Nanomechanics of functional and pathological amyloid materials

ProtAgents: protein discovery via large language model multi-agent collaborations combining physics and machine learning

Designing de novo proteins beyond those found in nature holds significant promise for advancements in both scientific and engineering applications. Current methodologies for protein design often rely on AI-based models, such as surrogate models that address end-to-end problems by linking protein structure to material properties or vice versa. However, these models frequently focus on specific material objectives or structural properties, limiting their flexibility when incorporating out-of-domain knowledge into the design process or comprehensive data analysis is required. In this study, we introduce ProtAgents, a platform for de novo protein design based on Large Language Models (LLMs), where multiple AI agents with distinct capabilities collaboratively address complex tasks within a dynamic environment. The versatility in agent development allows for expertise in diverse domains, including knowledge retrieval, protein structure analysis, physics-based simulations, and results analysis. The dynamic collaboration between agents, empowered by LLMs, provides a versatile approach to tackling protein design and analysis problems, as demonstrated through diverse examples in this study. The problems of interest encompass designing new proteins, analyzing protein structures and obtaining new first-principles data - natural vibrational frequencies - via physics simulations. The concerted effort of the system allows for powerful automated and synergistic design of de novo proteins with targeted mechanical properties. The flexibility in designing the agents, on one hand, and their capacity in autonomous collaboration through the dynamic LLM-based multi-agent environment on the other hand, unleashes great potentials of LLMs in addressing multi-objective materials problems and opens up new avenues for autonomous materials discovery and design.

Hierarchical Protofilament Intertwining Rules the Formation of Mixed-Curvature Amyloid Polymorphs

Amyloid polymorphism is a hallmark of almost all amyloid species, yet the mechanisms underlying the formation of amyloid polymorphs and their complex architectures remain elusive. Commonly, two main mesoscopic topologies are found in amyloid polymorphs characterized by non-zero Gaussian and mean curvatures: twisted ribbons and helical fibrils, respectively. Here, a rich heterogeneity of configurations is demonstrated on insulin amyloid fibrils, where protofilament packing can occur, besides the common polymorphs, also in a combined mode forming mixed-curvature polymorphs. Through AFM statistical analysis, an extended array of heterogeneous architectures that are rationalized by mesoscopic theoretical arguments are identified. Notably, an unusual fibrillization pathway is also unraveled toward mixed-curvature polymorphs via the widespread recruitment and intertwining of protofilaments and protofibrils. The results present an original view of amyloid polymorphism and advance the fundamental understanding of the fibrillization mechanism from single protofilaments into mature amyloid fibrils.

In Situ Nanoencapsulation of Curcumin in Soy Protein Isolate Amyloid-like Aggregates for Enhanced Wound Healing

The importance of amyloid nanofibrils made from food proteins is rising in diverse fields, such as biomedicine and food science. These protein nanofibrils (PNFs) serve as versatile and sustainable building blocks for biomaterials, characterized by their high β-sheet content and an ordered hydrogen bond network. These properties offer both stability and flexibility, along with an extreme aspect ratio and reactive functional groups. Plant-derived amyloid nanofibrils, such as soy protein isolate (SPI) PNFs, are increasingly favored due to their affordability and sustainability compared with animal proteins. This study aimed to explore the formation and application of SPI amyloid-like aggregates (SPIA) and their nanoencapsulation of curcumin (Cur) for biomedical purposes, particularly in wound healing. Under specific conditions of low pH and high temperature, SPIA formed, exhibited an amyloid nature, and successfully encapsulated Cur, thereby enhancing its stability and availability. Spectroscopic and microscopic analyses confirmed structural changes in SPIA upon the incorporation of Cur and the fabrication of SPIA@Cur. The obtained results indicate that in the presence of Cur, SPIA forms faster, attributed to accelerated SPI denaturation, an increased nucleation rate, and enhanced self-assembly facilitated by Cur's hydrophobic interactions and π-π stacking with SPI peptides. In vitro studies demonstrated the biocompatibility, biodegradability, and antioxidant properties of SPIA@Cur along with controlled release behavior. In vivo experiments in male Wistar rats revealed that both SPIA and SPIA@Cur significantly accelerate wound closure compared with untreated wounds, with SPIA@Cur showing slightly better efficacy. The histological analysis supported enhanced wound healing, indicating the potential of SPIA@Cur for biomedical applications.

Synthetic control of actin polymerization and symmetry breaking in active protocells

Nonlinear biomolecular interactions on membranes drive membrane remodeling crucial for biological processes including chemotaxis, cytokinesis, and endocytosis. The complexity of biomolecular interactions, their redundancy, and the importance of spatiotemporal context in membrane organization impede understanding of the physical principles governing membrane mechanics. Developing a minimal in vitro system that mimics molecular signaling and membrane remodeling while maintaining physiological fidelity poses a major challenge. Inspired by chemotaxis, we reconstructed chemically regulated actin polymerization inside vesicles, guiding membrane self-organization. An external, undirected chemical input induced directed actin polymerization and membrane deformation uncorrelated with upstream biochemical cues, suggesting symmetry breaking. A biophysical model incorporating actin dynamics and membrane mechanics proposes that uneven actin distributions cause nonlinear membrane deformations, consistent with experimental findings. This protocellular system illuminates the interplay between actin dynamics and membrane shape during symmetry breaking, offering insights into chemotaxis and other cell biological processes.

Mechanobiological insight into brain diseases based on mechanosensitive channels: Common mechanisms and clinical potential

BACKGROUND

As physical signals, mechanical cues regulate the neural cells in the brain. The mechanosensitive channels (MSCs) perceive the mechanical cues and transduce them by permeating specific ions or molecules across the plasma membrane, and finally trigger a series of intracellular bioelectrical and biochemical signals. Emerging evidence supports that wide-distributed, high-expressed MSCs like Piezo1 play important roles in several neurophysiological processes and neurological disorders.

AIMS

To systematically conclude the functions of MSCs in the brain and provide a novel mechanobiological perspective for brain diseases.

METHOD

We summarized the mechanical cues and MSCs detected in the brain and the research progress on the functional roles of MSCs in physiological conditions. We then concluded the pathological activation and downstream pathways triggered by MSCs in two categories of brain diseases, neurodegenerative diseases and place-occupying damages. Finally, we outlined the methods for manipulating MSCs and discussed their medical potential with some crucial outstanding issues.

RESULTS

The MSCs present underlying common mechanisms in different brain diseases by acting as the "transportation hubs" to transduce the distinct signal patterns: the upstream mechanical cues and the downstream intracellular pathways. Manipulating the MSCs is feasible to alter the complicated downstream processes, providing them promising targets for clinical treatment.

CONCLUSIONS

Recent research on MSCs provides a novel insight into brain diseases. The common mechanisms mediated by MSCs inspire a wide range of therapeutic potentials targeted on MSCs in different brain diseases.

