Nucleated polymerisation in the presence of pre-formed seed filaments

Surface effects on functional amyloid formation

Functional amyloids formed by the protein FapC in Pseudomonas bacteria are key structural components of Pseudomonas biofilms, which mediate chronic infections and also contribute to antimicrobial resistance. Here, we combine kinetic experiments with mechanistic modelling to probe the role of surfaces in FapC functional amyloid formation. We find that nucleation of new fibrils is predominantly heterogeneous in vitro, being catalysed by reaction vessel walls but not by the air/water interface. Removal of such interfaces by using microdroplets greatly slows heterogeneous nucleation and reveals a hitherto undetected fibril surface-catalysed "secondary nucleation" reaction step. We tune the degree of catalysis by varying the interface chemistry of the reaction vessel and by adding nanoparticles with tailored surface properties that catalyse fibril nucleation. In so doing, we discover that the rate of nucleation is controlled predominantly by the strength with which FapC binds to the catalytic sites on the interface, and by its surface area. Surprisingly, neither primary nucleation rate nor catalytic site binding strength appear closely correlated to the charge and hydrophilicity of the interface. This indicates the importance of considering experimental design in terms of surface chemistry of the reaction container while also highlighting the notion that fibril nucleation during protein aggregation is a heterogeneous process.

Variance and higher moments in the sigmoidal self-assembly of branched fibrils

Self-assembly of functional branched filaments, such as actin filaments and microtubules, or dysfunctional ones, such as amyloid fibrils, plays important roles in many biological processes. Here, based on the master equation approach, we study the kinetics of the formation of the branched fibrils. In our model, a branched fibril has one mother branch and several daughter branches. A daughter branch grows from the side of a pre-existing mother branch or daughter branch. In our model, we consider five basic processes for the self-assembly of the branched filaments, namely, the nucleation, the dissociation of the primary nucleus of fibrils, the elongation, the fragmentation, and the branching. The elongation of a mother branch from two ends and the elongation of a daughter branch from two ends can, in principle, occur with four different rate constants associated with the corresponding tips. This leads to a pronounced impact of the directionality of growth on the kinetics of the self-assembly. Here, we have unified and generalized our four previously presented models of branched fibrillogenesis in a single model. We have obtained a system of non-linear ordinary differential equations that give the time evolution of the polymer numbers and the mass concentrations along with the higher moments as observable quantities.

Amyloid fibril formation kinetics of low-pH denatured bovine PI3K-SH3 monitored by three different NMR techniques

Introduction: Misfolding of amyloidogenic proteins is a molecular hallmark of neurodegenerative diseases in humans. A detailed understanding of the underlying molecular mechanisms is mandatory for developing innovative therapeutic approaches. The bovine PI3K-SH3 domain has been a model system for aggregation and fibril formation. Methods: We monitored the fibril formation kinetics of low pH-denatured recombinantly expressed [U-13C, 15N] labeled bovine PI3K-SH3 by a combination of solution NMR, high-resolution magic angle spinning (HR-MAS) NMR and solid-state NMR spectra. Solution NMR offers the highest sensitivity and, therefore, allows for the recording of two-dimensional NMR spectra with residue-specific resolution for individual time points of the time series. However, it can only follow the decay of the aggregating monomeric species. In solution NMR, aggregation occurs under quiescent experimental conditions. Solid-state NMR has lower sensitivity and allows only for the recording of one-dimensional spectra during the time series. Conversely, solid-state NMR is the only technique to detect disappearing monomers and aggregated species in the same sample by alternatingly recoding scalar coupling and dipolar coupling (CP)-based spectra. HR-MAS NMR is used here as a hybrid method bridging solution and solid-state NMR. In solid-state NMR and HR-MAS NMR the sample is agitated due to magic angle spinning. Results: Good agreement of the decay rate constants of monomeric SH3, measured by the three different NMR methods, is observed. Moderate MAS up to 8 kHz seems to influence the aggregation kinetics of seeded fibril formation only slightly. Therefore, under sufficient seeding (1% seeds used here), quiescent conditions (solution NMR), and agitated conditions deliver similar results, arguing against primary nucleation induced by MAS as a major contributor. Using solid-state NMR, we find that the amount of disappeared monomer corresponds approximately to the amount of aggregated species under the applied experimental conditions (250 µM PI3K-SH3, pH 2.5, 298 K, 1% seeds) and within the experimental error range. Data can be fitted by simple mono-exponential conversion kinetics, with lifetimes τ in the 14-38 h range. Atomic force microscopy confirms that fibrils substantially grew in length during the aggregation experiment. This argues for fibril elongation as the dominant growth mechanism in fibril mass (followed by the CP-based solid-state NMR signal). Conclusion: We suggest a combined approach employing both solution NMR and solid-state NMR, back-to-back, on two aliquots of the same sample under seeding conditions as an additional approach to follow monomer depletion and growth of fibril mass simultaneously. Atomic force microscopy images confirm fibril elongation as a major contributor to the increase in fibril mass.

