FiberApp: An Open-Source Software for Tracking and Analyzing Polymers, Filaments, Biomacromolecules, and Fibrous Objects

Polymers with controlled assembly and rigidity made with click-functional peptide bundles

The engineering of biological molecules is a key concept in the design of highly functional, sophisticated soft materials. Biomolecules exhibit a wide range of functions and structures, including chemical recognition (of enzyme substrates or adhesive ligands¹, for instance), exquisite nanostructures (composed of peptides², proteins³ or nucleic acids⁴), and unusual mechanical properties (such as silk-like strength³, stiffness⁵, viscoelasticity⁶ and resiliency⁷). Here we combine the computational design of physical (noncovalent) interactions with pathway-dependent, hierarchical 'click' covalent assembly to produce hybrid synthetic peptide-based polymers. The nanometre-scale monomeric units of these polymers are homotetrameric, α-helical bundles of low-molecular-weight peptides. These bundled monomers, or 'bundlemers', can be designed to provide complete control of the stability, size and spatial display of chemical functionalities. The protein-like structure of the bundle allows precise positioning of covalent linkages between the ends of distinct bundlemers, resulting in polymers with interesting and controllable physical characteristics, such as rigid rods, semiflexible or kinked chains, and thermally responsive hydrogel networks. Chain stiffness can be controlled by varying only the linkage. Furthermore, by controlling the amino acid sequence along the bundlemer periphery, we use specific amino acid side chains, including non-natural 'click' chemistry functionalities, to conjugate moieties into a desired pattern, enabling the creation of a wide variety of hybrid nanomaterials.

Nature of Amorphous Hydrophilic Block Affects Self-Assembly of an Artificial Viral Coat Polypeptide

Consensus motifs for sequences of both crystallizable and amorphous blocks in silks and natural structural analogues of silks vary widely. To design novel silklike polypeptides, an important question is therefore how the nature of either the crystallizable or the amorphous block affects the self-assembly and resulting physical properties of silklike polypeptides. We address herein the influence of the amorphous block on the self-assembly of a silklike polypeptide that was previously designed to encapsulate single DNA molecules into rod-shaped viruslike particles. The polypeptide has a triblock architecture, with a long N-terminal amorphous block, a crystallizable midblock, and a C-terminal DNA-binding block. We compare the self-assembly behavior of a triblock with a very hydrophilic collagen-like amorphous block (GXaaYaa)132 to that of a triblock with a less hydrophilic elastin-like amorphous block (GSGVP)80. The amorphous blocks have similar lengths and both adopt a random coil structure in solution. Nevertheless, atomic force microscopy revealed significant differences in the self-assembly behavior of the triblocks. If collagen-like amorphous blocks are used, there is a clear distinction between very short polypeptide-only fibrils and much longer fibrils with encapsulated DNA. If elastin-like amorphous blocks are used, DNA is still encapsulated, but the polypeptide-only fibrils are now much longer and their size distribution partially overlaps with that of the encapsulated DNA fibrils. We attribute the difference to the more hydrophilic nature of the collagen-like amorphous block, which more strongly opposes the growth of polypeptide-only fibrils than the elastin-like amorphous blocks. Our work illustrates that differences in the chemical nature of amorphous blocks can strongly influence the self-assembly and hence the functionality of engineered silklike polypeptides.

Modulation of Formation, Physicochemical Properties, and Digestion of Ovotransferrin Nanofibrils with Covalent or Non-Covalent Bound Gallic Acid

The impact of covalent or non-covalent bound gallic acid (GA) on the formation, physicochemical properties, and digestion of ovotransferrin (OTF) nanofibrils was comprehensively studied. Thioflavin T fluorescence results revealed that bound GA could inhibit OTF nanofibrillation and that the fibril-inhibitory activity of bound GA was dose dependent. Covalent bound GA exerted stronger inhibition on OTF nanofibrillation than an equal amount of non-covalent bound GA. Atomic force microscopy revealed that covalent bound GA shortened OTF nanofibrils significantly, while non-covalent bound GA did not change the contour length of OTF fibrils remarkably. Bound GA altered diameter of OTF nanofibrils. Both covalent and non-covalent bound GA could alter the zeta potential, surface hydrophobicity, and rheological properties of OTF nanofibrils. Bound GA endowed OTF nanofibrils with a strong antioxidant activity. In vitro gastrointestinal digestion results showed that covalent bound GA elevated the fibril digestion rate better than non-covalent bound GA. Polyphenol binding provided a new approach to modulating the physicochemical properties of protein nanofibrils.

