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.

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.

Minimalist Adjuvant-Free Nano-Vaccine Based on Antigen Self-Assembled Amyloid-Like Fibrils to Induce Potent Immune Response

The development of cancer vaccines is at the forefront of cancer immunotherapy. Most existing strategies to induce an efficient anti-tumor immune response rely on molecular adjuvants and the incorporation of complex synthetic vectors into vaccine formulations. In contrast, this study introduces a one-step engineering technique to assemble the model antigen, Ovalbumin (OVA), into amyloid aggregates, leveraging biomimetic folding and aggregation to create non-fibrillar OVA globular aggregates and OVA amyloid-like fibrils as single-component, adjuvant-free vaccines. Notably, the OVA amyloid-like fibrils induced stronger immune responses compared to the native form, as evidenced by robust humoral immune reactions and the establishment of immune memory. These enhanced responses can be attributed to the self-adjuvant effect of the unique assembled structure, which preserves antigenic epitopes, improves antigen stability, facilitates antigen internalization, prolongs retention at the injection site, enhances antigen trafficking to the lymphoid organs, and promotes increased secretion of antibodies and cytokines. Furthermore, the efficacy of the vaccine was validated in a high OVA-expressing tumor model, demonstrating the potential of OVA amyloid-like fibrils as an effective vaccine for cancer immunoprevention. This minimalist self-adjuvant vaccine strategy holds promising implications for cancer immunotherapy and can inform the design of other protein antigen-based vaccines.

Valorization of Protein Materials Through Mechanochemistry and Self-Assembly

The concept of combining mixing of solids by milling (a type of mechanochemistry) with aqueous self-assembly provides interesting possibilities for energy efficient production of advanced nanomaterials. Many proteins are outstanding building blocks for self-assembly, a prominent example being the conversion of proteins into protein nanofibrils (PNFs) - a structure related to amyloid fibrils. PNFs have attractive mechanical properties and have a tendency to form ordered materials. They are accordingly of interest as materials for bioplastics and potentially also for more high-tech applications. In this concept article we highlight our effort on valorization of such proteins with hydrophobic organic compounds such an organic dyes and drug molecules, by developing scalable methodology combining mechanochemistry and self-assembly. Compared to more established methodology, mechanochemical methodology is a valuable complement as it allows potential scalable production of hybrids between e. g. proteins and highly hydrophobic compounds - a class of hybrid material that is difficult to access by other means. This may allow for development of sustainable processes for fabrication of advanced protein-based materials derivable from renewable source materials.

Biodegradable and Implantable Triboelectric Nanogenerator Improved by β-Lactoglobulin Fibrils-Assisted Flexible PVA Porous Film

Triboelectric nanogenerators (TENGs) are highly promising as implantable, degradable energy sources and self-powered sensors. However, the degradable triboelectric materials are often limited in terms of contact electrification and mechanical properties. Here, a bio-macromolecule-assisted toughening strategy for PVA aerogel-based triboelectric materials is proposed. By introducing β-lactoglobulin fibrils (BF) into the PVA aerogel network, the material's mechanical properties while preserving its swelling resistance is significantly enhanced. Compared to pure PVA porous film, the BF-PVA porous film exhibits an eightfold increase in fracture strength (from 1.92 to 15.48 J) and a fourfold increase in flexibility (from 10.956 to 39.36 MPa). Additionally, the electrical output of BF-PVA in triboelectric performance tests increased nearly fivefold (from 45 to 203 V). Leveraging these enhanced properties, a biodegradable TENG (bi-TENG) for implantable muscle activity sensing is developed, achieving real-time monitoring of neuromuscular processes. This innovation holds significant potential for advancing implantable medical devices and promoting new applications in bio-integrated electronics.

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.

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.

Catalytic Nanomaterials by Conjugation of an Artificial Heme-Peroxidase to Amyloid Fibrils

The self-assembly of proteins and peptides into fibrillar amyloid aggregates is a highly promising route to define the next generation of functional nanomaterials. Amyloid fibrils, traditionally associated with neurodegenerative diseases, offer exceptional conformational and chemical stability and mechanical properties, and resistance to degradation. Here, we report the development of catalytic amyloid nanomaterials through the conjugation of a miniaturized artificial peroxidase (FeMC6*a) to a self-assembling amyloidogenic peptide derived from human transthyretin, TTR(105-115), whose sequence is YTIAALLSPYS. Our synthetic approach relies on fast and selective click ligation upon proper modification of both the peptide and FeMC6*a, leading to TTRLys108@FeMC6*a. Mixing unmodified TTR(105-115) with TTRLys108@FeMC6*a allowed the generation of enzyme-loaded amyloid fibrils, namely, FeMC6*a@fibrils. Catalytic studies, performed in aqueous solution at nearly neutral pH, using ABTS as a model substrate and H2O2 as the oxidizing agent revealed that the enzyme retains its catalytic activity. Moreover, the activity was found to depend on the TTRLys108@FeMC6*a/unmodified TTR(105-115) peptide ratio. In particular, those with the 2:100 ratio showed the highest activity in terms of initial rates and substrate conversion among the screened nanoconjugates and compared to the freely diffusing enzyme. Finally, the newly developed nanomaterials were integrated into a flow system based on a polyvinylidene difluoride membrane filter. Within this flow-reactor, multiple reaction cycles were performed, showcasing the reusability and stability of the catalytic amyloids over extended periods, thus offering significantly improved characteristics compared to the isolated FeMC6*a in the application to a number of practical scenarios.