Challenges for design of aggregation-resistant variants of granulocyte colony-stimulating factor

Non-native protein aggregation is a long-standing issue in pharmaceutical biotechnology. A rational design approach was used in order to identify variants of recombinant human granulocyte colony-stimulating factor (rhG-CSF) with lower aggregation propensity at solution conditions that are typical of commercial formulation. The approach used aggregation-prone-region (APR) predictors to select single amino acid substitutions that were predicted to decrease intrinsic aggregation propensity (IAP). The results of static light scattering temperature-ramps and chemical unfolding experiments demonstrated that none of the selected variants exhibited improved aggregation resistance, and the apparent conformational stability of each variant was lower than that of WT. Aggregation studies under partly denaturing conditions suggested that the IAP of at least one variant remained unaltered. Overall, this study highlights a general challenge in designing aggregation resistance for proteins, due to the need to accurately predict both APRs and conformational stability.

Kinetics theories to understand the mechanism of aggregation of a protein and to design strategies for its inhibition

Protein aggregation phenomenon is closely related to the formation of amyloids which results in many neurodegenerative diseases like Alzheimer's, Parkinson's, Huntington's, and Amyotrophic Lateral Sclerosis. In order to prevent and treat these diseases, a clear understanding of the mechanism of misfolding and self-assembly of peptides and proteins is very crucial. The aggregation of a protein may involve various microscopic events. Multiple simulations utilizing the solutions of the master equation have given a better understanding of the kinetic profiles involved in the presence and absence of a particular microscopic event. This review focuses on understanding the contribution of these molecular events to protein aggregation based on the analysis of kinetic profiles of aggregation. We also discuss the effect of inhibitors, which target various species of aggregation pathways, on the kinetic profile of protein aggregation. At the end of this review, some strategies for the inhibition of aggregation that can be utilized by combining the chemical kinetics approach with thermodynamics are proposed.

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.

Amyotrophic Lateral Sclerosis: Proteins, Proteostasis, Prions, and Promises

Amyotrophic lateral sclerosis (ALS) is characterized by the progressive degeneration of the motor neurons that innervate muscle, resulting in gradual paralysis and culminating in the inability to breathe or swallow. This neuronal degeneration occurs in a spatiotemporal manner from a point of onset in the central nervous system (CNS), suggesting that there is a molecule that spreads from cell-to-cell. There is strong evidence that the onset and progression of ALS pathology is a consequence of protein misfolding and aggregation. In line with this, a hallmark pathology of ALS is protein deposition and inclusion formation within motor neurons and surrounding glia of the proteins TAR DNA-binding protein 43, superoxide dismutase-1, or fused in sarcoma. Collectively, the observed protein aggregation, in conjunction with the spatiotemporal spread of symptoms, strongly suggests a prion-like propagation of protein aggregation occurs in ALS. In this review, we discuss the role of protein aggregation in ALS concerning protein homeostasis (proteostasis) mechanisms and prion-like propagation. Furthermore, we examine the experimental models used to investigate these processes, including in vitro assays, cultured cells, invertebrate models, and murine models. Finally, we evaluate the therapeutics that may best prevent the onset or spread of pathology in ALS and discuss what lies on the horizon for treating this currently incurable disease.

Network Hamiltonian models reveal pathways to amyloid fibril formation

Amyloid fibril formation is central to the etiology of a wide range of serious human diseases, such as Alzheimer's disease and prion diseases. Despite an ever growing collection of amyloid fibril structures found in the Protein Data Bank (PDB) and numerous clinical trials, therapeutic strategies remain elusive. One contributing factor to the lack of progress on this challenging problem is incomplete understanding of the mechanisms by which these locally ordered protein aggregates self-assemble in solution. Many current models of amyloid deposition diseases posit that the most toxic species are oligomers that form either along the pathway to forming fibrils or in competition with their formation, making it even more critical to understand the kinetics of fibrillization. A recently introduced topological model for aggregation based on network Hamiltonians is capable of recapitulating the entire process of amyloid fibril formation, beginning with thousands of free monomers and ending with kinetically accessible and thermodynamically stable amyloid fibril structures. The model can be parameterized to match the five topological classes encompassing all amyloid fibril structures so far discovered in the PDB. This paper introduces a set of network statistical and topological metrics for quantitative analysis and characterization of the fibrillization mechanisms predicted by the network Hamiltonian model. The results not only provide insight into different mechanisms leading to similar fibril structures, but also offer targets for future experimental exploration into the mechanisms by which fibrils form.

Internalisation and toxicity of amyloid-β 1-42 are influenced by its conformation and assembly state rather than size

Amyloid fibrils found in plaques in Alzheimer's disease (AD) brains are composed of amyloid-β peptides. Oligomeric amyloid-β 1-42 (Aβ42) is thought to play a critical role in neurodegeneration in AD. Here, we determine how size and conformation affect neurotoxicity and internalisation of Aβ42 assemblies using biophysical methods, immunoblotting, toxicity assays and live-cell imaging. We report significant cytotoxicity of Aβ42 oligomers and their internalisation into neurons. In contrast, Aβ42 fibrils show reduced internalisation and no toxicity. Sonicating Aβ42 fibrils generates species similar in size to oligomers but remains nontoxic. The results suggest that Aβ42 oligomers have unique properties that underlie their neurotoxic potential. Furthermore, we show that incubating cells with Aβ42 oligomers for 24 h is sufficient to trigger irreversible neurotoxicity.