Polyvinyl alcohol films incorporated with clove essential oil emulsions stabilized by soy protein isolate-derived amyloid fibrils: Fabrication, characterization, and its application for active packaging

This study aimed to prepare a novel emulsion film with high stability, using soy protein-derived amyloid fibrils (SAFs) as an emulsifier incorporating clove essential oil (CEO) as the active component, and the polyvinyl alcohol (PVA) matrix to stabilize the system. The results demonstrated that SAFs can successfully stabilize CEO. Emulsion prepared by SAFS and CEO (SAC) exhibited a small droplet size and better dispersibility compared with SPI and CEO (SC) emulsion. According to FT-IR results, PVA addition increased the hydrogen bond interactions among emulsion film components, thus further reinforcing the protein matrix, increasing the tensile strength (TS) (41.18 MPa) and elongation at break (E) (121.62 %) of the films. The uniform appearance of SAC-PVA (SACP) emulsion films was confirmed by SEM images. Furthermore, SACP emulsion films show distinctive barrier properties, optical properties, and outstanding antioxidant properties. Finally, emulsion films exhibited excellent preservation of strawberries, resulting in an effective decline of the decay rate.

gp120-derived amyloidogenic peptides form amyloid fibrils that increase HIV-1 infectivity

Apart from mediating viral entry, the function of the free HIV-1 envelope protein (gp120) has yet to be elucidated. Our group previously showed that EP2 derived from one β-strand in gp120 can form amyloid fibrils that increase HIV-1 infectivity. Importantly, gp120 contains ~30 β-strands. We examined whether gp120 might serve as a precursor protein for the proteolytic release of amyloidogenic fragments that form amyloid fibrils, thereby promoting viral infection. Peptide array scanning, enzyme degradation assays, and viral infection experiments in vitro confirmed that many β-stranded peptides derived from gp120 can indeed form amyloid fibrils that increase HIV-1 infectivity. These gp120-derived amyloidogenic peptides, or GAPs, which were confirmed to form amyloid fibrils, were termed gp120-derived enhancers of viral infection (GEVIs). GEVIs specifically capture HIV-1 virions and promote their attachment to target cells, thereby increasing HIV-1 infectivity. Different GAPs can cross-interact to form heterogeneous fibrils that retain the ability to increase HIV-1 infectivity. GEVIs even suppressed the antiviral activity of a panel of antiretroviral agents. Notably, endogenous GAPs and GEVIs were found in the lymphatic fluid, lymph nodes, and cerebrospinal fluid (CSF) of AIDS patients in vivo. Overall, gp120-derived amyloid fibrils might play a crucial role in the process of HIV-1 infectivity and thus represent novel targets for anti-HIV therapeutics.

Mechanically Ultra-Robust Fluorescent Elastomer for Elaborating Auxetic Composite

Fluorescent elastomers are predominantly fabricated through doping fluorescent components or conjugating chromophores into polymer networks, which often involves detrimental effects on mechanical performance and also makes large-scale production difficult. Inspired by the heteroatom-rich microphase separation structures assisted by intensive hydrogen bonds in natural organisms, an ultra-robust fluorescent polyurethane elastomer is reported, which features a remarkable fracture strength of 87.2 MPa with an elongation of 1797%, exceptional toughness of 678.4 MJ m-3 and intrinsic cyan fluorescence at 445 nm. Moreover, the reversible fluorescence variation with temperature could in situ reveal the microphase separation of the elastomer in real time. By taking advantage of mechanical properties, intrinsic fluorescence and hydrogen bonds-promoted interfacial bonding ability, this fluorescent elastomer can be utilized as an auxetic skeleton for the elaboration of an integrated auxetic composite. Compared with the auxetic skeleton alone, the integrated composite shows an improved mechanical performance while maintaining auxetic deformation in a large strain below 185%, and its auxetic process can be visually detected under ultraviolet light by the fluorescence of the auxetic skeleton. The concept of introducing hydrogen-bonded heteroatom-rich microphase separation structures into polymer networks in this work provides a promising approach to developing fluorescent elastomers with exceptional mechanical properties.

Sound-mediated nucleation and growth of amyloid fibrils

Mechanical energy, specifically in the form of ultrasound, can induce pressure variations and temperature fluctuations when applied to an aqueous media. These conditions can both positively and negatively affect protein complexes, consequently altering their stability, folding patterns, and self-assembling behavior. Despite much scientific progress, our current understanding of the effects of ultrasound on the self-assembly of amyloidogenic proteins remains limited. In the present study, we demonstrate that when the amplitude of the delivered ultrasonic energy is sufficiently low, it can induce refolding of specific motifs in protein monomers, which is sufficient for primary nucleation; this has been revealed by MD. These ultrasound-induced structural changes are initiated by pressure perturbations and are accelerated by a temperature factor. Furthermore, the prolonged action of low-amplitude ultrasound enables the elongation of amyloid protein nanofibrils directly from natively folded monomeric lysozyme protein, in a controlled manner, until it reaches a critical length. Using solution X-ray scattering, we determined that nanofibrillar assemblies, formed either under the action of sound or from natively fibrillated lysozyme, share identical structural characteristics. Thus, these results provide insights into the effects of ultrasound on fibrillar protein self-assembly and lay the foundation for the potential use of sound energy in protein chemistry.

Significance Statement

Understanding how and why proteins form amyloid fibrils is crucial for research into various diseases, including neurodegeneration. Ultrasound is routinely used in research settings as a tool for generating amyloid seeds (nucleation sites) from mature fibrils, which accelerate the rate of fibril growth. However, ultrasound can have various effects on aqueous media including temperature, extreme shear, and free radicals. Here we show that when the ultrasound parameters are precisely adjusted, they can be utilized as a tool for amyloid growth directly from the natively folded monomers. Thus, it is possible to induce minor changes in the folding of proteins, which trigger nucleation and accelerate amyloid growth. This knowledge lays the foundation for the potential use of sound in protein chemistry.

Clues to the Design of Aggregation-Resistant Insulin from Proline Scanning of Highly Amyloidogenic Peptides Derived from the N-Terminal Segment of the A-Chain

Insulin aggregation poses a significant problem in pharmacology and medicine as it occurs during prolonged storage of the hormone and in vivo at insulin injection sites. We have recently shown that dominant forces driving the self-assembly of insulin fibrils are likely to arise from intermolecular interactions involving the N-terminal segment of the A-chain (ACC1-13). Here, we study how proline substitutions within the pilot GIVEQ sequence of this fragment affect its propensity to aggregate in both neutral and acidic environments. In a reasonable agreement with in silico prediction based on the Cordax algorithm, proline substitutions at positions 3, 4, and 5 turn out to be very effective in preventing aggregation according to thioflavin T-fluorescence-based kinetic assay, infrared spectroscopy, and atomic force microscopy (AFM). Since the valine and glutamate side chains within this segment are strongly involved in the interactions with the insulin receptor, we have focused on the possible implications of the Q → P substitution for insulin's stability and interactions with the receptor. To this end, comparative molecular dynamics (MD) simulations of the Q5P mutant and wild-type insulin were carried out for both free and receptor-bound (site 1) monomers. The results point to a mild destabilization of the mutant vis à vis the wild-type monomer, as well as partial preservation of key contacts in the complex between Q5P insulin and the receptor. We discuss the implications of these findings in the context of the design of aggregation-resistant insulin analogues retaining hormonal activity.

Variance and higher moments in the sigmoidal self-assembly of branched fibrils

Self-assembly of functional branched filaments, such as actin filaments and microtubules, or dysfunctional ones, such as amyloid fibrils, plays important roles in many biological processes. Here, based on the master equation approach, we study the kinetics of the formation of the branched fibrils. In our model, a branched fibril has one mother branch and several daughter branches. A daughter branch grows from the side of a pre-existing mother branch or daughter branch. In our model, we consider five basic processes for the self-assembly of the branched filaments, namely, the nucleation, the dissociation of the primary nucleus of fibrils, the elongation, the fragmentation, and the branching. The elongation of a mother branch from two ends and the elongation of a daughter branch from two ends can, in principle, occur with four different rate constants associated with the corresponding tips. This leads to a pronounced impact of the directionality of growth on the kinetics of the self-assembly. Here, we have unified and generalized our four previously presented models of branched fibrillogenesis in a single model. We have obtained a system of non-linear ordinary differential equations that give the time evolution of the polymer numbers and the mass concentrations along with the higher moments as observable quantities.

