Nanomechanics of functional and pathological amyloid materials

Force spectra of single bacterial amyloid CsgA nanofibers

CsgA is a major protein subunit of Escherichia coli biofilms and plays key roles in bacterial adhesion and invasion. CsgA proteins can self-assemble into amyloid nanofibers, characterized by their hierarchical structures across multiple length scales, outstanding strength and their structural robustness under harsh environments. Here, magnetic tweezers were used to study the force spectra of CsgA protein at fibril levels. The two ends of a single nanofiber were directly connected between a magnetic bead and a glass slide using a previously reported tag-free method. We showed that a wormlike chain model could be applied to fit the typical force–extension curves of CsgA nanofibers and to estimate accordingly the mechanical properties. The bending stiffness of nanofibers increased with increasing diameters. The changes in extension of single CsgA fibers were found to be up to 17 fold that of the original length, indicating exceptional tensile properties. Our results provide new insights into the tensile properties of bacterial amyloid nanofibers and highlight the ultrahigh structural stability of the Escherichia coli biofilms.

Magnetic tweezers were used to study the force spectra of CsgA, a major protein subunit of Escherichia coli biofilms, at fibril level.

Processing Induced Changes in Food Proteins: Amyloid Formation during Boiling of Hen Egg White

Amyloid fibrils (AFs) are highly ordered protein nanofibers composed of cross β-structure that occur in nature, but that also accumulate in age-related diseases. Amyloid propensity is a generic property of proteins revealed by conditions that destabilize the native state, suggesting that food processing conditions may promote AF formation. This had only been shown for foie gras, but not in common foodstuffs. We here extracted a dense network of fibrillar proteins from commonly consumed boiled hen egg white (EW) using chemical and/or enzymatic treatments. Conversion of EW proteins into AFs during boiling was demonstrated by thioflavin T fluorescence, Congo red staining, and X-ray fiber diffraction measurements. Our data show that cooking converts approximately 1-3% of the protein in EW into AFs, suggesting that they are a common component of the human diet.

Nature-derived materials for the fabrication of functional biodevices

Nature provides an incredible source of inspiration, structural concepts, and materials toward applications to improve the lives of people around the world, while preserving ecosystems, and addressing environmental sustainability. In particular, materials derived from animal and plant sources can provide low-cost, renewable building blocks for such applications. Nature-derived materials are of interest for their properties of biodegradability, bioconformability, biorecognition, self-repair, and stimuli response. While long used in tissue engineering and regenerative medicine, their use in functional devices such as (bio)electronics, sensors, and optical systems for healthcare and biomonitoring is finding increasing attention. The objective of this review is to cover the varied nature derived and sourced materials currently used in active biodevices and components that possess electrical or electronic behavior. We discuss materials ranging from proteins and polypeptides such as silk and collagen, polysaccharides including chitin and cellulose, to seaweed derived biomaterials, and DNA. These materials may be used as passive substrates or support architectures and often, as the functional elements either by themselves or as biocomposites. We further discuss natural pigments such as melanin and indigo that serve as active elements in devices. Increasingly, combinations of different biomaterials are being used to address the challenges of fabrication and performance in human monitoring or medicine. Finally, this review gives perspectives on the sourcing, processing, degradation, and biocompatibility of these materials. This rapidly growing multidisciplinary area of research will be advanced by a systematic understanding of nature-inspired materials and design concepts in (bio)electronic devices.

The Influence of Pathogenic Mutations in α-Synuclein on Biophysical and Structural Characteristics of Amyloid Fibrils

Proteinaceous deposits of α-synuclein amyloid fibrils are a hallmark of human disorders including Parkinson's disease. The onset of this disease is also associated with five familial mutations of the gene encoding the protein. However, the mechanistic link between single point mutations and the kinetics of aggregation, biophysical properties of the resulting amyloid fibrils, and an increased risk of disease is still elusive. Here, we demonstrate that the disease-associated mutations of α-synuclein generate different amyloid fibril polymorphs compared to the wild type protein. Remarkably, the α-synuclein variants forming amyloid fibrils of a comparable structure, morphology, and heterogeneity show similar microscopic steps defining the aggregation kinetics. These results demonstrate that a single point mutation can significantly alter the distribution of fibrillar polymorphs in α-synuclein, suggesting that differences in the clinical phenotypes of familial Parkinson's disease could be associated with differences in the mechanism of formation and the structural characteristics of the aggregates.

