Environmental conditions affect the kinetics of nucleation of amyloid fibrils and determine their morphology

Host defense amyloids: Biosensors of the immune system?

There is considerable evidence showing that highly ordered aggregate structures known as amyloids carry out essential biological roles in species ranging from bacteria to humans. Indeed, many antimicrobial peptides/proteins form amyloids to carry out their host defense functions and many amyloids are antimicrobial. The similarity of host defense amyloids from bacterial biofilms to the mammalian epididymal amyloid matrix implies highly conserved host defense structures/functions. With an emphasis on the epididymal amyloid matrix, here we review the common properties of host defense amyloids including unique traits that would allow them to function as powerful biosensors of the immune system.

Protein misfolding and amyloid nucleation through liquid-liquid phase separation

Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.

Investigating the binding interaction of quinoline yellow with bovine serum albumin and anti-amyloidogenic behavior of ferulic acid on QY-induced BSA fibrils

Protein aggregation induces profound changes in the structure along with the conformation of the protein, and is responsible for the pathogenesis of a number of neurodegenerative conditions such as Huntington's, Creutzfeldt-Jacob, Type II diabetes mellitus, Alzheimer's, etc. Numerous multi-spectroscopic approaches and in-silico experiments were utilized to investigate BSA's biomolecular interaction and aggregation in the presence of quinoline yellow. The present research investigation evaluated the interaction of BSA with the food colorant (QY) at two different pH (7.4 and 2.0). The development of the BSA-QY complex was established with UV visible and fluorescence spectroscopy. The quenching of fluorescence upon the interaction of BSA with QY revealed the static nature of quenching mechanism. The Kb value obtained from our result is 4. 54 × 10-4 M-1. The results from the competitive site marker study infer that quinoline yellow is binding with the sub-domain IB of bovine serum albumin, specifically on site III. Three-dimensional fluorescence and synchronous fluorescence spectroscopy were applied for monitoring the alterations in the microenvironment of BSA upon the addition of quinoline yellow. The results from turbidity and RLS studies showed that higher concentrations of QY (80-400 µM) triggered bovine serum albumin (BSA) aggregation at pH 2.0. At pH 7.4, QY couldn't manage to trigger bovine serum albumin aggregation, perhaps because of the repulsion between negatively charged dye (QY) and anionic bovine serum albumin. The results from far-UV CD, Congo Red, and scanning electron microscopy implicate that the QY-induced aggregates exhibit amyloid fibril-like structures. Molecular docking results revealed that hydrophobic interactions, hydrogen bonding, and Pi-Sulfur interactions contribute to QY-induced aggregation of BSA. Further, the amyloid inhibitory potential of ferulic acid (FA), a phenolic acid on QY-induced aggregation of BSA, has also been assessed. The QY-induced amyloid fibrils are FA-soluble, as confirmed by turbidity, RLS, and far-UV CD studies. Far-UV CD results showed that FA retains α helix and inhibits cross β sheet formation when the BSA samples were pre-incubated with increasing concentrations of FA (0-500 µM). Our findings conclude that QY dye successfully stimulates BSA aggregation, but ferulic acid inhibits QY-induced aggregation of BSA. Thus, FA can serve as a therapeutic agent and can help in the treatment of various amyloid-related conditions.

A glimpse into the structural properties of α-synuclein oligomers

α-Synuclein (αS) aggregation is the main neurological hallmark of a group of debilitating neurodegenerative disorders, collectively referred to as synucleinopathies, of which Parkinson's disease is the most prevalent. αS oligomers formed during the initial stages of aggregation are considered key pathogenic drivers of disease onset and progression, standing as privileged targets for therapeutic intervention and diagnosis. However, the structure of αS oligomers and the mechanistic basis of oligomer to fibril conversion are yet poorly understood, thereby precluding the rational formulation of strategies aimed at targeting oligomeric species. In this review, we delve into the recent advances in the structural and mechanistic characterization of αS oligomers. We also discuss how these advances are transforming our understanding of these elusive species and paving the way for oligomer-targeting therapeutics and diagnosis.

Pathways of amyloid fibril formation and protein aggregation

The main cause of many neurodegenerative diseases and systemic amyloidoses is protein and peptide aggregation and the formation of amyloid fibrils. The study of aggregation mechanisms, the discovery and description of aggregate structures, and a comprehensive understanding of the molecular mechanisms of amyloid formation are of great importance for the diagnostic processes at the molecular level and for the development of therapeutic strategies to counter aggregation-associated disorders. Given that understanding protein misfolding phenomena is directly related to the protein folding process, we will briefly explain the protein folding mechanism and then discuss the important factors involved in protein aggregation. In the following, we review different mechanisms of amyloid formation and finally represent the current knowledge on how amyloid fibrils are formed based on kinetic and thermodynamic factors.

Stress-mediated aggregation of disease-associated proteins in amyloid bodies

The formation of protein aggregates is a hallmark of many neurodegenerative diseases and systemic amyloidoses. These disorders are associated with the fibrillation of a variety of proteins/peptides, which ultimately leads to cell toxicity and tissue damage. Understanding how amyloid aggregation occurs and developing compounds that impair this process is a major challenge in the health science community. Here, we demonstrate that pathogenic proteins associated with Alzheimer's disease, diabetes, AL/AA amyloidosis, and amyotrophic lateral sclerosis can aggregate within stress-inducible physiological amyloid-based structures, termed amyloid bodies (A-bodies). Using a limited collection of small molecule inhibitors, we found that diclofenac could repress amyloid aggregation of the β-amyloid (1-42) in a cellular setting, despite having no effect in the classic Thioflavin T (ThT) in vitro fibrillation assay. Mapping the mechanism of the diclofenac-mediated repression indicated that dysregulation of cyclooxygenases and the prostaglandin synthesis pathway was potentially responsible for this effect. Together, this work suggests that the A-body machinery may be linked to a subset of pathological amyloidosis, and highlights the utility of this model system in the identification of new small molecules that could treat these debilitating diseases.

