Conducting nanowires built by controlled self-assembly of amyloid fibers and selective metal deposition

Broken but not beaten: Challenge of reducing the amyloids pathogenicity by degradation

BACKGROUND

The accumulation of ordered protein aggregates, amyloid fibrils, accompanies various neurodegenerative diseases (such as Parkinson's, Huntington's, Alzheimer's, etc.) and causes a wide range of systemic and local amyloidoses (such as insulin, hemodialysis amyloidosis, etc.). Such pathologies are usually diagnosed when the disease is already irreversible and a large amount of amyloid plaques have accumulated. In recent years, new drugs aimed at reducing amyloid levels have been actively developed. However, although clinical trials have demonstrated a reduction in amyloid plaque size with these drugs, their effect on disease progression has been controversial and associated with significant side effects, the reasons of which are not fully understood.

AIM OF REVIEW

The purpose of this review is to summarize extensive array of data on the effect of exogenous and endogenous factors (physico-mechanical effects, chemical effects of low molecular weight compounds, macromolecules and their complexes) on the structure and pathogenicity of mature amyloids for proposing future directions of the development of effective and safe anti-amyloid therapeutics.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Our analysis show that destruction of amyloids is in most cases incomplete and degradation products often retain the properties of amyloids (including high and sometimes higher than fibrils, cytotoxicity), accelerate amyloidogenesis and promote the propagation of amyloids between cells. Probably, the appearance of protein aggregates, polymorphic in structure and properties (such as amorphous aggregates, fibril fragments, amyloid oligomers, etc.), formed because of uncontrolled degradation of amyloids, may be one of the reasons for the ambiguous effectiveness and serious side effects of the anti-amyloid drugs. This means that all medications that are supposed to be used both for degradation and slow down the fibrillogenesis must first be tested on mature fibrils: the mechanism of drug action and cytotoxic, seeding, and infectious activity of the degradation products must be analyzed.

Amyloid-Templated Ceria Nanozyme Reinforced Microneedle for Diabetic Wound Treatments

Amyloid fibrils have emerged as excellent templates and building blocks for the development of ordered functional materials with considerable potential in biomedical applications. Here, lysozyme amyloid fibrils (Lys-AFs) are employed as templates for the in situ synthesis of ceria nanozymes (Lys-AFs-Ceria) with ultrafine dimensions, an optimized Ce3+/Ce4+ ratio, and uniform distribution on the fibril surface, addressing the challenges of low catalytic efficiency and high susceptibility to aggregation typical of traditional methods. As a proof of concept, it is further applied Lys-AFs-Ceria to develop hydrogel/microneedle for treating bacteria-infected diabetic wounds via non-covalent interactions between polyphenols and amyloid fibrils incorporating glucose oxidase (GOX). The hydrogel/microneedle facilitates superoxide dismutase and catalase cascade catalysis by Lys-AFs-Ceria, and integrates GOX-mediated glucose consumption, synergistically achieving glucose reduction, reactive oxygen species elimination, and hypoxia alleviation in the diabetic wound infection microenvironment. In addition to antibacterial properties and tissue regeneration promotion of Lys-AFs scaffold, Lys-AFs-Ceria regulates macrophages polarization toward an anti-inflammatory M2 state. Collectively, these attributes contribute to the enhanced efficacy of diabetic wound healing, with in vivo studies demonstrating increased healing efficiency following a single application, and more in general an effective strategy toward high-catalytic and stable nanozymes.

Unveiling the multifaceted potential of amyloid fibrils: from pathogenic myths to biotechnological marvels

Amyloid fibrils, historically stigmatized due to their association with diseases like Alzheimer's and Parkinson's, are now recognized as a distinct class of functional proteins with extraordinary potential. These highly ordered, cross-β-sheet protein aggregates are found across all domains of life, playing crucial physiological roles. In bacteria, functional amyloids like curli fibers are essential for surface adhesion, biofilm formation, and viral DNA packaging. Fungal prions exploit amyloid conformations to regulate translation, metabolism, and virulence, while mammalian amyloids are integral to melanin synthesis, hormone storage, and antimicrobial defense. The stability and hydrophobic nature of amyloid scaffolds underpin these diverse biological functions. Beyond their natural roles, amyloid fibrils offer unique capabilities in biomedicine, nanotechnology, and materials science. Their exceptional mechanical strength and biocompatibility make them ideal for controlled drug delivery, tissue engineering scaffolds, and enzyme immobilization. The intrinsic fluorescence and optical properties of certain amyloids open up innovative applications in biosensors, molecular probes, and optoelectronic devices. Furthermore, amyloid fibrils can template metal nanowires, enhance conducting materials, and form nanocomposites by integrating with polymers. This newfound appreciation for the functional diversity of amyloids has ignited intense research efforts to elucidate their molecular mechanisms, stability, and tunable properties. By unraveling the structural intricacies of functional amyloids, researchers aim to harness their remarkable attributes for groundbreaking biomedical therapies, advanced nanomaterials, and sustainable biotechnological innovations. This review explores the transformative journey of amyloids from pathological entities to biotechnological marvels, highlighting their vast potential across agriculture, environmental remediation, and industrial processes.

