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

Role of amino groups in the structural assembly of β-lactoglobulin nanofibers

In recent years, protein fibrillation has attracted extensive attention because of self-assembly mechanism. The structure of β-lactoglobulin (β-Lg) nanofibers, with all residues visible in the fibril core, remains elusive, and the mechanisms of side-chain interactions are poorly understood, complicating our understanding of their formation. Here, we identified 31 core building blocks of the full-length structure of β-Lg nanofibers via enzymatic hydrolysis combined with proteomic methods. Notably, all core building blocks included essential nonsecondary structural residues were crucial for maintaining cross-β structure. Amino groups were the main groups that stabilized the interstrand and intersheet stacking in the cross-β structure, and their absence resulted in nanofibers exhibiting a preference for lateral growth and a looser cross-β structure with increased interstrand and intersheet distances. Meanwhile, the number of nanofibers decreased by approximately 20.39 %, the kinetic self-assembly rate decreased, and the thermodynamic assembly energy-barrier increased, particularly during the lag phase of fibrillation. The position and quantity of amino groups affected the core building blocks of β-Lg nanofibers: 27 core building blocks were changed, and 9 core building blocks were lost in the absence of amino groups, severely inhibiting the conversion of α-helices to β-strands during β-Lg fibrillation. These results may provide new approaches and important information for revealing the assembly mechanism of nanofibers at the molecular level.

Effect of C- and N-Terminal Polyhistidine Tags on Aggregation of Influenza A Virus Nuclear Export Protein

Nuclear export protein (NEP) of the influenza A virus, being one of the key components of the virus life cycle, is a promising model for studying characteristics of formation of amyloids by viral proteins. Using atomic force microscopy, comparative study of aggregation properties of the recombinant NEP variants, including the protein of natural structure, as well as modified variants with N- and C-terminal affinity His6-tags, was carried out. All protein variants under physiological conditions are capable of forming aggregates of various morphologies: micelle-like nanoparticles, flexible protofibrils, rigid amyloid fibrils, etc. His6-tag attached to the C-terminus has the greatest effect on aggregation kinetics and morphology of nanoparticles, which indicates important role of the C-terminal domain in the process of protein self-assembly. Molecular dynamics simulation did not reveal substantial influence of the His6-containing fragments on the protein structure, but demonstrated some variations in the mobility of these fragments that may explain the observed differences in the aggregation kinetics of the different NEP variants. Hypothetical mechanisms for formation and interconversion of various aggregates are considered.

Chitosan oligosaccharides inhibit the fibrillation of insulin and disassemble its preformed fibrils

In the current study, we first established that chitosan oligosaccharides (COS) have significant anti-fibrillogenic and fibril-destabilising effects on bovine insulin in vitro that proportionally expand with concentration growth. The obtained data were supported by the Thioflavin T (ThT) assay, circular dichroism (CD), attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy, and atomic force microscopy (AFM). Interestingly, coincubation of insulin with COS in the ratio of 1 to 10 over 48 h at 37 °C leads to full prevention of insulin aggregation, and in the case of preformed fibrils, results in their destabilisation and disaggregation. Moreover, both a cationic polymer of allylamine (PAH) and a sulphated oligosaccharide (CROS) prepared from carrageenan had no inhibitory effect on insulin amyloid formation. Thus, we proposed that COS modulates insulin amyloid formation due to the presence of linear sugar units, the degree of polymerization, and the free amino group providing a positive charge. These findings highlight the potential implications of COS as a promising substance for the treatment of insulin-dependent diabetes mellitus and localised insulin-derived amyloidosis and, moreover, provide a new insight into the mechanism of the anti-diabetic and antitoxic properties of chitosan and chitosan-based agents.

Inhibitory effect of plain and functionalized graphene nanoplateles on hen egg white lysozyme fibrillation

Protein fibrillation is a phenomenon associated with misfolding and the production of highly ordered nanofibrils, which may cause serious degenerative diseases such as Parkinson's disease, Alzheimer's disease, and type 2 diabetes. Upon contact with biological fluids, the nanomaterials are immediately covered by proteins and interact with them. In this study, the effects of Graphene NanoPlateles (Plain-GNPs) and their modified forms with a carboxyl group (GNPs -COOH) and an amine group (GNPs -NH2) are evaluated on the fibrillation process of Hen Egg White Lysozyme (HEWL). The fibrillation process of HEWL was studied using thioflavin-T, Circular Dichroism spectrometry, and Atomic Force Microscopy. Plain-GNPs significantly decreased the fibrillation process at different stages, including nucleation, exponential fibrillation phases, and end-mature fibril products. However, GNPs-COOH and GNPs-NH2 affected the final fluorescence of ThT. The species formed in the presence of Plain-GNPs showed less toxicity in SH-SY5Y cells, which could be applicable for therapeutic purposes.

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.

Predicting Symptom Onset in Sporadic Alzheimer Disease With Amyloid PET

BACKGROUND AND OBJECTIVES

To predict when cognitively normal individuals with brain amyloidosis will develop symptoms of Alzheimer disease (AD).