Bovine liver catalase turns into three conformational states after exposure to an anionic surfactant

The mechanism by which anionic surfactants promote amyloid fibril is not well understood. Here, we investigated how sodium dodecyl sulfate (SDS), a negatively charged surfactant, affects the fibrillation of the partially unfolded random-coiled bovine liver catalase (BLC) at a pH of 2.0. We used several methods, including turbidity, RLS kinetics, intrinsic fluorescence, ThT fluorescence, far-UV CD, and TEM imaging, to evaluate the conformational changes of BLC in vitro in response to SDS treatment. BLC is a multimeric protein and well folded at physiological pH but forms a random coil structure at pH 2.0. Intrinsic fluorescence and far-UV CD data showed that below 0.1 mM SDS, random coiled BLC turned into a native-like structure. BLC incubated with an SDS concentration ranging from 0.1 to 2.0 mM led to the formation of aggregates. The ThT fluorescence intensity was enhanced in the aggregated BLC samples (0.1-2.0 mM SDS), and cross beta-sheeted structure was detected by the far UV CD measurements. BLC adopts a complete alpha-helical structure upon interacting with SDS at a more than 2.0 mM concentration at pH 2.0. Understanding the mechanism of surfactant- or lipid-induced fibrillation is important for therapeutic purposes.

A Systematic Compilation of Human SH3 Domains: A Versatile Superfamily in Cellular Signaling

SRC homology 3 (SH3) domains are fundamental modules that enable the assembly of protein complexes through physical interactions with a pool of proline-rich/noncanonical motifs from partner proteins. They are widely studied modular building blocks across all five kingdoms of life and viruses, mediating various biological processes. The SH3 domains are also implicated in the development of human diseases, such as cancer, leukemia, osteoporosis, Alzheimer's disease, and various infections. A database search of the human proteome reveals the existence of 298 SH3 domains in 221 SH3 domain-containing proteins (SH3DCPs), ranging from 13 to 720 kilodaltons. A phylogenetic analysis of human SH3DCPs based on their multi-domain architecture seems to be the most practical way to classify them functionally, with regard to various physiological pathways. This review further summarizes the achievements made in the classification of SH3 domain functions, their binding specificity, and their significance for various diseases when exploiting SH3 protein modular interactions as drug targets.

SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges

Inhibiting the aggregation of amyloid peptides with endogenous peptides has broad interest due to their intrinsically high biocompatibility and low immunogenicity. Here, we investigated the inhibition mechanism of the prostatic acidic phosphatase fragment SEVI (semen-derived enhancer of viral infection) against Aβ42 fibrillization using atomistic discrete molecular dynamic simulations. Our result revealed that SEVI was intrinsically disordered with dynamic formation of residual helices. With a high positive net charge, the self-aggregation tendency of SEVI was weak. Aβ42 had a strong aggregation propensity by readily self-assembling into β-sheet-rich aggregates. SEVI preferred to interact with Aβ42, rather than SEVI themselves. In the heteroaggregates, Aβ42 mainly adopted β-sheets buried inside and capped by SEVI in the outer layer. SEVI could bind to various Aβ aggregation species─including monomers, dimers, and proto-fibrils─by capping the exposed β-sheet elongation edges. The aggregation processes Aβ42 from the formation of oligomers to conformational nucleation into fibrils and fibril growth should be inhibited as their β-sheet elongation edges are being occupied by the highly charged SEVI. Overall, our computational study uncovered the molecular mechanism of experimentally observed inhibition of SEVI against Aβ42 aggregation, providing novel insights into the development of therapeutic strategies against Alzheimer's disease.

Investigating the Effects of NaCl on the Formation of AFs from Gluten in Cooked Wheat Noodles

To clarify the effect of NaCl concentration (0-2.0%) on the formation of amyloid fibrils (AFs) in cooked wheat noodles, the morphology, surface hydrophobicity, secondary structure, molecular weight distribution, microstructure, and crystal structure of AFs were investigated in this paper. Fluorescence data and Congo red stain images confirmed the presence of AFs and revealed that the 0.4% NaCl concentration promoted the production of AFs. The surface hydrophobicity results showed that the hydrophobicity of AFs increased significantly from 3942.05 to 6117.57 when the salt concentration increased from 0 to 0.4%, indicating that hydrophobic interactions were critical for the formation of AFs. Size exclusion chromatography combined with gel electrophoresis plots showed that the effect of NaCl on the molecular weight of AFs was small and mainly distributed in the range of 5-7.1 KDa (equivalent to 40-56 amino acid residues). X-ray diffraction and AFM images showed that the 0.4% NaCl concentration promoted the formation and longitudinal growth of AFs, while higher NaCl concentrations inhibited the formation and expansion of AFs. This study contributes to the understanding of the mechanism of AF formation in wheat flour processing and provides new insight into wheat gluten aggregation behavior.

Identifying Biological and Biophysical Features of Different Maturation States of α-Synuclein Amyloid Fibrils

Protein aggregates, hereunder amyloid fibrils, can undergo a maturation process, whereby early formed aggregates undergo a structural and physicochemical transition leading to more mature species. In the case of amyloid-related diseases, such maturation confers distinctive biological properties of the aggregates, which may account for a range of diverse pathological subtypes. Here, we present a protocol for the preparation of α-synuclein amyloid fibrils differing in the level of their maturation. We utilize widely accessible biophysical techniques to characterize the structure and morphology and a simple thermal treatment procedure to test their thermodynamic stability. Their biological properties are probed by means of binding to native plasma membrane sheets originating from mammalian cell lines.

Preparation and Investigation of Crucial Oligomers in the Early Stages of Aβ40 and Aβ42 Aggregation

Amyloid aggregation is a hallmark in many neuropathologies and other diseases of tremendous impact. It is increasingly evident that neuronal death associated with Alzheimer's disease (AD) is mainly produced by oligomers of the amyloid-β (Aβ) peptide. Yet little is known about the detailed structural and biophysical mechanisms of their formation. This lack of complete understanding comes from the labile nature and handling complexity of the oligomers. Consequently, providing reproducible and robust protocols for oligomer preparation is of particular importance.In this study, we describe detailed methods for the preparation and isolation of micellar oligomers of Aβ that evolve towards larger and more stable oligomers enriched in beta-sheet structure and able to acquire a higher capacity to fibrillate. We also describe briefly some biophysical experiments allowing oligomer characterization.