Peptide Self-assembly: From Ordered to Disordered

Biomolecular self-assembly is a ubiquitous occurrence in nature that gives rise to sophisticated superstructures that enable the implementation of complex biological functions. It encompasses both ordered structures, such as the DNA double helix, and disordered structures, such as the nucleolus and other nonmembranous organelles. In contrast to these highly organized ordered structures, which exhibit specific patterns or symmetry, disordered structures are characterized by their flexible and randomized molecular organization, which provides versatility, dynamicity, and adaptability to biological systems and contributes to the complexity and functionality of living organisms. However, these disordered structures usually exist in a thermodynamically metastable state. This means that these disordered structures are unstable and difficult to observe due to their short existence time. Achieving disordered structures through precise control of the assembly process and ensuring their stability and integrity pose significant challenges. Currently, ongoing research efforts are focused on the self-assembly of proteins with intrinsically disordered regions (IDRs). However, the structural complexity and instability of proteins present prohibitive difficulties in elucidating the multiscale self-assembly process. Therefore, simple peptides, as a segment of proteins, hold great promise in constructing self-assembly systems for related research. Since our finding on droplet-like disordered structures that occur transiently during the peptide self-assembly (PSA), our research is centered around the dynamic evolution of peptide supramolecular systems, particularly the modulation of a variety of assembled structures ranging from ordered to disordered.In this Account, we narrate our recent research endeavors on supramolecular structures formed by PSA, spanning from ordered structures to disordered structures. We delve into the mechanisms of structural regulation, shedding light on how these peptide-based structures can be controlled more precisely. Moreover, we emphasize the functional applications that arise from these structures. To begin, we conduct a comprehensive overview of various types of ordered structures that emerge from PSA, showcasing their diverse applications. Following, we elaborate on the discovery and development of droplet-like disordered structures that arise during PSA. A mechanistic study on multistep self-assembly processes mediated by liquid-liquid phase separation (LLPS) is critically emphasized. Ordered structures with different morphologies and functions can be obtained by subtly controlling and adjusting the metastable liquid droplets. In particular, we have recently developed solid glasses with long-range disorder, including noncovalent biomolecular glass based on amino acid and peptide derivatives, as well as high-entropy glass based on cyclic peptides. This demonstrates the great potential of using biologically derived molecules to create green and sustainable glassy materials.

Acetone-induced structural variant of insulin amyloid fibrils

Self-propagating polymorphism of amyloid fibrils is a distinct manifestation of non-equilibrium conditions under which protein aggregation typically occurs. Structural variants of fibrils can often be accessed through physicochemical perturbations of the de novo aggregation process. On the other hand, tiny changes in the amino acid sequence of the parent protein may also result in structurally distinguishable amyloid fibrils. Here, we show that in the presence of acetone, the low-pH fibrillization pathway of bovine insulin (BI) leads to a new type of amyloid with the infrared features (split amide I' band with the maximum at 1623 cm-1) bearing a striking resemblance to those of the previously reported fibrils from recombinant LysB31-ArgB32 human insulin analog formed in the absence of the co-solvent. Insulin fibrils formed in the presence ([BI-ace]) and absence ([BI]) of acetone cross-seed each other and pass their infrared features to the daughter generations of fibrils. We have used dimethyl sulfoxide (DMSO) coupled to in situ infrared spectroscopy measurements to probe the stability of fibrils against chemical denaturation. While both types of fibrils eventually undergo DMSO-induced disassembly coupled to a β-sheet→coil transition, in the case of [BI-ace] amyloid, the denaturation is preceded by the fibrils transiently acquiring the [BI]-like infrared characteristics. We argue that this effect is caused by DMSO-induced dehydration of [BI-ace]. In support to this hypothesis, we show that, even in the absence of DMSO, the infrared features of [BI-ace] disappear upon drying. We discuss this very peculiar aspect of [BI-ace] fibrils in the context of recently accessed in silico models of plausible structural variants of insulin protofilaments.

Bioinspired Amino Acid Based Materials in Bionanotechnology: From Minimalistic Building Blocks and Assembly Mechanism to Applications

Inspired by natural hierarchical self-assembly of proteins and peptides, amino acids, as the basic building units, have been shown to self-assemble to form highly ordered structures through supramolecular interactions. The fabrication of functional biomaterials comprised of extremely simple biomolecules has gained increasing interest due to the advantages of biocompatibility, easy functionalization, and structural modularity. In particular, amino acid based assemblies have shown attractive physical characteristics for various bionanotechnology applications. Herein, we propose a review paper to summarize the design strategies as well as research advances of amino acid based supramolecular assemblies as smart functional materials. We first briefly introduce bioinspired reductionist design strategies and assembly mechanism for amino acid based molecular assembly materials through noncovalent interactions in condensed states, including self-assembly, metal ion mediated coordination assembly, and coassembly. In the following part, we provide an overview of the properties and functions of amino acid based materials toward applications in nanotechnology and biomedicine. Finally, we give an overview of the remaining challenges and future perspectives on the fabrication of amino acid based supramolecular biomaterials with desired properties. We believe that this review will promote the prosperous development of innovative bioinspired functional materials formed by minimalistic building blocks.

From Fundamental Amyloid Protein Self-Assembly to Development of Bioplastics

Proteins can self-assemble into a range of nanostructures as a result of molecular interactions. Amyloid nanofibrils, as one of them, were first discovered with regard to the relevance of neurodegenerative diseases but now have been exploited as building blocks to generate multiscale materials with designed functions for versatile applications. This review interconnects the mechanism of amyloid fibrillation, the current approaches to synthesizing amyloid protein-based materials, and the application in bioplastic development. We focus on the fundamental structures of self-assembled amyloid fibrils and how external factors can affect protein aggregation to optimize the process. Protein self-assembly is essentially the autonomous congregation of smaller protein units into larger, organized structures. Since the properties of the self-assembly can be manipulated by changing intrinsic factors and external conditions, protein self-assembly serves as an excellent building block for bioplastic development. Building on these principles, general processing methods and pathways from raw protein sources to mature state materials are proposed, providing a guide for the development of large-scale production. Additionally, this review discusses the diverse properties of protein-based amyloid nanofibrils and how they can be utilized as bioplastics. The economic feasibility of the protein bioplastics is also compared to conventional plastics in large-scale production scenarios, supporting their potential as sustainable bioplastics for future applications.

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.

Wheat gluten amyloid fibrils: Conditions, mechanism, characterization, application, and future perspectives

Amyloid fibrils have excellent structural characteristics, such as a high aspect ratio, excellent stiffness, and a wide availability of functional groups on the surface. More studies are now focusing on the formation of amyloid fibrils using food proteins. Protein fibrillation is now becoming recognized as a promising strategy for enhancing the function of food proteins and expanding their range of applications. Wheat gluten is rich in glutamine (Q), hydrophobic amino acids, and the α-helix structure with high β-sheet tendency. These characteristics make it very easy for wheat gluten to form amyloid fibrils. The conditions, formation mechanism, characterization methods, and application of amyloid fibrils formed by wheat gluten are summarized in this review. Further exploration of amyloid fibrils formed by wheat gluten will reveal how they can play a significant role in food, biology, and other fields, especially in medicine.

