Template-directed self-assembly and growth of insulin amyloid fibrils

Protein aggregation and neurodegenerative disease: Structural outlook for the novel therapeutics

Before the controversial approval of humanized monoclonal antibody lecanemab, which binds to the soluble amyloid-β protofibrils, all the treatments available earlier, for Alzheimer's disease (AD) were symptomatic. The researchers are still struggling to find a breakthrough in AD therapeutic medicine, which is partially attributable to lack in understanding of the structural information associated with the intrinsically disordered proteins and amyloids. One of the major challenges in this area of research is to understand the structural diversity of intrinsically disordered proteins under in vitro conditions. Therefore, in this review, we have summarized the in vitro applications of biophysical methods, which are aimed to shed some light on the heterogeneity, pathogenicity, structures and mechanisms of the intrinsically disordered protein aggregates associated with proteinopathies including AD. This review will also rationalize some of the strategies in modulating disease-relevant pathogenic protein entities by small molecules using structural biology approaches and biophysical characterization. We have also highlighted tools and techniques to simulate the in vivo conditions for native and cytotoxic tau/amyloids assemblies, urge new chemical approaches to replicate tau/amyloids assemblies similar to those in vivo conditions, in addition to designing novel potential drugs.

Amyloidogenesis: What Do We Know So Far?

The study of protein aggregation, and amyloidosis in particular, has gained considerable interest in recent times. Several neurodegenerative diseases, such as Alzheimer's (AD) and Parkinson's (PD) show a characteristic buildup of proteinaceous aggregates in several organs, especially the brain. Despite the enormous upsurge in research articles in this arena, it would not be incorrect to say that we still lack a crystal-clear idea surrounding these notorious aggregates. In this review, we attempt to present a holistic picture on protein aggregation and amyloids in particular. Using a chronological order of discoveries, we present the case of amyloids right from the onset of their discovery, various biophysical techniques, including analysis of the structure, the mechanisms and kinetics of the formation of amyloids. We have discussed important questions on whether aggregation and amyloidosis are restricted to a subset of specific proteins or more broadly influenced by the biophysiochemical and cellular environment. The therapeutic strategies and the significant failure rate of drugs in clinical trials pertaining to these neurodegenerative diseases have been also discussed at length. At a time when the COVID-19 pandemic has hit the globe hard, the review also discusses the plausibility of the far-reaching consequences posed by the virus, such as triggering early onset of amyloidosis. Finally, the application(s) of amyloids as useful biomaterials has also been discussed briefly in this review.

Characterization of insulin cross-seeding: the underlying mechanism reveals seeding and denaturant-induced insulin fibrillation proceeds through structurally similar intermediates

Insulin rapidly fibrillates in the presence of amyloid seeds from different sources. To address its cross-reactivity we chose the seeds of seven model proteins and peptides along with the seeds of insulin itself. Model candidates were selected/designed according to their size, amino acid sequence, and hydrophobicity. We found while some seeds provided catalytic ends for inducing the formation of non-native insulin conformers and increase fibrillation, others attenuated insulin fibrillation kinetics. We also observed competition between the intermediate insulin conformers which formed with urea and amyloid seeds in entering the fibrillogenic pathway. Simultaneous incubation of insulin with urea and amyloid seeds resulted in the formation of nearly similar insulin intermediate conformers which synergistically enhance insulin fibrillation kinetics. Given these results, it is highly likely that, structurally, there is a specific intermediate in different pathways of insulin fibrillation that governs fibrillation kinetics and morphology of the final mature fibril. Overall, this study provides a novel mechanistic insight into insulin fibrillation and gives new information on how seeds of different proteins are capable of altering insulin fibrillation kinetics and morphology. This report, for the first time, tries to answer an important question that why fibrillation of insulin is either accelerated or attenuated in the presence of amyloid fibril seeds from different sources.