Amyloid detection in neurodegenerative diseases using MOFs

Neurodegenerative diseases (amyloid diseases such as Alzheimer's and Parkinson's), stemming from protein misfolding and aggregation, encompass a spectrum of disorders with severe systemic implications. Timely detection is pivotal in managing these diseases owing to their significant impact on organ function and high mortality rates. The diverse array of amyloid disorders, spanning localized and systemic manifestations, underscores the complexity of these conditions and highlights the need for advanced detection methods. Traditional approaches have focused on identifying biomarkers using imaging techniques (PET and MRI) or invasive procedures. However, recent efforts have focused on the use of metal-organic frameworks (MOFs), a versatile class of materials known for their unique properties, in revolutionizing amyloid disease detection. The high porosity, customizable structures, and biocompatibility of MOFs enable their integration with biomolecules, laying the groundwork for highly sensitive and specific biosensors. These sensors have been employed using electrochemical and photophysical techniques that target amyloid species under neurodegenerative conditions. The adaptability of MOFs allows for the precise detection and quantification of amyloid proteins, offering potential advancements in early diagnosis and disease management. This review article delves into how MOFs contribute to detecting amyloid diseases by categorizing their uses based on different sensing methods, such as electrochemical (EC), electrochemiluminescence (ECL), fluorescence, Förster resonance energy transfer (FRET), up-conversion luminescence resonance energy transfer (ULRET), and photoelectrochemical (PEC) sensing. The drawbacks of MOF biosensors and the challenges encountered in the field are also briefly explored from our perspective.

Using silver nanoparticle-decorated whey protein isolate amyloid fibrils to modify the electrode surface used for electrochemical detection of para-nitrophenol

Due to their organized structures, remarkable stiffness, and nice biocompatibility and biodegradability, amyloid fibrils serve as building blocks for versatile sustainable materials. Silver nanoparticles (AgNPs) are commonly used as the nano-catalysts for various electrochemical reactions. Given their large specific surface area and high surface energy, AgNPs exhibit high aggregation propensity, which hampers their electrocatalytic performance. Food protein wastes have been identified to be associated with climate change and environmental impacts, and a surplus of whey proteins in dairy industries causes high biological and chemical demands, and greenhouse gas emissions. This study is aimed at constructing sustainable electrode surface modifiers using AgNP-deposited whey protein amyloid fibrils (AgNP/WPI-AFs). AgNP/WPI-AFs were synthesized and characterized via spectroscopic techniques, electron microscopy, and X-ray diffraction. Next, the electrocatalytic performance of AgNP/WPI-AF modified electrode was assessed via para-nitrophenol (p-NP) reduction combined with various electrochemical analyses. Moreover, the reaction mechanism of p-NP electrocatalysis on the surface of AgNP/WPI-AF modified electrode was investigated. The detection range, limit of detection, sensitivity, and selectivity of the AgNP/WPI-AF modified electrode were evaluated accordingly. This work not only demonstrates an alternative for whey valorization but also highlights the feasibility of using amyloid-based hybrid materials as the electrode surface modifier for electrochemical sensing purposes.

DRGD-linked charged EKKE dimeric dodecapeptide: pH-based amyloid nanostructures and their application in lead and uranium binding

Peptides have been reported to undergo self-assembly into diverse nanostructures, influenced by several parameters, including their amino acid sequence, pH, charge, solvent, and temperature. Inspired by natural systems, researchers have developed biomimetic peptides capable of self-assembling into supramolecular functional structures. The present study explored a newly designed peptide sequence, EKKEDRGDEKKE, where E = glutamic acid, K = lysine, D = aspartic acid, G = glycine, and R = arginine, with a metal binding DRGD sequence incorporated between the exclusively charged EKKE peptide. We investigated the formation and the potential of the EKKEDRGDEKKE peptide in retaining the structure and morphology adopted by the individual EKKE peptide. According to a combination of experimental techniques such as thioflavin T fluorescence, field emission-scanning electron microscopy, atomic force microscopy, and circular dichroism, it was evident that the EKKEDRGDEKKE peptide displayed a pH-dependent propensity to adopt amyloid-like structures. Furthermore, the self-assembled entities formed under acidic, basic, and neutral conditions exhibited morphological variations, which resembled that observed for the exclusively charged EKKE peptide. Furthermore, the incorporation of the functional DRGD motif resulted in promising binding to two toxic metal ions, lead (Pb) and uranium (U), as evidenced by a range of spectroscopic techniques, including UV-visible spectroscopy, atomic absorption spectroscopy, fluorescence spectroscopy, and X-ray photoelectron spectroscopy. The use of the amyloid-forming EKKEDRGDEKKE scaffold can also be extended to potential biomedical applications.

Amyloid engineering - how terminal capping modifies morphology and secondary structure of supramolecular peptide aggregates

The effects of peptide N- and C-termini on aggregation behavior have been scarcely studied. Herein, we examine (105-115) peptide fragments of transthyretin (TTR) containing various functional groups at both termini and study their impact on the morphology and the secondary structure. We synthesized TTR(105-115) peptides functionalized with α-amino (H-), N-acetyl-α-amino (Ac-) or N,N-dimethyl-α-amino (DiMe-) groups at the N-terminus, and with amide (-NH2) or carboxyl (-OH) functions at the C-terminus. We also investigated quasi-racemic mixtures by mixing the L-enantiomers with the D-enantiomer capped by H- and -NH2 groups. We observed that fibril formation is promoted by the sufficient number of hydrogen bonds at peptides' termini. Moreover, the final morphology of the aggregates can be controlled by the functional groups at the N-terminus. Remarkably, all quasi-racemic mixtures resulted in the robust formation of fibrils. Overall, this work illustrates how modifications of peptide termini may help to engineer supramolecular aggregates with a predicted morphology.