Formation of hen egg white lysozyme derived amyloid-based hydrogels using different gelation agents: A potential tool for drug delivery

Amyloids are highly stable protein fibrillar aggregates that get deposited in various parts of our body and cause detrimental diseases. But in nature, the presence of functional amyloids is also noted in bacteria that help them by forming hyphae, biofilm, protein reservoirs, signalling messengers, etc. Keeping this perspective in mind, the idea behind this research was to develop functional amyloids in the form of hydrogel and analyse its potential in the biomedical sector as a drug-delivery tool. The synthesis and characterisation of three types of amyloid-based hydrogels have been reported in this work. Hen Egg-White Lysozyme (HEWL) protein was chosen as the principal ingredient as it is extensively used as a standard protein for studying amyloidogenesis and has inherent antibacterial properties. Comparative studies of different hydrogel properties exhibited variations in the hydrogels based on compositional differences in them. Finally, a drug release assay was done on the synthesized hydrogels to explore their potential as drug delivery tools.

Single-Crystal-to-Single-Crystal Topochemical Synthesis of a Collagen-inspired Covalent Helical Polymer

There is much demand for crystalline covalent helical polymers. Inspired by the helical structure of collagen, we synthesized a covalent helical polymer wherein the repeating dipeptide Gly-Pro units are connected by triazole linkages. We synthesized an azide and alkyne-modified dipeptide monomer made up of the repeating amino acid sequence of collagen. In its crystals, the monomer molecules aligned in head-to-tail fashion with proximally placed azide and alkyne forming supramolecular helices. At 60 °C, the monomer underwent single-crystal-to-single-crystal (SCSC) topochemical azide-alkyne cycloaddition polymerization, yielding a covalent helical polymer as confirmed by single-crystal X-ray diffraction (SCXRD) analysis. Compared to the monomer crystals, the polymer single-crystals were very strong and showed three-fold increase in Young's modulus, which is higher than collagen, many synthetic polymers and other materials. The crystals of this covalent helical polymer could bear loads as high as 1.5 million times of their own weight without deformation. These crystals could also withstand high compression force and did not disintegrate even at an applied force of 98 kN. Such light-weight strong materials are in demand for various technological applications.

Fast Probing Amyloid Polymorphism via Nanopore Translocation

Neurodegenerative diseases are characterized by the presence of cross-β-sheet amyloid fibrils and a rich mesoscopic polymorphism, requiring noninvasive detection with high fidelity. Here, we introduce a methodology that can probe via a sensitive synthetic nanopore the complex polymorphism of amyloid fibrils by an automated and fast screening protocol. Statistically analyzing the translocation events on two model amyloid systems derived from β-lactoglobulin and lysozyme allows extracting the cross-sectional configuration of hydrated amyloid fibrils from current block amplitude and correlating dwell time with fibril length. These findings are consistent with the amyloid polymorphs observed in solution by atomic force microscopy. Furthermore, the ionic current signal of a single translocation event can reveal abnormally aggregated conformations of amyloid fibrils without potential artifacts associated with microscopy methods. This study introduces an effective approach to physically discriminating and separating amyloid and may serve in the rapid diagnosis of early aggregating pathological amyloidosis.

Biomimetic Structural Proteins: Modular Assembly and High Mechanical Performance

Protein-based biomaterials attract growing interests due to their encoded and programmable robust mechanical properties, superelasticity, plasticity, shape adaptability, excellent interfacial behavior, etc., derived from sequence-guided backbone structures, particularly compared to chemically synthetic counterparts in materials science and biomedical engineering. For example, protein materials have been successfully fabricated as (1) artificial implants (man-made tendons, cartilages, or dental tissues), due to programmable chemistry and biocompatibility; (2) smart biodevices with temperature/light-response and self-healing effects; and (3) impact resistance materials having great mechanical performance due to biomimetics. However, the existing method of regenerating protein materials from natural sources has two critical issues, low yield and structural damage, making it unable to meet demands. Therefore, it is crucial to develop an alternative strategy for fabricating protein materials. Heterologous expression of natural proteins with a modular assembly approach is an effective strategy for material preparation. Standardized, easy-to-assemble protein modules with specific structures and functions are developed through experimental and computational tools based on natural functional protein sequences. Through recombination and heterologous expression, these artificial protein modules become keys to material fabrication. Undergoing an assembly process similar to supramolecular self-assembly of proteins in cells, biomimetic modules can be fabricated for formation of macroscopic materials such as fibers and adhesives. This strategy inspired by synthetic biology and supramolecular chemistry is important for improving target protein yields and assembly integrity. It also preserves and optimizes the mechanical functions of structural proteins, accelerating the design and fabrication of artificial protein materials.In this Account, we overview recent studies on fabricating biomimetic protein materials to elucidate the concept of modular assembly. We discuss the design of biomimetic structural proteins at the molecular level, providing a wealth of details determining the bulk properties of materials. Additinally, we describe the modular self-assembly and assembly driven by inducing molecules, and mechanical properties and applications of resulting fibers. We used these strategies to develop fiber materials with high tensile strength, high toughness, and properties such as anti-icing and high-temperature resistance. We also extended this approach to design protein-based adhesives with ultra-strong adhesion, biocompatibility, and biodegradability for surgical applications such as wound sealing and healing. Other protein materials, including films and hydrogels, have been developed through chemical assembly routes. Finally, we describe exploiting synthetic biology and chemistry to overcome bottlenecks in structural protein modular design, biosynthesis, and material assembly and our perspectives for future development in structural biomaterials.

Embedding Living Cells with a Mechanically Reinforced and Functionally Programmable Hydrogel Fiber Platform

Living materials represent a new frontier in functional material design, integrating synthetic biology tools to endow materials with programmable, dynamic, and life-like characteristics. However, a major challenge in creating living materials is balancing the tradeoff between structural stability, mechanical performance, and functional programmability. To address this challenge, a sheath-core living hydrogel fiber platform that synergistically integrates living bacteria with hydrogel fibers to achieve both functional diversity and structural and mechanical robustness is proposed. In the design, microfluidic spinning is used to produce hydrogel fiber, which offers advantages in both structural and functional designability due to their hierarchical porous architectures that can be tailored and their mechanical performance that can be enhanced through a variety of post-processing approaches. By introducing living bacteria, the platform is endowed with programmable functionality and life-like capabilities. This work reconstructs the genetic circuits of living bacteria to express chromoproteins and fluorescent proteins as two prototypes that enable the coloration of living fibers and sensing water pollutants by monitoring the amount of fluorescent protein expressed. Altogether, this study establishes a structure-property-function optimized living hydrogel fiber platform, providing a new tool for accelerating the practical applications of the emerging living material systems.

Lipid-induced polymorphic amyloid fibril formation by α-synuclein

Many proteins that self-assemble into amyloid and amyloid-like fibers can adopt diverse polymorphic forms. These forms have been observed both in vitro and in vivo and can arise through variations in the steric-zipper interactions between β-sheets, variations in the arrangements between protofilaments, and differences in the number of protofilaments that make up a given fiber class. Different polymorphs arising from the same precursor molecule not only exhibit different levels of toxicity, but importantly can contribute to different disease conditions. However, the factors which contribute to formation of polymorphic forms of amyloid fibrils are not known. In this work, we show that in the presence of 1,2-dimyristoyl-sn-glycero-3-phospho-L-serine, a highly abundant lipid in the plasma membrane of neurons, the aggregation of α-synuclein is markedly accelerated and yields a diversity of polymorphic forms under identical experimental conditions. This morphological diversity includes thin and curly fibrils, helical ribbons, twisted ribbons, nanotubes, and flat sheets. Furthermore, the amyloid fibrils formed incorporate lipids into their structures, which corroborates the previous report of the presence of α-synuclein fibrils with high lipid content in Lewy bodies. Thus, the present study demonstrates that an interface, such as that provided by a lipid membrane, can not only modulate the kinetics of α-synuclein amyloid aggregation but also plays an important role in the formation of morphological variants by incorporating lipid molecules in the process of amyloid fibril formation.

