix architecture that is involved in several fundamental cell processes. In the context of bone biology, little is known about the influence of the mineral surface on fibronectin supramolecular assembly. We investigate fibronectin morphological properties induced by its adsorption onto a model mineral matrix of hydroxyapatite (HA). Fibronectin adsorption onto HA spontaneously induces its aggregation and fibrillation. In some cases, fibronectin fibrils are even found connected into a dense network that is close to the matrix synthesized by cultured cells. Fibronectin adsorption-induced self-assembly is a time-dependant process that is sensitive to bulk concentration. The N-terminal domain of the protein, known to be implicated in its self-association, does not significantly inhibit the protein self-assembly while increasing ionic strength in the bulk alters both aggregation and fibrillation. The addition of a non-ionic surfactant during adsorption tends to promote aggregation with respect to fibrillation. Ultimately, fibronectin fibrils appear to be partially structured like amyloid fibrils as shown by thioflavine T staining. Taken together, our results suggest that there might be more than one single organization route involved in fibronectin self-assembly onto hydroxyapatite. The underlying mechanisms are discussed with respect to Fn conformation, Fn/surface and Fn/Fn interactions, and a model of fibronectin fibrillogenesis onto hydroxyapatite is proposed.     

Influence of protein hydrolysis on the growth kinetics of β-lg fibrils

Recently it was found that protein hydrolysis is an important step in the formation of β-lactoglobulin fibrils at pH 2 and elevated temperatures. The objective of the present study was to further investigate the influence of hydrolysis on the kinetics of fibril formation. Both the hydrolysis of β-lactoglobulin and the growth of the fibrils were followed as a function of time and temperature, using SDS polyacrylamide gel electrophoresis and a Thioflavin T fluorescence assay. As an essential extension to existing models, the quantification of the effect of the hydrolysis on the fibrillar growth was established by a simple polymerization model including a hydrolysis step.     

Towards Ratiometric Sensing of Amyloid Fibrils In Vitro

The aggregation of amyloid‐β peptide and its accumulation in the human brain has an important role in the etiology of Alzheimer’s disease. Thioflavin T has been widely used as a fluorescent marker for these amyloid aggregates. Nevertheless, its complex photophysical behavior, with strong wavelength dependencies of all its fluorescence properties, requires searching for new fluorescent probes. The use of 2‐(2′‐hydroxyphenyl)imidazo[4,5‐b]pyridine (HPIP), which shows two emission bands and a rich excited‐state behavior due to the existence of excited‐state intramolecular processes of proton transfer and charge transfer, is proposed. These properties result in a high sensitivity of HPIP fluorescence to its microenvironment and cause a large differential fluorescence enhancement of the two bands upon binding to aggregates of the amyloid‐β peptide. Based on this behavior, a very sensitive ratiometric method is established for the detection and quantification of amyloid fibrils, which can be combined with the monitoring of fluorescence anisotropy. The binding selectivity of HPIP is discussed on the basis of the apparent binding equilibrium constants of this probe to amyloid‐β (1–42) fibrils and to the nonfibrillar protein bovine serum albumin. Finally, an exhaustive comparison between HPIP and thioflavin T is presented to discuss the sensitivity and specificity of these probes to amyloid aggregates and the significant advantages of the HPIP dye for quantitative determinations.