Characterization of amyloid-like metal-amino acid assemblies with remarkable catalytic activity

While enzymes are potentially useful in various applications, their limited operational stability and production costs have led to an extensive search for stable catalytic agents that will retain the efficiency, specificity, and environmental-friendliness of natural enzymes. Despite extensive efforts, there is still an unmet need for improved enzyme mimics and novel concepts to discover and optimize such agents. Inspired by the catalytic activity of amyloids and the formation of amyloid-like assemblies by metabolites, our group pioneered the development of novel metabolite-metal co-assemblies (bio-nanozymes) that produce nanomaterials mimicking the catalytic function of common metalloenzymes that are being used for various technological applications. In addition to their notable activity, bio-nanozymes are remarkably safe as they are purely composed of amino acids and minerals that are harmless to the environment. The bio-nanozymes exhibit high efficiency and exceptional robustness, even under extreme conditions of temperature, pH, and salinity that are impractical for enzymes. Our group has recently also demonstrated the formation of ordered amino acid co-assemblies showing selective and preferential interactions comparable to the organization of residues in folded proteins. The identified bio-nanozymes can be used in various applications including environmental remediation, synthesis of new materials, and green energy.

Salt-Promoted Fibrillation of Legume Proteins Enhanced Interfacial Modulus for Stabilization of HIPEs Encapsulating Carotenoids with Improved Nutritional Performance

The thermal acidic-treatment-induced fibrillation of legume proteins isolated from cowpea and mung bean was demonstrated to be promoted by salt. Worm-like thin prefibrilar intermediates were formed in low salt concentrations (0-75 mM), which twisted to be the thick and mature amyloid-like fibrils with multistrands as the salt content was elevated (150-300 mM). Absorption of the fibrils fabricated in high salt concentrations to the oil/water interface constructed the protein layer with a significantly higher interfacial modulus compared with the one formed by the fibrils fabricated in low salt concentrations. Consequently, they showed the superiority in stabilizing high internal phase emulsions (HIPEs) with oil volume fraction ratios higher than 74%. HIPEs stabilized by the high salt-concentration-induced legume protein fibrils had stronger capabilities not only in encapsulating liposoluble carotenoids but also in protecting their stability against heating, ultraviolet, and iron ion stimulus, compared with the one stabilized by the low-salt-concentration-induced legume protein fibrils. Bioaccessibilities of the carotenoids in simulating gastrointestinal (GI) digestion were significantly improved after encapsulation by the HIPEs, which were interestingly increased with the elevation of salt concentrations utilized for preparing the legume protein fibrils. Furthermore, the carotenoids-loading-HIPEs were injectable and showed in vivo nutritional functions of mitigating colitis.

Exploring the potential of amyloids in biomedical applications: A review

Amyloid is defined as a fibrous quaternary structure formed by assembling protein or peptide monomers into intermolecularly hydrogen linked β-sheets. There is a prevalent issue with protein aggregation and the buildup of amyloid molecules, which results in human neurological illnesses including Alzheimer's and Parkinson's. But it is now evident that many organisms, like bacteria, fungi as well as humans, use the same fibrillar structure to carry out a variety of biological functions, such as structure and protection supporting interface transitions and cell-cell recognition, protein control and storage, epigenetic inheritance, and memory. Recent discoveries of self-assembling amyloidogenic peptides and proteins, based on the amyloid core structure, give rise to interesting biomaterials with potential uses in numerous industries. These functions dramatically diverge from the initial conception of amyloid fibrils as intrinsically diseased entities. Apart from the natural ability of amyloids to spontaneously arrange themselves and their exceptional material characteristics, this aspect has prompted extensive research into engineering artificial amyloids for generating various nanostructures, molecular substances, and combined materials. Here, we discuss significant developments in the artificial design of useful amyloids as well as how amyloid materials serve as examples of how function emerges from protein self-assembly at various length scales.

Food amyloid fibrils are safe nutrition ingredients based on in-vitro and in-vivo assessment

Food protein amyloid fibrils have superior technological, nutritional, sensorial, and physical properties compared to native monomers, but there is as yet insufficient understanding of their digestive fate and safety for wide consumption. By combining SDS-PAGE, ELISA, fluorescence, AFM, MALDI-MS, CD, microfluidics, and SAXS techniques for the characterization of β-lactoglobulin and lysozyme amyloid fibrils subjected to in-vitro gastrointestinal digestion, here we show that either no noticeable conformational differences exist between amyloid aggregates and their monomer counterparts after the gastrointestinal digestion process (as in β-lactoglobulin), or that amyloid fibrils are digested significantly better than monomers (as in lysozyme). Moreover, in-vitro exposure of human cell lines and in-vivo studies with C. elegans and mouse models, indicate that the digested fibrils present no observable cytotoxicity, physiological abnormalities in health-span, nor accumulation of fibril-induced plaques in brain nor other organs. These extensive in-vitro and in-vivo studies together suggest that the digested food amyloids are at least equally as safe as those obtained from the digestion of corresponding native monomers, pointing to food amyloid fibrils as potential ingredients for human nutrition.

Gold nanoparticle-coated apoferritin conductive nanowires

Gold-metallic nanofibrils were prepared from three different iso-apoferritin (APO) proteins with different Light/Heavy (L/H) subunit ratios (from 0% up to 100% L-subunits). We show that APO protein fibrils have the ability to in situ nucleate and grow gold nanoparticles (AuNPs) simultaneously assembled on opposite strands of the fibrils, forming hybrid inorganic-organic metallic nanowires. The AuNPs are arranged following the pitch of the helical APO protein fiber. The mean size of the AuNPs was similar in the three different APO protein fibrils studied in this work. The AuNPs retained their optical properties in these hybrid systems. Conductivity measurements showed ohmic behavior like that of a continuous metallic structure.