Amyloid adhesin production in activated sludge is enhanced in lab-scale sequencing batch reactors: Feeding regime impacts microbial community and amyloid distribution

Amyloid adhesins are β-sheet-rich extracellular proteins thought to contribute to bioflocculation. They are present in activated sludge to varying extent. However, it remains unclear which operational conditions promote their production. To this end, the abundance and distribution of amyloids and their potential producers were monitored in two lab-scale reactors operated in sequencing batch mode with an unaerated and aerated reaction phase. Various feeding regimes ranging from feast-famine to nearly continuous feeding were applied. Thioflavin T staining revealed more amyloids in the lab-scale reactors during all operational stages compared to the full-scale industrial and municipal inocula. Furthermore, the feeding regime impacted the distribution of produced amyloids from dense clusters during feast-famine conditions towards a dispersed distribution during nearly continuous feeding. This dispersed presence did not negatively impact the bioflocculation (towards average floc size and shear sensitivity). 16S rRNA sequencing detected several known EPS and amyloid producers. More continuous and, hence, partially aerobic feeding promoted the relative abundance of denitrifiers. Sequential Thioflavin T staining and fluorescence in situ hybridization identified Zoogloea and Ca. Competibacter as potential amyloid producers under the applied conditions. This experiment confirms that amyloid producers need to be triggered for production and that the feeding regime impacts the microbial community composition, which in turn influences the amyloid production and distribution.

How important is the N-terminal acetylation of alpha-synuclein for its function and aggregation into amyloids?

N-α-acetylation is a frequently occurring post-translational modification in eukaryotic proteins. It has manifold physiological consequences on the regulation and function of several proteins, with emerging studies suggesting that it is a global regulator of stress responses. For decades, in vitro biochemical investigations into the precise role of the intrinsically disordered protein alpha-synuclein (αS) in the etiology of Parkinson's disease (PD) were performed using non-acetylated αS. The N-terminus of α-synuclein is now unequivocally known to be acetylated in vivo, however, there are many aspects of this post-translational modifications that are not understood well. Is N-α-acetylation of αS a constitutive modification akin to most cellular proteins, or is it spatio-temporally regulated? Is N-α-acetylation of αS relevant to the as yet elusive function of αS? How does the N-α-acetylation of αS influence the aggregation of αS into amyloids? Here, we provide an overview of the current knowledge and discuss prevailing hypotheses on the impact of N-α-acetylation of αS on its conformational, oligomeric, and fibrillar states. The extent to which N-α-acetylation of αS is vital for its function, membrane binding, and aggregation into amyloids is also explored here. We further discuss the overall significance of N-α-acetylation of αS for its functional and pathogenic implications in Lewy body formation and synucleinopathies.

Rapid restructurization of conformationally-distinct alpha-synuclein amyloid fibrils at an elevated temperature

Protein aggregation in the form of amyloid fibrils is linked with the onset and progression of more than 30 amyloidoses, including multiple neurodegenerative disorders, such as Alzheimer's or Parkinson's disease. Despite countless studies and years of research, the process of such aggregate formation is still not fully understood. One peculiar aspect of amyloids is that they appear to be capable of undergoing structural rearrangements even after the fibrils have already formed. Such a phenomenon was reported to occur in the case of alpha-synuclein and amyloid beta aggregates after a long period of incubation. In this work, we examine whether incubation at an elevated temperature can induce the restructurization of four different conformation alpha-synuclein amyloid fibrils. We show that this structural alteration occurs in a relatively brief time period, when the aggregates are incubated at 60 °C. Additionally, it appears that during this process multiple conformationally-distinct alpha-synuclein fibrils all shift towards an identical secondary structure.

Role of salts and solvents on the defibrillation of food dye "sunset yellow" induced hen egg white lysozyme amyloid fibrils

Several food dyes are known to induce amyloid fibrillation when interacting with proteins. Here, we studied the role of sunset yellow (SY) in the amyloid fibrillation of hen egg white lysozyme (HEWL) and characterized the changes using spectroscopy techniques. Turbidity results showed that SY dye induces aggregation in HEWL in concentrations dependent manner. The aggregation induced by SY dye is kinetically very fast, no lag phase was detected, and the kinetics process follows an isodesmic kinetics pathway. The SY-dye induce aggregates have cross-β secondary structure confirmed by far-UV CD measurements. The effect of salts and solvents was also seen on SY-induced aggregates. Turbidity, far-UV CD, and kinetics results suggest that certain concentrations of NaCl and (NH₄)₂SO₄ solubilize the SY-induce amyloid fibrils, but (NH₄)₂SO₄ is more effective. Similarly, solvents are also solubilized the SY-induces HEWL amyloid fibrillation but the order of defibrillation is as follows: Isopropanol> ethanol > methanol which signified that isopropanol is more effective than other solvents. The salts and solvents data suggest that the electrostatic, as well as hydrophobic interaction, is responsible for SY-induced amyloid fibrillation. These conformational changes should be examined, more seriously for the purpose of food safety.

Investigating the Sequence Determinants of the Curling of Amyloid Fibrils Using Ovalbumin as a Case Study

Highly ordered, straight amyloid fibrils readily lend themselves to structure determination techniques and have therefore been extensively characterized. However, the less ordered curly fibrils remain relatively understudied, and the structural organization underlying their specific characteristics remains poorly understood. We found that the exemplary curly fibril-forming protein ovalbumin contains multiple aggregation prone regions (APRs) that form straight fibrils when isolated as peptides or when excised from the full-length protein through hydrolysis. In the context of the intact full-length protein, however, the regions separating the APRs facilitate curly fibril formation. In fact, a meta-analysis of previously reported curly fibril-forming proteins shows that their inter-APRs are significantly longer and more hydrophobic when compared to straight fibril-forming proteins, suggesting that they may cause strain in the amyloid state. Hence, inter-APRs driving curly fibril formation may not only apply to our model protein but rather constitute a more general mechanism.

Ion-Mediated Morphological Diversity in Protein Amyloid Systems

Salt ions are considered among the major determinants ruling protein folding, stability, and self-assembly in the context of amyloid-related diseases, protein drug development, and functional biomaterials. Here, we report that Hofmeister ions not only determine the rate constants of the aggregation reaction for human insulin and hen egg white lysozyme but also control the generation of a plethora of amyloid-like morphologies ranging from the nanoscale to the microscale. We anticipate that the latter is a result of a balance between colloidal and conformational stability combined with an ion-specific effect and highlight the importance of salt ions in controlling the biological functions of protein aggregates.