NMR insights into the pre-amyloid ensemble and secretion targeting of the curli subunit CsgA

The biofilms of Enterobacteriaceae are fortified by assembly of curli amyloid fibres on the cell surface. Curli not only provides structural reinforcement, but also facilitates surface adhesion. To prevent toxic intracellular accumulation of amyloid precipitate, secretion of the major curli subunit, CsgA, is tightly regulated. In this work, we have employed solution state NMR spectroscopy to characterise the structural ensemble of the pre-fibrillar state of CsgA within the bacterial periplasm, and upon recruitment to the curli pore, CsgG, and the secretion chaperone, CsgE. We show that the N-terminal targeting sequence (N) of CsgA binds specifically to CsgG and that its subsequent sequestration induces a marked transition in the conformational ensemble, which is coupled to a preference for CsgE binding. These observations lead us to suggest a sequential model for binding and structural rearrangement of CsgA at the periplasmic face of the secretion machinery.

Protein assembly systems in natural and synthetic biology

The traditional view of protein aggregation as being strictly disease-related has been challenged by many examples of cellular aggregates that regulate beneficial biological functions. When coupled with the emerging view that many regulatory proteins undergo phase separation to form dynamic cellular compartments, it has become clear that supramolecular assembly plays wide-ranging and critical roles in cellular regulation. This presents opportunities to develop new tools to probe and illuminate this biology, and to harness the unique properties of these self-assembling systems for synthetic biology for the purposeful manipulation of biological function.

Thermo- and pH-responsive fibrillization of squid suckerin A1H1 peptide

Stimuli-responsive smart materials have attracted considerable attention with numerous applications in nanotechnology, sensing, and biomedicine. Suckerin family proteins found in squid ring teeth represent such a class of peptide-based smart materials with their self-assemblies featuring excellent thermo-plasticity and pH-dependence. Similar to block copolymers, suckerin proteins are comprised of two repeating sequence motifs, where M1 motifs are abundant in alanine and histidine residues and M2 are rich in glycine. Experimental studies of suckerin assemblies suggested that M1 regions mainly formed nano-confined β-sheets within an amorphous matrix made of M2 modules stabilizing these β-rich nano-assemblies. The histidine-containing M1 modules are believed to govern the pH- and temperature-sensitive properties of suckerin assemblies. To better understand the stimuli-responsive properties of suckerin assemblies at the molecular level, we systematically studied the self-assembly dynamics of A1H1 peptides - a representative M1 sequence - at different temperatures and pH conditions with atomistic discrete molecular dynamic simulations. Our simulations with twenty A1H1 peptides demonstrated that below the transition temperature Tagg, they could readily self-assemble from isolated monomers into well-defined β-sheet nanostructures by both primary and secondary nucleation of β-sheets and subsequent aggregation growth via elongation and coagulation. Interestingly, the dissociation of pre-formed A1H1 β-sheet nanostructures featured a melting temperature Tm higher than Tagg, exhibiting the thermal hysteresis that is characteristic of first-order phase transitions with high energy barriers. In acidic environments where all histidine residues were protonated, the stability of the A1H1 β-sheet nano-assemblies was reduced and the β-rich assemblies easily dissociated into unstructured monomers at significantly lower temperatures than in the neutral solution. The computationally derived molecular mechanisms for pH- and temperature-dependent A1H1 self-assembly will help to understand the supramolecular assembly structures and functions of the large suckerin family and aid in the future design of peptide-based stimuli-responsive smart materials.

Advances in biomolecule inspired polymeric material decorated interfaces for biological applications

With the development of surface modification technology, interface properties have great effects on the interaction between biomedical materials and cells and biomolecules, which significantly affects the biocompatibility and functionality of materials. As an orderly and perfect system, biological organisms in nature effectively integrate all kinds of bio-interfaces with physiological functions, which shed light on the importance of biomolecules in organisms. It gives birth to a bio-inspiration strategy to design and fabricate smart materials with specific functionalities, e.g. osteogenic and chondrocytic induced materials inspired by bone sialoprotein and chondroitin sulfate. Through this mimicking approach, various functional materials were utilized to decorate the interfaces and further optimize the performance of biomedical materials, which would widely expand their applications. In this review, followed by a summary and brief introduction of surface modification methods, we highlight recent advances in the fabrication of functional polymeric materials inspired by a range of biomolecules for decorating interfaces. Then, the other applications of biomolecule inspired materials including tissue engineering, diagnosis and treatment of diseases and physiological function regulation are presented and the future outlook is discussed as well.