Stabilization of dry protein coatings with compatible solutes

Exposure of protein modified surfaces to air may be necessary in several applications. For example, air contact may be inevitable during the implantation of biomedical devices, for analysis of protein modified surfaces, or for sensor applications. Protein coatings are very sensitive to dehydration and can undergo significant and irreversible alterations of their conformations upon exposure to air. With the use of two compatible solutes from extremophilic bacteria, ectoine and hydroxyectoine, the authors were able to preserve the activity of dried protein monolayers for up to >24 h. The protective effect can be explained by the preferred exclusion model; i.e., the solutes trap a thin water layer around the protein, retaining an aqueous environment and preventing unfolding of the protein. Horseradish peroxidase (HRP) immobilized on compact TiO₂ was used as a model system. Structural differences between the compatible solute stabilized and unstabilized protein films, and between different solutes, were analyzed by static time-of-flight secondary ion mass spectrometry (ToF-SIMS). The biological activity difference observed in a colorimetric activity assay was correlated to changes in protein conformation by application of principal component analysis to the static ToF-SIMS data. Additionally, rehydration of the denatured HRP was observed in ToF-SIMS with an exposure of denatured protein coatings to ectoine and hydroxyectoine solutions.

Versatile multi-functionalization of protein nanofibrils for biosensor applications

Protein nanofibrils offer advantages over other nanostructures due to the ease in their self-assembly and the versatility of surface chemistry available. Yet, an efficient and general methodology for their post-assembly functionalization remains a significant challenge. We introduce a generic approach, based on biotinylation and thiolation, for the multi-functionalization of protein nanofibrils self-assembled from whey proteins. Biochemical characterization shows the effects of the functionalization onto the nanofibrils' surface, giving insights into the changes in surface chemistry of the nanostructures. We show how these methods can be used to decorate whey protein nanofibrils with several components such as fluorescent quantum dots, enzymes, and metal nanoparticles. A multi-functionalization approach is used, as a proof of principle, for the development of a glucose biosensor platform, where the protein nanofibrils act as nanoscaffolds for glucose oxidase. Biotinylation is used for enzyme attachment and thiolation for nanoscaffold anchoring onto a gold electrode surface. Characterization via cyclic voltammetry shows an increase in glucose-oxidase mediated current response due to thiol-metal interactions with the gold electrode. The presented approach for protein nanofibril multi-functionalization is novel and has the potential of being applied to other protein nanostructures with similar surface chemistry.

β-sheet propensity controls the kinetic pathways and morphologies of seeded peptide aggregation

The effect of seeds in templating the morphology of peptide aggregates is examined using molecular dynamics simulations and a coarse-grained peptide representation. Varying the nature of the aggregate seed between β-sheet, amorphous, and β-barrel seeds leads to different aggregation pathways and to morphologically different aggregates. Similar effects are seen by varying the β-sheet propensity of the free peptides. For a fibrillar seed and free peptides of high β-sheet propensity, fibrillar growth occurred by means of direct attachment (without structural rearrangement) of free individual peptides and small ordered oligomers onto the seed. For a fibrillar seed and free peptides of low β-sheet propensity, fibrillar growth occurred through a dock-lock mechanism, in which the free peptides first docked onto the seed, and then locked on, extending and aligning to join the fibril. Amorphous seeds absorbed free peptides into themselves indiscriminately, with any fibrillar rearrangement subsequent to this absorption by means of a condensation-ordering transition. Although the mechanisms observed by varying peptide β-sheet propensity are diverse, the initial pathways can always be broken down into the following steps: (i) the free peptides diffuse in the bulk and attach individually to the seed; (ii) the free peptides diffuse and aggregate among themselves; (iii) the free peptide oligomers collide with the seed; and (iv) the free oligomers merge with the seed and rearrange in a manner dependent on the backbone flexibility of both the free and seed peptides. Our simulations indicate that it is possible to sequester peptides from amorphous aggregates into fibrils, and also that aggregate morphology (and thus cytoxicity) can be controlled by introducing seeds of aggregate-compatible peptides with differing β-sheet propensities into the system.