One-pot synthesis of fibrillar-shaped functional nanomaterial using microbial transglutaminase

Recently, functional nanowire production using amyloids as a scaffold for protein immobilization has attracted attention. However, protein immobilization on amyloid fibrils often caused protein inactivation. In this study, we investigated protein immobilization using enzymatic peptide ligation to suppress protein inactivation during immobilization. We attempted to immobilize functional molecules such as green fluorescent protein (GFP) and Nanoluc to a transthyretin (TTR) amyloid using microbial transglutaminase (MTG), which links the glutamine side chain to the primary amine. Linkage between amyloid fibrils and functional molecules was achieved through the MTG substrate sequence, and the functional molecules-loaded nanowires were successfully fabricated. We also found that the synthetic process from amyloidization to functional molecules immobilization could be achieved in a single-step procedure.All rights reserved.

Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides

Screening amino acid sequence space via experiments to discover peptides that self-assemble into amyloid fibrils is challenging. We have developed a computational peptide assembly design (PepAD) algorithm that enables the discovery of amyloid-forming peptides. Discontinuous molecular dynamics (DMD) simulation with the PRIME20 force field combined with the FoldAmyloid tool is used to examine the fibrilization kinetics of PepAD-generated peptides. PepAD screening of ∼10,000 7-mer peptides resulted in twelve top-scoring peptides with two distinct hydration properties. Our studies revealed that eight of the twelve in silico discovered peptides spontaneously form amyloid fibrils in the DMD simulations and that all eight have at least five residues that the FoldAmyloid tool classifies as being aggregation-prone. Based on these observations, we re-examined the PepAD-generated peptides in the sequence pool returned by PepAD and extracted five sequence patterns as well as associated sequence signatures for the 7-mer amyloid-forming peptides. Experimental results from Fourier transform infrared spectroscopy (FTIR), thioflavin T (ThT) fluorescence, circular dichroism (CD), and transmission electron microscopy (TEM) indicate that all the peptides predicted to assemble in silico assemble into antiparallel β-sheet nanofibers in a concentration-dependent manner. This is the first attempt to use a computational approach to search for amyloid-forming peptides based on customized settings. Our efforts facilitate the identification of β-sheet-based self-assembling peptides, and contribute insights towards answering a fundamental scientific question: "What does it take, sequence-wise, for a peptide to self-assemble?".

Controlling Amyloid Fibril Properties Via Ionic Liquids: The Representative Case of Ethylammonium Nitrate and Tetramethylguanidinium Acetate on the Amyloidogenesis of Lysozyme

Protein aggregation into amyloid fibrils has been observed in several pathological conditions and exploited in nanotechnology. It is also key in several biochemical processes. In this work, we show that ionic liquids (ILs), a vast class of organic electrolytes, can finely tune amyloid properties, opening a new landscape in basic science and applications. The representative case of ethylammonium nitrate (EAN) and tetramethyl-guanidinium acetate (TMGA) ILs on lysozyme is considered. First, atomic force microscopy has shown that the addition of EAN and TMGA leads to thicker and thinner amyloid fibrils of greater and lower electric potential, respectively, with diameters finely tunable by IL concentration. Optical tweezers and neutron scattering have shed light on their mechanism of action. TMGA interacts with the protein hydration layer only, making the relaxation dynamics of these water molecules faster. EAN interacts directly with the protein instead, making it mechanically unstable and slowing down its relaxation dynamics.

Molecular dynamics study on the effects of charged amino acid distribution under low pH condition to the unfolding of hen egg white lysozyme and formation of beta strands

Aggregation of unfolded or misfolded proteins into amyloid fibrils can cause various diseases in humans. However, the fibrils synthesized in vitro can be developed toward useful biomaterials under some physicochemical conditions. In this study, atomistic molecular dynamics simulations were performed to address the mechanism of beta-sheet formation of the unfolded hen egg-white lysozyme (HEWL) under a high temperature and low pH. Simulations of the protonated HEWL at pH 2 and the non-protonated HEWL at pH 7 were performed at the highly elevated temperature of 450 K to accelerate the unfolding, followed by the 333 K temperature to emulate some previous in vitro studies. The simulations showed that HEWL unfolded faster, and higher beta-strand contents were observed at pH 2. In addition, one of the simulation replicas at pH 2 showed that the beta-strand forming sequence was consistent with the 'K-peptide', proposed as the core region for amyloidosis in previous experimental studies. Beta-strand formation mechanisms at the earlier stage of amyloidosis were explained in terms of the radial distribution of the amino acids. The separation between groups of positively charged sidechains from the hydrophobic core corresponded to the clustering of the hydrophobic residues and beta-strand formation.

Polysorbate 80 controls Morphology, structure and stability of human insulin Amyloid-Like spherulites

Amyloid protein aggregates are not only associated with neurodegenerative diseases and may also occur as unwanted by-products in protein-based therapeutics. Surfactants are often employed to stabilize protein formulations and reduce the risk of aggregation. However, surfactants alter protein-protein interactions and may thus modulate the physicochemical characteristics of any aggregates formed. Human insulin aggregation was induced at low pH in the presence of varying concentrations of the surfactant polysorbate 80. Various spectroscopic and imaging methods were used to study the aggregation kinetics, as well as structure and morphology of the formed aggregates. Molecular dynamics simulations were employed to investigate the initial interaction between the surfactant and insulin. Addition of polysorbate 80 slowed down, but did not prevent, aggregation of insulin. Amyloid spherulites formed under all conditions, with a higher content of intermolecular beta-sheets in the presence of the surfactant above its critical micelle concentration. In addition, a denser packing was observed, leading to a more stable aggregate. Molecular dynamics simulations suggested a tendency for insulin to form dimers in the presence of the surfactant, indicating a change in protein-protein interactions. It is thus shown that surfactants not only alter aggregation kinetics, but also affect physicochemical properties of any aggregates formed.

