Optimized sonoreactor for accelerative amyloid-fibril assays through enhancement of primary nucleation and fragmentation

Surface Modification of Ultrasonic Cavitation by Surfactants Improves Detection Sensitivity of α-Synuclein Amyloid Seeds

The rapid amplification and sensitive detection of α-synuclein (αSyn) seeds is an efficient approach for the early diagnosis of Parkinson's disease. Ultrasonication stands out as a promising method for the rapid amplification of αSyn seeds because of its robust fibril fragmentation capability. However, ultrasonication also induces the primary nucleation of αSyn monomers, deteriorating the seed detection sensitivity by generating seed-independent fibrils. In this study, we show that an addition of surfactants to the αSyn monomer solution during αSyn seed detection under ultrasonication remarkably improves the detection sensitivity of the αSyn seeds by a factor of 100-1000. Chemical kinetic analysis reveals that these surfactants reduce the rate of primary nucleation while promoting the fragmentation of the αSyn fibrils under ultrasonication. These effects are attributed to the modification of the ultrasonic cavitation surface by the surfactants. Our study enhances the utility of ultrasonication in clinical assays targeting αSyn seeds as the Parkinson's disease biomarker.

Supersaturation, a Critical Factor Underlying Proteostasis of Amyloid Fibril Formation

From a physicochemical viewpoint, amyloid fibril formation is a phase transition from soluble to crystal-like sates limited by supersaturation. It occurs only above solubility (i.e., the solubility limit) coupled with a breakdown of supersaturation. Although many studies have examined the role of molecular chaperones in the context of proteostasis, the role of supersaturation has not been addressed. Moreover, although molecular chaperone-dependent disaggregations have been reported for preformed amyloid fibrils, amyloid fibrils will not dissolve above the solubility of monomers, even if agitations fragment long fibrils to shorter amyloid particles. On the other hand, on considering a reversible and coupled equilibrium of interactions, folding/unfolding and amyloid formation/disaggregation, molecules stabilizing native states can work as a disaggregase reversing the amyloid fibrils to monomers. It is likely that the proteostasis network has various intra- and extracellular components which disaggregate preformed amyloid fibrils as well as prevent amyloid formation. Further studies with a view of solubility and supersaturation will be essential for comprehensive understanding of proteostasis.

Effects of sound energy on proteins and their complexes

Mechanical energy in the form of ultrasound and protein complexes intuitively have been considered as two distinct unrelated topics. However, in the past few years, increasingly more attention has been paid to the ability of ultrasound to induce chemical modifications on protein molecules that further change protein-protein interaction and protein self-assembling behavior. Despite efforts to decipher the exact structure and the behavior-modifying effects of ultrasound on proteins, our current understanding of these aspects remains limited. The limitation arises from the complexity of both phenomena. Ultrasound produces multiple chemical, mechanical, and thermal effects in aqueous media. Proteins are dynamic molecules with diverse complexation mechanisms. This review provides an exhaustive analysis of the progress made in better understanding the role of ultrasound in protein complexation. It describes in detail how ultrasound affects an aqueous environment and the impact of each effect separately and when combined with the protein structure and fold, the protein-protein interaction, and finally the protein self-assembly. It specifically focuses on modifying role of ultrasound in amyloid self-assembly, where the latter is associated with multiple neurodegenerative disorders.

Macromolecular crowding and supersaturation protect hemodialysis patients from the onset of dialysis-related amyloidosis

Dialysis-related amyloidosis (DRA), a serious complication among long-term hemodialysis patients, is caused by amyloid fibrils of β2-microglobulin (β2m). Although high serum β2m levels and a long dialysis vintage are the primary and secondary risk factors for the onset of DRA, respectively, patients with these do not always develop DRA, indicating that there are additional risk factors. To clarify these unknown factors, we investigate the effects of human sera on β2m amyloid fibril formation, revealing that sera markedly inhibit amyloid fibril formation. Results from over 100 sera indicate that, although the inhibitory effects of sera deteriorate in long-term dialysis patients, they are ameliorated by maintenance dialysis treatments in the short term. Serum albumin prevents amyloid fibril formation based on macromolecular crowding effects, and decreased serum albumin concentration in dialysis patients is a tertiary risk factor for the onset of DRA. We construct a theoretical model assuming cumulative effects of the three risk factors, suggesting the importance of monitoring temporary and accumulated risks to prevent the development of amyloidosis, which occurs based on supersaturation-limited amyloid fibril formation in a crowded milieu.

Supersaturation-Dependent Formation of Amyloid Fibrils

The supersaturation of a solution refers to a non-equilibrium phase in which the solution is trapped in a soluble state, even though the solute’s concentration is greater than its thermodynamic solubility. Upon breaking supersaturation, crystals form and the concentration of the solute decreases to its thermodynamic solubility. Soon after the discovery of the prion phenomena, it was recognized that prion disease transmission and propagation share some similarities with the process of crystallization. Subsequent studies exploring the structural and functional association between amyloid fibrils and amyloidoses solidified this paradigm. However, recent studies have not necessarily focused on supersaturation, possibly because of marked advancements in structural studies clarifying the atomic structures of amyloid fibrils. On the other hand, there is increasing evidence that supersaturation plays a critical role in the formation of amyloid fibrils and the onset of amyloidosis. Here, we review the recent evidence that supersaturation plays a role in linking unfolding/folding and amyloid fibril formation. We also introduce the HANABI (HANdai Amyloid Burst Inducer) system, which enables high-throughput analysis of amyloid fibril formation by the ultrasonication-triggered breakdown of supersaturation. In addition to structural studies, studies based on solubility and supersaturation are essential both to developing a comprehensive understanding of amyloid fibrils and their roles in amyloidosis, and to developing therapeutic strategies.

