Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility.

RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.

Interfacial Electrostatic Self-Assembly of Amyloid Fibrils into Multifunctional Protein Films.

Amyloid fibrils have generated steadily increasing traction in the development of natural and artificial materials. However, it remains a challenge to construct bulk amyloid films directly from amyloid fibrils due to their intrinsic brittleness. Here, a facile and general methodology to fabricate macroscopic and tunable amyloid films via fast electrostatic self-assembly of amyloid fibrils at the air-water interface is introduced. Benefiting from the excellent templating properties of amyloid fibrils for nanoparticles (such as conductive carbon nanotubes or magnetic Fe3 O4 nanoparticles), multifunctional amyloid films with tunable properties are constructed. As proof-of-concept demonstrations, a magnetically oriented soft robotic swimmer with well-confined movement trajectory is prepared. In addition, a smart magnetic sensor with high sensitivity to external magnetic fields is fabricated via the combination of the conductive and magnetic amyloid films. This strategy provides a convenient, efficient, and controllable approach for the preparation of amyloid-based multifunctional films and related smart devices.

Nature-Inspired Circular-Economy Recycling for Proteins: Proof of Concept.

The billion tons of synthetic-polymer-based materials (i.e. plastics) produced yearly are a great challenge for humanity. Nature produces even more natural polymers, yet they are sustainable. Proteins are sequence-defined natural polymers that are constantly recycled when living systems feed. Digestion is the protein depolymerization into amino acids (the monomers) followed by their re-assembly into new proteins of arbitrarily different sequence and function. This breaks a common recycling paradigm where a material is recycled into itself. Organisms feed off of random protein mixtures that are "recycled" into new proteins whose identity depends on the cell's specific needs. In this study, mixtures of several peptides and/or proteins are depolymerized into their amino acid constituents, and these amino acids are used to synthesize new fluorescent, and bioactive proteins extracellularly by using an amino-acid-free, cell-free transcription-translation (TX-TL) system. Specifically, three peptides (magainin II, glucagon, and somatostatin 28) are digested using thermolysin first and then using leucine aminopeptidase. The amino acids so produced are added to a commercial TX-TL system to produce fluorescent proteins. Furthermore, proteins with high relevance in materials engineering (ß-lactoglobulin films, used for water filtration, or silk fibroin solutions) are successfully recycled into biotechnologically relevant proteins (fluorescent proteins, catechol 2,3-dioxygenase).

Interconnect-Free Multibit Arithmetic and Logic Unit in a Single Reconfigurable 3 µm2 Plasmonic Cavity.

Processing information with conventional integrated circuits remains beset by the interconnect bottleneck: circuits made of smaller active devices need longer and narrower interconnects, which have become the prime source of power dissipation and clock rate saturation. Optical interchip communication provides a fast and energy-saving option that still misses a generic on-chip optical information processing by interconnect-free and reconfigurable Boolean arithmetic logic units (ALU). Considering metal plasmons as a platform with dual optical and electronic compatibilities, we forge interconnect-free, ultracompact plasmonic Boolean logic gates and reconfigure them, at will, into computing ALU without any redesign nor cascaded circuitry. We tailor the plasmon mode landscape of a single 2.6 µm2 planar gold cavity and demonstrate the operation and facile reconfiguration of all 2-input logic gates. The potential for higher complexity of the same logic unit is shown by a multi-input excitation and a phase control to realize an arithmetic 2-bit adder.

An antiviral trap made of protein nanofibrils and iron oxyhydroxide nanoparticles.

Minimizing the spread of viruses in the environment is the first defence line when fighting outbreaks and pandemics, but the current COVID-19 pandemic demonstrates how difficult this is on a global scale, particularly in a sustainable and environmentally friendly way. Here we introduce and develop a sustainable and biodegradable antiviral filtration membrane composed of amyloid nanofibrils made from food-grade milk proteins and iron oxyhydroxide nanoparticles synthesized in situ from iron salts by simple pH tuning. Thus, all the membrane components are made of environmentally friendly, non-toxic and widely available materials. The membrane has outstanding efficacy against a broad range of viruses, which include enveloped, non-enveloped, airborne and waterborne viruses, such as SARS-CoV-2, H1N1 (the influenza A virus strain responsible for the swine flu pandemic in 2009) and enterovirus 71 (a non-enveloped virus resistant to harsh conditions, such as highly acidic pH), which highlights a possible role in fighting the current and future viral outbreaks and pandemics.

