The amyloid state and its association with protein misfolding diseases

Amyloid fibrils for β-carotene delivery - Influence of self-assembled structures on binding and in vitro release behavior

Two whey protein isolate amyloid fibrils (WPIF) with different structure were prepared, and the effects of these structures on binding of β-carotene (BC) and in vitro digestibility were evaluated. Whey protein isolate (WPI) in water (80 °C, pH 2.0) self-assembled into elongated WPIF (E-WPIF), whereas WPI formed to worm-like WPIF (W-WPIF) in trifluoroethanol. Compared to E-WPIF, W-WPIF showed higher surface hydrophobicity, indicating exposure of more hydrophobic residues. The encapsulation efficiency and loading capacity of BC in W-WPIF were higher than that of E-WPIF. The hydrophobic interaction were the main driving forces of WPIF/BC. During gastric digestion, WPIF lost intact fibrils structures, resulting in unordered small aggregates and most BC still bound to them. Then they were destroyed in the following intestinal digestion, leading to the release of BC. Compared with W-WPIF/BC, E-WPIF/BC had higher release of BC in gastrointestinal digestion due to weaker binding of BC and better digestibility of E-WPIF.

Lipid-induced condensate formation from the Alzheimer's Aβ peptide triggers amyloid aggregation

The onset and development of Alzheimer's disease is linked to the accumulation of pathological aggregates formed from the normally monomeric amyloid-β peptide within the central nervous system. These Aβ aggregates are increasingly successfully targeted with clinical therapies at later stages of the disease, but the fundamental molecular steps in early stage disease that trigger the initial nucleation event leading to the conversion of monomeric Aβ peptide into pathological aggregates remain unknown. Here, we show that the Aβ peptide can form biomolecular condensates on lipid bilayers both in molecular assays and in living cells. Our results reveal that these Aβ condensates can significantly accelerate the primary nucleation step in the amyloid conversion cascade that leads to the formation of amyloid aggregates. We show that Aβ condensates contain phospholipids, are intrinsically heterogeneous, and are prone to undergo a liquid-to-solid transition leading to the formation of amyloid fibrils. These findings uncover the liquid-liquid phase separation behavior of the Aβ peptide and reveal a molecular step very early in the amyloid-β aggregation process.

Confinement-Induced Self-Assembly of Protein Nanofibrils Probed by Microfocus X-ray Scattering

We here explore confinement-induced assembly of whey protein nanofibrils (PNFs) into microscale fibers using microfocused synchrotron X-ray scattering. Solvent evaporation aligns the PNFs into anisotropic fibers, and the process is followed in situ by scattering experiments within a droplet of PNF dispersion. We find an optimal temperature at which the order parameter of the protein fiber is maximized, suggesting that the degree of order results from a balance between the time scales of the forced alignment and the rotational diffusion of the fibrils. Furthermore, the assembly process is shown to depend on the nanoscale morphology and flexibility of the PNFs. Stiff/straight PNFs with long persistence lengths (∼2 μm) align at the air-water interface, with anisotropy decreasing toward the center of the droplet as Marangoni flows increase entanglement toward the center. By contrast, flexible/curved PNFs with shorter persistence lengths (<100 nm) align more uniformly throughout the droplet, likely due to enhanced local entanglements. Straight PNFs pack tightly, forming smaller clusters with short intercluster distances, while curved PNFs form intricate, adaptable networks with larger characteristic distances and more varied structures.

PRMT1-methylated MSX1 phase separates to control palate development

Little is known about the regulation and function of phase separation in craniofacial developmental disorders. MSX1 mutations are associated with human cleft palate, the most common craniofacial birth defect. Here, we show that MSX1 phase separation is a vertebrate-conserved mechanism underlying embryonic palatal fusion. Notably, MSX1 phase separation is triggered by its intrinsically disordered protein region (IDR) and regulated by PRMT1-catalyzed methylation, specifically asymmetric dimethylation of arginine in the MSX1 IDR including R150 and R157. Hypomethylated MSX1 due to methylation site mutations and PRMT1 deficiency consistently leads to abnormal MSX1 phase separation to form less dynamic gel-like condensates, resulting in proliferation defects of embryonic palatal mesenchymal cells and cleft palate. Besides, high frequency mutations in the MSX1 IDR, especially R157S, have been identified in humans with cleft palate. Overall, we reveal the function and regulatory pathway of MSX1 phase separation as a conserved mechanism underlying cleft palate, providing a proof-of-concept example of a phenotype-associated phase separation mechanism associated with craniofacial developmental disorders.

Transient interactions between the fuzzy coat and the cross-β core of brain-derived Aβ42 filaments

Several human disorders, including Alzheimer's disease (AD), are characterized by the aberrant formation of amyloid fibrils. In many cases, the amyloid core is flanked by disordered regions, known as fuzzy coat. The structural properties of fuzzy coats, and their interactions with their environments, however, have not been fully described to date. Here, we generate conformational ensembles of two brain-derived amyloid filaments of Aβ42, corresponding respectively to the familial and sporadic forms of AD. Our approach, called metadynamic electron microscopy metainference (MEMMI), provides a characterization of the transient interactions between the fuzzy coat and the cross-β core of the filaments. These calculations indicate that the familial AD filaments are less soluble than the sporadic AD filaments, and that the fuzzy coat contributes to solubilizing both types of filament. These results illustrate how the metainference approach can help analyze cryo-EM maps for the characterization of the properties of amyloid fibrils.

From Self-Assembly to Drug Delivery: Understanding and Exploring Protein Fibrils

It is crucial to comprehend protein misfolding and aggregation in the domains of biomedicine, pharmaceuticals, and proteins. Amyloid fibrils are formed when proteins misfold and assemble, resulting in the debilitating illness known as "amyloidosis". This work investigates lysozyme fibrillation with pluronics (F68 and F127). The effect of pluronics on protein aggregation and fibrillation has been studied mechanistically using a combination of calorimetric and spectroscopic techniques. TEM images and the ThT binding experiment were used to analyze the conformation of protein fibrils, and the results showed that pluronics accelerated the fibrillation process. When pluronics interact with protein at different stages of fibrillation, their pre- and postmicellar concentrations show a decrease in ΔHm° value as the time of incubation increases. This indicates the formation of amorphous aggregates due to which endothermic enthalpy is observed. As a consequence, it was investigated if these generated aggregates can also act as drug delivery vehicle; therefore, the work was carried out with 5-fluorouracil and cytarabine. The endothermic enthalpy of interaction suggests that hydrophobic interaction is more prevalent when cytarabine is employed with protein fibrils, whereas the electrostatic interaction is more prevalent when 5-fluorouracil is combined with it. The former drug, however, showed a greater adsorption than the latter on the surface of protein fibrils. It is therefore determined that 5-fluorouracil has relatively significant adsorption on fibril surfaces, whereas cytarabine has weak adsorption and is easily desorbed in cells. Consequently, the combination of LFF127 and 5-FU is lethal to malignant cells. The drug encapsulation and delivery aspect of protein fibrils/aggregates needs further exploration.

Amyloid inspired single amino acid (phenylalanine)-based supramolecular functional assemblies: from disease to device applications

In the evolving landscape of biomolecular supramolecular chemistry, recent studies on phenylalanine (Phe) have revealed important insights into the versatile nature of this essential aromatic amino acid. Phe can spontaneously self-assemble into fibrils with amyloid-like properties linked to the neurological disorder phenylketonuria (PKU). Apart from its pathological implications, Phe also displays complex phase behavior and can undergo structural changes in response to external stimuli. Its ability to co-assemble with other amino acids opens up new possibilities for studying biomolecular interactions. Furthermore, Phe's coordination with metal ions has led to the development of enzyme-mimicking catalytic systems for applications in organic chemistry, environmental monitoring, and healthcare. Research on L and D enantiomers of Phe, particularly on bio-MOFs, has highlighted their potential in advanced technologies, including bioelectronic devices. This review provides a comprehensive overview of the advancements in Phe-based supramolecular assemblies, emphasizing their interdisciplinary relevance. The Phe assemblies show great potential for future therapeutic and functional biomaterial developments, from disease treatments to innovations in bionanozymes and bioelectronics. This review presents a compelling case for the ongoing exploration of Phe's biomolecular supramolecular chemistry as a fundamental framework for developing sustainable and efficient methodologies across various scientific disciplines.