METHODS

Brain amyloid burden was measured by amyloid PET with Pittsburgh compound B. The mean cortical standardized uptake value ratio (SUVR) was transformed into a timescale with the use of longitudinal data.

RESULTS

Amyloid accumulation was evaluated in 236 individuals who underwent >1 amyloid PET scan. The average age was 66.5 ± 9.2 years, and 12 individuals (5%) had cognitive impairment at their baseline amyloid PET scan. A tipping point in amyloid accumulation was identified at a low level of amyloid burden (SUVR 1.2), after which nearly all individuals accumulated amyloid at a relatively consistent rate until reaching a high level of amyloid burden (SUVR 3.0). The average time between levels of amyloid burden was used to estimate the age at which an individual reached SUVR 1.2. Longitudinal clinical diagnoses for 180 individuals were aligned by the estimated age at SUVR 1.2. In the 22 individuals who progressed from cognitively normal to a typical AD dementia syndrome, the estimated age at which an individual reached SUVR 1.2 predicted the age at symptom onset (R ² = 0.54, p < 0.0001, root mean square error [RMSE] 4.5 years); the model was more accurate after exclusion of 3 likely misdiagnoses (R ² = 0.84, p < 0.0001, RMSE 2.8 years).

CONCLUSION

The age at symptom onset in sporadic AD is strongly correlated with the age at which an individual reaches a tipping point in amyloid accumulation.

Effective inhibition of insulin amyloid fibril aggregation by nickel(II) complexes containing heterocyclic thiosemicarbazones

The sensitivity of protein molecular structures makes them susceptible to aggregation in conditions unfavorable for the maintenance of their native folds. The aggregation of proteins leads to many disorders, but the inhibition of amyloid fibril formation using metal-containing small molecules is gaining popularity. Herein we report the effect of nickel(II) complexes (N1, N2, N3, and N4) bearing thiosemicarbazones on the inhibition of amyloid fibril formation by insulin. The interactions of the complexes with amyloid fibrils were investigated using various biophysical techniques, including light scattering, intrinsic fluorescence assay, thioflavin T (ThT) assay, and Fourier transform-infrared spectroscopy. The results revealed that the phenyl-substituted N3 was an efficient inhibitor of amyloid fibril formation and maintained the insulin in its native structure despite conditions promoting fibrillation. Nickel(II) complexes containing indole based thiosemicarbazones were efficient in inhibiting the amyloid fibril formation and maintaining the insulin in its native structure in unfavorable conditions.

The impaired unfolded protein-premelanosome protein and transient receptor potential channels-autophagy axes in apoptotic melanocytes in vitiligo

Vitiligo is an autoimmune skin disease, characterized by depigmentation and epidermal melanocytes loss. The specific mechanisms underlying vitiligo have not been fully understood. As a result, treating vitiligo is a dermatological challenge. Recently, much attention has been paid to the dysfunction and interaction of organelles under environmental stress. The impaired organelles could generate misfolded proteins, particularly accumulated toxic premelanosome protein (PMEL) amyloid oligomers, activating the autoimmune system and cause melanocyte damage. Unfolded protein response (UPR) dysfunction accelerates toxic PMEL accumulation. Herein, we presented a narrative review on UPR's role in vitiligo, the misfolded PMEL-induced attack of the autoimmune system under autophagy dysfunction caused by abnormal activation of transient receptor potential (TRP) channels and the background of UPR system defects in melanocytes. All of these mechanisms were integrated to form UPR/PMEL-TRP channels/autophagy axis, providing a new understanding of vitiligo pathogenesis.

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.

Effects of Ions and Small Compounds on the Structure of Aβ42 Monomers

Aggregation of amyloid-β (Aβ) proteins in the brain is a hallmark of Alzheimer's disease. This phenomenon can be promoted or inhibited by adding small molecules to the solution where Aβ is embedded. These molecules affect the ensemble of conformations sampled by Aβ monomers even before aggregation starts. Here, we perform extensive all-atom replica exchange molecular dynamics (REMD) simulations to provide a comparative study of the ensemble of conformations sampled by Aβ₄₂ monomers in solutions that promote (i.e., aqueous solution containing NaCl) and inhibit (i.e., aqueous solutions containing scyllo-inositol or 4-aminophenol) aggregation. Simulations performed in pure water are used as our reference. We find that secondary-structure content is only affected in an antagonistic manner by promoters and inhibitors at the C-terminus and the central hydrophilic core. Moreover, the end of the C-terminus binds more favorably to the central hydrophobic core region of Aβ₄₂ in NaCl adopting a type of strand-loop-strand structure that is disfavored by inhibitors. Nonpolar residues that form the dry core of larger aggregates of Aβ₄₂ (e.g., PDB ID 2BEG) are found at close proximity in these strand-loop-strand structures, suggesting that their formation could play an important role in initiating nucleation. In the presence of inhibitors, the C-terminus binds the central hydrophilic core with a higher probability than in our reference simulation. This sensitivity of the C-terminus, which is affected in an antagonistic manner by inhibitors and promoters, provides evidence for its critical role in accounting for aggregation.

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.

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.