Tendon Repair and Regeneration Using Bioinspired Fibrillation Engineering That Mimicked the Structure and Mechanics of Natural Tissue

Replicating the controlled nanofibrillar architecture of collagenous tissue represents a promising approach in the design of tendon replacements that have tissue-mimicking biomechanics─outstanding mechanical strength and toughness, defect tolerance, and fatigue and fracture resistance. Guided by this principle, a fibrous artificial tendon (FAT) was constructed in the present study using an engineering strategy inspired by the fibrillation of a naturally spun silk protein. This bioinspired FAT featured a highly ordered molecular and nanofibrillar architecture similar to that of soft collagenous tissue, which exhibited the mechanical and fracture characteristics of tendons. Such similarities provided the motivation to investigate FAT for applications in Achilles tendon defect repair. In vitro cellular morphology and expression of tendon-related genes in cell culture and in vivo modeling of tendon injury clearly revealed that the highly oriented nanofibrils in the FAT substantially promoted the expression of tendon-related genes combined with the Achilles tendon structure and function. These results provide confidence about the potential clinical applications of the FAT.

Synthetic control of actin polymerization and symmetry breaking in active protocells

Non-linear biomolecular interactions on the membranes drive membrane remodeling that underlies fundamental biological processes including chemotaxis, cytokinesis, and endocytosis. The multitude of biomolecules, the redundancy in their interactions, and the importance of spatiotemporal context in membrane organization hampers understanding the physical principles governing membrane mechanics. A minimal, in vitro system that models the functional interactions between molecular signaling and membrane remodeling, while remaining faithful to cellular physiology and geometry is powerful yet remains unachieved. Here, inspired by the biophysical processes underpinning chemotaxis, we reconstituted externally-controlled actin polymerization inside giant unilamellar vesicles, guiding self-organization on the membrane. We show that applying undirected external chemical inputs to this system results in directed actin polymerization and membrane deformation that are uncorrelated with upstream biochemical cues, indicating symmetry breaking. A biophysical model of the dynamics and mechanics of both actin polymerization and membrane shape suggests that inhomogeneous distributions of actin generate membrane shape deformations in a non-linear fashion, a prediction consistent with experimental measurements and subsequent local perturbations. The active protocellular system demonstrates the interplay between actin dynamics and membrane shape in a symmetry breaking context that is relevant to chemotaxis and a suite of other biological processes.

Histidine modulates amyloid-like assembly of peptide nanomaterials and confers enzyme-like activity

Amyloid-like assembly is not only associated with pathological events, but also leads to the development of novel nanomaterials with unique properties. Herein, using Fmoc diphenylalanine peptide (Fmoc-F-F) as a minimalistic model, we found that histidine can modulate the assembly behavior of Fmoc-F-F and induce enzyme-like catalysis. Specifically, the presence of histidine rearranges the β structure of Fmoc-F-F to assemble nanofilaments, resulting in the formation of active site to mimic peroxidase-like activity that catalyzes ROS generation. A similar catalytic property is also observed in Aβ assembled filaments, which is correlated with the spatial proximity between intermolecular histidine and F-F. Notably, the assembled Aβ filaments are able to induce cellular ROS elevation and damage neuron cells, providing an insight into the pathological relationship between Aβ aggregation and Alzheimer's disease. These findings highlight the potential of histidine as a modulator in amyloid-like assembly of peptide nanomaterials exerting enzyme-like catalysis.

Biomineralization in Barnacle Base Plate in Association with Adhesive Cement Protein

Barnacles strongly attach to various underwater substrates by depositing and curing a proteinaceous cement that forms a permanent adhesive layer. The protein MrCP20 present within the calcareous base plate of the acorn barnacle Megabalanus rosa (M. rosa) was investigated for its role in regulating biomineralization and growth of the barnacle base plate, as well as the influence of the mineral on the protein structure and corresponding functional role. Calcium carbonate (CaCO3) growth on gold surfaces modified by 11-mercaptoundecanoic acid (MUA/Au) with or without the protein was followed using quartz crystal microbalance with dissipation monitoring (QCM-D), and the grown crystal polymorph was identified by Raman spectroscopy. It is found that MrCP20 either in solution or on the surface affects the kinetics of nucleation and growth of crystals and stabilizes the metastable vaterite polymorph of CaCO3. A comparative study of mass uptake calculated by applying the Sauerbrey equation to the QCM-D data and quantitative X-ray photoelectron spectroscopy determined that the final surface density of the crystals as well as the crystallization kinetics are influenced by MrCP20. In addition, polarization modulation infrared reflection-absorption spectroscopy of MrCP20 established that, during crystal growth, the content of β-sheet structures in MrCP20 increases, in line with the formation of amyloid-like fibrils. The results provide insights into the molecular mechanisms by which MrCP20 regulates the biomineralization of the barnacle base plate, while favoring fibril formation, which is advantageous for other functional roles such as adhesion and cohesion.

Secretion-Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface

Protein-based biomaterials have played a key role in tissue engineering, and additional exciting applications as self-healing materials and sustainable polymers are emerging. Over the past few decades, recombinant expression and production of various fibrous proteins from microbes have been demonstrated; however, the resulting proteins typically must then be purified and processed by humans to form usable fibers and materials. Here, we show that the Gram-positive bacterium Bacillus subtilis can be programmed to secrete silk through its translocon via an orthogonal signal peptide/peptidase pair. Surprisingly, we discover that this translocation mechanism drives the silk proteins to assemble into fibers spontaneously on the cell surface, in a process we call secretion-catalyzed assembly (SCA). Secreted silk fibers form self-healing hydrogels with minimal processing. Alternatively, the fibers retained on the membrane provide a facile route to create engineered living materials from Bacillus cells. This work provides a blueprint to achieve autonomous assembly of protein biomaterials in useful morphologies directly from microbial factories.

Aβ42 fibril and non-fibril oligomers characterization using a nanopipette

The Aβ42 aggregates with different structures and morphology was investigated through a single molecule label-free technique. To this end, the quartz nanopipettes were functionalized with polyethylene glycol. The set of Aβ42- epigallocatechin-3-gallate fibrils with length (from 85 nm to 250 nm) obtained by sonication was detected. The comparison of experimental and computed value of the amplitude of relative current blockade using a geometrical model show that for fibrils longer than 80 nm, the discriminating parameter is their diameter. Then, non-fibril oligomers obtain from Aβ42(Osaka) aggregation at different time seed was investigated. The analysis of the amplitude of relative current blockade shows that detected oligomers are smaller than 30 nm regardless the aggregation time. In addition, the wide distributions of the dwell time suggests the polymorph character of the sample.