Modulating the Mechanical Performance of Macroscale Fibers through Shear-Induced Alignment and Assembly of Protein Nanofibrils

Protein-based fibers are used by nature as high-performance materials in a wide range of applications, including providing structural support, creating thermal insulation, and generating underwater adhesives. Such fibers are commonly generated through a hierarchical self-assembly process, where the molecular building blocks are geometrically confined and aligned along the fiber axis to provide a high level of structural robustness. Here, this approach is mimicked by using a microfluidic spinning method to enable precise control over multiscale order during the assembly process of nanoscale protein nanofibrils into micro- and macroscale fibers. By varying the flow rates on chip, the degree of nanofibril alignment can be tuned, leading to an orientation index comparable to that of native silk. It is found that the Young's modulus of the resulting fibers increases with an increasing level of nanoscale alignment of the building blocks, suggesting that the mechanical properties of macroscopic fibers can be controlled through varying the level of ordering of the nanoscale building blocks. Capitalizing on strategies evolved by nature, the fabrication method allows for the controlled formation of macroscopic fibers and offers the potential to be applied for the generation of further novel bioinspired materials.

Prebiotic Peptides: Molecular Hubs in the Origin of Life

The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.

Self-Assembly of Aromatic Amino Acid Enantiomers into Supramolecular Materials of High Rigidity

Most natural biomolecules may exist in either of two enantiomeric forms. Although in nature, amino acid biopolymers are characterized by l-type homochirality, incorporation of d-amino acids in the design of self-assembling peptide motifs has been shown to significantly alter enzyme stability, conformation, self-assembly behavior, cytotoxicity, and even therapeutic activity. However, while functional metabolite assemblies are ubiquitous throughout nature and play numerous important roles including physiological, structural, or catalytic functions, the effect of chirality on the self-assembly nature and function of single amino acids is not yet explored. Herein, we investigated the self-assembly mechanism of amyloid-like structure formation by two aromatic amino acids, phenylalanine (Phe) and tryptophan (Trp), both previously found as extremely important for the nucleation and self-assembly of aggregation-prone peptide regions into functional structures. Employing d-enantiomers, we demonstrate the critical role that amino acid chirality plays in their self-assembly process. The kinetics and morphology of pure enantiomers is completely altered upon their coassembly, allowing to fabricate different nanostructures that are mechanically more robust. Using diverse experimental techniques, we reveal the different molecular arrangement and self-assembly mechanism of the dl-racemic mixtures that resulted in the formation of advanced supramolecular materials. This study provides a simple yet sophisticated engineering model for the fabrication of attractive materials with bionanotechnological applications.

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.

Comparative experiments of electrical conductivity from whey protein concentrates conventional film and nanofibril film

We compared the electrical conductivity from two different aggregates of whey protein concentrates (WPC) film: conventional amorphous aggregation at natural pH (pH 6.5) and amyloid fibrils at a low pH (pH 2.0) far away from the isoelectric point. The two types of film fabricated by these solutions with different aggregate structures showed large variations in electrical conductivity and other properties. The WPC fibril film (pH 2.0) exhibited higher electrical conductivity than that of the conventional WPC film (pH 6.5), improved mechanical properties and oil resistance, due to varying morphology, higher surface hydrophobicity and more (absolute value) surface charge of film-forming solutions. The evidence from this study suggests that fibrilized WPC with high-ordered and β-sheets-rich structures fabricated high electrical conductivity film, which broadens the potential application of fibrils as functional bio-nanomaterials.

Soft-Matter Nanotubes: A Platform for Diverse Functions and Applications

Self-assembled organic nanotubes made of single or multiple molecular components can be classified into soft-matter nanotubes (SMNTs) by contrast with hard-matter nanotubes, such as carbon and other inorganic nanotubes. To date, diverse self-assembly processes and elaborate template procedures using rationally designed organic molecules have produced suitable tubular architectures with definite dimensions, structural complexity, and hierarchy for expected functions and applications. Herein, we comprehensively discuss every functions and possible applications of a wide range of SMNTs as bulk materials or single components. This Review highlights valuable contributions mainly in the past decade. Fifteen different families of SMNTs are discussed from the viewpoints of chemical, physical, biological, and medical applications, as well as action fields (e.g., interior, wall, exterior, whole structure, and ensemble of nanotubes). Chemical applications of the SMNTs are associated with encapsulating materials and sensors. SMNTs also behave, while sometimes undergoing morphological transformation, as a catalyst, template, liquid crystal, hydro-/organogel, superhydrophobic surface, and micron size engine. Physical functions pertain to ferro-/piezoelectricity and energy migration/storage, leading to the applications to electrodes or supercapacitors, and mechanical reinforcement. Biological functions involve artificial chaperone, transmembrane transport, nanochannels, and channel reactors. Finally, medical functions range over drug delivery, nonviral gene transfer vector, and virus trap.