Stochastic master equation for early protein aggregation in the transthyretin amyloid disease

It is significant to understand the earliest molecular events occurring in the nucleation of the amyloid aggregation cascade for the prevention of amyloid related diseases such as transthyretin amyloid disease. We develop chemical master equation for the aggregation of monomers into oligomers using reaction rate law in chemical kinetics. For this stochastic model, lognormal moment closure method is applied to track the evolution of relevant statistical moments and its high accuracy is confirmed by the results obtained from Gillespie's stochastic simulation algorithm. Our results show that the formation of oligomers is highly dependent on the number of monomers. Furthermore, the misfolding rate also has an important impact on the process of oligomers formation. The quantitative investigation should be helpful for shedding more light on the mechanism of amyloid fibril nucleation.

The catalytic nature of protein aggregation

The formation of amyloid fibrils from soluble peptide is a hallmark of many neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Characterization of the microscopic reaction processes that underlie these phenomena have yielded insights into the progression of such diseases and may inform rational approaches for the design of drugs to halt them. Experimental evidence suggests that most of these reaction processes are intrinsically catalytic in nature and may display enzymelike saturation effects under conditions typical of biological systems, yet a unified modeling framework accounting for these saturation effects is still lacking. In this paper, we therefore present a universal kinetic model for biofilament formation in which every fundamental process in the reaction network can be catalytic. The single closed-form expression derived is capable of describing with high accuracy a wide range of mechanisms of biofilament formation and providing the first integrated rate law of a system in which multiple reaction processes are saturated. Moreover, its unprecedented mathematical simplicity permits us to very clearly interpret the effects of increasing saturation on the overall kinetics. The effectiveness of the model is illustrated by fitting it to the data of in vitro Aβ40 aggregation. Remarkably, we find that primary nucleation becomes saturated, demonstrating that it must be heterogeneous, occurring at interfaces and not in solution.

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.

Synaptic vesicle mimics affect the aggregation of wild-type and A53T α-synuclein variants differently albeit similar membrane affinity

α-Synuclein misfolding results in the accumulation of amyloid fibrils in Parkinson's disease. Missense protein mutations (e.g. A53T) have been linked to early onset disease. Although α-synuclein interacts with synaptic vesicles in the brain, it is not clear what role they play in the protein aggregation process. Here, we compare the effect of small unilamellar vesicles (lipid composition similar to synaptic vesicles) on wild-type (WT) and A53T α-synuclein aggregation. Using biophysical techniques, we reveal that binding affinity to the vesicles is similar for the two proteins, and both interact with the helix long axis parallel to the membrane surface. Still, the vesicles affect the aggregation of the variants differently: effects on secondary processes such as fragmentation dominate for WT, whereas for A53T, fibril elongation is mostly affected. We speculate that vesicle interactions with aggregate intermediate species, in addition to monomer binding, vary between WT and A53T, resulting in different consequences for amyloid formation.

An Easy Path for Correlative Electron and Super-Resolution Light Microscopy

A number of new Correlative Light and Electron Microscopy approaches have been developed over the past years, offering the opportunity to combine the specificity and bio-compatibility of light microscopy with the high resolution achieved in electron microscopy. More recently, these approaches have taken one step further and also super-resolution light microscopy was combined with transmission or scanning electron microscopy. This combination usually requires moving the specimen between different imaging systems, an expensive set-up and relatively complicated imaging workflows. Here we present a way to overcome these difficulties by exploiting a commercially available wide-field fluorescence microscope integrated in the specimen chamber of a Scanning Electron Microscope (SEM) to perform correlative LM/EM studies. Super-resolution light microscopy was achieved by using a recently developed algorithm - the Super-Resolution Radial Fluctuations (SRRF) - to improve the resolution of diffraction limited fluorescent images. With this combination of hardware/software it is possible to obtain correlative super-resolution light and scanning electron microscopy images in an easy and fast way. The imaging workflow is described and demonstrated on fluorescently labelled amyloid fibrils, fibrillar protein aggregates linked to the onset of multiple neurodegenerative diseases, revealing information about their polymorphism.

The growth of amyloid fibrils: rates and mechanisms

Amyloid fibrils are β-sheet-rich linear protein polymers that can be formed by a large variety of different proteins. These assemblies have received much interest in recent decades, due to their role in a range of human disorders. However, amyloid fibrils are also found in a functional context, whereby their structural, mechanical and thermodynamic properties are exploited by biological systems. Amyloid fibrils form through a nucleated polymerisation mechanism with secondary processes acting in many cases to amplify the number of fibrils. The filamentous nature of amyloid fibrils implies that the fibril growth rate is, by several orders of magnitude, the fastest step of the overall aggregation reaction. This article focusses specifically on in vitro experimental studies of the process of amyloid fibril growth, or elongation, and summarises the state of knowledge of its kinetics and mechanisms. This work attempts to provide the most comprehensive summary, to date, of the available experimental data on amyloid fibril elongation rate constants and the temperature and concentration dependence of amyloid fibril elongation rates. These data are compared with those from other types of protein polymers. This comparison with data from other polymerising proteins is interesting and relevant because many of the basic ideas and concepts discussed here were first introduced for non-amyloid protein polymers, most notably by the Japanese school of Oosawa and co-workers for cytoskeletal filaments.