De novo design of peptides that coassemble into β sheet-based nanofibrils

Peptides’ hierarchical coassembly into nanostructures enables controllable fabrication of multicomponent biomaterials. In this work, we describe a computational and experimental approach to design pairs of charge-complementary peptides that selectively coassemble into β-sheet nanofibers when mixed together but remain unassembled when isolated separately. The key advance is a peptide coassembly design (PepCAD) algorithm that searches for pairs of coassembling peptides. Six peptide pairs are identified from a pool of ~10⁶ candidates via the PepCAD algorithm and then subjected to DMD/PRIME20 simulations to examine their co-/self-association kinetics. The five pairs that spontaneously aggregate in kinetic simulations selectively coassemble in biophysical experiments, with four forming β-sheet nanofibers and one forming a stable nonfibrillar aggregate. Solid-state NMR, which is applied to characterize the coassembling pairs, suggests that the in silico peptides exhibit a higher degree of structural order than the previously reported CATCH(+/−) peptides.

Microbially Synthesized Polymeric Amyloid Fiber Promotes β-Nanocrystal Formation and Displays Gigapascal Tensile Strength

The ability of amyloid proteins to form stable β-sheet nanofibrils has made them potential candidates for material innovation in nanotechnology. However, such a nanoscale feature has rarely translated into attractive macroscopic properties for mechanically demanding applications. Here, we present a strategy by fusing amyloid peptides with flexible linkers from spidroin; the resulting polymeric amyloid proteins can be biosynthesized using engineered microbes and wet-spun into macroscopic fibers. Using this strategy, fibers from three different amyloid groups were fabricated. Structural analyses unveil the presence of β-nanocrystals that resemble the cross-β structure of amyloid nanofibrils. These polymeric amyloid fibers have displayed strong and molecular-weight-dependent mechanical properties. Fibers made of a protein polymer containing 128 repeats of the FGAILSS sequence displayed an average ultimate tensile strength of 0.98 ± 0.08 GPa and an average toughness of 161 ± 26 MJ/m³, surpassing most recombinant protein fibers and even some natural spider silk fibers. The design strategy and the biosynthetic approach can be expanded to create numerous functional materials, and the macroscopic amyloid fibers will enable a wide range of mechanically demanding applications.

Layered assembly of cationic and anionic supramolecular polymers

The chemical synthesis and the supramolecular assembly of an aromatic oligoamine are described. The self-assembly of the cationic oligomers in aqueous solution leads to the formation of vesicular objects. The assembly process of the oligomers is monitored by absorption and fluorescence spectroscopy and the formed vesicles are characterized by atomic force and transmission electron microscopy. The electrostatic complementarity of anionic supramolecular polymers sheets and the cationic vesicles is used for a layered assembly process.

Functionalized Prion-Inspired Amyloids for Biosensor Applications

Protein amyloid nanofibers provide a biocompatible platform for the development of functional nanomaterials. However, the functionalities generated up to date are still limited. Typical building blocks correspond to aggregation-prone proteins and peptides, which must be modified by complex and expensive reactions post-assembly. There is high interest in researching alternative strategies to tailor amyloid-based nanostructures’ functionality on demand. In the present study, the biotin-streptavidin system was exploited for this purpose. Prion-inspired heptapeptides (Ac-NYNYNYN-NH₂, Ac-QYQYQYQ-NH₂, and Ac-SYSYSYS-NH₂) were doped with biotin-conjugated counterparts and assembled into amyloid-like fibers under mild conditions. The scaffolds’ versatile functionalization was demonstrated by decorating them with different streptavidin conjugates, including gold nanoparticles, quantum dots, and enzymes. In particular, they were functionalized with peroxidase or phosphatase activities using streptavidin conjugated with horseradish peroxidase and alkaline phosphatase, respectively. Modification of amyloid-like nanostructures has generally been restricted to the addition of a single protein moiety. We functionalized the fibrils simultaneously with glucose oxidase and horseradish peroxidase, coupling these activities to build up a nanostructured glucose biosensor. Overall, we present a simple, modular, and multivalent approach for developing amyloid-based nanomaterials functionalized with any desired combination of chemical and biological moieties.

Bacterial extracellular matrix as a natural source of biotechnologically multivalent materials

The extracellular matrix (ECM) is an intricate megastructure made by bacterial cells to form architecturally complex biostructures called biofilms. Protection of cells, modulation of cell-to-cell signalling, cell differentiation and environmental sensing are functions of the ECM that reflect its diverse chemical composition. Proteins, polysaccharides and eDNA have specific functionalities while cooperatively interacting to sustain the architecture and biological relevance of the ECM. The accumulated evidence on the chemical heterogeneity and specific functionalities of ECM components has attracted attention because of their potential biotechnological applications, from agriculture to the water and food industries. This review compiles information on the most relevant bacterial ECM components, the biophysical and chemical features responsible for their biological roles, and their potential to be further translated into biotechnological applications.