Data-mining unveils structure-property-activity correlation of viral infectivity enhancing self-assembling peptides

Gene therapy via retroviral vectors holds great promise for treating a variety of serious diseases. It requires the use of additives to boost infectivity. Amyloid-like peptide nanofibers (PNFs) were shown to efficiently enhance retroviral gene transfer. However, the underlying mode of action of these peptides remains largely unknown. Data-mining is an efficient method to systematically study structure-function relationship and unveil patterns in a database. This data-mining study elucidates the multi-scale structure-property-activity relationship of transduction enhancing peptides for retroviral gene transfer. In contrast to previous reports, we find that not the amyloid fibrils themselves, but rather µm-sized β-sheet rich aggregates enhance infectivity. Specifically, microscopic aggregation of β-sheet rich amyloid structures with a hydrophobic surface pattern and positive surface charge are identified as key material properties. We validate the reliability of the amphiphilic sequence pattern and the general applicability of the key properties by rationally creating new active sequences and identifying short amyloidal peptides from various pathogenic and functional origin. Data-mining-even for small datasets-enables the development of new efficient retroviral transduction enhancers and provides important insights into the diverse bioactivity of the functional material class of amyloids.

Self-Assembly of Insulin-Derived Chimeric Peptides into Two-Component Amyloid Fibrils: The Role of Coulombic Interactions

Canonical amyloid fibrils are composed of covalently identical polypeptide chains. Here, we employ kinetic assays, atomic force microscopy, infrared spectroscopy, circular dichroism, and molecular dynamics simulations to study fibrillization patterns of two chimeric peptides, ACC1-13E8 and ACC1-13K8, in which a potent amyloidogenic stretch derived from the N-terminal segment of the insulin A-chain (ACC1-13) is coupled to octaglutamate or octalysine segments, respectively. While large electric charges prevent aggregation of either peptide at neutral pH, stoichiometric mixing of ACC1-13E8 and ACC1-13K8 triggers rapid self-assembly of two-component fibrils driven by favorable Coulombic interactions. The low-symmetry nonpolar ACC1-13 pilot sequence is crucial in enforcing the fibrillar structure consisting of parallel β-sheets as the self-assembly of free poly-E and poly-K chains under similar conditions results in amorphous antiparallel β-sheets. Interestingly, ACC1-13E8 forms highly ordered fibrils also when paired with nonpolypeptide polycationic amines such as branched polyethylenimine, instead of ACC1-13K8. Such synthetic polycations are more effective in triggering the fibrillization of ACC1-13E8 than poly-K (or poly-E in the case of ACC1-13K8). The high conformational flexibility of these polyamines makes up for the apparent mismatch in periodicity of charged groups. The results are discussed in the context of mechanisms of heterogeneous disease-related amyloidogenesis.

Cryo-EM structure and polymorphic maturation of a viral transduction enhancing amyloid fibril

Amyloid fibrils have emerged as innovative tools to enhance the transduction efficiency of retroviral vectors in gene therapy strategies. In this study, we used cryo-electron microscopy to analyze the structure of a biotechnologically engineered peptide fibril that enhances retroviral infectivity. Our findings show that the peptide undergoes a time-dependent morphological maturation into polymorphic amyloid fibril structures. The fibrils consist of mated cross-β sheets that interact by the hydrophobic residues of the amphipathic fibril-forming peptide. The now available structural data help to explain the mechanism of retroviral infectivity enhancement, provide insights into the molecular plasticity of amyloid structures and illuminate the thermodynamic basis of their morphological maturation.

Generative design of de novo proteins based on secondary structure constraints using an attention-based diffusion model

We report two generative deep learning models that predict amino acid sequences and 3D protein structures based on secondary structure design objectives via either overall content or per-residue structure. Both models are robust regarding imperfect inputs and offer de novo design capacity as they can discover new protein sequences not yet discovered from natural mechanisms or systems. The residue-level secondary structure design model generally yields higher accuracy and more diverse sequences. These findings suggest unexplored opportunities for protein designs and functional outcomes within the vast amino acid sequences beyond known proteins. Our models, based on an attention-based diffusion model and trained on a dataset extracted from experimentally known 3D protein structures, offer numerous downstream applications in conditional generative design of various biological or engineering systems. Future work may include additional conditioning, and an exploration of other functional properties of the generated proteins for various properties beyond structural objectives.

De novo amyloid peptides with subtle sequence variations differ in their self-assembly and nanomechanical properties

Proteinaceous amyloids are well known for their widespread pathological roles but lately have emerged also as key components in several biological functions. The remarkable ability of amyloid fibers to form tightly packed conformations in a cross β-sheet arrangement manifests in their robust enzymatic and structural stabilities. These characteristics of amyloids make them attractive for designing proteinaceous biomaterials for various biomedical and pharmaceutical applications. In order to design customizable and tunable amyloid nanomaterials, it is imperative to understand the sensitivity of the peptide sequence for subtle changes based on amino acid position and chemistry. Here we report our results from four rationally-designed amyloidogenic decapeptides that subtly differ in hydrophobicity and polarity at positions 5 and 6. We show that making the two positions hydrophobic renders the peptide with enhanced aggregation and material properties while introducing polar residues in position 5 dramatically changes the structure and nanomechanical properties of the fibrils formed. A charged residue at position 6, however, abrogates amyloid formation. In sum, we show that subtle changes in the sequence do not make the peptide innocuous but rather sensitive to aggregation, reflected in the biophysical and nanomechanical properties of the fibrils. We conclude that tolerance of peptide amyloid for changes in the sequence, however small they may be, should not be neglected for the effective design of customizable amyloid nanomaterials.

Choice of Protein, Not Its Amyloid-Fold, Determines the Success of Amyloid-Based Scaffolds for Cartilage Tissue Regeneration

The formation of fibrocartilage during articular cartilage regeneration remains a clinical problem affecting adequate restoration of articular cartilage in joints. To stimulate chondrocytes to form articular cartilage, we investigated the use of amyloid fibril-based scaffolds. The proteins α-synuclein, β-lactoglobulin, and lysozyme were induced to self-assemble into amyloid fibrils and, during dialysis, formed micrometer scale amyloid networks that resemble the cartilage extracellular matrix. Our results show that lysozyme amyloid micronetworks supported chondrocyte viability and extracellular matrix deposition, while α-synuclein and β-lactoglobulin maintained cell viability. With this study, we not only confirm the possible use of amyloid materials for tissue regeneration but also demonstrate that the choice of protein, rather than its amyloid-fold per se, affects the cellular response and tissue formation.

Realization of Amyloid-like Aggregation as a Common Cause for Pathogenesis in Diseases

Amyloids were conventionally referred to as extracellular and intracellular accumulation of Aβ42 peptide, which causes the formation of plaques and neurofibrillary tangles inside the brain leading to the pathogenesis in Alzheimer's disease. Subsequently, amyloid-like deposition was found in the etiology of prion diseases, Parkinson's disease, type II diabetes, and cancer, which was attributed to the aggregation of prion protein, α-Synuclein, islet amyloid polypeptide protein, and p53 protein, respectively. Hence, traditionally amyloids were considered aggregates formed exclusively by proteins or peptides. However, since the last decade, it has been discovered that other metabolites, like single amino acids, nucleobases, lipids, glucose derivatives, etc., have a propensity to form amyloid-like toxic assemblies. Several studies suggest direct implications of these metabolite assemblies in the patho-physiology of various inborn errors of metabolisms like phenylketonuria, tyrosinemia, cystinuria, and Gaucher's disease, to name a few. In this review, we present a comprehensive literature overview that suggests amyloid-like structure formation as a common phenomenon for disease progression and pathogenesis in multiple syndromes. The review is devoted to providing readers with a broad knowledge of the structure, mode of formation, propagation, and transmission of different extracellular amyloids and their implications in the pathogenesis of diseases. We strongly believe a review on this topic is urgently required to create awareness about the understanding of the fundamental molecular mechanism behind the origin of diseases from an amyloid perspective and possibly look for a common therapeutic strategy for the treatment of these maladies by designing generic amyloid inhibitors.