Statistical Mechanics of Globular Oligomer Formation by Protein Molecules

The misfolding and aggregation of proteins into linear fibrils is widespread in human biology, for example, in connection with amyloid formation and the pathology of neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. The oligomeric species that are formed in the early stages of protein aggregation are of great interest, having been linked with the cellular toxicity associated with these conditions. However, these species are not characterized in any detail experimentally, and their properties are not well understood. Many of these species have been found to have approximately spherical morphology and to be held together by hydrophobic interactions. We present here an analytical statistical mechanical model of globular oligomer formation from simple idealized amphiphilic protein monomers and show that this correlates well with Monte Carlo simulations of oligomer formation. We identify the controlling parameters of the model, which are closely related to simple quantities that may be fitted directly from experiment. We predict that globular oligomers are unlikely to form at equilibrium in many polypeptide systems but instead form transiently in the early stages of amyloid formation. We contrast the globular model of oligomer formation to a well-established model of linear oligomer formation, highlighting how the differing ensemble properties of linear and globular oligomers offer a potential strategy for characterizing oligomers from experimental measurements.

Parallel chromatography and in situ scattering to interrogate competing protein aggregation pathways

Protein aggregation can follow different pathways, and these can result in different net aggregation rates and kinetic profiles. α-chymotypsinogen A (aCgn) was used as a model system to quantitatively and qualitatively assess an approach that combines ex situ size-exclusion chromatography (SEC) with in situ laser scattering (LS) to monitor aggregation vs. time. Aggregation was monitored for a series of temperatures and initial dimer (ID) levels for starting conditions that were primarily (> 97%) monomer, and under initial-rate conditions (limited to low monomer conversion-less than 20% monomer mass loss), as these conditions are of most to interest to many pharmaceutical and biotechnology applications. SEC results show that modest decreases of ID levels can greatly reduce monomer loss rates, but do not affect the effective activation energy for aggregation. The normalized aggregation rates determined from LS were typically ∼ 1 order of magnitude higher than the corresponding rates from SEC. Furthermore, LS signals vs. time became variable and highly nonlinear with decreasing ID level, temperature, and/or total protein concentration. Temperature-cycling LS experiments showed this corresponded to conditions where dimer/oligomer "seeding" was suppressed, and high levels of reversible oligomers ("prenuclei") were formed prior to "nucleation" and growth of stable aggregates. In those conditions, aggregation rates inferred from LS and SEC are greatly different, as the techniques monitor different stages of the aggregation process. Overall, the results illustrate an approach for interrogating non-native protein aggregation pathways, and potential pitfalls if one relies on a single method to monitor aggregation-this holds more generally than the particular methods here.

Oil Palm Phenolics Inhibit the In Vitro Aggregation of β-Amyloid Peptide into Oligomeric Complexes

Alzheimer's disease is a severe neurodegenerative disease characterized by the aggregation of amyloid-β peptide (Aβ) into toxic oligomers which activate microglia and astrocytes causing acute neuroinflammation. Multiple studies show that the soluble oligomers of Aβ42 are neurotoxic and proinflammatory, whereas the monomers and insoluble fibrils are relatively nontoxic. We show that Aβ42 aggregation is inhibited in vitro by oil palm phenolics (OPP), an aqueous extract from the oil palm tree (Elaeis guineensis). The data shows that OPP inhibits stacking of β-pleated sheets, which is essential for oligomerization. We demonstrate the inhibition of Aβ42 aggregation by (1) mass spectrometry; (2) Congo Red dye binding; (3) 2D-IR spectroscopy; (4) dynamic light scattering; (5) transmission electron microscopy; and (6) transgenic yeast rescue assay. In the yeast rescue assay, OPP significantly reduces the cytotoxicity of aggregating neuropeptides in yeast genetically engineered to overexpress these peptides. The data shows that OPP inhibits (1) the aggregation of Aβ into oligomers; (2) stacking of β-pleated sheets; and (3) fibrillar growth and coalescence. These inhibitory effects prevent the formation of neurotoxic oligomers and hold potential as a means to reduce neuroinflammation and neuronal death and thereby may play some role in the prevention or treatment of Alzheimer's disease.