Six-fold director field configuration in amyloid nematic and cholesteric phases

Chiral liquid crystals, or cholesteric phases, have been widely studied in the last decades, leading to fundamental advances and a multitude of applications and technologies. In general, the rich phenomenology of these systems depends directly on the molecular traits and conditions of the system, imposing precise symmetry to the resulting nematic field. By selecting amyloid fibrils as model filamentous chiral colloids, we report an unprecedented breadth of liquid crystalline morphologies, where up to six distinct configurations of the nematic field are observed under identical conditions. Amyloid-rich droplets show homogeneous, bipolar, radial, uniaxial chiral and radial chiral nematic fields, with additional parabolic focal conics in bulk. Variational and scaling theories allow rationalizing the experimental evidence as a subtle interplay between surface and bulk energies. Our experimental and theoretical findings deepen the understanding of chiral liquid crystals under confinement, opening to a more comprehensive exploitation of these systems in related functional materials.

Inducible Fibril Formation of Silk-Elastin Diblocks

Silk-elastin block copolymers have such physical and biological properties that make them attractive biomaterials for applications ranging from tissue regeneration to drug delivery. Silk-elastin block copolymers that only assemble into fibrils at high concentrations can be used for a template-induced fibril assembly. This can be achieved by additionally including template-binding blocks that promote high local concentrations of polymers on the template, leading to a template-induced fibril assembly. We hypothesize that template-inducible silk-fibril formation, and hence high critical concentrations for fibril formation, requires careful tuning of the block lengths, to be close to a critical set of block lengths that separates fibril forming from nonfibril forming polymer architectures. Therefore, we explore herein the impact of tuning block lengths for silk-elastin diblock polypeptides on fibril formation. For silk-elastin diblocks E^S _m -S^Q _n , in which the elastin pentamer repeat is E^S = GSGVP and the crystallizable silk octamer repeat is S^Q = GAGAGAGQ, we find that no fibril formation occurs for n = 6 but that the n = 10 and 14 diblocks do show concentration-dependent fibril formation. For n = 14 diblocks, no effect is observed of the length m (with m = 40, 60, 80) of the amorphous block on the lengths of the fibrils. In contrast, for the n = 10 diblocks that are closest to the critical boundary for fibril formation, we find that long amorphous blocks (m = 80) oppose the growth of fibrils at low concentrations, making them suitable for engineering template-inducible fibril formation.

Active Modulation of States of Prestress in Self-Assembled Short Peptide Gels

Peptide hydrogels are excellent candidates for medical therapeutics due to their tuneable viscoelastic properties, however, in vivo they will be subject to various osmotic pressures, temperature changes, and biological co-solutes, which could alter their performance. Peptide hydrogels formed from the synthetic peptide I3K have a temperature-induced hardening of their shear modulus by a factor of 2. We show that the addition of uncross-linked poly( N-isopropylacrylamide) chains to the peptide gels increases the gels' temperature sensitivity by 3 orders of magnitude through the control of osmotic swelling and cross-linking. Using machine learning combined with single-molecule fluorescence microscopy, we measured the modulation of states of prestress in the gels on the level of single peptide fibers. A new self-consistent mixture model was developed to simultaneously quantify the energy and the length distributions of the states of prestress. Switching the temperature from 20 to 40 °C causes 6-fold increases in the number of states of prestress. At the higher temperature, many of the fibers experience constrained buckling with characteristic small wavelength oscillations in their curvature.