Understanding the Formation of Apoferritin Amyloid Fibrils.

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

Removal of radioactive cesium from contaminated water by whey protein amyloids-carbon hybrid filters.

We report on the application of an innovative whey protein amyloids-carbon hybrid filter for the removal and disposal of the long-lived radioactive fission product 137Cs from aqueous samples. Test experiments revealed a reduction of 137Cs radioactivity by a factor of 340 compared to the initial solution, with an efficiency as high as 99.7%. The adsorption capacity of the membrane was explored by performing several cycles of filtration, indicating a potential retention of more than 115 MBq per gram of filtering material at the applied experimental conditions. These results pave the way for further investigations on the applicability of this filter material to other nuclear fission products.

Self-Winding Gelatin-Amyloid Wires for Soft Actuators and Sensors.

The origin of self-winding mechanisms in plants' tendrils has fascinated scientists for centuries and continues to inspire developments in material science and nanotechnology. Here, bioinspired water-responsive wires that replicate these mechanisms, including the formation of coils and chiral perversions, are presented. A right-handed gelatin matrix is loaded with rigid left-handed amyloid fibrils and roll-dry-spun into wires in which self-winding activation emerges from simultaneous bending and twisting deformations. Wire bending is a consequence of amyloid fibrils' concentration and distribution within the wire, whereas twisting is controlled by amyloid fibrils' orientation. The resultant wires can be functionalized by organic molecules and inorganic nanoparticles, and potential applications in magnetic actuators and sensors are demonstrated. The simple fabrication method and the remarkable spontaneous self-winding response of these gelatin-amyloid wires exemplify how biomaterials based on mixed proteins have striking potential to develop advanced and tunable properties that can serve robotics, soft machines, and engineering systems.

Amyloid Fibril-Templated High-Performance Conductive Aerogels with Sensing Properties.

Amyloid fibrils have garnered increasing attention as viable building blocks for functional material design and synthesis, especially those derived from food and agricultural wastes. Here, amyloid fibrils generated from ß-lactoglobulin, a by-product from cheese industries, have been successfully used as a template for the design of a new class of high-performance conductive aerogels with sensing properties. These mechanically stable aerogels with three-dimensional porous architecture have a large surface area (≈159 m2 g-1), low density (≈0.044 g cm-3), and high electrical conductivity (≈0.042 S cm-1). A pressure sensing device is developed from these aerogels based on their combined electrical conductivity and compressible properties. More interestingly, these aerogels can be employed to design novel enzyme sensors by exploiting the proteinaceous nature of amyloid fibrils. This study expands the scope of structured amyloid fibrils as scaffolds for in situ polymerization of conducting polymers, offering new opportunities to design materials with multiple functionalities.

Single plasmon spatial and spectral sorting on a crystalline two-dimensional plasmonic platform.

In the context of the emerging field of quantum plasmonics, we demonstrate in this manuscript the wavelength-dependent propagation and sorting of single plasmons launched in a two-dimensional crystalline gold flake by a broadband quantum nanoemitter. The stream of single plasmons in the visible is produced by a nanodiamond hosting a single nitrogen-vacancy color center positioned in the near field of the mesoscopic metallic microplatelet. Spatially and spectrally resolved images of the single plasmon propagation in the pristine hexagonal flake, and then in the same structure after insertion of a Bragg mirror, are obtained by filtered image-plane acquisitions on a leakage-radiation microscope. Our work on two-dimensional crystalline structures paves the way to future fundamental studies and applications in quantum plasmonics.

Amyloid Fibrils Aerogel for Sustainable Removal of Organic Contaminants from Water.