Concentration dependent switch in the kinetic pathway of lysozyme fibrillation: Spectroscopic and microscopic analysis

Formation of amyloid fibrils is found to be a general tendency of many proteins. Investigating the kinetic mechanisms and structural features of the intermediates and the final fibrillar state is essential to understand their role in amyloid diseases. Lysozyme, a notable model protein for amyloidogenic studies, readily formed fibrils in vitro at neutral pH in the presence of urea. It, however, showed two different kinetic pathways under varying urea concentrations when probed with thioflavin T (ThT) fluorescence. In 2M urea, lysozyme followed a nucleation-dependent fibril formation pathway which was not altered by varying the protein concentration from 2mg/ml to 8mg/ml. In 4M urea, the protein exhibited concentration dependent change in the mechanism. At lower protein concentrations, lysozyme formed fibrils without any detectable nuclei (nucleation-independent polymerization pathway). When the concentration of the protein was increased above 3mg/ml, the protein followed nucleation-dependent polymerization pathway as observed in the case of 2M urea condition. This was further verified using microscopic images of the fibrils. The kinetic parameters such as lag time, elongation rate, and fibrillation half-time, which were derived from ThT fluorescence changes, showed linear dependency against the initial protein concentration suggested that under the nucleation-dependent pathway conditions, the protein followed primary-nucleation mechanism without any significant secondary nucleation events. The results also suggested that the differences in the initial protein conformation might alter the mechanism of fibrillation; however, at the higher protein concentrations lysozyme shifted to nucleation-dependent pathway.

The contribution of biophysical and structural studies of protein self-assembly to the design of therapeutic strategies for amyloid diseases

Many neurodegenerative disorders, including Alzheimer's, Parkinson's and the prion diseases, are characterized by a conformational conversion of normally soluble proteins or peptides into pathological species, by a process of misfolding and self-assembly that leads ultimately to the formation of amyloid fibrils. Recent studies support the idea that multiple intermediate species with a wide variety of degrees of neuronal toxicity are generated during such processes. The development of a high level of knowledge of the nature and structure of the pathogenic amyloid species would significantly enhance efforts to underline the molecular origins of these disorders and also to develop both accurate diagnoses and effective therapeutic interventions for these types of conditions. In this review, we discuss recent biophysical and structural information concerning different types of amyloid aggregates and the way in which such information can guide rational therapeutic approaches designed to target specific pathogenic events that occur during the development of these highly debilitating and increasingly common diseases.

Pyroglutamate-modified Aβ(3-42) affects aggregation kinetics of Aβ(1-42) by accelerating primary and secondary pathways

The aggregation into amyloid fibrils of amyloid-β (Aβ) peptides is a hallmark of Alzheimer's disease. A variety of Aβ peptides have been discovered in vivo, with pyroglutamate-modified Aβ (pEAβ) forming a significant proportion. pEAβ is mainly localized in the core of plaques, suggesting a possible role in inducing and facilitating Aβ oligomerization and accumulation. Despite this potential importance, the aggregation mechanism of pEAβ and its influence on the aggregation kinetics of other Aβ variants have not yet been elucidated. Here we show that pEAβ(3-42) forms fibrils much faster than Aβ(1-42) and the critical concentration above which aggregation was observed was drastically decreased by one order of magnitude compared to Aβ(1-42). We elucidated the co-aggregation mechanism of Aβ(1-42) with pEAβ(3-42). At concentrations at which both species do not aggregate as homofibrils, mixtures of pEAβ(3-42) and Aβ(1-42) aggregate, suggesting the formation of mixed nuclei. We show that the presence of pEAβ(3-42) monomers increases the rate of primary nucleation of Aβ(1-42) and that fibrils of pEAβ(3-42) serve as highly efficient templates for elongation and catalytic surfaces for secondary nucleation of Aβ(1-42). On the other hand, the addition of Aβ(1-42) monomers drastically decelerates the primary and secondary nucleation of pEAβ(3-42) while not altering the pEAβ(3-42) elongation rate. In addition, even moderate concentrations of fibrillar Aβ(1-42) prevent pEAβ(3-42) aggregation, likely due to non-reactive binding of pEAβ(3-42) monomers to the surfaces of Aβ(1-42) fibrils. Thus, pEAβ(3-42) accelerates aggregation of Aβ(1-42) by affecting all individual reaction steps of the aggregation process while Aβ(1-42) dramatically slows down the primary and secondary nucleation of pEAβ(3-42).

Physical principles of filamentous protein self-assembly kinetics

The polymerization of proteins and peptides into filamentous supramolecular structures is an elementary form of self-organization of key importance to the functioning biological systems, as in the case of actin biofilaments that compose the cellular cytoskeleton. Aberrant filamentous protein self-assembly, however, is associated with undesired effects and severe clinical disorders, such as Alzheimer's and Parkinson's diseases, which, at the molecular level, are associated with the formation of certain forms of filamentous protein aggregates known as amyloids. Moreover, due to their unique physicochemical properties, protein filaments are finding extensive applications as biomaterials for nanotechnology. With all these different factors at play, the field of filamentous protein self-assembly has experienced tremendous activity in recent years. A key question in this area has been to elucidate the microscopic mechanisms through which filamentous aggregates emerge from dispersed proteins with the goal of uncovering the underlying physical principles. With the latest developments in the mathematical modeling of protein aggregation kinetics as well as the improvement of the available experimental techniques it is now possible to tackle many of these complex systems and carry out detailed analyses of the underlying microscopic steps involved in protein filament formation. In this paper, we review some classical and modern kinetic theories of protein filament formation, highlighting their use as a general strategy for quantifying the molecular-level mechanisms and transition states involved in these processes.