Design of metalloenzyme mimics based on self-assembled peptides for organophosphorus pesticides detection

Organophosphorus pesticides (OPs) detection has attracted considerable attention because of the extensive application of OPs. In this research, non-toxic and high-performance metalloenzyme mimics of Zn²⁺-bonding peptides were developed by obtaining inspiration from phosphotriesterase (PTE) and nanofiber formation. Furthermore, based on the electrochemical activity of p-nitrophenol (PNP), the electrochemical sensor of metalloenzyme mimics was developed. By examining the effect of the active sites of peptides and fibril formation on the degradation of OPs, the optimal metalloenzyme mimic was selected. Furthermore, optimal metalloenzyme mimics were combined with NiCo₂O₄ to develop an electrochemical sensor of OPs. By monitoring square wave voltammetry (SWV) signals of PNP degraded from OPs, the amounts of OPs in actual samples could be determined in 15 min. We discovered that both the active sites of α metal and β metal were required for metalloenzyme mimics; Zn²⁺ promoted peptide fibrosis and especially acted as a cofactor for degrading OPs. Compared to traditional methods, the electrochemical sensor of metalloenzyme mimics was sensitive, reliable, and non-toxic; furthermore, the detection limit of methyl paraoxon was as low as 0.08 µM. The metalloenzyme mimics will be a promising material for detecting OPs in the food industry and environment fields.

Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation

Escherichia coli is a Gram-negative bacterium that colonises the human intestine and virulent strains can cause severe diarrhoeal and extraintestinal diseases. The protein SslE is secreted by a range of pathogenic and commensal E. coli strains. It can degrade mucins in the intestine, promotes biofilm maturation and it is a major determinant of infection in virulent strains, although how it carries out these functions is not well understood. Here, we examine SslE from the commensal E. coli Waksman and BL21 (DE3) strains and the enterotoxigenic H10407 and enteropathogenic E2348/69 strains. We reveal that SslE has a unique and dynamic structure in solution and in response to acidification within mature biofilms it can form a unique aggregate with amyloid-like properties. Furthermore, we show that both SslE monomers and aggregates bind DNA in vitro and co-localise with extracellular DNA (eDNA) in mature biofilms, and SslE aggregates may also associate with cellulose under certain conditions. Our results suggest that interactions between SslE and eDNA are important for biofilm maturation in many E. coli strains and SslE may also be a factor that drives biofilm formation in other SslE-secreting bacteria.

Sunset Yellow Dye Induces Amorphous Aggregation in β-Lactoglobulin at Acidic pH: A Multi-Techniques Approach

Protein aggregation is of two types: (i) amorphous and (ii) amyloid fibril. Several extrinsic factors (temperature, pH, and small ligands) stimulate protein aggregation in vitro. In this study, we have examined the role of sunset yellow (SY) on the β-lactoglobulin (BLG) aggregation at pH 2.0. We have used spectroscopic (turbidity, Rayleigh light scattering (RLS), far-UV CD) and microscopic (transmission electron microscopy [TEM]) techniques to describe the effects of SY on BLG aggregation. Our results showed that BLG aggregation is dependent on SY concentrations. Very low concentrations (0.0–0.07 mM) of SY were unable to induce aggregation, while SY in the concentrations range of 0.1–5.0 mM induces aggregation in BLG. The kinetics of SY-stimulated aggregation is very fast and monomeric form of BLG directly converted into polymeric aggregates. The kinetics results also showed SY-induced BLG aggregation disappeared in the presence of NaCl. The far-UV CD and TEM results indicated the amorphous nature of SY-induced BLG aggregates. We believe that our results clearly suggest that SY dye effectively stimulates BLG aggregation.

Polymorphism of Alpha-Synuclein Amyloid Fibrils Depends on Ionic Strength and Protein Concentration

Protein aggregate formation is linked with multiple amyloidoses, including Alzheimer's and Parkinson's diseases. Currently, the understanding of such fibrillar structure formation and propagation is still not sufficient, the outcome of which is a lack of potent, anti-amyloid drugs. The environmental conditions used during in vitro protein aggregation assays play an important role in determining both the aggregation kinetic parameters, as well as resulting fibril structure. In the case of alpha-synuclein, ionic strength has been shown as a crucial factor in its amyloid aggregation. In this work, we examine a large sample size of alpha-synuclein aggregation reactions under thirty different ionic strength and protein concentration combinations and determine the resulting fibril structural variations using their dye-binding properties, secondary structure and morphology. We show that both ionic strength and protein concentration determine the structural variability of alpha-synuclein amyloid fibrils and that sometimes even identical conditions can result in up to four distinct types of aggregates.

Interplay between epigallocatechin-3-gallate and ionic strength during amyloid aggregation

The formation and accumulation of protein amyloid aggregates is linked with multiple amyloidoses, including neurodegenerative Alzheimer's or Parkinson's disease. The mechanism of such fibril formation is impacted by various environmental conditions, which greatly complicates the search for potential anti-amyloid compounds. One of these factors is solution ionic strength, which varies between different aggregation protocols during in vitro drug screenings. In this work, we examine the interplay between ionic strength and a well-known protein aggregation inhibitor-epigallocatechin-3-gallate. We show that changes in solution ionic strength have a major impact on the compound's inhibitory effect, reflected in both aggregation times and final fibril structure. We also observe that this effect is unique to different amyloid-forming proteins, such as insulin, alpha-synuclein and amyloid-beta.

Kinetics of aggregation of amyloid β under different shearing conditions: Experimental and modelling analyses

Amyloid β (Aβ40) is a class of amyloidogenic proteins known to aggregate into a fibrillar network. The rate of aggregation and fibril yield is sensitive to external energy input, such as shear. In this work, simple shear and shaking experiments are performed on Aβ40 solution using a Couette cell and an orbital shaker, respectively. Experiments show that, under uniform shear, both the mass of fibrils and aggregation rate increase with the shear rate. In the case of orbital shaking, the lag time decreases with the rotational speed of the shaker, but the final fibril mass is the same for all agitation speeds. To explain this contrasting behavior of aggregation kinetics, a population balance model is developed to account for the effect of shear on the aggregation of Aβ. The kinetic model includes primary nucleation, secondary nucleation, elongation, fragmentation, and depolymerization steps. The effect of steady uniform shear is encoded in the depolymerization rate constant (k_d), and it is shown that k_d decreases with shear rate initially and saturates at high shear rates. A competition between elongation and depolymerization rates yields different equilibrium masses of fibril at different shear rates. The model results agree quantitatively well with experimental data on the rate of aggregation and mass of fibrils as a function of shear rate. The modeling framework can be used to explain the shear rate-dependent aggregation of other amyloidogenic proteins.