Understanding the Formation of Apoferritin Amyloid Fibrils

We present the optimization of experimental conditions to yield long, rigid apoferritin protein amyloid fibrils, as well as the corresponding fibrillation pathway. Fibril growth kinetics was followed using atomic force microscopy (AFM), transmission electron microscopy (TEM), dynamic light scattering (DLS), circular dichroism (CD), fourier-transform infrared spectroscopy (FTIR), and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Among the morphologies identified, we show that the conditions result in small aggregates, as well as medium and long fibrils. Extended incubation times led to progressive unfolding and hydrolysis of the proteins into very short peptide fragments. AFM, SDS-PAGE, and CD support a universal common fibrillation mechanism in which hydrolyzed fragments play the central role. These collective results provide convincing evidence that protein unfolding and complete hydrolysis of the proteins into very short peptide sequences are essential for the formation of the final apoferritin amyloid-like fibrils.

Amyloid-Like Aggregation in Diseases and Biomaterials: Osmosis of Structural Information

The discovery that the polypeptide chain has a remarkable and intrinsic propensity to form amyloid-like aggregates endowed with an extraordinary stability is one of the most relevant breakthroughs of the last decades in both protein/peptide chemistry and structural biology. This observation has fundamental implications, as the formation of these assemblies is systematically associated with the insurgence of severe neurodegenerative diseases. Although the ability of proteins to form aggregates rich in cross-β structure has been highlighted by recent studies of structural biology, the determination of the underlying atomic models has required immense efforts and inventiveness. Interestingly, the progressive molecular and structural characterization of these assemblies has opened new perspectives in apparently unrelated fields. Indeed, the self-assembling through the cross-β structure has been exploited to generate innovative biomaterials endowed with promising mechanical and spectroscopic properties. Therefore, this structural motif has become the fil rouge connecting these diversified research areas. In the present review, we report a chronological recapitulation, also performing a survey of the structural content of the Protein Data Bank, of the milestones achieved over the years in the characterization of cross-β assemblies involved in the insurgence of neurodegenerative diseases. A particular emphasis is given to the very recent successful elucidation of amyloid-like aggregates characterized by remarkable molecular and structural complexities. We also review the state of the art of the structural characterization of cross-β based biomaterials by highlighting the benefits of the osmosis of information between these two research areas. Finally, we underline the new promising perspectives that recent successful characterizations of disease-related amyloid-like assemblies can open in the biomaterial field.

Metal-Protein Hybrid Materials with Desired Functions and Potential Applications

Metal nanohybrids are fast emerging functional nanomaterials with advanced structures, intriguing physicochemical properties, and a broad range of important applications in current nanoscience research. Significant efforts have been devoted toward design and develop versatile metal nanohybrid systems. Among numerous biological components, diverse proteins offer avenues for making advanced multifunctional systems with unusual properties, desired functions, and potential applications. This review discusses the rational design, properties, and applications of metal-protein nanohybrid materials fabricated from proteins and inorganic components. The construction of functional biomimetic nanohybrid materials is first briefly introduced. The properties and functions of these hybrid materials are then discussed. After that, an overview of promising application of biomimetic metal-protein nanohybrid materials is provided. Finally, the key challenges and outlooks related to this fascinating research area are also outlined.

Protein aggregation: in silico algorithms and applications

Protein aggregation is a topic of immense interest to the scientific community due to its role in several neurodegenerative diseases/disorders and industrial importance. Several in silico techniques, tools, and algorithms have been developed to predict aggregation in proteins and understand the aggregation mechanisms. This review attempts to provide an essence of the vast developments in in silico approaches, resources available, and future perspectives. It reviews aggregation-related databases, mechanistic models (aggregation-prone region and aggregation propensity prediction), kinetic models (aggregation rate prediction), and molecular dynamics studies related to aggregation. With a multitude of prediction models related to aggregation already available to the scientific community, the field of protein aggregation is rapidly maturing to tackle new applications.

Fabrication of fluorescent nanospheres by heating PEGylated tetratyrosine nanofibers

Aromatic polypeptides have recently drawn the interest of the research community for their capability to self-assemble into a variety of functional nanostructures. Due to their interesting mechanical, electrical and optical properties, these nanostructures have been proposed as innovative materials in different biomedical, biotechnological and industrial fields. Recently, several efforts have been employed in the development of these innovative materials as nanoscale fluorescence (FL) imaging probes. In this context, we describe the synthesis and the functional properties of a novel fluorescent tyrosine (Tyr, Y)-based nanospheres, obtained by heating at 200 °C a solution of the PEGylated tetra-peptide PEG6-Y4. At room temperature, this peptide self-assembles into not fluorescent low ordered water-soluble fibrillary aggregates. After heating, the aggregation of different polyphenolic species generates Y4-based nanospheres able to emit FL into blue, green and red spectral regions, both in solution and at the solid state. The aggregation features of PEG6-Y4 before and after heating were studied using a set of complementary techniques (Fluorescence, CD, FT-IR, Small and Wide-Angle X-ray Scattering and SEM). After a deep investigation of their optoelectronic properties, these nanospheres could be exploited as promising tools for precise biomedicine in advanced nanomedical technologies (local bioimaging, light diagnostics, therapy, optogenetics and health monitoring).