The Amyloid Phenomenon and Its Significance in Biology and Medicine

The misfolding of proteins is now recognized to be the origin of a large number of medical disorders. One particularly important group of such disorders is associated with the aggregation of misfolded proteins into amyloid structures, and includes conditions ranging from Alzheimer's and Parkinson's diseases to type II diabetes. Such conditions already affect over 500 million people in the world, a number that is rising rapidly, and at present these disorders cannot be effectively treated or prevented. This review provides an overview of this field of science and discusses recent progress in understanding the nature and properties of the amyloid state, the kinetics and mechanism governing its formation, the origins of its links with disease, and the manner in which its formation may be inhibited or suppressed. This latter topic is of particular importance, both to enhance our knowledge of the maintenance of protein homeostasis in living organisms and also to address the development of therapeutic strategies through which to combat the loss of homeostasis and the associated onset and progression of disease.

Quantifying the Mechanical Anisotropy in Poly(3-hexylthiophene) Nanofibers

Correlating the structure with nanomechanical property of semicrystalline conjugated-polymer crystal is of essential importance for the performance improvement and design of flexible electronic devices. Although it is well-known that the semicrystalline conjugated-polymer crystal exhibits anisotropic structure owing to the π-π and layer stacking of highly coplanar conjugated backbones, the structure-nanomechanical property relationship is missing. Here, we investigated the axial mechanical anisotropy of the P3HT nanofiber by using thermal shape-fluctuation analysis and a three-point bending test based on atomic force microscopy. Our results show that Young's modulus in the layer-stacking direction (E_L) is 1-2 orders of magnitude greater than that in the π-conjugated backbone direction (E_B). We attribute this mechanical anisotropy to the π-stacking of the P3HT backbone, but the layer stacking will decrease E_L, which weakens the mechanical anisotropy. Moreover, we demonstrated that the P3HT nanofiber shows a loading-rate-independent Young's modulus and deformation-dependent resilience in the layer-stacking direction.

Accelerated charge transfer in water-layered peptide assemblies

Bioinspired assemblies bear massive potential for energy generation and storage. Yet, biological molecules have severe limitations for charge transfer. Here, we report l-tryptophan-d-tryptophan assembling architectures comprising alternating water and peptide layers. The extensive connection of water molecules results in significant dipole-dipole interactions and piezoelectric response that can be further engineered by doping via iodine adsorption or isotope replacement with no change in the chemical composition. This simple system and the new doping strategies supply alternative solutions for enhancing charge transfer in bioinspired supramolecular architectures.

Rigid Tightly Packed Amino Acid Crystals as Functional Supramolecular Materials

The formation of ordered nanostructures by metabolites is gaining increased interest due to the simplicity of the building blocks and their natural occurrence. Specifically, aromatic amino acids possess the ability to form ordered supramolecular interactions due to their limited solubility in aqueous solution. Unexpectedly, l-tyrosine (l-Tyr) is almost 2 orders of magnitude less soluble in water compared to l-phenylalanine (l-Phe). However, the underlying mechanism is not fully understood as l-Tyr is more polar. Here, we explore the utilization of insoluble tyrosine assemblies for technological applications and their molecular basis by manipulating the basic building blocks of tightly packed dimers. We show that the addition of an amyloid inhibition agent increases l-Tyr solubility due to the disruption of the dimer formation. The molecular organization grants the l-Tyr crystal higher thermal stability and mechanical properties between three amino acids. Additionally, l-Tyr crystals are shown to generate high and stable piezoelectric power outputs under mechanical pressure in a sandwich device. By incorporating the rigid l-Tyr crystals into a soft polymer, a mechano-responsive bending composite was fabricated. Furthermore, the l-Tyr crystalline needles exhibit an active photowaveguiding property, making them promising candidates for the generation of photonic biomaterial-based devices. The present work exemplifies a feasible strategy to explore physical properties of supramolecular self-assemblies comprises minimalistic naturally occurring building blocks and their applications in energy harvesting, photonic devices, stretchable electronics, and soft robotics.

Patterned Amyloid Materials Integrating Robustness and Genetically Programmable Functionality

The precise manipulation, localization, and assembly of biological and bioinspired molecules into organized structures have greatly promoted material science and bionanotechnology. Further technological innovation calls for new patternable soft materials with the long-sought qualities of environmental tolerance and functional flexibility. Here, we report a patterned amyloid material (PAM) platform for producing hierarchically ordered structures that integrate these material attributes. This platform, combining soft lithography with generic amyloid monomer inks (consisting of genetically engineered biofilm proteins dissolved in hexafluoroisopropanol), along with methanol-assisted curing, enables the spatially controlled deposition and in situ reassembly of amyloid monomers. The resulting patterned structures exhibit spectacular chemical and thermal stability and mechanical robustness under harsh conditions. The PAMs can be programmed for a vast array of multilevel functionalities, including anchoring nanoparticles, enabling diverse fluorescent protein arrays, and serving as self-supporting porous sheets for cellular growth. This PAM platform will not only drive innovation in biomanufacturing but also broaden the applications of patterned soft architectures in optics, electronics, biocatalysis, analytical regents, cell engineering, medicine, and other areas.