Mica Lattice Orientation of Epitaxially Grown Amyloid β25-35 Fibrils

β-amyloid (Aβ) peptides form self-organizing fibrils in Alzheimer's disease. The biologically active, toxic Aβ25-35 fragment of the full-length Aβ-peptide forms a stable, oriented filament network on the mica surface with an epitaxial mechanism at the timescale of seconds. While many of the structural and dynamic features of the oriented Aβ25-35 fibrils have been investigated before, the β-strand arrangement of the fibrils and their exact orientation with respect to the mica lattice remained unknown. By using high-resolution atomic force microscopy, here, we show that the Aβ25-35 fibrils are oriented along the long diagonal of the oxygen hexagon of mica. To test the structure and stability of the oriented fibrils further, we carried out molecular dynamics simulations on model β-sheets. The models included the mica surface and a single fibril motif built from β-strands. We show that a sheet with parallel β-strands binds to the mica surface with its positively charged groups, but the C-terminals of the strands orient upward. In contrast, the model with antiparallel strands preserves its parallel orientation with the surface in the molecular dynamics simulation, suggesting that this model describes the first β-sheet layer of the mica-bound Aβ25-35 fibrils well. These results pave the way toward nanotechnological construction and applications for the designed amyloid peptides.

Biotechnological applications of amyloid fibrils

Protein aggregates and amyloid fibrils have special qualities and are used in a variety of biotechnological applications. They are extensively employed in bioremediation, biomaterials, and biocatalysis. Because of their capacity to encapsulate and release pharmaceuticals and their sensitivity to certain molecules, respectively, they are also used in drug delivery and biosensor applications. They have also demonstrated potential in the domains of food and bioremediation. Additionally, amyloid peptides have drawn interest in biological applications, especially in the investigation of illnesses like Parkinson's and Alzheimer's. The unique characteristics of amyloid fibrils, namely their mechanical strength and β-sheet structure, make them adaptable to a wide range of biotechnological uses. Even with their promise, one important factor to keep in mind before widely using modified amyloid materials is their potential toxicity. Thus, current research aims to overcome safety concerns while maximizing their potential.

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.

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

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

Deciphering amyloid fibril molecular maturation through FLIM-phasor analysis of thioflavin T

The investigation of amyloid fibril formation is paramount for advancing our understanding of neurodegenerative diseases and for exploring potential correlated therapeutic strategies. Moreover, the self-assembling properties of amyloid fibrils show promise for the development of advanced protein-based biomaterials. Among the methods employed to monitor protein aggregation processes, fluorescence has emerged as a powerful tool. Its exceptional sensitivity enables the detection of early-stage aggregation events that are otherwise challenging to observe. This research underscores the pivotal role of fluorescence analysis, particularly in investigating the aggregation processes of hen egg white lysozyme, a model protein extensively studied for insights into amyloid fibril formation. By combining classical spectroscopies with fluorescence microscopy and by exploiting the fluorescence properties (intensity and lifetime) of the thioflavin T, we were able to noninvasively monitor key and complex molecular aspects of the process. Intriguingly, the fluorescence lifetime imaging-phasor analysis of thioflavin T fluorescence lifetime on structures at different stages of aggregation allowed to decipher the complex fluorescence decay behavior, highlighting that their changes rise from the combination of specific binding to amyloid typical cross-β structures and of the rigidity of the molecular environment.

Structure of Amyloid Peptide Ribbons Characterized by Electron Microscopy, Atomic Force Microscopy, and Solid-State Nuclear Magnetic Resonance

Polypeptides often self-assemble to form amyloid fibrils, which contain cross-β structural motifs and are typically 5-15 nm in width and micrometers in length. In many cases, short segments of longer amyloid-forming protein or peptide sequences also form cross-β assemblies but with distinctive ribbon-like morphologies that are characterized by a well-defined thickness (on the order of 5 nm) in one lateral dimension and a variable width (typically 10-100 nm) in the other. Here, we use a novel combination of data from solid-state nuclear magnetic resonance (ssNMR), dark-field transmission electron microscopy (TEM), atomic force microscopy (AFM), and cryogenic electron microscopy (cryoEM) to investigate the structures within amyloid ribbons formed by residues 14-23 and residues 11-25 of the Alzheimer's disease-associated amyloid-β peptide (Aβ14-23 and Aβ11-25). The ssNMR data indicate antiparallel β-sheets with specific registries of intermolecular hydrogen bonds. Mass-per-area values are derived from dark-field TEM data. The ribbon thickness is determined from AFM images. For Aβ14-23 ribbons, averaged cryoEM images show a periodic spacing of β-sheets. The combined data support structures in which the amyloid ribbon growth direction is the direction of intermolecular hydrogen bonds between β-strands, the ribbon thickness corresponds to the width of one β-sheet (i.e., approximately the length of one molecule), and the variable ribbon width is a variable multiple of the thickness of one β-sheet (i.e., a multiple of the repeat distance in a stack of β-sheets). This architecture for a cross-β assembly may generally exist within amyloid ribbons.