Apoferritin Amyloid-Fibril Directed the In Situ Assembly and/or Synthesis of Optical and Magnetic Nanoparticles

The coupling of proteins that can assemble, recognise or mineralise specific inorganic species is a promising strategy for the synthesis of nanoscale materials with a controllable morphology and functionality. Herein, we report that apoferritin protein amyloid fibrils (APO) have the ability to assemble and/or synthesise various metal and metal compound nanoparticles (NPs). As such, we prepared metal NP-protein hybrid bioconjugates with improved optical and magnetic properties by coupling diverse gold (AuNPs) and magnetic iron oxide nanoparticles (MNPs) to apoferritin amyloid fibrils and compared them to the well-known β-lactoglobulin (BLG) protein. In a second approach, we used of solvent-exposed metal-binding residues in APO amyloid fibrils as nanoreactors for the in situ synthesis of gold, silver (AgNPs) and palladium nanoparticles (PdNPs). Our results demonstrate, the versatile nature of the APO biotemplate and its high potential for preparing functional hybrid bionanomaterials. Specifically, the use of apoferritin fibrils as vectors to integrate magnetic MNPs or AuNPs is a promising synthetic strategy for the preparation of specific contrast agents for early in vivo detection using various bioimaging techniques.

Amyloid-Like Peptide Aggregates

Self-assembly of proteins and peptides into the amyloid fold is a widespread phenomenon in the natural world. The structural hallmark of self-assembly into amyloid fibrillar assemblies is the cross-beta motif, which conveys distinct morphological and mechanical properties. The amyloid fibril formation has contrasting results depending on the organism, in the sense that it can bestow an organism with the advantages of mechanical strength and improved functionality or, on the contrary, could give rise to pathological states. In this chapter we review the existing information on amyloid-like peptide aggregates, which could either be derived from protein sequences, but also could be rationally or de novo designed in order to self-assemble into amyloid fibrils under physiological conditions. Moreover, the development of self-assembled fibrillar biomaterials that are tailored for the desired properties towards applications in biomedical or environmental areas is extensively analyzed. We also review computational studies predicting the amyloid propensity of the natural amino acid sequences and the structure of amyloids, as well as designing novel functional amyloid materials.

Half a century of amyloids: past, present and future

Amyloid diseases are global epidemics with profound health, social and economic implications and yet remain without a cure. This dire situation calls for research into the origin and pathological manifestations of amyloidosis to stimulate continued development of new therapeutics. In basic science and engineering, the cross-β architecture has been a constant thread underlying the structural characteristics of pathological and functional amyloids, and realizing that amyloid structures can be both pathological and functional in nature has fuelled innovations in artificial amyloids, whose use today ranges from water purification to 3D printing. At the conclusion of a half century since Eanes and Glenner's seminal study of amyloids in humans, this review commemorates the occasion by documenting the major milestones in amyloid research to date, from the perspectives of structural biology, biophysics, medicine, microbiology, engineering and nanotechnology. We also discuss new challenges and opportunities to drive this interdisciplinary field moving forward.

An integrated, optofluidic system with aligned optical waveguides, microlenses, and coupling prisms for fluorescence sensing

An improved, laser-induced fluorescence-based micro-optical biosensor was designed and fabricated, with cyclic olefin copolymer (COC) optical waveguides, a poly(methyl methacrylate) (PMMA) fluidic substrate with an array of microlenses, and a COC coupling prism integrated with the waveguide substrate or cover plate. The double-sided hot embossed fluidic substrate had sampling zone microchannels on the bottom and microlenses on the top. Dissolved COC injected into polydimethylsiloxane (PDMS) lost molds embedded the waveguides in the PMMA cover plate and formed the integrated coupling prism. The embedded COC waveguide was flycut down to 50 μm. The cover plate and shallow, 1:20 aspect ratio, microchannels were thermal fusion bonded using a pressure-assisted boiling point control system, without sagging. The large COC prism coupled better to the waveguide. The highest intensity evanescent excitation of the waveguide was obtained near the critical angle. The maximum signal-to-noise ratio (SNR) was 119 and the lowest detection limit was 7.34 × 10-20 mol at a SNR of 2 for a 100 μm wide by 50 μm deep waveguide. The microlenses highly focused the fluorescent radiation in the sampling zone. The microfabricated waveguide enables rapid, low-cost detection of fluorescent samples with high SNR, a low detection limit, and high sampling efficiency.

Link Between Diabetes and Alzheimer's Disease due to the Shared Amyloid Aggregation and Deposition Involving both Neurodegenerative Changes and Neurovascular Damages

Diabetes and Alzheimer’s disease are two highly prevalent diseases among the aging population and have become major public health concerns in the 21st century, with a significant risk to each other. Both of these diseases are increasingly recognized to be multifactorial conditions. The terms “diabetes type 3” or “brain diabetes” have been proposed in recent years to provide a complete view of the potential common pathogenic mechanisms between these diseases. While insulin resistance or deficiency remains the salient hallmarks of diabetes, cognitive decline and non-cognitive abnormalities such as impairments in visuospatial function, attention, cognitive flexibility, and psychomotor speed are also present. Furthermore, amyloid aggregation and deposition may also be drivers for diabetes pathology. Here, we offer a brief appraisal of social impact and economic burden of these chronic diseases and provide insight into amyloidogenesis through considering recent advances of amyloid-β aggregates on diabetes pathology and islet amyloid polypeptide on Alzheimer’s disease. Exploring the detailed knowledge of molecular interaction between these two amyloidogenic proteins opens new opportunities for therapies and biomarker development.

Non-Equilibrium Polymerization of Cross-β Amyloid Peptides for Temporal Control of Electronic Properties

Hydrophobic collapse plays crucial roles in protein functions, from accessing the complex three-dimensional structures of native enzymes to the dynamic polymerization of non-equilibrium microtubules. However, hydrophobic collapse can also lead to the thermodynamically downhill aggregation of aberrant proteins, which has interestingly led to the development of a unique class of soft nanomaterials. There remain critical gaps in the understanding of the mechanisms of how hydrophobic collapse can regulate such aggregation. Demonstrated herein is a methodology for non-equilibrium amyloid polymerization through mutations of the core sequence of Aβ peptides by a thermodynamically activated moiety. An out of equilibrium state is realized because of the negative feedback from the transiently formed cross-β amyloid networks. Such non-equilibrium amyloid nanostructures were utilized to access temporal control over its electronic properties.