Water contamination by organic pollutants is ubiquitous and hence a global concern due to detrimental effects on the environment and human health. Here, it is demonstrated that amyloid fibrils aerogels are ideal adsorbers for removing organic pollutants from water. To this end, amyloid fibrils prepared from ß-lactoglobulin, the major constituent of milk whey protein, are used as building blocks for the fabrication of the aerogels. The adsorption of Bentazone, Bisphenol A, and Ibuprofen, as model pollutants, is evaluated under quasi-static conditions, without use of energy or pressure. Through adsorption by amyloid fibrils aerogel, excellent removal efficiencies of 92%, 78%, and 98% are demonstrated for Bentazone, Bisphenol A, and Ibuprofen, respectively. Furthermore, the maximum adsorption capacity of amyloid fibrils aerogel for Bentazone, Bisphenol A, and Ibuprofen is 54.2, 50.6, and 69.6 mg g-1 , respectively. To shed light on the adsorption equilibrium process, adsorption isotherms, binding constants, saturation limits, and the effect of pH are evaluated. Finally, the regeneration of the aerogel over three consecutive cycles is studied, exhibiting high reusability with no significant changes in its removal performance. These results point at amyloid fibrils aerogels as a sustainable, efficient, and inexpensive technology for alleviating the ubiquitous water contamination by organic pollutants.

Amyloid hybrid membranes for bacterial & genetic material removal from water and their anti-biofouling properties.

Water scarcity and contamination by biological pollutants are global challenges that significantly affect public health. Reverse osmosis, nanofiltration and ultrafiltration technologies are very effective for the elimination of pathogens and most contaminants but associated with considerable capital and operating costs, high energy consumption and the use of chlorinated chemicals to suppress membrane fouling. Additionally, the pressure needed by these techniques may disrupt the pathogenic microbial cell membranes, causing the release of genetic material (fragments of DNA, RNA and plasmids) into the water. Here, we introduce the simultaneous removal of both bacteria and associated genetic material using amyloid hybrid membranes, via a combined adsorption and size exclusion mechanism. Amyloid hybrid membranes can remove upto and beyond 99% of the genetic material by adsorption, where amyloid fibrils act as the primary adsorbing material. When the same membranes are surface-modified using chitosan, the anti-biofouling performance of the membranes improved significantly, with a bacterial removal efficiency exceeding 6 log.

Ubiquitous aluminium contamination in water and amyloid hybrid membranes as a sustainable possible solution.

We develop a membrane technology based on amyloid fibrils to remove aluminium from water and minimize its exposure to humans. We study aluminium adsorption by amyloid fibrils by evaluating the binding isotherms, the thermodynamics and the effects of different parameters. Amyloid-based membranes demonstrate outstanding removal efficiencies beyond 98%.

Selective and Efficient Removal of Fluoride from Water: In Situ Engineered Amyloid Fibril/ZrO2 Hybrid Membranes.

We report a new strategy for efficient removal of F- from contaminated water streams, and it relies on carbon hybrid membranes made of amyloid fibril/ZrO2 nanoparticles (<10 nm). These membranes exhibit superior selectivity for F- against various competitive ions, with a distribution coefficient (Kd ) as high as 6820 mL g-1 , exceeding commercial ion-exchange resins (IRA-900) by 180 times and outdoing the performance of most commercial carbon-activated aluminum membranes. At both low and high (ca. 200 mg L-1 ) F- concentrations, the membrane efficiency exceeds 99.5 % removal. For real untreated municipal tap water (ca. 2.8 mg L-1 ) under continuous operating mode, data indicates that about 1750 kg water m-2 membrane can be treated while maintaining drinking water quality, and the saturated membranes can be regenerated and reused several times without decrease in performance. This technology is promising for mitigating the problem of fluoride water contamination worldwide.

Amyloid fibril-directed synthesis of silica core-shell nanofilaments, gels, and aerogels.