Probing physical properties of single amyloid fibrils using nanofluidic channels

Amyloid fibril formation is central to the pathology of many diseases, including neurodegenerative disorders such as Alzheimer's and Parkinson's disease. Amyloid fibrils can also have functional and scaffolding roles, for example in bacterial biofilms, and have also been exploited as useful biomaterials. Despite being linear protein homopolymers, amyloid fibrils can exhibit significant structural and morphological polymorphism, making it relevant to study them on the single fibril level. We here introduce the concept of nanofluidic channel analysis to the study of single, fluorescently-labeled amyloid fibrils in solution, monitoring the extension and emission intensity of individual fibrils confined in nanochannels with a depth of 300 nm and a width that gradually increases from 300 to 3000 nm. The change in fibril extension with channel width permitted accurate determination of the persistence length of individual fibrils using Odijk's theory for strongly confined polymers. The technique was applied to amyloid fibrils prepared from the Alzheimer's related peptide amyloid-β(1-42) and the Parkinson's related protein α-synuclein, obtaining mean persistence lengths of 5.9 ± 4.5 μm and 3.0 ± 1.6 μm, respectively. The broad distributions of fibril persistence lengths indicate that amyloid fibril polymorphism can manifest in their physical properties. Interestingly, the α-synuclein fibrils had lower persistence lengths than the amyloid-β(1-42) fibrils, despite being thicker. Furthermore, there was no obvious within-sample correlation between the fluorescence emission intensity per unit length of the labelled fibrils and their persistence lengths, suggesting that stiffness may not be proportional to thickness. We foresee that the nanofluidics methodology established here will be a useful tool to study amyloid fibrils on the single fibril level to gain information on heterogeneity in their physical properties and interactions.

Flexibility Analysis of DNA Nanotubes with Prescribed Circumferences and Their Pearl-Necklace Assemblies with Gold Nanoclusters

DNA has been demonstrated as a powerful platform for the construction of inorganic nanoparticles (NPs) into complex three-dimensional assemblies. Despite extensive research, the physical fundamental details of DNA nanostructures and their assemblies with NPs remain obscure. Here, we report the identification and quantification of the assembly details of programmable DNA nanotubes with monodisperse circumferences of a 4, 5, 6, 7, 8, or 10 DNA helix and their pearl-necklace-like assemblies with ultrasmall gold nanoparticles, Au₂₅ nanoclusters (AuNCs), liganded by -S(CH₂)_nNH₃⁺ (n = 3, 6, 11). The flexibilities of DNA nanotubes, analyzed via statistical polymer physics analysis through atomic force microscopy (AFM), demonstrate that ∼2.8 power exponentially increased with the DNA helix number. Moreover, the short-length liganded AuS(CH₂)₃NH₃⁺ NCs were observed to be able to form pearl-necklace-like DNA-AuNC assemblies stiffened than neat DNA nanotubes, while long-length liganded AuS(CH₂)₆NH₃⁺ and AuS(CH₂)₁₁NH₃⁺ NCs could fragment DNA nanotubular structures, indicating that DNA-AuNC assembling can be precisely manipulated by customizing the hydrophobic domains of the AuNC nanointerfaces. We prove the advantages of polymer science concepts in unraveling useful intrinsic information on physical fundamental details of DNA-AuNC assembling, which facilitates DNA-metal nanocomposite construction.

Gold nanoparticle-coated apoferritin conductive nanowires

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

Structural Quantification of the Surface-Confined Metal-Organic Precursors Simulated with the Lattice Monte Carlo Method

The diversity of surface-confined metal-organic precursor structures, which recently have been observed experimentally, poses a question of how the individual properties of a molecular building block determine those of the resulting superstructure. To answer this question, we use the Monte Carlo simulation technique to model the self-assembly of metal-organic precursors that precede the covalent polymerization of halogenated PAH isomers. For this purpose, a few representative examples of low-dimensional constructs were studied, and their basic structural features were quantified using such descriptors as the orientational order parameter, radial distribution function, and one- and two-dimensional structure factors. The obtained results demonstrated that the morphology of the precursor (and thus the subsequent polymer) could be effectively tuned by a suitable choice of molecular parameters, including size, shape, and intramolecular distribution of halogen substituents. Moreover, our theoretical investigations showed the effect of the main structural features of the precursors on the related indirect characteristics of these constructs. The results reported herein can be helpful in the custom designing and characterization of low-dimensional polymers with adjustable properties.

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.

Living electronics: A catalogue of engineered living electronic components

Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.

Dipeptide nanostructures: Synthesis, interactions, advantages and biomedical applications

Short peptides are important in the design of self-assembled materials due to their versatility and flexibility. Self-assembled dipeptides, a group of peptide nanostructures, have highly attractive uses in the field of biomedicine. Recently these materials have proved to be important nanostructures because of their biocompatibility, low-cost and simplicity of synthesis, functionality/easy tunability and nano dimensions. Although there are different studies on peptide and protein-based nanostructures, more information about self-assembled nanostructures for dipeptides is still required to discover the advantages, challenges, importance, synthesis, interactions, and applications. This review describes and discusses the self-assembled dipeptide nanostructures especially for biomedical applications.

Protein Design: From the Aspect of Water Solubility and Stability

Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.