Molecular Propeller Tethering on a Dipeptide Induces a One-Step Conversion of Its Secondary Structure on Water Surface Promoted by Chiral Supramolecular Assembly

Water provides a unique surface for the formation of directed self-assembly and transformation of secondary structures of peptides and proteins as witnessed in the biological systems. Herein a one-step transformation of an amyloid-derived dipeptide is reported from β-sheet to α-helix structures on the water surface, facilitated by chiral supramolecular assembly. The study utilizes various analytical techniques to elucidate the structural transformation and the supramolecular packing of the peptide assemblies. Organizations such as spherical aggregates and molecular nanowires containing β-sheet structure are converted into (2D) molecular sheets comprising a larger planar area yet with a molecular level thickness of α-helix structure. The conformational features of the β-sheet to α-helix structural transformation are dominated by the intermolecular H-bonding, π-π stacking, and C─H···π interactions. Strikingly, the dynamic changes in the dihedral (intramolecular) angle between the aromatic rings of the dipeptide at the water surface alter the molecular packing and shorten the intermolecular H-bonds with larger binding energies required for the secondary structural transformation. Thus, the novel one-step strategy reports herein offers a simple, efficient, and hitherto unprecedented way of chiral supramolecular assembly directed total secondary structural transformation of the dipeptide on water surface.

Anti-amyloidogenic hexapeptide-coated gold nanoparticles for enhanced inhibition of amyloid formation: A promising therapeutic approach

Under specific external stimulus, misfolded and natively disordered globular proteins undergo irreversible transformation into pathogenic β-sheet-rich insoluble fibrillar structure, and deposition of theses fibrils in cells and tissues leads to disorders like Alzheimer's, Dementia, Type II diabetes, and many more. Here, we have developed a positively-charged Arg-containing hexapeptide, SqP7, and elucidated its anti-amyloidogenic propensity on in vitro HEWL amyloid formation under acidic and neutral fibrillation conditions using computational tools and several biophysical techniques. SqP7, at a five-fold molar excess, displayed excellent amyloid inhibition capability at both pH conditions (~83 % and 72 % inhibition under acidic and neutral fibrillation conditions, respectively), and was further chosen as a coating agent on gold nanoparticles. This was done to investigate whether coating of this peptide on gold nanoparticles has any effect on its anti-amyloidogenic efficiency and effective inhibition concentration. The synthesized SqP7-coated gold nanoparticles were characterized to be spherical and highly-dispersed having a mean diameter of 9.12 ± 2.08 nm. The anti-amyloidogenic capability of the synthesized SqP7-coated gold nanoparticles was further evaluated, and a 10-fold reduction in the effective inhibition concentration of SqP7 was observed. This peptide‑gold nanoparticle based integrated approach can lead to the development of highly effective therapeutics for amyloid-related diseases, offering improved prevention and treatment options.

Proteopathic seed amplification assays in easily accessible specimens for human synucleinopathies, tauopathies, and prionopathies: A scoping review

A hallmark event in neurodegenerative diseases is represented by the misfolding, aggregation and accumulation of proteins, leading to cellular and network dysfunction preceding the development of clinical symptoms by years. Early diagnosis represents a crucial issue in the field of neuroscience as it offers the potential to utilize this therapeutic window in the future to manage disease-modifying therapy. Seed amplification assays, including Real-Time Quaking-Induced Conversion (RT-QuIC) and Protein Misfolding Cyclic Amplification (PMCA), have emerged in recent years as innovative techniques developed to detect minute amounts of amyloidogenic proteins. These techniques can utilize various biological fluids and tissues, with most evidence to date regarding their potential diagnostic use focusing on cerebrospinal fluid. In this scoping review, we aimed to investigate and discuss the available evidence regarding the diagnostic use of these assays on easily accessible biological fluids and tissues in patients affected by synucleinopathies, tauopathies or prion diseases. From a systematic search on two databases, Scopus and Pubmed, we identified 49 studies. Although most identified studies have used skin and olfactory mucosa as biological samples, there is preliminary evidence suggesting the potential implementation of these techniques using fluids as blood, saliva and tears. The results achieved so far, as well as methodological aspects and limitations to overcome, are discussed.

Liquid-liquid phase separation of tau and α-synuclein: A new pathway of overlapping neuropathologies

Liquid-liquid phase separation (LLPS) is a critical phenomenon that leads to the formation of liquid-like membrane-less organelles within cells. Advances in our understanding of condensates reveal their significant roles in biology and highlight how their dysregulation may contribute to disease. Recent evidence indicates that the high protein concentration in coacervates may lead to abnormal protein aggregation associated with several neurodegenerative diseases. The presence of condensates containing multiple amyloidogenic proteins may play a role in the co-deposition and comorbidity seen in neurodegeneration. This review first provides a brief overview of the physicochemical bases and molecular determinants of LLPS. It then summarizes our understanding of Tau and α-synuclein (AS) phase separation, key proteins in Alzheimer's and Parkinson's diseases. By integrating recent findings on complex Tau and AS coacervation, this article offers a fresh perspective on how LLPS may contribute to the pathological overlap in neurodegenerative disorders and provide a novel therapeutic target to mitigate or prevent such conditions.

Beyond Misfolding: A New Paradigm for the Relationship Between Protein Folding and Aggregation

Aggregation is intricately linked to protein folding, necessitating a precise understanding of their relationship. Traditionally, aggregation has been viewed primarily as a sequential consequence of protein folding and misfolding. However, this conventional paradigm is inherently incomplete and can be deeply misleading. Remarkably, it fails to adequately explain how intrinsic and extrinsic factors, such as charges and cellular macromolecules, prevent intermolecular aggregation independently of intramolecular protein folding and structure. The pervasive inconsistencies between protein folding and aggregation call for a new framework. In all combined reactions of molecules, both intramolecular and intermolecular rate (or equilibrium) constants are mutually independent; accordingly, intrinsic and extrinsic factors independently affect both rate constants. This universal principle, when applied to protein folding and aggregation, indicates that they should be treated as two independent yet interconnected processes. Based on this principle, a new framework provides groundbreaking insights into misfolding, Anfinsen's thermodynamic hypothesis, molecular chaperones, intrinsic chaperone-like activities of cellular macromolecules, intermolecular repulsive force-driven aggregation inhibition, proteome solubility maintenance, and proteinopathies. Consequently, this paradigm shift not only refines our current understanding but also offers a more comprehensive view of how aggregation is coupled to protein folding in the complex cellular milieu.

Integrated Network-Based Analysis of Diseases Associated with Amyloid Deposition Through a Disease-Protein-Drug Network

Background: At present, the complexity that governs the associations between different biological entities is understood better than ever before, owing to high-throughput techniques and systems biology. Networks of interactions are necessary not only for the visualization of these complex relationships but also because their analysis tends to be valuable for the extraction of novel biological knowledge. Methods: For this reason, we constructed a disease-protein-drug network, focusing on a category of rare protein-misfolding diseases, known as amyloidoses, and on other pathological conditions also associated with amyloid deposition. Apart from the amyloidogenic proteins that self-assemble into fibrils, we also included other co-deposited proteins found in amyloid deposits. Results: In this work, protein-protein, protein-drug, and disease-drug associations were collected to create a heterogenous network. Through disease-based and drug-based analyses, we highlighted commonalities between diseases and proposed an approved drug with prospects of repurposing. Conclusions: The identified disease associations and drug candidates are proposed for further study that will potentially help treat diseases associated with amyloid deposition.