Amyloid fibrils have evolved from purely pathological materials implicated in neurodegenerative diseases to efficient templates for last-generation functional materials and nanotechnologies. Due to their high intrinsic stiffness and extreme aspect ratio, amyloid fibril hydrogels can serve as ideal building blocks for material design and synthesis. Yet, in these gels, stiffness is generally not paired by toughness, and their fragile nature hinders significantly their widespread application. Here we introduce an amyloid-assisted biosilicification process, which leads to the formation of silicified nanofibrils (fibril-silica core-shell nanofilaments) with stiffness up to and beyond ∼20 GPa, approaching the Young's moduli of many metal alloys and inorganic materials. The silica shell endows the silicified fibrils with large bending rigidity, reflected in hydrogels with elasticity three orders of magnitude beyond conventional amyloid fibril hydrogels. A constitutive theoretical model is proposed that, despite its simplicity, quantitatively interprets the nonmonotonic dependence of the gel elasticity upon the filaments bundling promoted by shear stresses. The application of these hybrid silica-amyloid hydrogels is demonstrated on the fabrication of mechanically stable aerogels generated via sequential solvent exchange, supercritical [Formula: see text] removal, and calcination of the amyloid core, leading to aerogels of specific surface area as high as 993 [Formula: see text]/g, among the highest values ever reported for aerogels. We finally show that the scope of amyloid hydrogels can be expanded considerably by generating double networks of amyloid and hydrophilic polymers, which combine excellent stiffness and toughness beyond those of each of the constitutive individual networks.

Assessing the Binding Performance of Amyloid-Carbon Membranes toward Heavy Metal Ions.

Amyloid-carbon hybrid membranes have exceptional performance in removing heavy metal ions from water because of the presence of multiple binding sites on the amyloid fibrils, but the binding process is still not fully understood. To understand the mechanisms of amyloid-metal ion binding, we perform adsorption isotherms on a model system given by ß-lactoglobulin amyloid fibrils and four representative heavy metal ions: chromium (Cr), nickel (Ni), silver (Ag), and platinum (Pt). Furthermore, to get a comprehensive thermodynamic picture of the binding process between amino acid residues and heavy metals, we here use isothermal titration calorimetry on native ß-lactoglobulin monomers and amyloid fibrils exposed to the two model metal ions, that is, silver and chromium. A conclusive thermodynamic insight on the binding process emerges by direct measurements of enthalpy and entropy changes, association binding constant, and average number of binding sites of the protein monomer and amyloid fibril. As a result of the strong amyloid binding affinity between amino acids and metal ions, when the protein is converted into amyloid fibrils and assembled into membranes, the resulting amyloid-activated carbon hybrids remove all the tested heavy metals with efficiencies beyond 99%. Importantly, the efficiency remains stable during several consecutive cycles, demonstrating a high adsorption capacity and a long lifetime and reusability of the membranes. The recovery of adsorbed precious metal ions converted into elemental metals is shown to be a general feature of these membranes, with platinum and silver successfully recovered from saturated hybrid membranes by a simple thermal reduction. The separation performance, evaluated on real electroplating industrial wastewater containing chromium and nickel, is found to exceed 99% at a permeability as high as 2.92 × 10-16 m2, that is, at least 4 orders of magnitude higher than typical nanofiltration membranes, conclusively validating the technology under stringent real conditions.

Sustainable technologies for water purification from heavy metals: review and analysis.

Water pollution is a global problem threatening the entire biosphere and affecting the life of many millions of people around the world. Not only is water pollution one of the foremost global risk factors for illness, diseases and death, but it also contributes to the continuous reduction of the available drinkable water worldwide. Delivering valuable solutions, which are easy to implement and affordable, often remains a challenge. Here we review the current state-of-the-art of available technologies for water purification and discuss their field of application for heavy metal ion removal, as heavy metal ions are the most harmful and widespread contaminants. We consider each technology in the context of sustainability, a largely neglected key factor, which may actually play a pivotal role in the implementation of each technology in real applications, and we introduce a compact index, the Ranking Efficiency Product (REP), to evaluate the efficiency and ease of implementation of the various technologies in this broader perspective. Emerging technologies, for which a detailed quantitative analysis and assessment is not yet possible according to this methodology, either due to scarcity or inhomogeneity of data, are discussed in the final part of the manuscript.