Modulation of Insulin Amyloid Fibrillization in Imidazolium-Based Ionic Liquids with Hofmeister Series Anions

Amyloid fibrils have immense potential to become the basis of modern biomaterials. The formation of amyloid fibrils in vitro strongly depends on the solvent properties. Ionic liquids (ILs), alternative solvents with tunable properties, have been shown to modulate amyloid fibrillization. In this work, we studied the impact of five ILs with 1-ethyl-3-methylimidazolium cation [EMIM⁺] and anions of Hofmeisterseries hydrogen sulfate [HSO₄^-], acetate [AC^-], chloride [Cl^-], nitrate [NO₃^-], and tetrafluoroborate [BF₄^-] on the kinetics of insulin fibrillization and morphology, and the structure of insulin fibrils when applying fluorescence spectroscopy, AFM and ATR-FTIR spectroscopy. We found that the studied ILs were able to speed up the fibrillization process in an anion- and IL-concentration-dependent manner. At an IL concentration of 100 mM, the efficiency of the anions at promoting insulin amyloid fibrillization followed the reverse Hofmeister series, indicating the direct binding of ions with the protein surface. At a concentration of 25 mM, fibrils with different morphologies were formed, yet with similar secondary structure content. Moreover, no correlation with the Hofmeister ranking was detected for kinetics parameters. IL with the kosmotropic strongly hydrated [HSO₄^-] anion induced the formation of large amyloid fibril clusters, while the other kosmotropic anion [AC^-] along with [Cl^-] led to the formation of fibrils with similar needle-like morphologies to those formed in the IL-free solvent. The presence of the ILs with the chaotropic anions [NO₃^-] and [BF₄^-] resulted in longer laterally associated fibrils. The effect of the selected ILs was driven by a sensitive balance and interplay between specific protein-ion and ion-water interactions and non-specific long-range electrostatic shielding.

Probing the Protein Folding Energy Landscape: Dissociation of Amyloid-β Fibrils by Laser-Induced Plasmonic Heating

Insoluble amyloid fibrils made from proteins and peptides are difficult to be degraded in both living and artificial systems. The importance of studying their physical stability lies primarily with their association with human neurodegenerative diseases, but also owing to their potential role in multiple bio-nanomaterial applications. Here, gold nanorods (AuNRs) were utilized to investigate the plasmonic heating properties and dissociation of amyloid-β fibrils formed by different peptide fragments (Aβ_16-22/Aβ_25-35/Aβ_1-42) related to the Alzheimer's disease. It is demonstrated that AuNRs were able to break mature amyloid-β fibrils from both the full length (Aβ_1-42) and peptide fragments (Aβ_16-22/Aβ_25-35) within minutes by triggering ultrahigh localized surface plasmon resonance (LSPR) heating. The LSPR energy absorbed by the amyloids to unfold and move to higher levels in the protein folding energy landscape can be measured directly and in situ by luminescence thermometry using lanthanide-based upconverting nanoparticles. We also show that Aβ_16-22 fibrils, with the largest persistence length, displayed the highest resistance to breakage, resulting in a transition from rigid fibrils to short flexible fibrils. These findings are consistent with molecular dynamics simulations indicating that Aβ_16-22 fibrils possess the highest thermostability due to their highly ordered hydrogen bond networks and antiparallel β-sheet orientation, hence affected by an LSPR-induced remodeling rather than melting. The present results introduce original strategies for disassembling amyloid fibrils noninvasively in liquid environment; they also introduce a methodology to probe the positioning of amyloids on the protein folding and aggregation energy landscape via nanoparticle-enabled plasmonic and upconversion nanothermometry.

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.

Full-colour Jabuticaba-like nanostructures via the multiplex and orthogonal self-assembly of protein-conjugated quantum dots with engineered biofilms

The integration of inorganic components with bacterial biofilms is of great significance for expanding the functionality of artificial biological materials. However, so far, the complexities and functionalities of biofilm-based scaffolds assembled via metal-peptide coordination chemistries remain limited. Here, we present a platform for the multiplexed and specific coupling of recombinant protein-functionalized fluorescent red-green-blue (RGB) quantum dots (QDs) with engineered biofilms to form Jabuticaba-like nanostructures. Full-color living Jabuticaba-like nanostructures have been achieved through the interaction of extracellular peptides that are fabricated by biofilms with the proteins that modify the surface of the RGB QDs through orthogonal SpyTag/SpyCatcher, IsopeptagN/PilinN, and IsopeptagC/PilinC pairs. We envision that living cell populations will enable the multiplexable, scalable and bottom-up assembly of versatile materials that integrate both abiotic and biotic components into multifunctional systems.

Application of Amyloid-Based Hybrid Membranes in Drug Delivery

The properties of amyloid fibrils, e.g., unique structural characteristics and superior biocompatibility, make them a promising vehicle for drug delivery. Here, carboxymethyl cellulose (CMC) and whey protein isolate amyloid fibril (WPI-AF) were used to synthesize amyloid-based hybrid membranes as vehicles for the delivery of cationic and hydrophobic drugs (e.g., methylene blue (MB) and riboflavin (RF)). The CMC/WPI-AF membranes were synthesized via chemical crosslinking coupled with phase inversion. The zeta potential and scanning electron microscopy results revealed a negative charge and a pleated surface microstructure with a high content of WPI-AF. FTIR analysis showed that the CMC and WPI-AF were cross-linked via glutaraldehyde and the interacting forces between membrane and MB or RF was found to be electrostatic interaction and hydrogen bonding, respectively. Next, the in vitro drug release from membranes was monitored using UV-vis spectrophotometry. Additionally, two empirical models were used to analyze the drug release data and relevant rate constant and parameters were determined accordingly. Moreover, our results indicated that in vitro drug release rates depended on the drug–matrix interactions and transport mechanism, which could be controlled by altering the WPI-AF content in membrane. This research provides an excellent example of utilizing two-dimensional amyloid-based materials for drug delivery.

Cryo-EM structure of a catalytic amyloid fibril

Catalytic amyloid fibrils are novel types of bioinspired, functional materials that combine the chemical and mechanical robustness of amyloids with the ability to catalyze a certain chemical reaction. In this study we used cryo-electron microcopy to analyze the amyloid fibril structure and the catalytic center of amyloid fibrils that hydrolyze ester bonds. Our findings show that catalytic amyloid fibrils are polymorphic and consist of similarly structured, zipper-like building blocks that consist of mated cross-β sheets. These building blocks define the fibril core, which is decorated by a peripheral leaflet of peptide molecules. The observed structural arrangement differs from previously described catalytic amyloid fibrils and yielded a new model of the catalytic center.