Imidazo[2,1-b][1,3]thiazine Derivatives as Potential Modulators of Alpha-Synuclein Amyloid Aggregation

Insoluble amyloid fibrils accumulate in the intercellular spaces of organs and tissues, leading to various amyloidosis-related disorders in the human body. Specifically, Parkinson's disease is associated with the aggregation of alpha-synuclein. However, current treatments for Parkinson's primarily focus on managing motor symptoms and slowing disease progression. Efforts to prevent and halt the progression of these diseases involve the search for small molecular compounds. In this work, we synthesized imidazo[2,1-b][1,3]thiazines in an atom-economic way by cyclization of 2-alkynylthioimidazoles using 10% AuCl as the catalyst. We identified several compounds with specific functional groups capable of both inhibiting the aggregation of alpha-synuclein and redirecting the fibril formation pathway. The investigation into how these substances function revealed that imidazo[2,1-b][1,3]thiazine derivatives can influence alpha-synuclein aggregation in several ways. They not only inhibit the primary nucleation process and maintain a balance toward nonaggregated protein states but also stabilize smaller oligomeric species of alpha-synuclein and cause the formation of fibrils with unique structures and forms. These imidazo[2,1-b][1,3]thiazines could potentially be used in developing highly efficient, small molecular weight protein aggregation inhibitors.

Polymeric Nanodiscs Comprising 5-Fluorouracil for Inhibition of Protein Aggregation and Their Anti-Alzheimer's Activity in the Drosophila Model

Nanoconjugates are promising for therapeutic drug delivery and targeted applications due to the numerous opportunities to functionalize their surface. The present study reports the synthesis of 5-fluorouracil (5-FU)-entrapped polyvinylpyrrolidone (PVP) nanoconjugates, precisely 5-FU-PVP and 5-FU-PVP-Au, and the evaluation of protein aggregation inhibition efficiency. The 5-FU-loaded polymer nanoconjugates were functionalized with gold nanoparticles and analyzed using characterization techniques like dynamic light scattering, UV-visible spectroscopy, Fourier-transform infrared spectroscopy, and zeta potential analysis. These conjugates exhibit consistent morphology with a spherical, flat, disc-like structure. The 5-FU-PVP and 5-FU-PVP-Au nanoconjugates exhibited a high drug loading, up to 81% and 90%, respectively. The nanoconjugates exhibited prolonged drug delivery of 5-FU from 5-FU-PVP and 5-FU-PVP-Au, wherein 5-FU-PVP-Au depicted a higher drug release. They were investigated for inhibiting the protein hen egg white lysozyme (HEWL) aggregation by ThT fibril size measurement, binding assay, and electron microscopy, and the results showed that conjugates repressed the fibrillogenesis in HEWL. The prominent activity of amyloid aggregation inhibition for HEWL using 5-FU-PVP and 5-FU-PVP-Au was found to be 29 μg.mL-1 and 27 μg.mL-1, respectively. The dissociation of amyloid aggregates was achieved against 5-FU-PVP and 5-FU-PVP-Au at 27 μg.mL-1 and 25 μg.mL-1, respectively. Furthermore, the nanoconjugates were investigated for anti-Alzheimer's activity in the Drosophila model. A Drosophila model of Alzheimer's disease (AD) was developed that expressed Aβ42 peptides in the neuronal secretory system to comprehend the pathogenic effects of Aβ42 in vivo. All the results demonstrate that polymer nanoconjugates exhibit more effective inhibition of protein aggregation than bare drugs.

Heterotypic Interactions of Amyloid β and the Islet Amyloid Polypeptide Produce Mixed Aggregates with Non-Native Fibril Structure

Amyloid aggregates are hallmarks of the pathology of a wide range of diseases, including type 2 diabetes (T2D) and Alzheimer's disease (AD). Much epidemiological and pathological evidence points to significant overlap between AD and T2D. Individuals with T2D have a higher likelihood of developing AD; moreover, colocalized aggregates of amyloid β (Aβ) and the islet amyloid polypeptide (IAPP), the two main peptides implicated in the formation of toxic amyloid aggregates in AD and T2D, have also been identified in the brain. However, how these peptides interact with each other is not well understood, and the structural facets of heterotypic mixed fibrils formed via such interactions remain elusive. Here we use atomic force microscopy augmented with infrared spectroscopy to probe the secondary structure of individual aggregates formed via heterotypic interactions of Aβ and IAPP and provide unequivocal direct evidence of mixed aggregates. Furthermore, we show that co-aggregation of the peptides from the monomeric stage leads to the formation of unique polymorphs, in which both peptides undergo structural deviation from their native states, whereas seeding with preformed IAPP fibrils leads to aggregates similar to native Aβ. These findings highlight how heterotypic interactions between amyloidogenic peptides can lead to polymorphic diversity proteinopathies.

Anti-aggregation Properties of the Mini-Peptides Derived from Alpha Crystallin Domain of the Small Heat Shock Protein, Tpv HSP 14.3

The highly conserved alpha crystallin domain of the small heat shock proteins is essential for dimerization and also implicated in substrate interaction. In this study, we designed four novel mini-peptides from alpha crystallin domain of archaeal Small Heat Shock Protein Tpv HSP 14.3. Among the peptide designs, the mini-peptides 38SDLVLEAEMAGFDKKNIKVS57 and 40LVLEAEMAGFD50 overlapped to the sequences of β3-β4 region. The other two peptides 77YIDQRVDKVYKVVKLPVE94 and 107GILTVRMK114 correspond to β6-β7 region and β9, respectively. Functional activity of the peptides was evaluated by monitoring heat-induced aggregation of the model substrates alcohol dehydrogenase at 43 °C and citrate synthase at 45 °C. Our results showed that the (38-57) and the (77-94) fragments exhibited chaperone activity with both of the substrate proteins. The (40-50) fragment while exhibiting a noticeable protective effect (> 90%) when tested with citrate synthase showed an anti-chaperone property toward alcohol dehydrogenase. Unlike the (40-50) fragment, the (107-114) fragment did not show any chaperone activity with citrate synthase but exhibited the highest chaperone efficiency among four mini-peptides with alcohol dehydrogenase. The selectivity of the (40-50) and the (107-114) fragments in targeting the client proteins is most likely dependent on their surface hydrophobicity and/or charge as revealed by the sequence and exposed surface analyses.

Massively parallel genetic perturbation reveals the energetic architecture of an amyloid beta nucleation reaction

Amyloid protein aggregates are pathological hallmarks of more than fifty human diseases but how soluble proteins nucleate to form amyloids is poorly understood. Here we use combinatorial mutagenesis, a kinetic selection assay, and machine learning to massively perturb the energetics of the nucleation reaction of amyloid beta (Aβ42), the protein that aggregates in Alzheimer's disease. In total, we quantify the nucleation rates of >140,000 variants of Aβ42. This allows us to accurately quantify the changes in reaction activation energy for all possible amino acid substitutions in a protein for the first time and, in addition, to quantify >600 energetic interactions between mutations. The data reveal the simple and interpretable genetic architecture of an amyloid nucleation reaction. Strikingly, strong energetic couplings are rare and identify a subset of structural contacts in mature fibrils. Together with the activation energy changes, this strongly suggests that the Aβ42 nucleation reaction transition state is structured in a short C-terminal region, providing a structural model for the reaction that may initiate Alzheimer's disease. We believe this approach can be widely applied to probe the energetics and transition state structures of protein reactions.

Binding Interaction Between Two Mutant Myocilin Olfactomedin Domain Monomers in a Homodimer

In myocilin-associated glaucoma, pathogenic missense mutations accumulate mainly in the olfactomedin domain (mOLF) of myocilin. This makes the protein susceptible to aggregation, where mOLF-mOLF dimerization is possibly an initial stage. Nevertheless, there are no molecular level studies that have probed the nature of interactions occurring between two mOLF domains and the key characteristics of the resulting dimer complex. In this work, we used AlphaFold2 to obtain an I477N mutant mOLF structure with high quality followed by a stable I477N mOLF-mOLF homodimer model using molecular docking combined with molecular dynamics simulations. Moreover, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods coupled with per-residue energy decomposition studies are carried out to identify the key residues involved in the binding interaction. Based on these results, we provide insights into the molecular level understanding of the intermolecular interaction between two mOLF domains in an I477N homodimer. Hydrogen bonds, salt bridges, and favorable van der Waals interactions are observed in the binding interface of the homodimer. Additionally, our results suggest that I477N mutant mOLF aggregation could be a multistep process, beginning with an initial mOLF-mOLF dimerization mainly mediated by residues such as Asp395 and Arg681. Also, the peptides P1 (residues 326-337) and P3 (residues 426-442) of the mOLF domain, previously identified as pertinent for myocilin aggregation, could potentially contribute to a subsequent stage of myocilin aggregation, the first step being mOLF-mOLF dimerization.

