Shear forces affect self-assembly processes ranging from crystallization to fiber formation. Here, the effect of mild agitation on amyloid fibril formation was explored for four peptides and investigated in detail for A β 42, which is associated with Alzheimer’s disease. To gain mechanistic insights into the effect of mild agitation, nonseeded and seeded aggregation reactions were set up at various peptide concentrations with and without an inhibitor. First, an effect on fibril fragmentation was excluded by comparing the monomer-concentration dependence of aggregation kinetics under idle and agitated conditions. Second, using a secondary nucleation inhibitor, Brichos, the agitation effect on primary nucleation was decoupled from secondary nucleation. Third, an effect on secondary nucleation was established in the absence of inhibitor. Fourth, an effect on elongation was excluded by comparing the seeding potency of fibrils formed under idle or agitated conditions. We find that both primary and secondary nucleation steps are accelerated by gentle agitation. The increased shear forces facilitate both the detachment of newly formed aggregates from catalytic surfaces and the rate at which molecules are transported in the bulk solution to encounter nucleation sites on the fibril and other surfaces. Ultrastructural evidence obtained with cryogenic transmission electron microscopy and free-flow electrophoresis in microfluidics devices imply that agitation speeds up the detachment of nucleated species from the fibril surface. Our findings shed light on the aggregation mechanism and the role of detachment for efficient secondary nucleation. The results inform on how to modulate the relative importance of different microscopic steps in drug discovery and investigations.

Amyloids are elongated supramolecular protein self-assemblies. Their formation is a non-covalent assembly process and as such is fully reversible. Amyloid formation is associated with several neurodegenerative diseases, and the reversibility is key to maintaining the healthy state. Reversibility is also key to the performance of fibril-based biomaterials and functional amyloids. The reversibility can be observed by a range of spectroscopic, calorimetric, or surface-based techniques using as a starting state either a supersaturated monomer solution or diluted fibrils. Amyloid formation has the characteristics of a phase transition, and we provide some basic formalism for the reversibility and the derivation of the solubility/critical concentration. We also discuss conditions under which the dissociation of amyloids may be so slow that the process can be viewed as practically irreversible, for example, because it is slow relative to the experimental time frame or because the system at hand contains a source for constant monomer addition.

Formation of new amyloid fibrils and oligomers from monomeric protein on the surfaces of existing fibrils is an important driver of many disorders such as Alzheimer’s and Parkinson’s diseases. The structural basis of this secondary nucleation process, however, is poorly understood. Here, we ask whether secondary nucleation sites are found predominantly at rare growth defects: irregularities in the fibril core structure incorporated during their original assembly. We first demonstrate using the specific inhibitor of secondary nucleation, Brichos, that secondary nucleation sites on Alzheimer’s disease-associated fibrils composed of Aβ40 and Aβ42 peptides are rare compared to the number of protein molecules they contain. We then grow Aβ40 fibrils under conditions designed to eliminate most growth defects while leaving the regular fibril morphology unchanged, and confirm the latter using cryo-electron microscopy. We measure both the ability of these annealed fibrils to promote secondary nucleation and the stoichiometry of their secondary nucleation sites, finding that both are greatly reduced as predicted. Re-analysis of published data for other proteins suggests that fibril growth defects may also drive secondary nucleation generally across most amyloids. These findings could unlock structure-based drug design of therapeutics that aim to halt amyloid disorders by inhibiting secondary nucleation sites.

Intracellular deposits of neurofibrillary tau tangles and extracellular Aβ plaques are closely associated with Alzheimer's disease. The mapping of thermodynamic parameters, including solubility limits, indicates when a protein forms amyloid fibrils or remains in solution. This reveals the direction of change of the system and may help in understanding drift and steady states in living systems. Here we have developed methodology for tau solubility quantification and determined the solubility of the amyloidogenic core fragment of tau in vitro. We monitored the concentration of free tau304-380C322S fragment at 37 °C in phosphate buffer at pH 8.0 using three separate methods: HPLC-UV, derivatization with ortho-phthalaldehyde and scintillation counting. The measurements were repeated over time until a stable value was reached, implying that an equilibrium with fibrils had been established. The solubility measurements converged on a free monomer concentration of 6.1 ± 3.5 nM, which represents the solubility of the fragment under the current experimental conditions.

Inhibition of amyloid-β fibril formation by the human chaperone DNAJB6b through the binding of transient oligomers, detected with microfluidic diffusional sizing.

The transglycosylation behavior and capacity of two clan GH-D α-galactosidases, BoGal36A from the gut bacterium Bacteroides ovatus and Aga27A from the guar plant, was investigated and compared. The enzymes were screened for the ability to use para-nitrophenyl-α-galactoside (pNP-Gal), raffinose and locust bean gum (LBG) galactomannan as glycosyl donors with the glycosyl acceptors methanol, propanol, allyl alcohol, propargyl alcohol and glycerol using mass spectrometry. Aga27A was, in general, more stable in the presence of the acceptors. HPLC analysis was developed and used as a second screening method for reactions using raffinose or LBG as a donor substrate with methanol, propanol and glycerol as acceptors. Time-resolved reactions were set up with raffinose and methanol as the donor and acceptor, respectively, in order to develop an insight into the basic transglycosylation properties, including the ratio between the rate of transglycosylation (methyl galactoside synthesis) and rate of hydrolysis. BoGal36A had a somewhat higher ratio (0.99 compared to 0.71 for Aga27A) at early time points but was indicated to be more prone to secondary (product) hydrolysis in prolonged incubations. The methyl galactoside yield was higher when using raffinose (48% for BoGal36A and 38% for Aga27A) compared to LBG (27% for BoGal36A and 30% for Aga27A).