Influence of rigid wall on the nonlinear pulsation of nearby bubble

This paper mainly focuses on the nonlinear pulsation of a bubble near the rigid wall. Dynamics of near-wall bubble and free bubble are discussed and compared in details. Investigation reveals as the driving acoustic pressure amplitude increases, nonlinear pulsation of bubble becomes intense gradually. Besides, decreasing the viscosity of host liquid is advantageous for the nonlinear pulsation of bubble. Bifurcation diagrams of bubble radius show acoustic reflection of the rigid wall makes the initial bifurcation appear at low driving acoustic amplitude and on bubble with small ambient radius, and makes the bifurcation still exist for bubble in high-viscosity liquids. That indicates the rigid wall will produce enhancement on the nonlinearity of nearby bubble. As the bubble approaches the wall, the enhancement becomes strong. Moreover, research on the influence of driving frequency shows the rigid wall makes the frequency band corresponding to chaos around the resonant frequency of free bubble shift downward.

Comparative Analysis of the Relative Fragmentation Stabilities of Polymorphic Alpha-Synuclein Amyloid Fibrils

The division of amyloid fibril particles through fragmentation is implicated in the progression of human neurodegenerative disorders such as Parkinson's disease. Fragmentation of amyloid fibrils plays a crucial role in the propagation of the amyloid state encoded in their three-dimensional structures and may have an important role in the spreading of potentially pathological properties and phenotypes in amyloid-associated diseases. However, despite the mechanistic importance of fibril fragmentation, the relative stabilities of different types or different polymorphs of amyloid fibrils toward fragmentation remain to be quantified. We have previously developed an approach to compare the relative stabilities of different types of amyloid fibrils toward fragmentation. In this study, we show that controlled sonication, a widely used method of mechanical perturbation for amyloid seed generation, can be used as a form of mechanical perturbation for rapid comparative assessment of the relative fragmentation stabilities of different amyloid fibril structures. This approach is applied to assess the relative fragmentation stabilities of amyloid formed in vitro from wild type (WT) α-synuclein and two familial mutant variants of α-synuclein (A30P and A53T) that generate morphologically different fibril structures. Our results demonstrate that the fibril fragmentation stabilities of these different α-synuclein fibril polymorphs are all highly length dependent but distinct, with both A30P and A53T α-synuclein fibrils displaying increased resistance towards sonication-induced fibril fragmentation compared with WT α-synuclein fibrils. These conclusions show that fragmentation stabilities of different amyloid fibril polymorph structures can be diverse and suggest that the approach we report here will be useful in comparing the relative stabilities of amyloid fibril types or fibril polymorphs toward fragmentation under different biological conditions.

Development of HANABI, an ultrasonication-forced amyloid fibril inducer

Amyloid fibrils involved in amyloidoses are crystal-like aggregates, which are formed by breaking supersaturation of denatured proteins. Ultrasonication is an efficient method of agitation for breaking supersaturation and thus inducing amyloid fibrils. By combining an ultrasonicator and a microplate reader, we developed the HANABI (HANdai Amyloid Burst Inducer) system that enables high-throughput analysis of amyloid fibril formation. Among high-throughput approaches of amyloid fibril assays, the HANABI system has advantages in accelerating and detecting spontaneous amyloid fibril formation. HANABI is also powerful for amplifying a tiny amount of preformed amyloid fibrils by seeding. Thus, HANABI will contribute to creating therapeutic strategies against amyloidoses by identifying their biomarkers.

Half-Time Heat Map Reveals Ultrasonic Effects on Morphology and Kinetics of Amyloidogenic Aggregation Reaction

Ultrasonication has been recently adopted in amyloid-fibril assays because of its ability to accelerate fibril formation, being promising in the early stage diagnosis of amyloidoses in clinical applications. Although applications of this technique are expanding in the field of protein science, its effects on the aggregation reactions of amyloidogenic proteins are poorly understood. In this study, we comprehensively investigated the morphology and structure of resultant aggregates, kinetics of fibril formation, and seed-detection sensitivity under ultrasonication using β₂-microglobulin and compared these characteristics under shaking, which has been traditionally adopted in amyloid-fibril assays. To discuss the ultrasonic effects on the amyloid-fibril formation, we propose the half-time heat map, which describes the phase diagram of the aggregation reaction of amyloidogenic proteins. The experimental results show that ultrasonication greatly promotes fibril formation, especially in dilute monomer solutions, induces short-dispersed fibrils, and is capable of detecting ultra-trace-concentration seeds with a detection limit of 10 fM. Furthermore, we indicate that ultrasonication highly alters the energy landscape of an aggregation reaction due to the effect of ultrasonic cavitation. These insights contribute not only to our understanding of the effects of agitation on amyloidogenic aggregation reactions but also to their effective application in the clinical diagnosis of amyloidoses.