Small molecule inhibits BACE1 activity by a dual mechanism confirmed by simulations-based study

Alzheimer's disease (AD) is a progressive and largely incurable neurodegenerative disorder that affects millions of people worldwide. It is characterised by the accumulation of amyloid-beta plaques and neurofibrillary tangles in the brain. It is commenced by cleavage of amyloid precursor protein (APP) by β-secretase, β-site amyloid precursor protein cleaving enzyme (BACE1; also called Asp2, memapsin 2). Therefore, BACE1 is a prime target for developing therapeutics against AD. In this study, we have identified a small molecule that potentially inhibits the activity of BACE1 by interacting with the active site residues. Also, the flap region seems to be involved in enhancing the stability of the small molecule at the active site. We have used Umibecestat (CNP-520) as a positive control. Our in silico results show that the identified molecule has a much better orientation at the active site of BACE1 than Umibecestat and inhibits by blocking the active site and modulating flap dynamics. We have utilised virtual high-throughput screening assay, ADME profiling, and blood-brain-barrier crossing ability to narrow down potential leads. The two shortlisted molecules were then subjected to atomistic molecular dynamics simulations study. Overall, our study proposes a much better inhibitor and a rational molecule for lead development against AD.

Multispectroscopic and computational insights into amyloid fibril formation of alpha lactalbumin induced by sodium hexametaphosphate

The impact of sodium hexametaphosphate (SHMP) on the aggregation behavior of α-lactalbumin (α-LA) was studied at pH 7.4 and 2.0. Turbidity measurements showed a concentration-dependent aggregation of α-LA at pH 2.0 in the presence of SHMP, while no aggregation was observed at pH 7.4. Light scattering (LS) and Thioflavin-T (ThT) data revealed that the aggregation was rapid, following nucleation-independent pathways. In other kinetics experiments such as turbidity and ThT confirmed that SHMP-induced α-LA aggregation was dependent on SHMP concentration rather than incubation time. Once formed, the aggregates remained unchanged for up to five days. Intrinsic fluorescence studies indicated conformational changes in α-LA upon SHMP addition, and dye-binding assays with ThT and Congo Red demonstrated the formation of amyloid-like aggregates. Far-UV circular dichroism (CD) data suggested a structural transition from α-helical to β-structures in α-LA in the presence of SHMP at pH 2.0. Molecular docking studies confirmed stronger interactions between α-LA and SHMP at pH 2.0 (ΔG = -6.2 kcal/mol) compared to pH 7.4 (ΔG = -5.3 kcal/mol), driven by electrostatic forces and hydrogen bonding. These results suggest that SHMP induces amyloid-like aggregation of α-LA, particularly at acidic pH.

Trace_y: Software algorithms for structural analysis of individual helical filaments by three-dimensional contact point reconstruction atomic force microscopy

Atomic force microscopy (AFM) is a powerful and increasingly accessible technology that has a wide range of bio-imaging applications. AFM is capable of producing detailed three-dimensional topographical images with high signal-to-noise ratio, which enables the structural features of individual molecules to be studied without the need for ensemble averaging. Here, a software tool Trace_y, designed to reconstruct the three-dimensional surface envelopes of individual helical filament structures from topographical AFM images, is presented. Workflow using Trace_y is demonstrated on the structural analysis of individual helical amyloid protein fibrils where the assembly mechanism of heterogeneous, complex and diverse fibril populations due to structural polymorphism is not understood. The algorithms presented here allow structural information encoded in topographical AFM height images to be extracted and understood as three-dimensional (3D) contact point clouds. This approach will facilitate the use of AFM in structural biology to understand molecular structures and behaviors at individual molecule level.

Characterizing heterogeneity in amyloid formation processes

Protein aggregation is a complex process, consisting of a large number of pathways connecting monomers and mature amyloid fibrils. Recent advances in structure determination techniques, such as solid-state NMR and cryoEM, have allowed the determination of atomic resolution structures of fibril polymorphs, but most of the intermediate stages of the process including oligomer formation remain unknown. Proper characterization of the heterogeneity of the process is critical not only for physical and chemical understanding of the aggregation process but also for elucidation of the disease mechanisms and identification of therapeutic targets. This article reviews recent developments in the characterization of heterogeneity in amyloid formation processes.

Sequence-based identification of amyloidogenic β-hairpins reveals a prostatic acid phosphatase fragment promoting semen amyloid formation

β-Structure-rich amyloid fibrils are hallmarks of several diseases, including Alzheimer's (AD), Parkinson's (PD), and type 2 diabetes (T2D). While amyloid fibrils typically consist of parallel β-sheets, the anti-parallel β-hairpin is a structural motif accessible to amyloidogenic proteins in their monomeric and oligomeric states. Here, to investigate implications of β-hairpins in amyloid formation, potential β-hairpin-forming amyloidogenic segments in the human proteome were predicted based on sequence similarity with β-hairpins previously observed in Aβ, α-synuclein, and islet amyloid polypeptide, amyloidogenic proteins associated with AD, PD, and T2D, respectively. These three β-hairpins, established upon binding to the engineered binding protein β-wrapin AS10, are characterized by proximity of two sequence segments rich in hydrophobic and aromatic amino acids, with high β-aggregation scores according to the TANGO algorithm. Using these criteria, 2505 potential β-hairpin-forming amyloidogenic segments in 2098 human proteins were identified. Characterization of a test set of eight protein segments showed that seven assembled into Thioflavin T-positive aggregates and four formed β-hairpins in complex with AS10 according to NMR. One of those is a segment of prostatic acid phosphatase (PAP) comprising amino acids 185-208. PAP is naturally cleaved into fragments, including PAP(248-286) which forms functional amyloid in semen. We find that PAP(185-208) strongly decreases the protein concentrations required for fibril formation of PAP(248-286) and of another semen amyloid peptide, SEM1(86-107), indicating that it promotes nucleation of semen amyloids. In conclusion, β-hairpin-forming amyloidogenic protein segments could be identified in the human proteome with potential roles in functional or disease-related amyloid formation.

Landscape of intrinsically disordered proteins in mental disorder diseases

Disrupted genes linked to mental disorders sometimes exhibit characteristics of Intrinsically Disordered Proteins (IDPs). However, few studies have comprehensively explored the functional associations between protein disorder properties and different psychiatric disorders. In this study, we collected disrupted proteins for seven mental diseases (MDD, SCZ, BP, ID, AD, ADHD, ASD) and a control dataset from normal brains. After calculating the disorder scores for each protein, we thoroughly compared the proportions and functions of IDPs between differentially expressed proteins in each disease and healthy controls. Our findings revealed that disrupted proteins, particularly in ASD and ADHD, contain more IDPs than controls from normal brains. Distinct patterns in disorder properties were observed among different mental disorders. Functional enrichment analysis indicated that IDPs in mental disorders were associated with neurodevelopment, synaptic signaling, and gene expression regulatory pathways. In addition, we analyzed the proportion and function of liquid-phase-separated proteins (LLPS) in psychiatric disorders, finding that LLPS proteins are mainly enriched in pathways related to neurodevelopment and inter-synaptic signaling. Furthermore, to validate our findings, we conducted an analysis of differentially expressed genes in an ASD cohort, revealing that the encoded proteins also exhibit a higher proportion of IDPs. Notably, these IDPs were particularly enriched in pathways related to neurodevelopment, including head development, a process known to be disrupted in ASD. Our study sheds light on the crucial role of IDPs in psychiatric disorders, enhancing our understanding of their molecular mechanisms.