Mechanically rigid supramolecular assemblies formed from an Fmoc-guanine conjugated peptide nucleic acid

The variety and complexity of DNA-based structures make them attractive candidates for nanotechnology, yet insufficient stability and mechanical rigidity, compared to polyamide-based molecules, limit their application. Here, we combine the advantages of polyamide materials and the structural patterns inspired by nucleic-acids to generate a mechanically rigid fluorenylmethyloxycarbonyl (Fmoc)-guanine peptide nucleic acid (PNA) conjugate with diverse morphology and photoluminescent properties. The assembly possesses a unique atomic structure, with each guanine head of one molecule hydrogen bonded to the Fmoc carbonyl tail of another molecule, generating a non-planar cyclic quartet arrangement. This structure exhibits an average stiffness of 69.6 ± 6.8 N m-1 and Young's modulus of 17.8 ± 2.5 GPa, higher than any previously reported nucleic acid derived structure. This data suggests that the unique cation-free "basket" formed by the Fmoc-G-PNA conjugate can serve as an attractive component for the design of new materials based on PNA self-assembly for nanotechnology applications.

Protein Microgels from Amyloid Fibril Networks

Nanofibrillar forms of amyloidogenic proteins were initially discovered in the context of protein misfolding and disease but have more recently been found at the origin of key biological functionality in many naturally occurring functional materials, such as adhesives and biofilm coatings. Their physiological roles in nature reflect their great strength and stability, which has led to the exploration of their use as the basis of artificial protein-based functional materials. Particularly for biomedical applications, they represent attractive building blocks for the development of, for instance, drug carrier agents due to their inherent biocompatibility and biodegradability. Furthermore, the propensity of proteins to self-assemble into amyloid fibrils can be exploited under microconfinement, afforded by droplet microfluidic techniques. This approach allows the generation of multi-scale functional microgels that can host biological additives and can be designed to incorporate additional functionality, such as to aid targeted drug delivery.

Fibrous Aggregates of Short Peptides Containing Two Distinct Aromatic Amino Acid Residues

The aim of the study was the assessment of the ability of short peptides to form aggregates under physiological conditions. The dipeptides studied were derived from different aromatic amino acids (heteroaromatic peptides). Tripeptides were obtained from two distinct aromatic amino acids and cysteine or methionine residue in the C-terminal, N-terminal, or central position. The ability of the peptides to form fibrous aggregates under physiological conditions was evaluated using three independent methods: the Congo Red assay, the Thioflavin T assay, and microscopic examinations using normal and polarized light. Materials potentially useful for regenerative medicine were selected based on their cytotoxicity to the endothelial cell line EA.hy 926 and physicochemical properties of films formed by peptides. The required parameters of biocompatibility were fulfilled by H-PheCysTrp-OH, H-PheCysTyr-OH, H-PheTyrMet-OH, and H-TrpTyr-OH.

Coupled chemistry kinetics demonstrate the utility of functionalized Sup35 amyloid nanofibrils in biocatalytic cascades

Concerns over the environment are a central driver for designing cell-free enzymatic cascade reactions that synthesize non-petrol-based commodity compounds. An often-suggested strategy that would demonstrate the economic competitiveness of this technology is recycling of valuable enzymes through their immobilization. For this purpose, amyloid nanofibrils are an ideal scaffold to realize chemistry-free covalent enzyme immobilization on a material that offers a large surface area. However, in most instances, only single enzyme-functionalized amyloid fibrils have so far been studied. To embark on the next stage, here we displayed xylanase A, β-xylosidase, and an aldose sugar dehydrogenase on Sup35(1-61) nanofibrils to convert beechwood xylan to xylonolactone. We characterized this enzymatic cascade by measuring the time-dependent accumulation of xylose, xylooligomers, and xylonolactone. Furthermore, we studied the effects of relative enzyme concentrations, pH, temperature, and agitation on product formation. Our investigations revealed that a modular cascade with a mixture of xylanase and β-xylosidase, followed by product removal and separate oxidation of xylose with the aldose sugar dehydrogenase, is more productive than an enzyme mix containing all of these enzymes together. Moreover, we found that the nanofibril-coupled enzymes do not lose activity compared with their native state. These findings provide proof of concept of the feasibility of functionalized Sup35(1-61) fibrils as a molecular scaffold for biocatalytic cascades consisting of reusable enzymes that can be used in biotechnology.