Automated Ex Situ Assays of Amyloid Formation on a Microfluidic Platform

Increasingly prevalent neurodegenerative diseases are associated with the formation of nanoscale amyloid aggregates from normally soluble peptides and proteins. A widely used strategy for following the aggregation process and defining its kinetics involves the use of extrinsic dyes that undergo a spectral shift when bound to β-sheet-rich aggregates. An attractive route to carry out such studies is to perform ex situ assays, where the dye molecules are not present in the reaction mixture, but instead are only introduced into aliquots taken from the reaction at regular time intervals to avoid the possibility that the dye molecules interfere with the aggregation process. However, such ex situ measurements are time-consuming to perform, require large sample volumes, and do not provide for real-time observation of aggregation phenomena. To overcome these limitations, here we have designed and fabricated microfluidic devices that offer continuous and automated real-time ex situ tracking of the protein aggregation process. This device allows us to improve the time resolution of ex situ aggregation assays relative to conventional assays by more than one order of magnitude. The availability of an automated system for tracking the progress of protein aggregation reactions without the presence of marker molecules in the reaction mixtures opens up the possibility of routine noninvasive study of protein aggregation phenomena.

A minimal conformational switching-dependent model for amyloid self-assembly

Amyloid formation is associated with various pathophysiological conditions like Alzheimer’s and Parkinson’s diseases as well as many useful functions. The hallmark of amyloid assemblies is a conformational transition of the constituent proteins into a β - sheet rich filament. Accounting for this conformational transition in amyloidogenic proteins, we develop an analytically solvable model that can probe the dynamics of an ensemble of single filaments. Using the theory and Monte Carlo simulations, we show the presence of two kinetic regimes for the growth of a self-assembling filament – switching-dependent and –independent growth regimes. We observe a saturation in fibril elongation velocities at higher concentrations in the first regime, providing a novel explanation to the concentration-independence of growth velocities observed experimentally. We also compute the length fluctuation of the filaments to characterize aggregate heterogeneity. From the early velocities and length fluctuation, we propose a novel way of estimating the conformational switching rate. Our theory predicts a kinetic phase diagram that has three distinct phases – short oligomers/monomers, disordered aggregates and β -rich filaments. The model also predicts the force generation potential and the intermittent growth of amyloid fibrils evident from single molecular experiments. Our model could contribute significantly to the physical understanding of amyloid aggregation.

Dynamic Landau theory for supramolecular self-assembly

Although pathway-specific kinetic theories are fundamentally important to describe and understand reversible polymerisation kinetics, they come in principle at a cost of having a large number of system-specific parameters. Here, we construct a dynamical Landau theory to describe the kinetics of activated linear supramolecular self-assembly, which drastically reduces the number of parameters and still describes most of the interesting and generic behavior of the system in hand. This phenomenological approach hinges on the fact that if nucleated, the polymerisation transition resembles a phase transition. We are able to describe hysteresis, overshooting, undershooting and the existence of a lag time before polymerisation takes off, and pinpoint the conditions required for observing these types of phenomenon in the assembly and disassembly kinetics. We argue that the phenomenological kinetic parameter in our theory is a pathway controller, i.e., it controls the relative weights of the molecular pathways through which self-assembly takes place.

Asymptotic solutions of the Oosawa model for the length distribution of biofilaments

Nucleated polymerisation phenomena are general linear growth processes that underlie the formation of a range of biofilaments in nature, including actin and tubulin that are key components of the cellular cytoskeleton. The conventional theoretical framework for describing this process is the Oosawa model that takes into account homogeneous nucleation coupled to linear growth. In his original work, Oosawa provided an analytical solution to the total mass concentration of filaments; the time evolution of the full length distribution has, however, been challenging to access, in large part due to the nonlinear nature of the rate equations inherent in the description of such phenomena and to date analytical solutions for the filament distribution are known only in certain special cases. Here, by exploiting a technique based on the method of matched asymptotics, we present an analytical treatment of the Oosawa model that describes the shape of the length distribution of biofilaments reversibly growing through primary nucleation and filament elongation. Our work highlights the power of matched asymptotics for obtaining closed-form analytical solutions to nonlinear master equations in biophysics and allows us to identify the key time scales that characterize biological polymerization processes.

Quantitative assessment of prion infectivity in tissues and body fluids by real-time quaking-induced conversion

Prions are amyloid-forming proteins that cause transmissible spongiform encephalopathies through a process involving the templated conversion of the normal cellular prion protein (PrP(C)) to a pathogenic misfolded conformation. Templated conversion has been modelled in several in vitro assays, including serial protein misfolding amplification, amyloid seeding and real-time quaking-induced conversion (RT-QuIC). As RT-QuIC measures formation of amyloid fibrils in real-time, it can be used to estimate the rate of seeded conversion. Here, we used samples from deer infected with chronic wasting disease (CWD) in RT-QuIC to show that serial dilution of prion seed was linearly related to the rate of amyloid formation over a range of 10(-3) to 10(-8) µg. We then used an amyloid formation rate standard curve derived from a bioassayed reference sample (CWD+ brain homogenate) to estimate the prion seed concentration and infectivity in tissues, body fluids and excreta. Using these methods, we estimated that urine and saliva from CWD-infected deer both contained 1-5 LD50 per 10 ml. Thus, over the 1-2 year course of an infection, a substantial environmental reservoir of CWD prion contamination accumulates.