Exploring the Impact of Physiological C-Terminal Truncation on α-Synuclein Conformations to Unveil Mechanisms Regulating Pathological Aggregation

Emerging evidence suggests that physiological C-terminal truncation of α-synuclein (αS) plays a critical role in regulating liquid-liquid phase separation and promoting amyloid aggregation, processes implicated in neurodegenerative diseases such as Parkinson's disease (PD). However, the molecular mechanisms through which C-terminal truncation influences αS conformation and modulates its aggregation remain poorly understood. In this study, we investigated the impact of C-terminal truncation on αS conformational dynamics by comparing full-length αS1-140 with truncated αS1-103 monomers using atomistic discrete molecular dynamics simulations. Our findings revealed that both αS1-140 and αS1-103 primarily adopted helical conformations around residues 7-32, while residues 36-95, located in the second half of the N-terminal and NAC domains, predominantly formed a dynamic β-sheet core. The C-terminus of αS1-140 was largely unstructured and dynamically wrapped around the β-sheet core. While residues 1-95 exhibited similar secondary structure propensities in both αS1-140 and αS1-103, the dynamic capping by the C-terminus in αS1-140 slightly enhanced β-sheet formation around residues 36-95. In contrast, key aggregation-driving regions (residues 2-9, 36-42, 45-57, and 68-78) were dynamically shielded by the C-terminus in αS1-140, reducing their exposure and potentially preventing interpeptide interactions that drive aggregation. C-terminal truncation, on the other hand, increased the exposed surface area of these aggregation-prone regions, thereby enhancing interpeptide interactions, phase separation, and amyloid aggregation. Overall, our simulations provide valuable insights into the conformational effects of C-terminal truncation on αS and its role in promoting pathological aggregation.

Single-Molecule Kinetic Observation of Antibody Interactions with Growing Amyloid β Fibrils

Understanding the dynamic assembly process of amyloid β (Aβ) during fibril formation is essential for developing effective therapeutic strategies against Alzheimer's disease. Here, we employed high-speed atomic force microscopy to observe the growth of Aβ fibrils at the single-molecule level, focusing specifically on their interaction with anti-Aβ antibodies. Our findings show that fibril growth consists of intermittent periods of elongation and pausing, which are dictated by the alternating addition of Aβ monomers to protofilaments. We highlight the distinctive interaction of antibody 4396C, which specifically binds to the fibril ends in the paused state, suggesting a unique mechanism to hinder fibril elongation. Through real-time visualization of fibril growth and antibody interactions combined with molecular simulation, this study provides a refined understanding of Aβ assembly during fibril formation and suggests novel strategies for Alzheimer's therapy aimed at inhibiting the fibril elongation.

Advanced glycation end-products accelerate amyloid deposits in adipocyte's lipid droplets

Adipose tissue dysfunction is central to insulin resistance, and the emergence of type 2 diabetes (T2D) is associated with elevated levels of carbonyl metabolites from glucose metabolism. In this study, using methylglyoxal (MGO) and glycolaldehyde (GAD) carbonyl metabolites induced protein glycation, leading to misfolding and β-sheet formation and generation of advanced glycation end products (AGEs). The formed AGEs compromise adipocytes activity. Microscopic and spectroscopic assays were used to examine the impact of MGO and GAD on lipid droplet-associated proteins. The results provide information about how these conditions lead to the appearance of glycated and amyloidogenic proteins formation that hinders metabolism and autophagy in adipocytes. We measured the beneficial effects of metformin (MET), an anti-diabetic drug, on misfolded protein as assessed by thioflavin (ThT) spectroscopy and improved autophagy, determined by LC3 staining. In vitro findings were complemented by in vivo analysis of white adipose tissue (WAT), where lipid droplet-associated β-amyloid deposits were predominantly linked to adipose triglyceride lipase (ATGL), a lipid droplet protein. Bioinformatics, imaging, biochemical and MS/MS methods affirm ATGL's glycation and its role in β-sheet secondary structure formation. Our results highlighted the pronounced presence of amyloidogenic proteins in adipocytes treated with carbonyl compounds, potentially reshaping our understanding of adipocyte altered activity in the context of T2D. This in-depth exploration offers novel perspectives on related pathophysiology and underscores the potential of adipocytes as pivotal therapeutic targets, bridging T2D, amyloidosis, protein glycation, and adipocyte malfunction.

iAmyP: A Multi-view Learning for Amyloidogenic Hexapeptides Identification Based on Sequence Least Squares Programming

The development of peptide drug is hindered by the risk of amyloidogenic aggregation; if peptides tend to aggregate in this manner, they may be unsuitable for drug design. Computational methods aimed at predicting amyloidogenic sequences often face challenges in extracting high-quality features, and their predictive performance can be enchanced. To surmount these challenges, iAmyP was introduced as a specialized computational tool designed for predicting amyloidogenic hexapeptides. Utilizing multi-view learning, iAmyP incorporated sequence, structural, and evolutionary features, performing feature selection and feature fusion through recursive feature elimination and attention mechanisms. This amalgamation of features and subsequent feature selection and fusion lead to optimal performance facilitated by an optimization algorithm based on sequence least squares programming. Notably, iAmyP exhibited robust generalization for peptides with lengths of 7-10 amino acids. The role of hydrophobic amino acids in the aggregation process is critical, and a thorough analysis have significantly enhanced our insight into their significance in amyloidogenic hexapeptides. This tool represented an advancement in the development of peptide therapeutics by providing an understanding of amyloidogenic aggregation, establishing itself as a valuable framework for assessing amyloidogenic sequences. The data and code can be freely accessed at https://github.com/xialab-ahu/iAmyP .

Principles and Biomedical Applications of Self-Assembled Peptides: Potential Treatment of Type 2 Diabetes Mellitus

Type 2 diabetes mellitus (T2DM) is the most prevalent metabolic disorder worldwide. There have been tremendous efforts to find a safe and prolonged effective therapy for its treatment. Peptide hormones, from certain organisms in the human body, as the pharmaceutical agents, have shown outstanding profiles of efficacy and safety in plasma glucose regulation. Their therapeutic promises have undergone intensive investigations via examining their physicochemical and pharmacokinetic properties. Their major drawback is their short half-life in vivo. To address this challenge, researchers have recently started to apply the state-of-the-art molecular self-assembly on peptide hormones to form nanofibrillar structures, as a smart nanotherapeutic drug delivery technique, to tremendously enhance their prolonged bioactivity in vivo. This revolutionary therapeutic approach would significantly improve patient compliance. First, this review provides a comprehensive summary on the pathophysiology of T2DM, various efforts to treat this chronic disorder, and the limitations and drawbacks of these treatment approaches. Next, this review lays out detailed insights on various aspects of peptide self-assembly: adverse effects, potential applications in nanobiotechnology, thermodynamics and kinetics of the process, as well as the molecular structures of the self-assembled configurations. Furthermore, this review elucidates the recent efforts on applying reversible human-derived peptide self-assembly to generate highly organized smart nanostructured drug formulations known as nanofibrils to regulate and prolong the bioactivity of the human gut hormone peptides in vivo to treat T2DM. Finally, this review highlights the future research directions to advance the knowledge on the state-of-the-art peptide self-assembly process to apply the revolutionary smart nanotherapeutics for treatment of chronic disorders such as T2DM with highly improved patient compliance.

Enhanced Photodynamic Therapy for Neurodegenerative Diseases: Development of Azobenzene-Spiropyran@Gold Nanoparticles for Controlled Singlet Oxygen Generation

The development of durable photosensitizers is pivotal for advancing phototherapeutic applications in biomedicine. Here, we introduce a core-shell azobenzene-spiropyran structure on gold nanoparticles, engineered to enhance singlet oxygen generation. These nano-photosensitizers exhibit increased structural stability and thermal resistance, as demonstrated by slowed O-N-C bond recombination dynamics via in-situ Raman spectroscopy. Notably, the in-situ formation of merocyanine and a light-induced compact shell arrangement extend its half-life from 47 minutes to over 154 hours, significantly boosting singlet oxygen output. The nano-photosensitizer also shows high biocompatibility and notably inhibits tau protein aggregation in neural cells, even with phosphatase inhibitors. Further, it promotes dendritic growth in neuro cells, doubling typical lengths. This work not only advances chemical nanotechnology but also sets a foundation for developing long-lasting phototherapy agents for treating neurodegenerative diseases.