Diverse Aggregation Kinetics Predicted by a Coarse-Grained Peptide Model

Protein and peptide aggregation is a ubiquitous phenomenon with implications in medicine, pharmaceutical industry, and materials science. An important issue in peptide aggregation is the molecular mechanism of aggregate nucleation and growth. In many experimental studies, sigmoidal kinetics curves show a clear lag phase ascribed to nucleation; however, experimental studies also show downhill kinetics curves, where the monomers decay continuously and no lag phase can be seen. In this work, we study peptide aggregation kinetics using a coarse-grained implicit solvent model introduced in our previous work. Our simulations explore the hypothesis that the interplay between interchain attraction and intrachain bending stiffness controls the aggregation kinetics and transient aggregate morphologies. Indeed, our model reproduces the aggregation modes seen in experiment: no observed aggregation, nucleated aggregation, and rapid downhill aggregation. We find that the interaction strength is the primary parameter determining the aggregation mode, whereas the stiffness is a secondary parameter modulating the transient morphologies and aggregation rates: more attractive and stiff chains aggregate more rapidly and the transient morphologies are more ordered. We also explore the effects of the initial monomer concentration and the chain length. As the concentration decreases, the aggregation mode shifts from downhill to nucleated and no-aggregation. This concentration effect is in line with an experimental observation that the transition between downhill and nucleated kinetics is concentration-dependent. We find that longer peptides can aggregate at conditions where short peptides do not aggregate at all. It supports an experimental observation that the elongation of a homopeptide, e.g., polyglutamine, can increase the aggregation propensity.

Necessity of regulatory guidelines for the development of amyloid based biomaterials

Amyloid diseases are caused due to protein homeostasis failure where incorrectly folded proteins/peptides form cross-β-sheet rich amyloid fibrillar structures. Besides proteins/peptides, small metabolite assemblies also exhibit amyloid-like features. These structures are linked to several human and animal diseases. In addition, non-toxic amyloids with diverse physiological roles are characterized as a new functional class. This finding, along with the unique properties of amyloid like stability and mechanical strength, led to a surge in the development of amyloid-based biomaterials. However, the usage of these materials by humans and animals may pose a health risk such as the development of amyloid diseases and toxicity. This is possible because amyloid-based biomaterials and their fragments may assist seeding and cross-seeding mechanisms of amyloid formation in the body. This review summarizes the potential uses of amyloids as biomaterials, the concerns regarding their usage, and a prescribed workflow to initiate a regulatory approach.

Rapid Conversion of Amyloid-Beta 1-40 Oligomers to Mature Fibrils through a Self-Catalytic Bimolecular Process

The formation of fibrillar aggregates of the amyloid beta peptide (Aβ) in the brain is one of the hallmarks of Alzheimer’s disease (AD). A clear understanding of the different aggregation steps leading to fibrils formation is a keystone in therapeutics discovery. In a recent study, we showed that Aβ40 and Aβ42 form dynamic micellar aggregates above certain critical concentrations, which mediate a fast formation of more stable oligomers, which in the case of Aβ40 are able to evolve towards amyloid fibrils. Here, using different biophysical techniques we investigated the role of different fractions of the Aβ aggregation mixture in the nucleation and fibrillation steps. We show that both processes occur through bimolecular interplay between low molecular weight species (monomer and/or dimer) and larger oligomers. Moreover, we report here a novel self-catalytic mechanism of fibrillation of Aβ40, in which early oligomers generate and deliver low molecular weight amyloid nuclei, which then catalyze the rapid conversion of the oligomers to mature amyloid fibrils. This fibrillation catalytic activity is not present in freshly disaggregated low-molecular weight Aβ40 and is, therefore, a property acquired during the aggregation process. In contrast to Aβ40, we did not observe the same self-catalytic fibrillation in Aβ42 spheroidal oligomers, which could neither be induced to fibrillate by the Aβ40 nuclei. Our results reveal clearly that amyloid fibrillation is a multi-component process, in which dynamic collisions between different interacting species favor the kinetics of amyloid nucleation and growth.

AbsoluRATE: An in-silico method to predict the aggregation kinetics of native proteins

Protein aggregation has two aspects, namely, mechanistic and kinetics. Understanding protein aggregation kinetics is critical for prediction of progression of diseases caused by amyloidosis, accumulation of aggregates in biotherapeutics during storage and engineering commercial nano-biomaterials. In this work, we have collected experimentally determined absolute protein aggregation rates and developed an SVM based regression model to predict absolute rates of protein and peptide aggregation near-physiological conditions. The regression model achieved a correlation coefficient of 0.72 with MAE of 0.91 (natural log of k_app, where k_app is in hour^-1) using leave-one-out cross-validation on a dataset of 82 non-redundant proteins/peptides. The model accounts for the experimental conditions (such as temperature, pH, ionic and protein concentration) and sequence-based properties. The amino acid sequence features revealed by this model as being important for aggregation kinetics, are also associated with the aggregation mechanism. In particular, inherent aggregation propensity of the protein/peptide sequence and number of aggregation prone regions (APRs) unpunctuated by the gatekeeping residues, were found to play important roles in the prediction of the absolute aggregation rates. This analysis shows that mechanism and kinetics of protein aggregation are coupled via common sequence attributes. The aggregation kinetic prediction method developed in this work is available at https://web.iitm.ac.in/bioinfo2/absolurate-pred/index.html.