Kinetic pathways to peptide aggregation on surfaces: the effects of β-sheet propensity and surface attraction

Mechanisms of peptide aggregation on hydrophobic surfaces are explored using molecular dynamics simulations with a coarse-grained peptide representation. Systems of peptides are studied with varying degrees of backbone rigidity (a measure of β-sheet propensity) and degrees of attraction between their hydrophobic residues and the surface. Multiple pathways for aggregation are observed, depending on the surface attraction and peptide β-sheet propensity. For the case of a single-layered β-sheet fibril forming on the surface (a dominant structure seen in all simulations), three mechanisms are observed: (a) a condensation-ordering transition where a bulk-formed amorphous aggregate binds to the surface and subsequently rearranges to form a fibril; (b) the initial formation of a single-layered fibril in the bulk depositing flat on the surface; and (c) peptides binding individually to the surface and nucleating fibril formation by individual peptide deposition. Peptides with a stiffer chiral backbone prefer mechanism (b) over (a), and stronger surface attractions prefer mechanism (c) over (a) and (b). Our model is compared to various similar experimental systems, and an agreement was found in terms of the surface increasing the degree of fibrillar aggregation, with the directions of fibrillar growth matching the crystallographic symmetry of the surface. Our simulations provide details of aggregate growth mechanisms on scales inaccessible to either experiment or atomistic simulations.

Techniques for Monitoring Protein Misfolding and Aggregation in Vitro and in Living Cells

Protein misfolding and aggregation have been considered important in understanding many neurodegenerative diseases and recombinant biopharmaceutical production. Therefore, various traditional and modern techniques have been utilized to monitor protein aggregation in vitro and in living cells. Fibril formation, morphology and secondary structure content of amyloidogenic proteins in vitro have been monitored by molecular probes, TEM/AFM, and CD/FTIR analyses, respectively. Protein aggregation in living cells has been qualitatively or quantitatively monitored by numerous molecular folding reporters based on either fluorescent protein or enzyme. Aggregation of a target protein is directly correlated to the changes in fluorescence or enzyme activity of the folding reporter fused to the target protein, which allows non-invasive monitoring aggregation of the target protein in living cells. Advances in the techniques used to monitor protein aggregation in vitro and in living cells have greatly facilitated the understanding of the molecular mechanism of amyloidogenic protein aggregation associated with neurodegenerative diseases, optimizing culture conditions to reduce aggregation of biopharmaceuticals expressed in living cells, and screening of small molecule libraries in the search for protein aggregation inhibitors.

TRPM8 and Nav1.8 sodium channels are required for transthyretin-induced calcium influx in growth cones of small-diameter TrkA-positive sensory neurons

Background

Familial amyloidotic polyneuropathy (FAP) is a peripheral neuropathy caused by the extracellular accumulation and deposition of insoluble transthyretin (TTR) aggregates. However the molecular mechanism that underlies TTR toxicity in peripheral nerves is unclear. Previous studies have suggested that amyloidogenic proteins can aggregate into oligomers which disrupt intracellular calcium homeostasis by increasing the permeability of the plasma membrane to extracellular calcium. The aim of the present study was to examine the effect of TTR on calcium influx in dorsal root ganglion neurons.

Results

Levels of intracellular cytosolic calcium were monitored in dorsal root ganglion (DRG) neurons isolated from embryonic rats using the calcium-sensitive fluorescent indicator Fluo4. An amyloidogenic mutant form of TTR, L55P, induced calcium influx into the growth cones of DRG neurons, whereas wild-type TTR had no significant effect. Atomic force microscopy and dynamic light scattering studies confirmed that the L55P TTR contained oligomeric species of TTR. The effect of L55P TTR was decreased by blockers of voltage-gated calcium channels (VGCC), as well as by blockers of Na_v1.8 voltage-gated sodium channels and transient receptor potential M8 (TRPM8) channels. siRNA knockdown of TRPM8 channels using three different TRPM8 siRNAs strongly inhibited calcium influx in DRG growth cones.