Facile synthesis of EGCG modified Au nanoparticles and their inhibitory effects on amyloid protein aggregation

Preventing β-amyloid (Aβ) peptide aggregation by Au nanoparticles (NPs) is a promising strategy for the treatment of Alzheimer's disease. However, construction of Au nanostructures with easy preparation and high therapeutic efficiency is still a challenge. Herein, one-step pulsed laser ablation in water is used to fabricate epigallocatechin-3-gallate (EGCG) modified Au (Au-EGCG) NPs with uniform size. The as-obtained Au-EGCG NPs can effectively inhibit β-amyloid (1-42) peptide (Aβ42) aggregation by the interaction with peptides, which is confirmed by transmission electron microscopy (TEM), fluorescence spectroscopy (thioflavin T (ThT), tyrosine and 8-anilinonaphthalene-1-sulfonic acid (ANS) assays), and Fourier transform infrared (FT-IR) spectroscopy. Besides, they can also effectively attenuate Aβ42-induced cytotoxicity based on the cell viability experiments. This work provides a facile approach to synthesize the surface-functionalized Au NPs for enhanced inhibition of Aβ aggregation and amelioration of Aβ-induced cytotoxicity.

NMR studies of amyloid interactions

Amyloid fibrils are insoluble, fibrous nanostructures that accumulate extracellularly in biological tissue during the progression of several human disorders, including Alzheimer's disease (AD) and type 2 diabetes. Fibrils are assembled from protein monomers via the transient formation of soluble, cytotoxic oligomers, and have a common molecular architecture consisting of a spinal core of hydrogen-bonded protein β-strands. For the past 25 years, NMR spectroscopy has been at the forefront of research into the structure and assembly mechanisms of amyloid aggregates. Until the recent boom in fibril structure analysis by cryo-electron microscopy, solid-state NMR was unrivalled in its ability to provide atomic-level models of amyloid fibril architecture. Solution-state NMR has also provided complementary information on the early stages in the amyloid assembly mechanism. Now, both NMR modalities are proving to be valuable in unravelling the complex interactions between amyloid species and a diverse range of physiological metal ions, molecules and surfaces that influence the assembly pathway, kinetics, morphology and clearance in vivo. Here, an overview is presented of the main applications of solid-state and solution-state NMR for studying the interactions between amyloid proteins and biomembranes, glycosaminoglycan polysaccharides, metal ions, polyphenols, synthetic therapeutics and diagnostics. Key NMR methodology is reviewed along with examples of how to overcome the challenges of detecting interactions with aggregating proteins. The review heralds this new role for NMR in providing a comprehensive and pathologically-relevant view of the interactions between protein and non-protein components of amyloid. Coverage of both solid- and solution-state NMR methods and applications herein will be informative and valuable to the broad communities that are interested in amyloid proteins.

New Hypothesis on Enhancing β-Sheet Formation during the Tau Fragment Dimer Transition from a Flexible Monomer: Insights into Primary Nucleation Processes by Histidine Behaviors

Slight perturbations in pH can have significant effects on the primary nucleation processes of the tau protein. The behaviors of histidine due to its pivotal role in modulating H-bonding network interactions and electrostatic interactions have garnered considerable attention, as it can influence the structural characteristics and aggregation properties. However, the nucleation mechanisms and related intermediates are still unclear. In the current study, we performed nine independent replica exchange molecular dynamics simulations to investigate dimer formation involving R3(εδ) in conjunction with the R1, R2, and R4 monomers. Our findings substantiate that, in comparison to R1-R3(εδ) and R4-R3(εδ) systems, the R2-R3(εδ) systems consistently manifest the highest averaged β-sheet content, with the fundamental feature of R3(εδ) promoting R2 rearrangement. Our comprehensive analysis reveals that high-β-sheet-rich systems exhibit a conserved three/five β-strand structure. In these β-strand-rich systems, one chain [R1/R2/R4 or R3(εδ)] with robust intrachain H-bonding interactions coordinates with another chain through interchain H-bonding interactions, contributing to the overall stability. Furthermore, we discuss distinct histidine behaviors, including backbone/side chain interactions and donor/acceptor roles. This study provides a comprehensive understanding of the aggregation propensities of soluble tau oligomers and sheds light on the primary nucleation mechanism. It contributes to a new perspective for understanding protein folding and misfolding.

A review of recent clinical trials to evaluate disease-modifying therapies in the treatment of cardiac amyloidosis

Cardiac amyloidosis (CA) is a serious condition that results in infiltrative cardiomyopathy and heart failure with preserved ejection fraction (HFpEF) that is caused by the extracellular deposition of amyloid fibrils within heart tissue. While many important features of CA have been known for years, its prevalence in elderly patients with HF is increasingly being recognized. Plasma cells produce monoclonal immunoglobulin light chains which results in the formation and aggregation of amyloid fibrils that are responsible for AL amyloidosis. CA is classified as originating from either transthyretin (ATTR) or light chain (AL) amyloidosis. ATTR CA may result from a genetic mutation in the TTR gene, which is inherited (ATTRv), or from age-related deposition from wild-type ATTR (ATTRwt). Cardiac involvement in AL amyloidosis is attributed to either of two mechanisms: the extracellular deposition of amyloid fibril in the myocardium, or direct cardiotoxicity from the fibril aggregates. Typing of amyloid fibrils, a critical determinant of therapy, has also improved with wider availability of laser capture and mass spectrometry of histologic specimens. Specific and accurate evaluation of CA is now possible using cardiac magnetic resonance imaging and bone scintigraphy tracers. Survival in CA has improved markedly as novel chemotherapy agents have become available, but challenges remain in advanced disease. Broadening the amyloid-specific therapeutic landscape to include RNA inhibitors, fibril formation stabilizers and inhibitors, and immunotherapeutic targeting of amyloid deposits holds promise and may improve outcomes in systemic and cardiac amyloidoses. Treatment strategies for CA has recently undergone transformative changes, leading to some progress in outcomes for certain patients. Here, we discuss the basic features of CA as well as the emergence of novel, disease-modifying strategies that have been recently evaluated in clinical trials for the treatment of CA.

Optimal strategy for stabilizing protein folding intermediates

To manipulate the protein concentration at a certain functional state through chemical stabilizers is crucial for protein-related studies. It not only plays a key role in protein structure analysis and protein folding kinetics, but also affects protein functionality to a large extent and thus has wide applications in medicine, food industry, etc. However, due to concerns about side effects or financial costs of stabilizers, identifying optimal strategies for enhancing protein stability with a minimal amount of stabilizers is of great importance. Here, we prove that either for the fixed terminal time (including both finite and infinite cases) or for the free one, the optimal control strategy for stabilizing the folding intermediates with a linear strategy for stabilizer addition belongs to the class of bang-bang controls. The corresponding optimal switching time is derived analytically, whose phase diagram with respect to several key parameters is explored in detail. The bang-bang control will be broken when nonlinear strategies for stabilizer addition are adopted. Moreover, the above theory is applied to the stabilization of erythropoietin by ten different kinds of chemicals, providing theoretical guidance for the selection and rational usage of stabilizers. Our current study on optimal strategies for protein stabilizers not only offers deep insights into the general picture of protein folding kinetics but also provides valuable theoretical guidance on treatments for protein-related diseases in medicine.

Distance-Dependent Tryptophan-Induced Quenching of Thioflavin T Defines the Amyloid Core Architecture

Thioflavin T (ThT) is widely employed as a fluorogenic marker for amyloid formation. ThT fluorescence is utilized to detect amyloid fibrils as well as to follow aggregation kinetics. Here, we make a unique case to demonstrate that site-specific tryptophan-induced fluorescence quenching of ThT bound to the α-synuclein amyloid can define the central amyloid core. We show that distance-dependent quenching of amyloid-bound ThT by site-specifically incorporated tryptophan maps the proximal and distal locations of the polypeptide chain within amyloid fibrils. Our studies indicate that tryptophan-induced fluorescence quenching is dominated by the static quenching mechanism. Our findings underscore the utility of site-specific amino acid-based quenching of ThT fluorescence to characterize the core architecture of amyloid derived from a wide range of proteins.