The effects of nanobubbles on the assembly of glucagon amyloid fibrils

Some recent studies have shown that the surface and interface play an important role in the assembly and aggregation of amyloid proteins. However, it is unclear how the gas-liquid interface affects the protein assembly at the nanometer scale although the presence of gas-liquid interfaces is very common in in vitro experiments. Nanobubbles have a large specific surface area, which provides a stage for interactions with various proteins and peptides on the nanometer scale. In this work, nanobubbles produced in solution were employed for studying the effects of the gas-liquid interface on the assembly of glucagon proteins. Atomic force microscopy (AFM) studies showed that nanobubble-treated glucagon solution formed fibrils with an apparent height of 4.02 ± 0.71 nm, in contrast to the fibrils formed with a height of 2.14 ± 0.53 nm in the control. Transmission electron microscopy (TEM) results also showed that nanobubbles promoted the assembly of glucagon to form more fibrils. Thioflavin T (ThT) fluorescence and Fourier transform infrared (FTIR) analyses indicated that the nanobubbles induced the change of the glucagon conformation to a β-sheet structure. A mechanism that explains how nanobubbles affect the assembly of glucagon amyloid fibrils was proposed based on the above-mentioned experimental results. Given the fact that there are a considerable amount of nanobubbles existing in protein solutions, our results indicate that nanobubbles should be considered for fully understanding the protein aggregation events in vitro.

L. major apo-acyl carrier protein forms ordered aggregates due to an exposed phenylalanine, while phosphopantetheine inhibits aggregation in the holo-form

L. major acyl carrier protein (ACP) is a mitochondrial protein, involved in fatty acid biosynthesis. The protein is expressed as an apo-protein, and post-translationally modified at Ser 37 by a 4'-Phosphopantetheinyl transferase. Crystal structure of the apo-form of the protein at pH 5.5 suggests a four helix bundle fold, typical of ACP's. However, upon lowering the pH to 5.0, it undergoes a conformational transition from α-helix to β-sheet, and displays amyloid like properties. When left for a few days at room temperature at this pH, the protein forms fibrils, visible under Transmission electron microscopy (TEM). Using an approach combining NMR, biophysical techniques, and mutagenesis, we have identified a Phe residue present on helix II of ACP, liable for this change. Phosphopantetheinylation of LmACP, or mutation of Phe 45 to the corresponding residue in E. coli ACP (methionine), slows down the conformational change. Conversely, substitution of methionine 44 of E. coli ACP with a phenylalanine, causes enhanced ThT binding. Thus, we demonstrate the unique property of an exposed Phe in inducing, and phophopantetheine in inhibiting amyloidogenesis. Taken together, our study adds L. major acyl carrier protein to the list of ACPs that act as pH sensors.

Lysozyme Fibrils Alter the Mechanism of Insulin Amyloid Aggregation

Protein aggregation into amyloid fibrils is linked to multiple disorders. The understanding of how natively non-harmful proteins convert to these highly cytotoxic amyloid aggregates is still not sufficient, with new ideas and hypotheses being presented each year. Recently it has been shown that more than one type of protein aggregates may co-exist in the affected tissue of patients suffering from amyloid-related disorders, sparking the idea that amyloid aggregates formed by one protein may induce another protein’s fibrillization. In this work, we examine the effect that lysozyme fibrils have on insulin amyloid aggregation. We show that not only do lysozyme fibrils affect insulin nucleation, but they also alter the mechanism of its aggregation.

Protein aggregation: in silico algorithms and applications

Protein aggregation is a topic of immense interest to the scientific community due to its role in several neurodegenerative diseases/disorders and industrial importance. Several in silico techniques, tools, and algorithms have been developed to predict aggregation in proteins and understand the aggregation mechanisms. This review attempts to provide an essence of the vast developments in in silico approaches, resources available, and future perspectives. It reviews aggregation-related databases, mechanistic models (aggregation-prone region and aggregation propensity prediction), kinetic models (aggregation rate prediction), and molecular dynamics studies related to aggregation. With a multitude of prediction models related to aggregation already available to the scientific community, the field of protein aggregation is rapidly maturing to tackle new applications.

Dual effect of 2D WS2 nanoparticles on the lysozyme conformation

In the present work we studied the effect of 2D WS₂ nanoparticles on the conformational changes in lysozyme protein at different pH values (2.0-11.5). The contributions of various structural conformations (α-helix, β-sheets parallel and antiparallel, unordered structure and side groups) were determined by decomposition of Amid I absorbance bands. The 2D WS₂ were shown to have different impact on secondary structure depending on pH of the solution and protein concentration. The amyloid fibril presence was confirmed with confocal microscopy enhanced by gold support, and fluorescent spectroscopy with amyloid-sensitive dye Thioflavin T. Our data show that WS₂ can both inhibit and stimulate amyloid formation. Additionally, we have also reported an unusual spectroscopic behavior displayed by lysozyme, indicated by narrowing of Amide I and Amide II bands at pH 2.5 and 3.5 when incubated with 2D WS2 nanoparticles.

AggreRATE-Pred: a mathematical model for the prediction of change in aggregation rate upon point mutation

MOTIVATION

Protein aggregation is a major unsolved problem in biochemistry with implications for several human diseases, biotechnology and biomaterial sciences. A majority of sequence-structural properties known for their mechanistic roles in protein aggregation do not correlate well with the aggregation kinetics. This limits the practical utility of predictive algorithms.

RESULTS

We analyzed experimental data on 183 unique single point mutations that lead to change in aggregation rates for 23 polypeptides and proteins. Our initial mathematical model obtained a correlation coefficient of 0.43 between predicted and experimental change in aggregation rate upon mutation (P-value <0.0001). However, when the dataset was classified based on protein length and conformation at the mutation sites, the average correlation coefficient almost doubled to 0.82 (range: 0.74-0.87; P-value <0.0001). We observed that distinct sequence and structure-based properties determine protein aggregation kinetics in each class. In conclusion, the protein aggregation kinetics are impacted by local factors and not by global ones, such as overall three-dimensional protein fold, or mechanistic factors such as the presence of aggregation-prone regions.

AVAILABILITY AND IMPLEMENTATION

The web server is available at http://www.iitm.ac.in/bioinfo/aggrerate-pred/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

The protein-surfactant stoichiometry governs the conformational switching and amyloid nucleation kinetics of tau K18

Amyloids are pathological hallmarks of a number of debilitating neurodegenerative diseases. Understanding the molecular mechanism of protein amyloid assembly with an emphasis on structural characterization of early, key prefibrillar species is important for targeted drug design and clinical interventions. Tau is an intrinsically disordered, microtubule-binding protein which is also implicated in various neurodegenerative disorders such as frontotemporal dementia, Down's syndrome, Alzheimer's disease, etc. Earlier reports have demonstrated that tau aggregation in vitro is triggered by anionic inducers, presumably due to charge compensation which facilitates intermolecular association between the tau polypeptide chains. However, the molecular mechanism of tau amyloid aggregation, involving the structural characterization of amyloidogenic intermediates formed especially during early key steps, remains elusive. In this work, we have employed a spectroscopic toolbox to elucidate the mechanism of anionic surfactant-induced disorder-to-order amyloid transition of a tau segment. This study revealed that the amyloid assembly is mediated via binding-induced conformational switching into an early partially helical amyloid-competent intermediate. Additionally, protein and inducer concentration-dependent studies indicated that at the higher protein and/or inducer concentrations, competing off-pathway intermediates dampen the amyloid assembly which implies that the stoichiometry of protein and inducer plays a key regulatory role in the amyloid nucleation and fibril elongation kinetics.