Conclusions

These data suggest that activation of TRPM8 channels triggers the activation of Na_v1.8 channels which leads to calcium influx through VGCC. We suggest that TTR-induced calcium influx into DRG neurons may contribute to the pathophysiology of FAP. Furthermore, we speculate that similar mechanisms may mediate the toxic effects of other amyloidogenic proteins such as the β-amyloid protein of Alzheimer's disease.

Osmolyte controlled fibrillation kinetics of insulin: New insight into fibrillation using the preferential exclusion principle

Amyloid proteins are converted from their native-fold to long beta-sheet-rich fibrils in a typical sigmoidal time-dependent protein aggregation curve. This reaction process from monomer or dimer to oligomer to nuclei and then to fibrils is the subject of intense study. The main results of this work are based on the use of a well-studied model amyloid protein, insulin, which has been used in vitro by others. Nine osmolyte molecules, added during the protein aggregation process for the production of amyloid fibrils, slow-down or speed up the process depending on the molecular structure of each osmolyte. Of these, all stabilizing osmolytes (sugars) slow down the aggregation process in the following order: tri > di > monosaccharides, whereas destabilizing osmolytes (urea, guanidium hydrochloride) speed up the aggregation process in a predictable way that fits the trend of all osmolytes. With respect to kinetics, we illustrate, by adapting our earlier reaction model to the insulin system, that the intermediates (trimers, tetramers, pentamers, etc.) are at very low concentrations and that nucleation is orders of magnitude slower than fibril growth. The results are then collated into a cogent explanation using the preferential exclusion and accumulation of osmolytes away from and at the protein surface during nucleation, respectively. Both the heat of solution and the neutral molecular surface area of the osmolytes correlate linearly with two fitting parameters of the kinetic rate model, that is, the lag time and the nucleation rate prior to fibril formation. These kinetic and thermodynamic results support the preferential exclusion model and the existence of oligomers including nuclei and larger structures that could induce toxicity.

Light-induced aggregation of type I soluble tumor necrosis factor receptor

We evaluated the effect of UV-B light at 302 nm on a model therapeutic protein, 2.6 D type I soluble tumor necrosis factor receptor (sTNF-RI). This protein contains a single Trp at position 97 and seven native disulfide bonds along its interior from the N to the C-terminus. At a protein concentration of 0.1 mg/mL photoirradiation was found to induce the formation of soluble disulfide cross-linked dimers with greater levels of these species formed at pH 8 than at pH 5. Intermolecular disulfide formation was also directly correlated with the photoinduced unfolding of the protein as measured by changes in secondary structure by CD spectroscopy. Trp was implicated as the initiator of the observed photoreactions by the detection of the Trp oxidation products and the absence of dimer formation when Trp97 was replaced with Gln. Reactive oxygen species or triplet state species of Trp were not involved in the reaction suggesting that disulfides were cleaved through one-electron reduction by either hydrated or peptide bound electrons produced by the photoirradiated Trp resulting in thiyl radical formation with disruption of the protein structure and intermolecular cross-linking. Photodegradation was not prevented by deoxygenation, methionine or sucrose commonly used for formulation of biopharmaceuticals. To our knowledge this is the first report directly documenting disulfide mediated aggregation through thiyl radical formation initiated by photoirradiation of Trp.

Biological assemblies provide novel templates for the synthesis of hierarchical structures and facilitate cell adhesion