Proteomic Evidence for Amyloidogenic Cross-Seeding in Fibrinaloid Microclots

In classical amyloidoses, amyloid fibres form through the nucleation and accretion of protein monomers, with protofibrils and fibrils exhibiting a cross-β motif of parallel or antiparallel β-sheets oriented perpendicular to the fibre direction. These protofibrils and fibrils can intertwine to form mature amyloid fibres. Similar phenomena can occur in blood from individuals with circulating inflammatory molecules (and also some originating from viruses and bacteria). Such pathological clotting can result in an anomalous amyloid form termed fibrinaloid microclots. Previous proteomic analyses of these microclots have shown the presence of non-fibrin(ogen) proteins, suggesting a more complex mechanism than simple entrapment. We thus provide evidence against such a simple entrapment model, noting that clot pores are too large and centrifugation would have removed weakly bound proteins. Instead, we explore whether co-aggregation into amyloid fibres may involve axial (multiple proteins within the same fibril), lateral (single-protein fibrils contributing to a fibre), or both types of integration. Our analysis of proteomic data from fibrinaloid microclots in different diseases shows no significant quantitative overlap with the normal plasma proteome and no correlation between plasma protein abundance and their presence in fibrinaloid microclots. Notably, abundant plasma proteins like α-2-macroglobulin, fibronectin, and transthyretin are absent from microclots, while less abundant proteins such as adiponectin, periostin, and von Willebrand factor are well represented. Using bioinformatic tools, including AmyloGram and AnuPP, we found that proteins entrapped in fibrinaloid microclots exhibit high amyloidogenic tendencies, suggesting their integration as cross-β elements into amyloid structures. This integration likely contributes to the microclots' resistance to proteolysis. Our findings underscore the role of cross-seeding in fibrinaloid microclot formation and highlight the need for further investigation into their structural properties and implications in thrombotic and amyloid diseases. These insights provide a foundation for developing novel diagnostic and therapeutic strategies targeting amyloidogenic cross-seeding in blood clotting disorders.

Different charged biopolymers induce α-synuclein to form fibrils with distinct structures

The aggregation of α-synuclein (α-syn) into amyloid fibrils, a key process in the development of Parkinson's disease (PD) and other synucleinopathies, is influenced by a range of factors such as charged biopolymers, chaperones, and metabolites. However, the specific impacts of different biopolymers on α-syn fibril structure are not well understood. In our work, we found that different polyanions and polycations, such as polyphosphate (polyP), polyuridine (polyU), and polyamines (including putrescine, spermidine, and spermine), markedly altered the fibrillation kinetics of α-syn in vitro. Furthermore, the seeding assay revealed distinct cross-seeding capacities across different biopolymer-induced α-syn fibrils, suggesting the formation of structurally distinct strains under different conditions. Utilizing cryo-electron microscopy (cryo-EM), we further examined the detailed structural configuration of α-syn fibrils formed in the presence of these biopolymers. Notably, we found that while polyamines do not change the atomic structure of α-syn fibrils, polyU and polyP induce the formation of distinct amyloid fibrils, exhibiting a range of structural polymorphs. Our work offers valuable insights into how various charged biopolymers affect the aggregation process and the resultant structures of α-syn fibrils, thereby enhancing our understanding of the structural variations in α-syn fibrils across different pathological conditions.

CsgA gatekeeper residues control nucleation but not stability of functional amyloid

Functional amyloids, beneficial to the organism producing them, are found throughout life, from bacteria to humans. While disease-related amyloids form by uncontrolled aggregation, the fibrillation of functional amyloid is regulated by complex cellular machinery and optimized sequences, including so-called gatekeeper residues such as Asp. However, the molecular basis for this regulation remains unclear. Here we investigate how the introduction of additional gatekeeper residues affects fibril formation and stability in the functional amyloid CsgA from E. coli. Step-wise introduction of additional Asp gatekeepers gradually eliminated fibrillation unless preformed fibrils were added, illustrating that gatekeepers mainly affect nucleus formation. Once formed, the mutant CsgA fibrils were just as stable as wild-type CsgA. HSQC NMR spectra confirmed that CsgA is intrinsically disordered, and that the introduction of gatekeeper residues does not alter this ensemble. NMR-based Dark-state Exchange Saturation Transfer (DEST) experiments on the different CsgA variants, however, show a decrease in transient interactions between monomeric states and the fibrils, highlighting a critical role for these interactions in the fibrillation process. We conclude that gatekeeper residues affect fibrillation kinetics without compromising structural integrity, making them useful and selective modulators of fibril properties.

Amyloid Nanofibril-Assisted Spray Drying of Crumpled Supraparticles

Nanofibrils are known to improve the cohesion of supraparticle (SP) assemblies. However, tailoring the morphology of SPs using nanofibrillar additives is not well developed. Herein, β-lactoglobulin amyloid nanofibrils (ANFs) are investigated as means to impart morphological control over the assembly process of spray-dried SPs composed of 10-100 nm silica nanoparticles (SiNPs). Phytoglycogen (PG) and silver nanowires (AgNWs) are used to assess the influence of building block softness and aspect ratio, respectively. The results demonstrate that ANFs promote the onset of structural arrest during the particle consolidation enabling the preparation of corrugated SP morphologies. The critical ANF loading required to induce SP corrugation increases by roughly 1 vol% for every 10-nm increase in SiNP diameter, while the ensuing ANF network density decreases with SiNP volume fraction and increases with SiNP diameter. Results imply that ANF length starts to become influential when it approaches the SiNP diameter. ANFs display a reduced effectiveness in altering soft PG SP morphology compared with hard SiNPs of comparable size. In SiNP-AgNW SPs, ANFs induce a toroid-to-corrugated morphology transformation for sufficiently large SPs and small SiNPs. The results illustrate that ANFs are effective additives for the morphological engineering of spray-dried SPs important for numerous applications.

Diagnosis and therapy of Alzheimer's disease: Light-driven heterogeneous redox processes

Light-driven heterogeneous processes are promising approaches for diagnosing and treating Alzheimer's disease (AD) by regulating its relevant biomolecules. The molecular understanding of the heterogeneous interface environment and its interaction with target biomolecules is important. This review critically appraises the advances in AD early diagnosis and therapy employing heterogeneous light-driven redox processes, encompassing photoelectrochemical (PEC) biosensing, photodynamic therapy, photothermal therapy, PEC therapy, and photoacoustic therapy. The design strategies for heterogeneous interfaces based on target biomolecules and applications are also compiled. Finally, the remaining challenges and future perspectives are discussed. The present review may promote the fundamental understanding of AD diagnosis and therapy and facilitate interdisciplinary studies at the junction of nanotechnology and bioscience.

Massive experimental quantification of amyloid nucleation allows interpretable deep learning of protein aggregation

Protein aggregation is a pathological hallmark of more than fifty human diseases and a major problem for biotechnology. Methods have been proposed to predict aggregation from sequence, but these have been trained and evaluated on small and biased experimental datasets. Here we directly address this data shortage by experimentally quantifying the amyloid nucleation of >100,000 protein sequences. This unprecedented dataset reveals the limited performance of existing computational methods and allows us to train CANYA, a convolution-attention hybrid neural network that accurately predicts amyloid nucleation from sequence. We adapt genomic neural network interpretability analyses to reveal CANYA's decision-making process and learned grammar. Our results illustrate the power of massive experimental analysis of random sequence-spaces and provide an interpretable and robust neural network model to predict amyloid nucleation.