Functionalized Mesoporous Silicas Direct Structural Polymorphism of Amyloid-β Fibrils

The aggregation of amyloid-β (Aβ) is associated with the onset of Alzheimer's disease (AD) and involves a complex kinetic pathway as monomers self-assemble into fibrils. A central feature of amyloid fibrils is the existence of multiple structural polymorphs, which complicates the development of disease-relevant structure-function relationships. Developing these relationships requires new methods to control fibril structure. In this work, we evaluated the effect that mesoporous silicas (SBA-15) functionalized with hydrophobic (SBA-PFDTS) and hydrophilic groups (SBA-PEG) have on the aggregation kinetics and resulting structure of Aβ_1-40 fibrils. The hydrophilic SBA-PEG had little effect on amyloid kinetics, while as-synthesized and hydrophobic SBA-PFDTS accelerated aggregation kinetics. Subsequently, we quantified the relative population of fibril structures formed in the presence of each material using electron microscopy. Fibrils formed from Aβ_1-40 exposed to SBA-PEG were structurally similar to control fibrils. In contrast, Aβ_1-40 incubated with SBA-15 or SBA-PFDTS formed fibrils with shorter crossover distances that were more structurally representative of fibrils found in AD patient derived samples. Overall, our results suggest that mesoporous silicas and other exogenous materials are promising scaffolds for the de novo production of specific fibril polymorphs of Aβ_1-40 and other amyloidogenic proteins.

Understanding the self-assembly pathways of a single chain variant of monellin: A first step towards the design of sweet nanomaterials

Peptides and proteins possess an inherent tendency to self-assemble, prompting the formation of amyloid aggregates from their soluble and functional states. Amyloids are linked to many devastating diseases, but self-assembling proteins can also represent formidable tools to produce new and sustainable biomaterials for biomedical and biotechnological applications. The mechanism of fibrillar aggregation, which influences the morphology and the properties of the protein aggregates, depend on factors such as pH, ionic strength, temperature, agitation, and protein concentration. We have here used intensive mechanical agitation, with or without beads, to prompt the aggregation of the single-chain derivative of the plant protein monellin, named MNEI, which is a well characterized sweet protein. Transmission electron microscopy confirmed the formation of fibrils several micrometers long, morphologically different from the previously characterized fibers of MNEI. Changes in the protein secondary structures during the aggregation process were monitored by Fourier transform infrared spectroscopy, which detected differences in the conformation of the final aggregates obtained under mechanical agitation. Moreover, soluble oligomers could be detected in the early phases of aggregation by polyacrylamide gel-electrophoresis. These findings emphasize the existence of multiple pathways of fibrillar aggregation for MNEI, which could be exploited for the design of innovative protein-based biomaterials.

Disentangling the Amyloid Pathways: A Mechanistic Approach to Etiology

Amyloids are fibrillar protein aggregates associated with diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes and Creutzfeldt-Jakob disease. The process of amyloid polymerization involves three pathological protein transformations; from natively folded conformation to the cross-β conformation, from biophysically soluble to insoluble, and from biologically functional to non-functional. While amyloids share a similar cross-β conformation, the biophysical transformation can either take place spontaneously via a homogeneous nucleation mechanism (HON) or catalytically on an exogenous surface via a heterogeneous nucleation mechanism (HEN). Here, we postulate that the different nucleation pathways can serve as a mechanistic basis for an etiological classification of amyloidopathies, where hereditary forms generally follow the HON pathway, while sporadic forms follow seed-induced (prions) or surface-induced (including microbially induced) HEN pathways. Critically, the conformational and biophysical amyloid transformation results in loss-of-function (LOF) of the original natively folded and soluble protein. This LOF can, at least initially, be the mechanism of amyloid toxicity even before amyloid accumulation reaches toxic levels. By highlighting the important role of non-protein species in amyloid formation and LOF mechanisms of toxicity, we propose a generalized mechanistic framework that could help better understand the diverse etiology of amyloid diseases and offer new opportunities for therapeutic interventions, including replacement therapies.

M. Brito R. Structure and Aggregation Mechanisms in Amyloids

The aggregation of a polypeptide chain into amyloid fibrils and their accumulation and deposition into insoluble plaques and intracellular inclusions is the hallmark of several misfolding diseases known as amyloidoses. Alzheimer′s, Parkinson′s and Huntington’s diseases are some of the approximately 50 amyloid diseases described to date. The identification and characterization of the molecular species critical for amyloid formation and disease development have been the focus of intense scrutiny. Methods such as X-ray and electron diffraction, solid-state nuclear magnetic resonance spectroscopy (ssNMR) and cryo-electron microscopy (cryo-EM) have been extensively used and they have contributed to shed a new light onto the structure of amyloid, revealing a multiplicity of polymorphic structures that generally fit the cross-β amyloid motif. The development of rational therapeutic approaches against these debilitating and increasingly frequent misfolding diseases requires a thorough understanding of the molecular mechanisms underlying the amyloid cascade. Here, we review the current knowledge on amyloid fibril formation for several proteins and peptides from a kinetic and thermodynamic point of view, the structure of the molecular species involved in the amyloidogenic process, and the origin of their cytotoxicity.

Concentration-dependent polymorphism of insulin amyloid fibrils

Protein aggregation into highly structured fibrils has long been associated with several neurodegenerative disorders, such as Alzheimer's or Parkinson's disease. Polymorphism of amyloid fibrils increases the complexity of disease mechanisms and may be one of the reasons for the slow progress in drug research. Here we report protein concentration as another factor leading to polymorphism of insulin amyloid fibrils. Moreover, our data suggests that insulin amyloid conformation can self-replicate only via elongation, while seed-induced nucleation will lead to environment-defined conformation of fibrils. As similar observations were already described for a couple of other amyloid proteins, we suggest it to be a generic mechanism for self-replication of different amyloid fibril conformations.