Elasticity in Physically Cross-Linked Amyloid Fibril Networks.

We provide a constitutive model of semiflexible and rigid amyloid fibril networks by combining the affine thermal model of network elasticity with the Derjaguin-Landau-Vervey-Overbeek (DLVO) theory of electrostatically charged colloids. When compared to rheological experiments on ß-lactoglobulin and lysozyme amyloid networks, this approach provides the correct scaling of elasticity versus both concentration (G∼c^{2.2} and G∼c^{2.5} for semiflexible and rigid fibrils, respectively) and ionic strength (G∼I^{4.4} and G∼I^{3.8} for ß-lactoglobulin and lysozyme, independent from fibril flexibility). The pivotal role played by the screening salt is to reduce the electrostatic barrier among amyloid fibrils, converting labile physical entanglements into long-lived cross-links. This gives a power-law behavior of G with I having exponents significantly larger than in other semiflexible polymer networks (e.g., actin) and carrying DLVO traits specific to the individual amyloid fibrils.

Biophotonics of Native Silk Fibrils.

Native silk fibroin (NSF) is a unique biomaterial with extraordinary mechanical and biochemical properties. These key characteristics are directly associated with the physical transformation of unstructured, soluble NSF into highly organized nano- and microscale fibrils rich in ß-sheet content. Here, it is shown that this NSF fibrillation process is accompanied by the development of intrinsic fluorescence in the visible range, upon near-UV excitation, a phenomenon that has not been investigated in detail to date. Here, the optical and fluorescence characteristics of NSF fibrils are probed and a route for potential applications in the field of self-assembled optically active biomaterials and systems is explored. In particular, it is demonstrated that NSF can be structured into autofluorescent microcapsules with a controllable level of ß-sheet content and fluorescence properties. Furthermore, a facile and efficient fabrication route that permits arbitrary patterns of NSF microcapsules to be deposited on substrates under ambient conditions is shown. The resulting fluorescent NSF patterns display a high level of photostability. These results demonstrate the potential of using native silk as a new class of biocompatible photonic material.

Enzyme-Mimetic Antioxidant Luminescent Nanoparticles for Highly Sensitive Hydrogen Peroxide Biosensing.

Hydrogen peroxide (H2O2) is an abundant molecule associated with biological functions and reacts with natural enzymes, such as catalase. Even though direct H2O2 measurement can be used to diagnose pathological conditions, such as infection and inflammation, H2O2 quantification further enables the detection of disease biomarkers in enzyme-linked assays (e.g., ELISA) in which enzymatic reactions may generate or consume H2O2. Such a quantification is often measured optically with organic dyes in biological media that suffer, however, from poor stability. Currently, the optical H2O2 biosensing without organic-dyes in biological media and at low, submicromolar, concentrations has yet to be achieved. Herein, we rationally design biomimetic artificial enzymes based on antioxidant CeO2 nanoparticles that become luminescent upon their Eu3+ doping. We vary systematically their diameter from 4 to 16 nm and study their catalase-mimetic antioxidant activity, manifested as catalytic H2O2 decomposition in aqueous solutions, revealing a strong nanoparticle surface area dependency. The interaction with H2O2 influences distinctly the particle luminescence rendering them highly sensitive H2O2 biosensors down to 0.15 µM (5.2 ppb) in solutions for biological assays. Our results link two, so far, unrelated research domains, the CeO2 nanoparticle antioxidant activity and luminescence by rare-earth doping. When these enzyme-mimetic nanoparticles are coupled with alcohol oxidase, biosensing can be extended to ethanol exemplifying how their detection potential can be broadened to additional biologically relevant metabolites. The enzyme-mimetic nanomaterial developed here could serve as a starting point of sophisticated in vitro assays toward the highly sensitive detection of disease biomarkers.