Disulfide-Mediated Elongation of Amyloid Fibrils of α-Synuclein For Use in Producing Self-Healing Hydrogel and Dye-Absorbing Aerogel

Due to their mechanical robustness, biocompatibility, and nanoscale size, amyloid fibrils (AFs) have been considered as a potential nanomaterial for biological applications. Unfortunately, however, AFs are usually not fully extended because of their pre-mature breakage, which hampers their use to generate biocompatible suprastructures, although the amounts of AFs could be amplified via their self-propagation property. Here, we have demonstrated the full extension of AFs of α-synuclein (αS) by introducing a cysteine residue to its C-terminus which prevents the shear-induced fragmentation of AFs via site-directed disulfide bond formation on the exposed surface of AFs. These heat- and cold-resistant elongated AFs were entangled into self-healable hydrogels through a mild disulfide-exchange process in the presence of tris(2-carboxyethyl) phosphine, which subsequently developed into dye-absorbing aerogels upon freeze-drying without collapsing the three-dimensional internal fibrillar network. The resulting αS aerogel with high porosity and increased surface area was shown to be capable of absorbing both hydrophilic and hydrophobic substances. In addition, the aerogel was further engineered with 8-arm polyethylene glycol containing a sulfhydryl group to increase its drug loading capacity and protease susceptibility for drug unloading. The elongated AFs, therefore, have been suggested to play a pivotal component for the development of bio-nano-matrix for diverse biological applications including drug delivery, tissue engineering, and environmental remediation. STATEMENT OF SIGNIFICANCE: Due to accurate protein self-assembly process, α-synuclein forms an amyloid fibril which are the major component of Lewy bodies. In general, α-synuclein amyloid fibrils break under thermal fluctuations as these nanofibrils elongate to reach certain length. In this study, we have demonstrated the full extension of α-synuclein amyloid fibrils by introducing a cysteine residue to its C-terminus by forming site-directed disulfide bonds on the exposed surface of amyloid fibrils for the first time. The resulting elongated amyloid fibrils were mechanically robust and stable. By using elongated amyloid fibrils, we have made self-healable amyloid fibril hydrogel and dye-absorbing aerogel.

1D Colloidal chains: recent progress from formation to emergent properties and applications

Integrating nanoscale building blocks of low dimensionality (0D; i.e., spheres) into higher dimensional structures endows them and their corresponding materials with emergent properties non-existent or only weakly existent in the individual building blocks. Constructing 1D chains, 2D arrays and 3D superlattices using nanoparticles and colloids therefore continues to be one of the grand goals in colloid and nanomaterial science. Amongst these higher order structures, 1D colloidal chains are of particular interest, as they possess unique anisotropic properties. In recent years, the most relevant advances in 1D colloidal chain research have been made in novel synthetic methodologies and applications. In this review, we first address a comprehensive description of the research progress concerning various synthetic strategies developed to construct 1D colloidal chains. Following this, we highlight the amplified and emergent properties of the resulting materials, originating from the assembly of the individual building blocks and their collective behavior, and discuss relevant applications in advanced materials. In the discussion of synthetic strategies, properties, and applications, particular attention will be paid to overarching concepts, fresh trends, and potential areas of future research. We believe that this comprehensive review will be a driver to guide the interdisciplinary field of 1D colloidal chains, where nanomaterial synthesis, self-assembly, physical property studies, and material applications meet, to a higher level, and open up new research opportunities at the interface of classical disciplines.

Protein nanofibrils and their use as building blocks of sustainable materials

The development towards a sustainable society requires a radical change of many of the materials we currently use. Besides the replacement of plastics, derived from petrochemical sources, with renewable alternatives, we will also need functional materials for applications in areas ranging from green energy and environmental remediation to smart foods. Proteins could, with their intriguing ability of self-assembly into various forms, play important roles in all these fields. To achieve that, the code for how to assemble hierarchically ordered structures similar to the protein materials found in nature must be cracked. During the last decade it has been demonstrated that amyloid-like protein nanofibrils (PNFs) could be a steppingstone for this task. PNFs are formed by self-assembly in water from a range of proteins, including plant resources and industrial side streams. The nanofibrils display distinct functional features and can be further assembled into larger structures. PNFs thus provide a framework for creating ordered, functional structures from the atomic level up to the macroscale. This review address how industrial scale protein resources could be transformed into PNFs and further assembled into materials with specific mechanical and functional properties. We describe what is required from a protein to form PNFs and how the structural properties at different length scales determine the material properties. We also discuss potential chemical routes to modify the properties of the fibrils and to assemble them into macroscopic structures.

Lead(II) ions adsorption onto amyloid particulates: An in depth study

The production of new cost-effective biocompatible sorbent sustainable materials, with natural origins, able to remove heavy metals from water resources is nowadays highly desirable in order to reduce pollution and increase clean water availability. In this context, self-assembled protein materials with amyloid structures seem to have a great potential as natural platform for a broader development of highly-tunable structures. In this work we show how protein particulates, a generic form of protein aggregates, with spherical micro sized shape can be used as adsorbents of Pb²⁺ ions from aqueous solution. The effect of pH, ionic medium, ionic strength and temperature of the metal ion solution on the adsorption ability and affinity has been evaluated revealing the complexity of adsorption mechanisms which are the result of the balance of specific interactions with functional groups in protein structure and not specific ones common to all polypeptide chains, and possibly related to amyloid state and to modification of particulates hydration layer.