Early mechanisms of amyloid fibril nucleation in model and disease-related proteins

Protein amyloid aggregation is a hallmark in neuropathologies and other diseases of tremendous impact such as Alzheimer's or Parkinson's diseases. During the last decade, it has become increasingly evident that neuronal death is mainly induced by proteinaceous oligomers rather than the mature amyloid fibrils. Therefore, the earliest molecular events occurring during the amyloid aggregation cascade represent a growing interest of study. Important breakthroughs have been achieved using experimental data from different proteins, used as models, as well as systems related to diseases. Here, we summarize the structural properties of amyloid oligomeric and fibrillar aggregates and review the recent advances on how biophysical techniques can be combined with quantitative kinetic analysis and theoretical models to study the detailed mechanism of oligomer formation and nucleation of fibrils. These insights into the mechanism of early oligomerization and amyloid nucleation are of relevant interest in drug discovery and in the design of preventive strategies against neurodegenerative diseases.

Modulating amyloid fibrillation in a minimalist model peptide by intermolecular disulfide chemical reduction

Peptide structural transformation and aggregation is associated with a large number of outsider aetiology diseases, and it is intrinsically linked to amyloid peptide aggregation. Diphenylalanine self-assembled structures are used as robust minimalist beta amyloids not only to elucidate protein aggregation but also to generate hydrogels. Herein, we employed a neutral model peptide Ac-Phe-Phe-Cys-NH2 (Ac-FFC-NH2) to elucidate the role of intermolecular disulfide bonds in protein fibrillation. The Ac-FFC-NH2 peptide initially self-assembles into nanospheres that evolve to amyloid type fibrils under mild oxidative conditions. Incubation of the peptide in the presence of the chemical reduction agent TCEP inhibits the formation of the fibrils, detecting only spherical nanostructures with no secondary structure. Importantly, we triggered the transformation of the preformed linear straight amyloid fibrils to non-fibrillar structures by TCEP treatment. Under this condition, the amyloid bundles are transformed into rings, which evolve to a new spherical microstructure. We showed that the chemical reduction of intermolecular S-S in internal amyloid sequences might favour the off-path intermediates of amyloid fibril growth, even when the fibrils are formed. Our findings demonstrated that in internal amyloid sequences, the formation of intermolecular S-S promotes the formation of amyloid type fibrils; meanwhile, its reduction stabilises non-fibrillar structures. Altogether, this work provides fundamental understanding at the molecular and supramolecular level, thus facilitating the rational design of therapeutic tools for protein aggregation diseases.

The interaction of several herbal extracts with α-synuclein: Fibril formation and surface plasmon resonance analysis

Proteins from their native conformation convert into highly ordered fibrillar aggregation under particular conditions; that are described as amyloid fibrils. α-Synuclein (α-Syn) is a small natively unfolded protein that its fibrillation is the causative factor of Parkinson's disease. One important approach in the development of therapeutic agents is the use of small molecules (such as flavonoids) that could specifically and efficiently inhibit the aggregation process. In this study the effect of few herbal extract (Berberis, Quercus robur, Zizyphus vulgaris, Salix aegyptica) containing flavonoids were investigated on fibril formation of α-syn by using conventional methods such as ThT fluorescence, circular dichroism (CD) spectroscopy and transmission electron microscopy (TEM). The interaction of extracts were also analysed by surface plasmon resonance (SPR). Among extracts, Salix aegyptica revealed the highest inhibitory effect on fibril formation. As expected, Salix aegyptica extract also exhibited the highest affinity toward α-syn. Cell viability using MTT assay revealed that fibrils alone were more toxic than those containing the extract. Overall, we demonstrated that the affinity of compounds used in this study corresponds to their ability to arrest fibrillation and reduce cellular toxicity of α-syn fibrils.

Label-free detection of early oligomerization of α-synuclein and its mutants A30P/E46K through solid-state nanopores

A30P and E46K are two mutants of α-synuclein (α-Syn) associated with familial early-onset Parkinson's disease (PD), and amyloid fibrils of α-Syn are the hallmarks of this disease. Detecting the heterogeneous system in the oligomerization stage of α-Syn is crucial for understanding the fibril formation and in vivo toxicity of α-Syn oligomers. Over the last two decades, solid-state nanopore technology has been developed into a reliable and versatile method in single-molecule studies. In this work, we study the time-dependent kinetics of early oligomerization of wild-type α-Syn, A30P, and E46K mutants through silicon nitride solid-state nanopores. By testing A30P, E46K, and wild-type α-Syn samples with different incubation times-from 3 to 15 days-we identify three typical types of oligomers formed in the oligomerization stage and confirm that A30P and E46K mutants aggregate faster than wild-type α-Syn. The results imply that the distinct aggregation pathways and kinetics featured by wild-type α-Syn and mutations may account for their distinct cytotoxicity and pathology in PD-related studies.

Early Stage Alpha-Synuclein Amyloid Fibrils are Reservoirs of Membrane-Binding Species

The presence of αSN fibrils indisputably associates with the development of synucleinopathies. However, while certain fibril morphologies have been linked to downstream pathological phenotypes, others appear less harmful, leading to the concept of fibril strains, originally described in relation to prion disease. Indeed, the presence of fibrils does not associate directly with neurotoxicity. Rather, it has been suggested that the toxic compounds are soluble amyloidogenic oligomers, potentially co-existing with fibrils. Here, combining synchrotron radiation circular dichroism, transmission electron microscopy and binding assays on native plasma membrane sheets, we reveal distinct biological and biophysical differences between initial and matured fibrils, transformed within the timespan of few days. Immature fibrils are reservoirs of membrane-binding species, which in response to even gentle experimental changes release into solution in a reversible manner. In contrast, mature fibrils, albeit macroscopically indistinguishable from their less mature counterparts, are structurally robust, shielding the solution from the membrane active soluble species. We thus show that particular biological activity resides transiently with the fibrillating sample, distinct for one, but not the other, spontaneously formed fibril polymorph. These results shed new light on the principles of fibril polymorphism with consequent impact on future design of assays and therapeutic development.