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

Protein amyloid aggregation is a hallmark in neuropathologies and other diseases of tremendous impact such as Alzheimer's or Parkinson's diseases. During the last decade, it has become increasingly evident that neuronal death is mainly induced by proteinaceous oligomers rather than the mature amyloid fibrils. Therefore, the earliest molecular events occurring during the amyloid aggregation cascade represent a growing interest of study. Important breakthroughs have been achieved using experimental data from different proteins, used as models, as well as systems related to diseases. Here, we summarize the structural properties of amyloid oligomeric and fibrillar aggregates and review the recent advances on how biophysical techniques can be combined with quantitative kinetic analysis and theoretical models to study the detailed mechanism of oligomer formation and nucleation of fibrils. These insights into the mechanism of early oligomerization and amyloid nucleation are of relevant interest in drug discovery and in the design of preventive strategies against neurodegenerative diseases.

A BODIPY biosensor to detect and drive self-assembly of diphenylalanine

Diphenylalanine (FF), as the smallest unit and core recognition motif of β-amyloid (Aβ), could self-assemble into nanofibers, which induces an early onset of Alzheimer's disease (AD). Green/near-infrared fluorescent BODIPY probes were designed and synthesized to detect FF-assembly, providing unique insights into the chemical and molecular mechanism of Aβ aggregation and drug development for AD.

Revisiting the conformational state of albumin conjugated to gold nanoclusters: A self-assembly pathway to giant superstructures unraveled

Bovine serum albumin (BSA) is often employed as a proteinaceous component for synthesis of luminescent protein-stabilized gold nanoclusters (AuNC): intriguing systems with many potential applications. Typically, the formation of BSA-AuNC conjugate occurs under strongly alkaline conditions. Due to the sheer complexity of intertwined chemical and structural transitions taking place upon BSA-AuNC formation, the state of albumin enveloping AuNCs remains poorly characterized. Here, we study the conformational properties of BSA bound to AuNCs using an array of biophysical tools including vibrational spectroscopy, circular dichroism, fluorescence spectroscopy and trypsin digestion. The alkaline conditions of BSA-AuNC self-assembly appear to be primary responsible for the profound irreversible disruption of tertiary contacts, partial unfolding of native α-helices, hydrolysis of disulfide bonds and the protein becoming vulnerable to trypsin digestion. Further unfolding of BSA-AuNC by guanidinium hydrochloride (GdnHCl) is fully reversible equally in terms of albumin's secondary structure and conjugate's luminescent properties. This suggests that binding to AuNCs traps the albumin molecule in a state that is both partly disordered and refractory to irreversible misfolding. Indeed, when BSA-AuNC is subjected to conditions favoring self-association of BSA into amyloid-like fibrils, the buildup of non-native β-sheet conformation is less pronounced than in a control experiment with unmodified BSA. Unexpectedly, BSA-AuNC reveals a tendency to self-assemble into giant twisted superstructures of micrometer lengths detectable with transmission electron microscopy (TEM), a property absent in unmodified BSA. The process is accompanied by ordering of bound AuNCs into elongated streaks and simultaneous decrease in fluorescence intensity. The newly discovered self-association pathway appears to be specifically accessible to protein molecules with a certain restriction on structural dynamics which in the case of BSA-AuNC arises from binding to metal nanoclusters. Our results have been discussed in the context of mechanisms of protein misfolding and applications of BSA-AuNC.

Polyamine-induced, chiral expression from liquid crystalline peptide nanofilaments to long-range ordered nanohelices

We reported the condensation and transformation of peptide micelles into well-defined nanohelices through the incorporation of natural polyamines. The liquid-crystalline peptide micelles are assembled by a short dipeptide amphiphile driven by strong electrostatic repulsions and aromatic stacking attractions. By incorporating polyamines into the peptide solutions, like-charge attractions were achieved to induce the condensation of the like-charged nanofilaments into giant bundles. Intriguingly, by increasing the temperature or electrostatic screening effects, the nanofilaments within the bundles fuse with each other into well-defined flat ribbons which then spontaneously twisted into macroscopically aligned nanohelices. Moreover, the chiral interactions between the aromatic groups of adjacent peptides are inverted from right-handedness to left-handedness during the formation of nanohelices. The results provide new insights into the chiral evolution during peptide self-assembly and offer opportunities for the design of peptide materials with new properties, such as anisotropic hydrogels and long-range ordered chiral nanostructures.

Stable and optoelectronic dipeptide assemblies for power harvesting

Low biocompatibility or engineerability of conventional inorganic materials limits their extensive application for power harvesting in biological systems or at bio-machine interfaces. In contrast, intrinsically biocompatible peptide self-assemblies have shown promising potential as a new type of ideal components for eco-friendly optoelectronic energy-harvesting devices. However, the structural instability, weak mechanical strength, and inefficient optical or electrical properties severely impede their extensive application. Here, we demonstrate tryptophan-based aromatic dipeptide supramolecular structures to be direct wide-gap semiconductors. The molecular packings can be effectively modulated by changing the peptide sequence. The extensive and directional hydrogen bonding and aromatic interactions endow the structures with unique rigidity and thermal stability, as well as a wide-spectrum photoluminescence covering nearly the entire visible region, optical waveguiding, temperature/irradiation-dependent conductivity, and the ability to sustain quite high external electric fields. Furthermore, the assemblies display high piezoelectric properties, with a measured open-circuit voltage of up to 1.4 V. Our work provides insights into using aromatic short peptide self-assemblies for the fabrication of biocompatible, miniaturized electronics for power generation with tailored semiconducting optoelectronic properties and improved structural stability.