Functionalized Prion-Inspired Amyloids for Biosensor Applications

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

Examining the effect of bovine serum albumin on the properties and drug release behavior of β-lactoglobulin-derived amyloid fibril-based hydrogels

Herein, we report the use of β-lactoglobulin (β-LG) combined with bovine serum albumin (BSA) for the preparation of amyloid-based hydrogels with aim of delivering riboflavin. The incorporation of BSA enhanced β-LG fibrillogenesis and protected β-LG fibrils from losing fibrillar structure due to the pH shift. The mechanical properties of hydrogels were observed to be positively correlated with the number of amyloid fibrils. While the addition of BSA induced amyloid fibril formation, its presence between the fibril chains interfered with the entanglement of fibril chains, thus adversely affecting the hydrogels' mechanical properties. Hydrogels' surface microstructure became more compact as the number of amyloid fibrils rose and the presence of BSA could improve hydrogels' surface homogeneity. In vitro riboflavin (RF) release rate was found to be correlated with the number of fibrils and BSA-RF binding affinity. However, when the digestive enzymes were present, the influence of BSA-RF affinity was alleviated due to enzymes' destructive and/or degradative effects on BSA and/or hydrogels, thus the release rate relied on the number of fibrils, which could be adjusted by the amount of BSA. Results indicate that the additional component, BSA, plays an important role in modulating the properties and functions of β-LG fibril-based hydrogels.

Intrinsic electronic conductivity of individual atomically resolved amyloid crystals reveals micrometer-long hole hopping via tyrosines

Proteins are commonly known to transfer electrons over distances limited to a few nanometers. However, many biological processes require electron transport over far longer distances. For example, soil and sediment bacteria transport electrons, over hundreds of micrometers to even centimeters, via putative filamentous proteins rich in aromatic residues. However, measurements of true protein conductivity have been hampered by artifacts due to large contact resistances between proteins and electrodes. Using individual amyloid protein crystals with atomic-resolution structures as a model system, we perform contact-free measurements of intrinsic electronic conductivity using a four-electrode approach. We find hole transport through micrometer-long stacked tyrosines at physiologically relevant potentials. Notably, the transport rate through tyrosines (10⁵ s^-1) is comparable to cytochromes. Our studies therefore show that amyloid proteins can efficiently transport charges, under ordinary thermal conditions, without any need for redox-active metal cofactors, large driving force, or photosensitizers to generate a high oxidation state for charge injection. By measuring conductivity as a function of molecular length, voltage, and temperature, while eliminating the dominant contribution of contact resistances, we show that a multistep hopping mechanism (composed of multiple tunneling steps), not single-step tunneling, explains the measured conductivity. Combined experimental and computational studies reveal that proton-coupled electron transfer confers conductivity; both the energetics of the proton acceptor, a neighboring glutamine, and its proximity to tyrosine influence the hole transport rate through a proton rocking mechanism. Surprisingly, conductivity increases 200-fold upon cooling due to higher availability of the proton acceptor by increased hydrogen bonding.

SAPdb: A database of short peptides and the corresponding nanostructures formed by self-assembly

Nanostructures generated by self-assembly of peptides yield nanomaterials that have many therapeutic applications, including drug delivery and biomedical engineering, due to their low cytotoxicity and higher uptake by targeted cells owing to their high affinity and specificity towards cell surface receptors. Despite the promising implications of this rapidly expanding field, there is no dedicated resource to study peptide nanostructures. This study endeavours to create a repository of short peptides, which may prove to be the best models to study ordered nanostructures formed by peptide self-assembly. SAPdb has a repertoire of 1049 entries of experimentally validated nanostructures formed by the self-assembly of small peptides. It consists of 328 tripeptides, 701 dipeptides, and 20 single amino acids with some conjugate partners. Each entry encompasses comprehensive information about the peptide, such as chemical modifications, the type of nanostructure formed, experimental conditions like pH, temperature, solvent required for the self-assembly, etc. Our analysis indicates that peptides containing aromatic amino acids favour the formation of self-assembling nanostructures. Additionally, we observed that these peptides form different nanostructures under different experimental conditions. SAPdb provides this comprehensive information in a hassle-free tabulated manner at a glance. User-friendly browsing, searching, and analysis modules have been integrated for easy data retrieval, data comparison, and examination of properties. We anticipate SAPdb to be a valuable repository for researchers engaged in the burgeoning arena of nanobiotechnology. It is freely available at https://webs.iiitd.edu.in/raghava/sapdb.