Protein-Based Biological Materials: Molecular Design and Artificial Production

Polymeric materials produced from fossil fuels have been intimately linked to the development of industrial activities in the 20th century and, consequently, to the transformation of our way of living. While this has brought many benefits, the fabrication and disposal of these materials is bringing enormous sustainable challenges. Thus, materials that are produced in a more sustainable fashion and whose degradation products are harmless to the environment are urgently needed. Natural biopolymers─which can compete with and sometimes surpass the performance of synthetic polymers─provide a great source of inspiration. They are made of natural chemicals, under benign environmental conditions, and their degradation products are harmless. Before these materials can be synthetically replicated, it is essential to elucidate their chemical design and biofabrication. For protein-based materials, this means obtaining the complete sequences of the proteinaceous building blocks, a task that historically took decades of research. Thus, we start this review with a historical perspective on early efforts to obtain the primary sequences of load-bearing proteins, followed by the latest developments in sequencing and proteomic technologies that have greatly accelerated sequencing of extracellular proteins. Next, four main classes of protein materials are presented, namely fibrous materials, bioelastomers exhibiting high reversible deformability, hard bulk materials, and biological adhesives. In each class, we focus on the design at the primary and secondary structure levels and discuss their interplays with the mechanical response. We finally discuss earlier and the latest research to artificially produce protein-based materials using biotechnology and synthetic biology, including current developments by start-up companies to scale-up the production of proteinaceous materials in an economically viable manner.

Familial Alzheimer's Disease-Related Mutations Differentially Alter Stability of Amyloid-Beta Aggregates

Amyloid-beta (Aβ) deposition as senile plaques is a pathological hallmark of Alzheimer's disease (AD). AD is characterized by a large level of heterogeneity in amyloid pathology, whose molecular origin is poorly understood. Here, we employ NMR spectroscopy and MD simulation at ambient and high pressures and investigate how AD-related mutations in Aβ peptide influence the stability of Aβ aggregates. The pressure-induced monomer dissociation from Aβ aggregates monitored by NMR demonstrated that the Iowa (D23N), Arctic (E22G), and Osaka (ΔE22) mutations altered the pressure stability of Aβ40 aggregates in distinct manners. While the NMR data of monomeric Aβ40 showed only small localized effects of mutations, the MD simulation of mutated Aβ fibrils revealed their distinct susceptibility to elevated pressure. Our data propose a structural basis for the distinct stability of various Aβ fibrils and highlights "stability" as a molecular property potentially contributing to the large heterogeneity of amyloid pathology in AD.

Two dimensional (2D) materials and biomaterials for water desalination; structure, properties, and recent advances

BACKGROUND

An efficient solution to the global freshwater dilemma is desalination. MXene, Molybdenum Disulfide (MoS₂), Graphene Oxide, Hexagonal Boron Nitride, and Phosphorene are just a few examples of two-dimensional (2D) materials that have shown considerable promise in the development of 2D materials for water desalination. However, other promising materials for desalinating water are biomaterials. The benefits of bio-materials are their wide distribution, lack of toxicity, and superior capacity for water desalination.

METHODS

For the rational use of water and the advancement of sustainable development, it is of the utmost importance to research 2D-dimensional materials and biomaterials that are effective for water desalination. The scientific community has concentrated on wastewater remediation using bio-derived materials, such as nanocellulose, chitosan, bio-char, bark, and activated charcoal generated from plant sources, among the various endeavors to enhance access to clean water. Moreover, the 2D-materials and biomaterials may have ushered in a new age in the production of desalination materials and created a promising future.

RESULTS

The present review article focuses on and reviews the progress of 2D materials and biomaterials for water desalination. Their properties, surface, and structure, combined with water desalination applications, are highlighted. Further, the practicability and potential future directions of 2D materials and biomaterials are proposed. Thus, the current work provides information and discernments for developing novel 2D materials and biomaterials for wastewater desalination. Moreover, it aims to promote the contribution and advancement of materials for water desalination, fabrication, and industrial production.

Racemic Amino Acid Assembly Enables Supramolecular β-Sheet Transition with Property Modulations

Amino acids are the most simplistic bio-building blocks and perform a variety of functions in metabolic activities. Increasing publications report that amino acid-based superstructures present amyloid-like characteristics, arising from their supramolecular β-sheet secondary structures driven by hydrogen-bonding-connected supramolecular β-strands, which are formed by head-to-tail hydrogen bonds between terminal amino and carboxyl groups of the adjacent residues. Therefore, the establishment of the structure-function relationships is critical for exploring the properties and applications of amino acid assemblies. Among the naturally encoded self-assembling amino acids, tyrosine (Y)-based superstructures have been found to show diverse properties and functions including high rigidity, promoting melanin formations, mood regulations, and preventing anxiety, thus showing promising potential as next-generation functional biomaterials for biomedical and bio-machine interface applications. However, the development of Y-based organizations of functional features is severely limited due to the intrinsic difficulty of modulating the energetically stable supramolecular β-sheet structures. Herein, we report that by the racemic assembly of l-Y and d-Y, the supramolecular secondary structures are modulated from the antiparallel β-sheets in the enantiomeric assemblies to the parallel ones in the racemate counterparts, thus leading to higher degrees of freedom, which finally induce distinct organization kinetics and modulation of the physicochemical properties including the optical shifts, elastic softening, and the piezoelectric outputs of the superstructures.

Structural control of self-assembled peptide nanostructures to develop peptide vesicles for photodynamic therapy of cancer

Vesicles such as liposomes, polymersomes, and exosomes have been widely used as drug delivery carriers; however, peptide vesicles (peptidesomes) despite their potential utility are far less well developed. Peptidesomes are distinctive because peptides play dual roles as a self-assembly building block and a bioactive functional unit. In order for peptidesomes to become successful nanodrugs, the issues related to differences in nanostructural properties between in vitro and in vivo conditions should be addressed. Here, we delineate a multivariate approach to feedback control the structures of peptide building blocks, nanoparticle size, drug loading process, nanoparticle aggregation, cytotoxicity, cell targeting capability, endosome disruption function, protease resistance, and in vivo performance, which eventually enabled the successful development of a highly efficacious peptidesome for in vivo cancer therapy. This study lays the groundwork for the successful in vivo translation of peptide nanodrugs.

Functional Coating from Amyloid Superwetting Films

Tailoring the hydrophilicity of solid surfaces with a strong affinity to water has been extensively explored in the last 20 years, but studies have been limited to the single function of wettability. Here, the multifunctional properties of tailored surface films are extended from exhibiting superwettability to facilitating biological activities. It is shown that amyloid fibrils can be universally coated onto various substrates, such as fabrics (non-woven organic masks), metal meshes, polyethersulfone (PES), glass, and more, endowing the resulting surfaces with excellent performance in oil/water mixture and emulsion separation, antifouling, and antifogging. Moreover, the biocompatible crosslinked amyloid fibril coatings can serve as a platform for biocatalytic activities by immobilizing enzymes, as shown in the 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS) oxidation and Reactive Black 5 (RB5) degradation by laccase from Trametes versicolor. The study provides a universal approach to modifying surface morphology and chemical properties via fibrous protein templates, opening the way to unexplored bio-based applications and functionalities.

Ultra-lightweight living structural material for enhanced stiffness and environmental sensing

Natural materials such as bone, wood, and bamboo can inspire the fabrication of stiff, lightweight structural materials. Biofilms are one of the most dominant forms of life in nature. However, little is known about their physical properties as a structural material. Here we report an Escherichia coli biofilm having a Young's modulus close to 10 ​GPa with ultra-low density, indicating a high-performance structural material. The mechanical and structural characterization of the biofilm and its components illuminates its adaptable bottom-up design, consisting of lightweight microscale cells covered by a dense network of amyloid nanofibrils on the surface. We engineered E. coli such that 1) carbon nanotubes assembled on the biofilm, enhancing its stiffness to over 30 ​GPa, or that 2) the biofilm sensitively detected heavy metal as an example of an environmental toxin. These demonstrations offer new opportunities for developing responsive living structural materials to serve many real-world applications.