Cohesive and adhesive properties of crosslinked semiflexible biopolymer networks

Biomolecular semiflexible polymer networks with persistence lengths well above those of single polymeric chains serve important structural and adhesive roles in biology, biomaterials, food science and many other fields. While relationships between the structure and viscoelasticity of semiflexible polymer networks have been previously investigated, it remains challenging to systematically relate fibril and network properties to cohesive and adhesive properties that govern the function of these materials. To address this issue, here we utilize coarse-grained molecular dynamics simulations to thoroughly elucidate how the work of adhesion of a semiflexible polymer network to a surface depends on crosslink density and fibril persistence length. Two emergent characteristics of the network are its elasticity and its interfacial energy with the surface. Stiff networks that are either highly crosslinked or have high persistence length fibrils tend to have lower interfacial energy, and consequently, lower work of adhesion. For lightly crosslinked networks with flexible fibrils, considerable strain energy must be stored within the adhesive during detachment, which creates an additional penalty to detachment. Increasing persistence length while keeping crosslink density constant leads to porous, low density networks, leading to an optimal fibril persistence length at which maximum work of adhesion per mass density is attained for a given crosslink density. For any given fibril persistence length, increasing crosslink density has a slightly negative effect on network mass density and interfacial energy. A critical crosslink density is found, below which the networks have no significant load-bearing capacity. Lightly crosslinked networks above this threshold absorb more strain energy during desorption and consequently possess greater work of adhesion. The conflict between mass density and stiffness results in a non-monotonic trend between the ratio of work of adhesion to interfacial energy and persistence length. These findings provide physical insight into the adhesive mechanisms of biomaterials based on crosslinked semiflexible polymer networks, and reveal important design guidelines for bio-adhesives.

Rigid helical-like assemblies from a self-aggregating tripeptide

The structural versatility, biocompatibility and dynamic range of the mechanical properties of protein materials have been explored in functional biomaterials for a wide array of biotechnology applications. Typically, such materials are made from self-assembled peptides with a predominant β-sheet structure, a common structural motif in silk and amyloid fibrils. However, collagen, the most abundant protein in mammals, is based on a helical arrangement. Here we show that Pro-Phe-Phe, the most aggregation-prone tripeptide of natural amino acids, assembles into a helical-like sheet that is stabilized by the dry hydrophobic interfaces of Phe residues. This architecture resembles that of the functional PSMα3 amyloid, highlighting the role of dry helical interfaces as a core structural motif in amyloids. Proline replacement by hydroxyproline, a major constituent of collagen, generates minimal helical-like assemblies with enhanced mechanical rigidity. These results establish a framework for designing functional biomaterials based on ultrashort helical protein elements.

The Role of Structural Polymorphism in Driving the Mechanical Performance of the Alzheimer's Beta Amyloid Fibrils

Alzheimer's Disease (AD) is related with the abnormal aggregation of amyloid β-peptides Aβ₁₋₄₀ and Aβ₁₋₄₂, the latter having a polymorphic character which gives rise to U- or S-shaped fibrils. Elucidating the role played by the nanoscale-material architecture on the amyloid fibril stability is a crucial breakthrough to better understand the pathological nature of amyloid structures and to support the rational design of bio-inspired materials. The computational study here presented highlights the superior mechanical behavior of the S-architecture, characterized by a Young's modulus markedly higher than the U-shaped architecture. The S-architecture showed a higher mechanical resistance to the enforced deformation along the fibril axis, consequence of a better interchain hydrogen bonds' distribution. In conclusion, this study, focusing the attention on the pivotal multiscale relationship between molecular phenomena and material properties, suggests the S-shaped Aβ₁₋₄₂ species as a target of election in computational screen/design/optimization of effective aggregation modulators.