Solution conditions determine the relative importance of nucleation and growth processes in α-synuclein aggregation

The formation of amyloid fibrils by the intrinsically disordered protein α-synuclein is a hallmark of Parkinson disease. To characterize the microscopic steps in the mechanism of aggregation of this protein we have used in vitro aggregation assays in the presence of preformed seed fibrils to determine the molecular rate constant of fibril elongation under a range of different conditions. We show that α-synuclein amyloid fibrils grow by monomer and not oligomer addition and are subject to higher-order assembly processes that decrease their capacity to grow. We also find that at neutral pH under quiescent conditions homogeneous primary nucleation and secondary processes, such as fragmentation and surface-assisted nucleation, which can lead to proliferation of the total number of aggregates, are undetectable. At pH values below 6, however, the rate of secondary nucleation increases dramatically, leading to a completely different balance between the nucleation and growth of aggregates. Thus, at mildly acidic pH values, such as those, for example, that are present in some intracellular locations, including endosomes and lysosomes, multiplication of aggregates is much faster than at normal physiological pH values, largely as a consequence of much more rapid secondary nucleation. These findings provide new insights into possible mechanisms of α-synuclein aggregation and aggregate spreading in the context of Parkinson disease.

Nucleation-conversion-polymerization reactions of biological macromolecules with prenucleation clusters

The self-assembly of biomolecules, such as peptides and proteins, into filaments is conventionally understood as a nucleated polymerization reaction. However, detailed analysis of experimental observation has revealed recently that nucleation pathways generate growth-competent nuclei via a cascade of metastable intermediate species, which are omitted in conventional models of filamentous growth based on classical nucleation theory. Here we take an analytical approach to generalizing the classical theory of nucleated polymerization to include the formation of these prenucleation clusters, providing a quantitative general classification of the behavior exhibited by these nucleation-conversion-polymerization reactions. A phase diagram is constructed, and analytical predictions are derived for key experimental observables. Using this approach, we delineate the characteristic time scales that determine the nature of biopolymer growth phenomena.

The presence of an air-water interface affects formation and elongation of α-Synuclein fibrils

The aggregation of human α-Synuclein (α-Syn) into amyloid fibrils is related to the onset of multiple diseases termed synucleinopathies. Substantial evidence suggests that hydrophobic-hydrophilic interfaces promote the aggregation of amyloidogenic proteins and peptides in vitro. In this work the effect of the air-water interface (AWI) on α-Syn aggregation is investigated by means of thioflavin T binding measurements, dynamic light scattering, size-exclusion chromatography, electron microscopy, and atomic force microscopy. Measurements were performed with the monomeric protein alone or together with preformed seeds. In presence of the AWI, α-Syn aggregates readily into amyloid fibrils that remain adsorbed to the AWI. Instead, when the AWI is removed from the samples by replacing it with a solid-liquid interface, the interfacial aggregation of monomeric α-Syn is greatly reduced and no significant increase in ThT fluorescence is detected in the bulk, even at 900 μM concentration. Bulk aggregation is observed only when a sufficient amount of preformed seeds is added, and the initial slope of the kinetics scales with the amount of seeds as expected for first order kinetics. By contrast, in seeded experiments with the AWI, the initial slope is one order of magnitude lower and secondary nucleation pathways appear instead to be dominant. Thus, interfaces play multiple roles in the aggregation of α-Syn, influencing primary nucleation, aggregate elongation, and secondary nucleation processes. Interfacial effects must therefore be taken into account to achieve a complete understanding of protein aggregation events in vitro as well as in vivo.

Direct observation of heterogeneous amyloid fibril growth kinetics via two-color super-resolution microscopy

The self-assembly of normally soluble proteins into fibrillar amyloid structures is associated with a range of neurodegenerative disorders, such as Parkinson's and Alzheimer's diseases. In the present study, we show that specific events in the kinetics of the complex, multistep aggregation process of one such protein, α-synuclein, whose aggregation is a characteristic hallmark of Parkinson's disease, can be followed at the molecular level using optical super-resolution microscopy. We have explored in particular the elongation of preformed α-synuclein fibrils; using two-color single-molecule localization microscopy we are able to provide conclusive evidence that the elongation proceeds from both ends of the fibril seeds. Furthermore, the technique reveals a large heterogeneity in the growth rates of individual fibrils; some fibrils exhibit no detectable growth, whereas others extend to more than ten times their original length within hours. These large variations in the growth kinetics can be attributed to fibril structural polymorphism. Our technique offers new capabilities in the study of amyloid growth dynamics at the molecular level and is readily translated to the study of the self-assembly of other nanostructures.

Modelling amyloid fibril formation kinetics: mechanisms of nucleation and growth

Amyloid and amyloid-like fibrils are self-assembling protein nanostructures, of interest for their robust material properties and inherent biological compatibility as well as their putative role in a number of debilitating mammalian disorders. Understanding fibril formation is essential to the development of strategies to control, manipulate or prevent fibril growth. As such, this area of research has attracted significant attention over the last half century. This review describes a number of different models that have been formulated to describe the kinetics of fibril assembly. We describe the macroscopic implications of mechanisms in which secondary processes such as secondary nucleation, fragmentation or branching dominate the assembly pathway, compared to mechanisms dominated by the influence of primary nucleation. We further describe how experimental data can be analysed with respect to the predictions of kinetic models.