Mechanical mismatch and the lack of interactions between implants and the natural tissue environment are the major drawbacks in bone tissue engineering. Biomaterials mimicking the self-assembly process and the composition of the bone matrix should provide new route for fabricating biomaterials possessing novel osteoconductive and osteoinductive properties for bone repair. In the present study, we employ bio-inspired strategies to design de novo self-assembled chimeric protein hydrogels comprising leucine zipper motifs flanked by dentin matrix protein 1 domain, which was characterized as a mineralization nucleator. Results showed that this chimeric protein could function as a hydroxyapatite nucleator in pseudo-physiological buffer with the formation of highly oriented apatites similar to biogenic bone mineral. It could also function as an inductive substrate for osteoblast adhesion, promote cell surface integrin presentation and clustering, and modulate the formation of focal contacts. Such biomimetic "bottom-up" construction with dual osteoconductive and osteoinductive properties should open new avenues for bone tissue engineering.Mechanical mismatch and the lack of interactions between implants and the natural tissue environment are the major drawbacks in bone tissue engineering. Biomaterials mimicking the self-assembly process and the composition of the bone matrix should provide new route for fabricating biomaterials possessing novel osteoconductive and osteoinductive properties for bone repair. In the present study, we employ bio-inspired strategies to design de novo self-assembled chimeric protein hydrogels comprising leucine zipper motifs flanked by dentin matrix protein 1 domain, which was characterized as a mineralization nucleator. Results showed that this chimeric protein could function as a hydroxyapatite nucleator in pseudo-physiological buffer with the formation of highly oriented apatites similar to biogenic bone mineral. It could also function as an inductive substrate for osteoblast adhesion, promote cell surface integrin presentation and clustering, and modulate the formation of focal contacts. Such biomimetic "bottom-up" construction with dual osteoconductive and osteoinductive properties should open new avenues for bone tissue engineering.

Highly accelerated self-assembly and fibrillation of prion peptides on solid surfaces

The conformational change of cellular prion protein (PrP(C)) to its infectious isoform (PrP(Sc)) is a hallmark of prion diseases. We have developed a novel solid surface-based system for efficient prion fibrillation in vitro by immobilizing prion peptides onto a chemically activated solid surface. The self-assembly of prion peptides into fibrils was more highly accelerated on the solid surface than in solution after 72 h of incubation at 37 degrees C. According to our observation using ex situ atomic force microscopy, fibrils were over 200 nm long and 5-8 nm in diameter. Amyloid-like properties of fibrils self-assembled on the solid surface were confirmed by multiple analyses with circular dichroism and amyloid-specific dyes such as Congo red and thioflavin T. The fibril formation of prion peptides was substantially affected by the incubation temperature, and preformed fibrils disassembled after additional heat treatment at 100 Odegrees . The solid surface-based prion fibrillation system developed in the present work may become a useful tool for the in vitro study of prion aggregation. The adoption of this system will allow the efficient investigation of environmental factors and inhibitor screening.

Microfluidic self-assembly of insulin monomers into amyloid fibrils on a solid surface

We report the self-assembly of insulin monomers into amyloid fibrils within microchannels. To demonstrate the microfluidic amyloid formation and fibril growth on a solid surface, we seeded the internal surfaces of the microchannels with insulin monomers via N-hydroxysuccinimide ester activation and continuously flushed a fresh insulin solution through the microchannels. According to our analysis using optical and fluorescence microscopy, insulin amyloid preferentially formed in the center of the microchannels and, after reaching a certain density, spread to the side walls of the microchannels. By using ex situ atomic force microscopy, we observed the growth of amyloid fibrils inside the microchannels, which occurred at a much higher rate than that in bulk systems. After 12 h of incubation, insulin formed amyloid spherulites having "Maltese cross" extinction patterns within the microchannels according to the polarized microscopic analysis. Microfluidic amyloid formation enabled low consumption of reagents, reduction of incubation time, and simultaneous observation of amyloid formation under different conditions. This work will contribute to the rapid analysis of amyloid formation associated with many protein misfolding diseases.

Amyloid Fibrils: From Disease to Design. New Biomaterial Applications for Self-Assembling Cross-β Fibrils

Amyloid fibrils are self-assembling protein aggregates. They are essentially insoluble and resilient nanofibres that offer great potential as materials for nanotechnology and bionanotechnology. Fibrils are associated with several debilitating diseases, for example Alzheimer’s disease, but recent advances suggest they also have positive functions in nature and can be formed in vitro from generic proteins. This article explores how the unique nanotopography and advantageous properties of fibrils may be used to develop tools for probing cell behaviour, protein-based biomimetic materials for supporting cells, or platforms for biosensors and enzyme immobilization.