Protein Nanofibrils and Their Hydrogel Formation with Metal Ions

Protein nanofibrils (PNFs) have been prepared by whey protein fibrillation at low pH and in the presence of different metal ions. The effect of the metal ions was systematically studied both in terms of PNF suspension gelation behavior and fibrillation kinetics. A high valence state and a small ionic radius (e.g., Sn4+) of the metal ion resulted in the formation of hydrogels already at a metal ion concentration of 30 mM, whereas an intermediate valence state and larger ionic radius (Co2+, Ni2+, Al3+) resulted in the hydrogel formation occurring at 60 mM. A concentration of 120 mM of Na+ was needed to form a PNF hydrogel, while lower concentrations showed liquid behaviors similar to the reference PNF solution where no metal ions had been introduced. The hydrogel mechanics were investigated at steady-state conditions after 24 h of incubation/gelation, revealing that more acidic (smaller and more charged) metal ions induced ca. 2 orders of magnitude higher storage modulus as compared to the less acidic metal ions (with smaller charge and larger radius) for the same concentration of metal ions. The viscoelastic nature of the hydrogels was attributed to the ability of the metal ions to coordinate water molecules in the vicinity of the PNFs. The presence of metal ions in the solutions during the growth of the PNFs typically resulted in curved fibrils, whereas an upper limit of the concentration existed when oxides/hydroxides were formed, and the hydrogels lost their gel properties due to phase separation. Thioflavin T (ThT) fluorescence was used to determine the rate of the fibrillation to form 50% of the total PNFs (t1/2), which decreased from 2.3 to ca. 0.5 h depending on the specific metal ions added.

Preparation, Functionalization, Modification, and Applications of Nanostructured Gold: A Critical Review

Gold nanoparticles (Au NPs) play a significant role in science and technology because of their unique size, shape, properties and broad range of potential applications. This review focuses on the various approaches employed for the synthesis, modification and functionalization of nanostructured Au. The potential catalytic applications and their enhancement upon modification of Au nanostructures have also been discussed in detail. The present analysis also offers brief summaries of the major Au nanomaterials synthetic procedures, such as hydrothermal, solvothermal, sol-gel, direct oxidation, chemical vapor deposition, sonochemical deposition, electrochemical deposition, microwave and laser pyrolysis. Among the various strategies used for improving the catalytic performance of nanostructured Au, the modification and functionalization of nanostructured Au produced better results. Therefore, various synthesis, modification and functionalization methods employed for better catalytic outcomes of nanostructured Au have been summarized in this review.

Conformational Transitions upon Maturation Rule Surface and pH-Responsiveness of α-Lactalbumin Microparticulates

De novo designed protein supramolecular structures are nowadays attracting much interest as highly performing biomaterials. While a clear advantage is provided by the intrinsic biocompatibility and biodegradability of protein and peptide building blocks, developing sustainable and green bottom up approaches for finely tuning the material properties still remains a challenge. Here, we present an experimental study on the formation of protein microparticles in the form of particulates from the protein α-lactalbumin using bulk mixing in water solution and high temperature. Once formed, the structure and stability of these spherical protein condensates change upon further thermal incubation while the size of aggregates does not significantly increase. Combining advanced microscopy and spectroscopy methods, we prove that this process, named maturation, is characterized by a gradual increase of amyloid-like structure in protein particulates, an enhancement in surface roughness and in molecular compactness, providing a higher stability and resistance of the structure in acidic environments. When dissolved at pH 2, early stage particulates disassemble into a homogeneous population of small oligomers, while the late stage particulates remain unaffected. Particulates at the intermediate stage of maturation partially disassemble into a heterogeneous population of fragments. Importantly, differently matured microparticles show different features when loading a model lipophilic molecule. Our findings suggest conformational transitions localized at the interface as a key step in the maturation of amyloid protein condensates, promoting this phenomenon as an intrinsic knob to tailor the properties of protein microparticles formed via bulk mixing in aqueous solution. This provides a simple and sustainable platform for the design and realization of protein microparticles for tailored applications.

Metal-Protein Hybrid Materials with Desired Functions and Potential Applications

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

Guided Assembly and Patterning of Intrinsically Fluorescent Amyloid Fibers with Long-Range Order

Fibrillar amyloids exhibit a fascinating range of mechanical, optical, and electronic properties originating from their characteristic β-sheet-rich structure. Harnessing these functionalities in practical applications has so far been hampered by a limited ability to control the amyloid self-assembly process at the macroscopic scale. Here, we use core-shell electrospinning with microconfinement to assemble amyloid-hybrid fibers, consisting of densely aggregated fibrillar amyloids stabilized by a polymer shell. Up to centimeter-long hybrid fibers with micrometer diameter can be arranged into aligned and ordered arrays and deposited onto substrates or produced as free-standing networks. Properties that are characteristic of amyloids, including their high elastic moduli and intrinsic fluorescence signature, are retained in the hybrid fiber cores, and we show that they fully persist through the macroscopic fiber patterns. Our findings suggest that microlevel confinement is key for the guided assembly of amyloids from monomeric proteins.