Modular genetic design of multi-domain functional amyloids: insights into self-assembly and functional properties

Engineering functional amyloids through a modular genetic strategy represents new opportunities for creating multifunctional molecular materials with tailored structures and performance. Despite important advances, how fusion modules affect the self-assembly and functional properties of amyloids remains elusive. Here, using Escherichia coli curli as a model system, we systematically studied the effect of flanking domains on the structures, assembly kinetics and functions of amyloids. The designed amyloids were composed of E. coli biofilm protein CsgA (as amyloidogenic cores) and one or two flanking domains, consisting of chitin-binding domains (CBDs) from Bacillus circulans chitinase, and/or mussel foot proteins (Mfps). Incorporation of fusion domains did not disrupt the typical β-sheet structures, but indeed affected assembly rate, morphology, and stiffness of resultant fibrils. Consequently, the CsgA-fusion fibrils, particularly those containing three domains, were much shorter than the CsgA-only fibrils. Furthermore, the stiffness of the resultant fibrils was heavily affected by the structural feature of fusion domains, with β-sheet-containing domains tending to increase the Young's modulus while random coil domains decreasing the Young's modulus. In addition, fibrils containing CBD domains showed higher chitin-binding activity compared to their CBD-free counterparts. The CBD-CsgA-Mfp3 construct exhibited significantly lower binding activity than Mfp5-CsgA-CBD due to inappropriate folding of the CBD domain in the former construct, in agreement with results based upon molecular dynamics modeling. Our study provides new insights into the assembly and functional properties of designer amyloid proteins with increasing complex domain structures and lays the foundation for the future design of functional amyloid-based structures and molecular materials.

Influence of crowding and surfaces on protein amyloidogenesis: A thermo-kinetic perspective

The last few decades have irreversibly implicated protein self-assembly and aggregation leading to amyloid fibril formation in proteopathies that include several neurodegenerative diseases. Emerging studies recognize the importance of eliciting the pathways leading to protein aggregation in the context of the crowded intracellular environment rather than in conventional in vitro conditions. It is found that crowded environments can have acceleratory as well as inhibitory effects on protein aggregation, depending on the interplay of underlying factors on the crucial rate limiting steps. The aggregation mechanism and transient species formed along the pathway are further altered when they interface with natural and artificial surfaces in the cellular milieu. An increasing number of studies probe the autocatalytic nature of amyloid surfaces as well as membrane bilayer effects on amyloidogenesis. Moreover, exposure to modern nanosurfaces via nanomedicines and other sources potentially invokes beneficial or deleterious biological response that needs rigorous investigation. Mounting evidences indicate that nanoparticles can either promote or impede amyloid aggregation, spurring efforts to tune their interactions for developing effective anti-amyloid strategies. Mechanistic insights into nanoparticle mediated aggregation pathways are therefore crucial for engineering anti-amyloid nanoparticle strategies that are biocompatible and sustainable. This review is a compilation of studies that contribute to the current understanding of the altering effects of molecular crowding as well as natural and artificial surfaces on protein amyloidogenesis.

A first-passage approach to the thermal breakage of a discrete one-dimensional chain

Using the first passage method for a Markov process, we theoretically study the fragmentation rate of a discrete one-dimensional chain (Rouse model). The fragmentation occurs due to thermal fluctuations. Assuming equilibrium initial conditions, we obtain an expression for the fragmentation rate of the one-dimensional filament as a function of the number of monomers, the position of the breaking point along the filament, the ratio of the bond energy to the thermal energy, and the Rouse relaxation time. We also obtain the fragmentation rate for a fixed initial configuration of the chain by numerically solving a Volterra equation. Our results reduce to those of previous theoretical studies at the appropriate limits, and spell out the role of the relevant time scales. The prediction of our model for the fragmentation rate of insulin fibrils under optimal growth conditions for the solution appears to be consistent with experimental data from other studies.

Subtyping of circulating exosome-bound amyloid β reflects brain plaque deposition

Despite intense interests in developing blood measurements of Alzheimer’s disease (AD), the progress has been confounded by limited sensitivity and poor correlation to brain pathology. Here, we present a dedicated analytical platform for measuring different populations of circulating amyloid β (Aβ) proteins – exosome-bound vs. unbound – directly from blood. The technology, termed amplified plasmonic exosome (APEX), leverages in situ enzymatic conversion of localized optical deposits and double-layered plasmonic nanostructures to enable sensitive, multiplexed population analysis. It demonstrates superior sensitivity (~200 exosomes), and enables diverse target co-localization in exosomes. Employing the platform, we find that prefibrillar Aβ aggregates preferentially bind with exosomes. We thus define a population of Aβ as exosome-bound (Aβ42+ CD63+) and measure its abundance directly from AD and control blood samples. As compared to the unbound or total circulating Aβ, the exosome-bound Aβ measurement could better reflect PET imaging of brain amyloid plaques and differentiate various clinical groups.

Detecting Alzheimer’s disease from blood samples is challenging because amyloid β blood levels are lower than the ELISA detection limit. Here the authors capture amyloid β bound to circulating exosomes on a plasmonic nanosensor, followed by enzymatic amplification to improve detection sensitivity.