Enhancing amyloid beta inhibition and disintegration by natural compounds: A study utilizing spectroscopy, microscopy and cell biology

Amyloid proteins and peptides play a pivotal role in the etiology of various neurodegenerative diseases, including Alzheimer's disease (AD). Synthetically designed small molecules/ peptides/ peptidomimetics show promise towards inhibition of various kinds of amyloidosis. However, exploration of compounds isolated from natural extracts having such potential is lacking. Herein, we have investigated the repurposing of a traditional Indian medicine Lasunadya Ghrita (LG) in AD. LG is traditionally used to treat gut dysregulation and mental illnesses. Various extracts of LG were obtained, characterized, and analyzed for inhibition of Aβ aggregation. Biophysical studies show that the water extract of LG (LGWE) is more potent in inhibiting Aβ peptide aggregation and defibrillation of Aβ40/Aβ42 aggregates. NMR studies showed that LGWE binds to the central hydrophobic area and C-terminal residues of Aβ40/Aβ42, thereby modulating the aggregation, and reducing cell membrane damage. Additionally, LGWE rescues Aβ toxicity in neuronal SH-SY5Y cells evident from decreases in ROS generation, membrane leakage, cellular apoptosis, and calcium dyshomeostasis. Notably, LGWE is non-toxic to neuronal cells and mouse models. Our study thus delves into the mechanistic insights of a repurposed drug LGWE with the potential to ameliorate Aβ induced neuroinflammation.

Authentic hSAA related with AA amyloidosis: New method of purification, folding and amyloid polymorphism

The secondary amyloidosis of humans is caused by the formation of hSAA fibrils in different organs and tissues. Until now hSAA was thought to have low amyloidogenicity in vitro and the majority of SAA aggregation experiments were done using murine protein or hSAA non-pathogenic isoforms. In this work a novel purification method for recombinant hSAA was introduced, enabling to obtain monomeric protein capable of amyloid aggregation under physiological conditions. The stability and amyloid aggregation of hSAA have been examined using a wide range of biophysical methods. It was shown that the unfolding of monomeric protein occurs through the formation of molten globule-like intermediate state. Polymorphism of hSAA amyloids was discovered to depend on the solution pH. At pH 8.5, rapid protein aggregation occurs, which leads to the formation of twisted short fibrils. Even a slight decrease of the pH to 7.8 results in delayed aggregation with the formation of long straight amyloids composed of laterally associated protofilaments. Limited proteolysis experiments have shown that full-length hSAA is involved in the formation of intermolecular interactions in both amyloid polymorphs. The results obtained, and the experimental approach used in this study can serve as a basis for further research on the mechanism of authentic hSAA amyloid formation.

Aggregation of the amyloid-β peptide (Aβ40) within condensates generated through liquid-liquid phase separation

The deposition of the amyloid-β (Aβ) peptide into amyloid fibrils is a hallmark of Alzheimer's disease. Recently, it has been reported that some proteins can aggregate and form amyloids through an intermediate pathway involving a liquid-like condensed phase. These observations prompted us to investigate the phase space of Aβ. We thus explored the ability of Aβ to undergo liquid-liquid phase separation, and the subsequent liquid-to-solid transition that takes place within the resulting condensates. Through the use of microfluidic approaches, we observed that the 40-residue form of Αβ (Αβ40) can undergo liquid-liquid phase separation, and that accessing a liquid-like intermediate state enables Αβ40 to self-assemble and aggregate into amyloid fibrils through this pathway. These results prompt further studies to investigate the possible role of Αβ liquid-liquid phase separation and its subsequent aggregation in the context of Alzheimer's disease and more generally on neurodegenerative processes.

Aggregation Rules of Short Peptides

The elucidation of aggregation rules for short peptides (e.g., tetrapeptides and pentapeptides) is crucial for the precise manipulation of aggregation. In this study, we derive comprehensive aggregation rules for tetrapeptides and pentapeptides across the entire sequence space based on the aggregation propensity values predicted by a transformer-based deep learning model. Our analysis focuses on three quantitative aspects. First, we investigate the type and positional effects of amino acids on aggregation, considering both the first- and second-order contributions. By identifying specific amino acids and amino acid pairs that promote or attenuate aggregation, we gain insights into the underlying aggregation mechanisms. Second, we explore the transferability of aggregation propensities between tetrapeptides and pentapeptides, aiming to explore the possibility of enhancing or mitigating aggregation by concatenating or removing specific amino acids at the termini. Finally, we evaluate the aggregation morphologies of over 20,000 tetrapeptides, regarding the morphology distribution and type and positional contributions of each amino acid. This work extends the existing aggregation rules from tripeptide sequences to millions of tetrapeptide and pentapeptide sequences, offering experimentalists an explicit roadmap for fine-tuning the aggregation behavior of short peptides for diverse applications, including hydrogels, emulsions, or pharmaceuticals.

Unraveling the Structure and Dynamics of Ac-PHF6-NH2 Tau Segment Oligomers

The aggregation of the proteins tau and amyloid-β is a salient feature of Alzheimer's disease, the most common form of neurodegenerative disorders. Upon aggregation, proteins transition from their soluble, monomeric, and functional state into insoluble, fibrillar deposits through a complex process involving a variety of intermediate species of different morphologies, including monomers, toxic oligomers, and insoluble fibrils. To control and direct peptide aggregation, a complete characterization of all species present and an understanding of the molecular processes along the aggregation pathway are essential. However, this is extremely challenging due to the transient nature of oligomers and the complexity of the reaction networks. Therefore, we have employed a combined approach that allows us to probe the structure and kinetics of oligomeric species, following them over time as they form fibrillar structures. Targeting the tau protein peptide segment Ac-PHF6-NH2, which is crucial for the aggregation of the full protein, soft nano-electrospray ionization combined with ion mobility mass spectrometry has been employed to study the kinetics of heparin-induced intact oligomer formation. The oligomers are identified and characterized using high-resolution ion mobility mass spectrometry, demonstrating that the addition of heparin does not alter the structure of the oligomeric species. The kinetics of fibril formation is monitored through a Thioflavin T fluorescence assay. Global fitting of the kinetic data indicates that secondary nucleation plays a key role in the aggregation of the Ac-PHF6-NH2 tau segment, while the primary nucleation rate is greatly accelerated by heparin.

A Peptide Strategy for Inhibiting Different Protein Aggregation Pathways

Protein aggregation correlates with many human diseases. Protein aggregates differ in structure and shape. Strategies to develop effective aggregation inhibitors that reach the clinic failed so far. Here, we developed a family of peptides targeting early aggregation stages for both amorphous and fibrillar aggregates of proteins unrelated in sequence and structure. They act on dynamic precursors before mechanistic differentiation takes place. Using peptide arrays, we first identified peptides inhibiting the amorphous aggregation of a molten globular, aggregation-prone mutant of the Axin tumor suppressor. Optimization revealed that the peptides activity did not depend on their sequences but rather on their molecular determinants: a composition of 20-30 % flexible, 30-40 % aliphatic and 20-30 % aromatic residues, a hydrophobicity/hydrophilicity ratio close to 1, and an even distribution of residues of different nature throughout the sequence. The peptides also suppressed fibrillation of Tau, a disordered protein that forms amyloids in Alzheimer's disease, and slowed down that of Huntingtin Exon1, an amyloidogenic protein in Huntington's disease, both entirely unrelated to Axin. Our compounds thus target early stages of different aggregation mechanisms, inhibiting both amorphous and amyloid aggregation. Such cross-mechanistic, multi-targeting aggregation inhibitors may be lead compounds for developing drug candidates against various protein aggregation diseases.

Monitoring and analysis of mitochondrial precursor protein aggregates in the cytosol

The vast majority of mitochondrial precursor proteins is synthesized in the cytosol and subsequently imported into the organelle with the help of targeting signals that are present within these proteins. Disruptions in mitochondrial import will result in the accumulation of the organellar precursors in the cytosol of the cell. If mislocalized proteins exceed their critical concentrations, they become prone to aggregation. Under certain circumstances, protein aggregation becomes an irreversible process, which eventually endangers cellular health. Impairment in mitochondrial biogenesis and its effect on cellular protein homeostasis were recently linked to neurodegeneration, therefore placing this process in the center of attention. In this chapter, we are presenting a set of techniques that allows to monitor and study mitochondrial precursor protein aggregates upon mitochondrial dysfunction in the cytosol of both yeast and human cells.