Directionality of growth and kinetics of branched fibril formation

The self-assembly of fibrils is a subject of intense interest, primarily due to its relevance to the formation of pathological structures. Some fibrils develop branches via the so-called secondary nucleation. In this paper, we use the master equation approach to model the kinetics of formation of branched fibrils. In our model, a branched fibril consists of one mother branch and several daughter branches. We consider five basic processes of fibril formation, namely, nucleation, elongation, branching, fragmentation, and dissociation of the primary nucleus of fibrils into free monomers. Our main focus is on the effect of the directionality of growth on the kinetics of fibril formation. We consider several cases. At first, the mother branch may elongate from one or from both ends, while the daughter branch elongates only from one end. We also study the case of branched fibrils with bidirectionally growing daughter branches, tangentially to the main stem, which resembles the intertwining process. We derive a set of ordinary differential equations for the moments of the number concentration of fibrils, which can be solved numerically. Assuming that the primary nucleus of fibrils dissociates with the fragmentation rate, in the limit of the zero branching rate, our model reproduces the results of a previous model that considers only the three basic processes of nucleation, elongation, and fragmentation. We also use the experimental parameters for the fibril formation of Huntingtin fragments to investigate the effect of unidirectional vs bidirectional elongation of the filaments on the kinetics of fibrillogenesis.

Amyloid-Like Peptide Aggregates

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

Transition of Ultrathick Polyamide Tubes into Vesicles with Great Stability

This work reports on the transition of a polyamide ultrathick wall microtubes to microvesicles through self-assembly. An amphiphilic polyamide is synthesized first by the solution polycondensation of sodium isophthalate-5-sulfonate (SIPA) and poly(propylene glycol) bis(2-aminopropyl ether) 2000. Then, its self-assembly in aqueous solution is investigated through direct hydration. The size and morphology of the self-assemblies is investigated by transmission electron microscope (TEM), scanning electron microscope (SEM), atomic force microscope (AFM), and optical microscope (OM) measurements. The result shows that the as-prepared polyamide first self-assembles to thick walled tubes, then these tubes can gradually evolve to ultrathick wall microvesicles with an unusually thick membrane above 330 nm. Both the transition pathway and the mechanism are investigated in micromicroscopy. Most importantly, the microvesicles show great thermal and chemical stability. The novel superstable self-assembly structures as well as the transition mechanism presented here offer a promising perspective for the application in the scope of the biological membrane movements and nanoelectromechanics in medical devices.

Tubulin Double Helix: Lateral and Longitudinal Curvature Changes of Tubulin Protofilament

By virtue of their native structures, tubulin dimers are protein building blocks that are naturally preprogrammed to assemble into microtubules (MTs), which are cytoskeletal polymers. Here, polycation-directed (i.e., electrostatically tunable) assembly of tubulins is demonstrated by conformational changes to the tubulin protofilament in longitudinal and lateral directions, creating tubulin double helices and various tubular architectures. Synchrotron small-angle X-ray scattering and transmission electron microscopy reveal a remarkable range of nanoscale assembly structures: single- and double-layered double-helix tubulin tubules. The phase transitions from MTs to the new assemblies are dependent on the size and concentration of polycations. Two characteristic scales that determine the number of observed phases are the size of polycation compared to the size of tubulin (≈4 nm) and to MT diameter (≈25 nm). This work suggests the feasibility of using polycations that have scissor- and glue-like properties to achieve "programmable breakdown" of protein nanotubes, tearing MTs into double-stranded tubulins and building up previously undiscovered nanostructures. Importantly, a new role of tubulins is defined as 2D shape-controllable building blocks for supramolecular architectures. These findings provide insight into the design of protein-based functional materials, for example, as metallization templates for nanoscale electronic devices, molecular screws, and drug delivery vehicles.

Synergism of Multicomponent Catalysis: One-Dimensional Pt-Rh-Pd Nanochain Catalysts for Efficient Methanol Oxidation

Designing Pt-based alloy catalysts with multicomponent composition and a controllable structure is important to improve the utilization efficiency of precious metals and catalytic activity, but it still face a lot of challenges for simple preparation. Herein, we used insulin amyloid fibrils as templates and their own one-dimensional spiral structure to synthesize Pt-Rh-Pd ternary alloy nanochains under mild conditions. The prepared Pt-Rh-Pd alloy nanochains (NCs) have uniform diameter, and the particle size is only 2 nm. This ultrafine structure increases the specific surface area of the catalyst to a certain extent, and the synergistic effect of the three metals improves the catalytic performance. Compared with commercial Pt/C and binary Pt-Rh NCs, the as-presented Pt-Rh-Pd NCs show better methanol oxidation activity ability and stability against CO poisoning. The peak current density of front sweep is 1.48 mA cm-2, which is 1.7 times higher than that of commercial Pt/C (0.89 mA cm-2) and 1.4 times higher than that of the Pt-Rh NCs (1.07 mA cm-2), indicating great application potential as high-performance electrocatalysts in fuel cells.

Self-assembled peptide-inorganic nanoparticle superstructures: from component design to applications

Peptides have become excellent platforms for the design of peptide-nanoparticle hybrid superstructures, owing to their self-assembly and binding/recognition capabilities. Morover, peptide sequences can be encoded and modified to finely tune the structure of the hybrid systems and pursue functionalities that hold promise in an array of high-end applications. This feature article summarizes the different methodologies that have been developed to obtain self-assembled peptide-inorganic nanoparticle hybrid architectures, and discusses how the proper encoding of the peptide sequences can be used for tailoring the architecture and/or functionality of the final systems. We also describe the applications of these hybrid superstructures in different fields, with a brief look at future possibilities towards the development of new functional hybrid materials.