Morphological Determinants of Carbon Nanomaterial-Induced Amyloid Peptide Self-Assembly

Hybridizing carbon nanomaterials (CNMs) with amyloid fibrils—the ordered nanostructures self-assembled by amyloidogenic peptides—has found promising applications in bionanotechology. Understanding fundamental interactions of CNMs with amyloid peptides and uncovering the determinants of their self-assembly structures and dynamics are, therefore, pivotal for enriching and enabling this novel class of hybrid nanomaterials. Here, we applied atomistic molecular dynamics simulations to investigate the self-assembly of two amyloid peptides—the amyloidogenic core residues 16-22 of amyloid-β (Aβ₁₆₋₂₂) and the non-amyloid-β core of α-synuclein (NACore₆₈₋₇₈)—on the surface of carbon nanotubes (CNT) with different sizes and chirality. Our computational results showed that with small radial CNTs, both types of peptides could form β-sheets wrapping around the nanotube surface into a supercoiled morphology. The angle between β-strands and nanotube axes in the supercoil structure depended mainly on the peptide sequence and CNT radius, but also weakly on the CNT chirality. Large radial CNTs and the extreme case of the flat graphene nanosheet, on the other hand, could nucleate amyloid fibrils perpendicular to the surface. Our results provided new insights of hybridizing CNMs with amyloid peptides and also offered a novel approach to manipulate the morphology of CNM-induced amyloid assembly by tuning the surface curvature, peptide sequence, and molecular ratio between peptides and available CNM surface area, which may be useful in engineering nanocomposites with high-order structures.

Formation of α-synuclein aggregates in aqueous ethylammonium nitrate solutions

The effect of adding ethylammonium nitrate (EAN), which is an ionic liquid (IL), on the aggregate formation of α-synuclein (α-Syn) in aqueous solution has been investigated. FTIR and Raman spectroscopy were used to investigate changes in the secondary structure of α-Syn and in the states of water molecules and EAN. The results presented here show that the addition of EAN to α-Syn causes the formation of an intermolecular β-sheet structure in the following manner: native disordered state → polyproline II (PPII)-helix → intermolecular β-sheet (α-Syn amyloid-like aggregates: α-SynA). Although cations and anions of EAN play roles in masking the charged side chains and PPII-helix-forming ability involved in the formation of α-SynA, water molecules are not directly related to its formation. We conclude that EAN-induced α-Syn amyloid-like aggregates form at hydrophobic associations in the middle of the molecules after masking the charged side chains at the N- and C-terminals of α-Syn.

Islet Amyloid Polypeptide: A Partner in Crime With Aβ in the Pathology of Alzheimer's Disease

Diabetes affects hundreds of millions of patients worldwide. Despite the advances in understanding the disease and therapeutic options, it remains a leading cause of death and of comorbidities globally. Islet amyloid polypeptide (IAPP), or amylin, is a hormone produced by pancreatic β-cells. It contributes to the maintenance of glucose physiological levels namely by inhibiting insulin and glucagon secretion as well as controlling adiposity and satiation. IAPP is a highly amyloidogenic polypeptide forming intracellular aggregates and amyloid structures that are associated with β-cell death. Data also suggest the relevance of unprocessed IAPP forms as seeding for amyloid buildup. Besides the known consequences of hyperamylinemia in the pancreas, evidence has also pointed out that IAPP has a pathological role in cognitive function. More specifically, IAPP was shown to impair the blood–brain barrier; it was also seen to interact and co-deposit with amyloid beta peptide (Aß), and possibly with Tau, within the brain of Alzheimer's disease (AD) patients, thereby contributing to diabetes-associated dementia. In fact, it has been suggested that AD results from a metabolic dysfunction in the brain, leading to its proposed designation as type 3 diabetes. Here, we have first provided a brief perspective on the IAPP amyloidogenic process and its role in diabetes and AD. We have then discussed the potential interventions for modulating IAPP proteotoxicity that can be explored for therapeutics. Finally, we have proposed the concept of a “diabetes brain phenotype” hypothesis in AD, which may help design future IAPP-centered drug developmentstrategies against AD.

Growth, Polymorphism, and Spatially Controlled Surface Immobilization of Biotinylated Variants of IAPP21-27 Fibrils

The islet amyloid polypeptide (IAPP) is a regulatory peptide that can aggregate into fibrillar structures associated with type 2 diabetes. In this study, the IAPP_21-27 segment was modified with a biotin linker at the N-terminus (Btn-GNNFGAIL) to immobilize peptide fibrils on streptavidin-coated surfaces. Key residues for fibril formation of the N-terminal biotinylated IAPP_21-27 segment were identified by using an alanine scanning approach combined with molecular dynamics simulations, thioflavin T fluorescence measurements, and scanning electron microscopy. Significant contributions of phenylalanine (F23), leucine (L27), and isoleucine (I26) for the fibrillation of the short peptide segment were identified. The fibril morphologies of the peptide variants differed depending on their primary sequence, ranging from flexible and semiflexible to stiff and crystal-like structures. These insights could advance the design of new functional hybrid bionanomaterials and fibril-engineered surface coatings using short peptide segments. To validate this concept, the biotinylated fibrils were immobilized on streptavidin-coated surfaces under spatial control.