Simple moment-closure model for the self-assembly of breakable amyloid filaments

In this work, we derive a simple mathematical model from mass-action equations for amyloid fiber formation that takes into account the primary nucleation, elongation, and length-dependent fragmentation. The derivation is based on the principle of minimum free energy under certain constraints and is mathematically related to the partial equilibrium approximation. Direct numerical comparisons confirm the usefulness of our simple model. We further explore its basic kinetic and equilibrium properties, and show that the current model is a straightforward generalization of that with constant fragmentation rates.

Amyloid-like fibril elongation follows michaelis-menten kinetics

A number of proteins can aggregate into amyloid-like fibrils. It was noted that fibril elongation has similarities to an enzymatic reaction, where monomers or oligomers would play a role of substrate and nuclei/fibrils would play a role of enzyme. The question is how similar these processes really are. We obtained experimental data on insulin amyloid-like fibril elongation at the conditions where other processes which may impact kinetics of fibril formation are minor and fitted it using Michaelis-Menten equation. The correlation of the fit is very good and repeatable. It speaks in favour of enzyme-like model of fibril elongation. In addition, obtained and values at different conditions may help in better understanding influence of environmental factors on the process of fibril elongation.

A label-free, quantitative assay of amyloid fibril growth based on intrinsic fluorescence

Kinetic assay of seeded growth: The graph shows the variation in intrinsic fluorescence intensity of amyloid fibrils. Fluorescence increases during the seeded aggregation of α-synuclein seeds with α-synuclein monomeric protein (blue curve) but not when α-synuclein seeds are incubated with β-synuclein monomeric protein (black curve), thus showing that no seeded growth occurred in this case.

Role of elongation and secondary pathways in S6 amyloid fibril growth

The concerted action of a large number of individual molecular level events in the formation and growth of fibrillar protein structures creates a significant challenge for differentiating between the relative contributions of different self-assembly steps to the overall kinetics of this process. The characterization of the individual steps is, however, an important requirement for achieving a quantitative understanding of this general phenomenon which underlies many crucial functional and pathological pathways in living systems. In this study, we have applied a kinetic modeling approach to interpret experimental data obtained for the aggregation of a selection of site-directed mutants of the protein S6 from Thermus thermophilus. By studying a range of concentrations of both the seed structures, used to initiate the reaction, and of the soluble monomer, which is consumed during the growth reaction, we are able to separate unambiguously secondary pathways from primary nucleation and fibril elongation. In particular, our results show that the characteristic autocatalytic nature of the growth process originates from secondary processes rather than primary nucleation events, and enables us to derive a scaling law which relates the initial seed concentration to the onset of the growth phase.

Nanomechanical properties of single amyloid fibrils

Amyloid fibrils are traditionally associated with neurodegenerative diseases like Alzheimer's disease, Parkinson's disease or Creutzfeldt-Jakob disease. However, the ability to form amyloid fibrils appears to be a more generic property of proteins. While disease-related, or pathological, amyloid fibrils are relevant for understanding the pathology and course of the disease, functional amyloids are involved, for example, in the exceptionally strong adhesive properties of natural adhesives. Amyloid fibrils are thus becoming increasingly interesting as versatile nanobiomaterials for applications in biotechnology. In the last decade a number of studies have reported on the intriguing mechanical characteristics of amyloid fibrils. In most of these studies atomic force microscopy (AFM) and atomic force spectroscopy play a central role. AFM techniques make it possible to probe, at nanometer length scales, and with exquisite control over the applied forces, biological samples in different environmental conditions. In this review we describe the different AFM techniques used for probing mechanical properties of single amyloid fibrils on the nanoscale. An overview is given of the existing mechanical studies on amyloid. We discuss the difficulties encountered with respect to the small fibril sizes and polymorphic behavior of amyloid fibrils. In particular, the different conformational packing of monomers within the fibrils leads to a heterogeneity in mechanical properties. We conclude with a brief outlook on how our knowledge of these mechanical properties of the amyloid fibrils can be exploited in the construction of nanomaterials from amyloid fibrils.

From macroscopic measurements to microscopic mechanisms of protein aggregation

The ability to relate bulk experimental measurements of amyloid formation to the microscopic assembly processes that underlie protein aggregation is critical in order to achieve a quantitative understanding of this complex phenomenon. In this review, we focus on the insights from classical and modern theories of linear growth phenomena and discuss how theory allows the roles of growth and nucleation processes to be defined through the analysis of experimental in vitro time courses of amyloid formation. Moreover, we discuss the specific signatures in the time course of the reactions that correspond to the actions of primary and secondary nucleation processes, and outline strategies for identifying and characterising the nature of the dominant process responsible in each case for the generation of new aggregates. We highlight the power of a global analysis of experimental time courses acquired under different conditions, and discuss how such an analysis allows a rigorous connection to be established between the macroscopic measurements and the rates of the individual microscopic processes that underlie the phenomenon of amyloid formation.