Phasor-FLIM analysis of Thioflavin T self-quenching in Concanavalin amyloid fibrils

The formation of amyloid structures has traditionally been related to human neurodegenerative pathologies and, in recent years, the interest in these highly stable nanostructures was extended to biomaterial sciences. A common method to monitor amyloid growth is the analysis of Thioflavin T fluorescence. The use of this highly selective dye, diffused worldwide, allows mechanistic studies of supramolecular assemblies also giving back important insight on the structure of these aggregates. Here we present experimental evidence of self-quenching effect of Thioflavin T in presence of amyloid fibrils. A significant reduction of fluorescence lifetime of this dye which is not related to the properties of analyzed amyloid structures is found. This result is achieved by coupling Fluorescence Lifetime Imaging Microscopy with phasor approach as suitable model-free methods and constitute a serious warning that have to be taken in account if is dye is used for quantitative studies.

Biofilm architecture: An emerging synthetic biology target

Synthetic biologists are exploiting biofilms as an effective mechanism for producing various outputs. Metabolic optimization has become commonplace as a method of maximizing system output. In addition to production pathways, the biofilm itself contributes to the efficacy of production. The purpose of this review is to highlight opportunities that might be leveraged to further enhance production in preexisting biofilm production systems. These opportunities may be used with previously established production systems as a method of improving system efficiency further. This may be accomplished through the reduction in the cost of establishing and maintaining biofilms, and maintenance of the enhancement of product yield per unit of time, per unit of area, or per unit of required input.

The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX)4 and Coumarin-(RXDX)4 Conjugate β-Sheets

pH-Switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X = Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)₄ systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X = Ala are found to be unstable at both pHs, while conjugates with X = Val, Leu, Ile, and Phe are found to form stable β-sheets at least at neutral pH. The coumarin-(RFDF)₄ conjugate is found to have the largest relative entropy value of 0.884 ± 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)₄ containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.

Bottom-up synthesis of protein-based nanomaterials from engineered β-solenoid proteins

Biomolecular self-assembly is an emerging bottom-up approach for the synthesis of novel nanomaterials. DNA and viruses have both been used to create scaffolds but the former lacks chemical diversity and the latter lack spatial control. To date, the use of protein scaffolds to template materials on the nanoscale has focused on amyloidogenic proteins that are known to form fibrils or two-protein systems where a second protein acts as a cross-linker. We previously developed a unique approach for self-assembly of nanomaterials based on engineering β-solenoid proteins (BSPs) to polymerize into micrometer-length fibrils. BSPs have highly regular geometries, tunable lengths, and flat surfaces that are amenable to engineering and functionalization. Here, we present a newly engineered BSP based on the antifreeze protein of the beetle Rhagium inquisitor (RiAFP-m9), which polymerizes into stable fibrils under benign conditions. Gold nanoparticles were used to functionalize the RiAFP-m9 fibrils as well as those assembled from the previously described SBAFP-m1 protein. Cysteines incorporated into the sequences provide site-specific gold attachment. Additionally, silver was deposited on the gold-labelled fibrils by electroless plating to create nanowires. These results bolster prospects for programable self-assembly of BSPs to create scaffolds for functional nanomaterials.

Short to ultrashort peptide-based hydrogels as a platform for biomedical applications

Short peptides have attracted significant attention from researchers in the past few years due to their easy design, synthesis and characterization, diverse functionalisation possibilities, low cost, possibility to make a large range of hierarchical nanostructures and most importantly their high biocompatibility and biodegradability. Generally, short peptides are also relatively more stable than their longer variants, non-immunogenic in nature and many of them self-assemble to provide an exciting range of nanostructures, including hydrogels. Thus, the development of short peptide-based hydrogels has become an area of intense investigation. Although these hydrogels have a water content of greater than 90%, they are surprisingly highly stable structures, and thus have been used for various biomedical applications, including cell therapeutics, drug delivery, tissue engineering and regeneration, contact lenses, biosensors, and wound healing, by different researchers. Herein, we review the progress of research in the rapidly expanding field of short to ultrashort peptide-based hydrogels and their possible applications. Special attention is paid to address and review this field with regard to the stability of peptide-based hydrogels, particularly to enzymatic degradation.

Mobile obstacles accelerate and inhibit the bundle formation in two-patch colloidal particle

Aggregation of protein into bundles is responsible for many neurodegenerative diseases. In this work, we show how two-patch colloidal particles self-assemble into chains and a sudden transition to bundles takes place by tuning the patch size and solvent condition. We study the kinetics of formation of chains, bundles, and networklike structures using patchy Brownian cluster dynamics. We also analyze the ways to inhibit and accelerate the formation of these bundles. We show that in the presence of inert immobile obstacles, the kinetics of formation of bundles slows down. However, in the presence of mobile aggregating particles, which exhibit interspecies hard sphere repulsion and intraspecies attraction, the kinetics of bundle formation accelerates slightly. We also show that if we introduce mobile obstacles, which exhibit interspecies attraction and intraspecies hard sphere repulsion, the kinetics of formation of bundles is inhibited. This is similar to the inhibitory effect of peptide P4 on the formation of insulin fibers. We are providing a model of mobile obstacles undergoing directional interactions to inhibit the formation of bundles.