Unified theoretical description of the kinetics of protein aggregation

Solution conditions chosen for the production of amyloid can also promote formation of significant extents of amorphous protein aggregate. In one interpretation, the amyloid and amorphous aggregation pathways are considered to be in competition with each other. An alternative conceptualization involves considering amorphous aggregation as an obligatory intermediate process of the amyloid formation pathway. Here, we review recently developed macroscopic-level theories of protein aggregation that unify these two competing models into a single paradigm. Key features of the unified model included (1) a description of the amorphous aggregate as a second liquid phase with the degree of liquid-like character determined by the mobility of the monomer within it, and (2) heterogeneous growth pathways based on nucleation, growth, and fragmentation of amyloid occurring within different phases and at their interfacial boundary. Limiting-case behaviors of the protein aggregation reaction, either singly involving amyloid or amorphous aggregate production, and mixed-case behaviors, involving competitive and/or facilitated growth of amorphous and amyloid species, are presented and reviewed in context. This review principally describes an approach developed by Hirota and Hall 2019 (Hirota, N. and Hall, D. 2019. Protein Aggregation Kinetics: A Unified Theoretical Description. Chapter 7 of 'Protein Solubility and Amorphous Aggregation: From Academic Research to Applications in Drug Discovery and Bioindustry' edited by Y. Kuroda and F. Arisaka. CMC Publishers). Sections of that work are translated from the original Japanese and republished here with the full permission of CMC Publishing Corporation.

Primary, Secondary, Tertiary and Quaternary Structure Levels in Linear Polysaccharides: From Random Coil, to Single Helix to Supramolecular Assembly

Polysaccharides are ubiquitous in nature and represent an essential class of biopolymers with multiple levels of conformation and structural hierarchy. However, a standardized structural nomenclature, as in the case of proteins, is still lacking due to uncertainty on their hierarchical organization. In this work we use carrageenans as model polysaccharides to demonstrate that several structural levels exist and can be unambiguously resolved by statistical analysis on high resolution Atomic Force Microscopy images, supported by spectroscopic, X-ray scattering and rheological techniques. In direct analogy with proteins, we identify primary, secondary, tertiary and quaternary structures. The structure-property relationship induced by monovalent ions for κ-, ι- and the non-gelling control λ-carrageenan is established from the single chain regime to the occurrence of hydrogels at higher concentrations. For κ-carrageenan in the presence of potassium, a disorder-order transition from random coil to single helix is first observed (secondary structure), followed by intrachain supercoiling events (tertiary structure) and macroscopic anisotropic domains which are parts of a network (quaternary structure) with tunable elasticity up to ∼10³ Pa. In contrast, κ-carrageenan in the presence of sodium only produces changes in secondary structure without supercoiling events, prior to formation of gels, highlighting the ion-specificity of the process. Loosely intertwined single helices are observed for ι-carrageenan in the presence of sodium and potassium chloride, providing an elastic mesh with many junction zones, while λ-carrageenan does not undergo any structural change. A generality of the observed behavior may be inferred by extending these observations to a distinct class of polysaccharides, the weak carboxylic polyelectrolyte Gellan gum. These results advance our understanding of ion-specific structural changes of polysaccharides and the physical mechanisms responsible for their gelation.

Amyloid fragments and their toxicity on neural cells

The formation of amyloid fibrils from soluble proteins is a common form of self-assembly phenomenon that has fundamental connections with biological functions and human diseases. Lysozyme was converted from its soluble native state into highly organized amyloid fibrils. Ultrasonic treatment was used to break amyloid fibrils to fibrillar fragments–seeds. Atomic force microscopy and fluorescence microscopy was employed to characterize the morphology of the amyloid assemblies and neural cells–amyloid complexes. Our results demonstrate that prefibrillar intermediated and their mixture with proteins exhibit toxicity, although native proteins and fibrils appear to have no effect on number of cells. Our findings confirm that innocuous hen lysozyme can be engineered to produce both cytotoxic fibrillar fragments and non-toxic mature amyloid fibrils. Our work further strengthens the claim that amyloid conformation, and not the identity of the protein, is key to cellular toxicity and the underlying specific cell death mechanism.

Progress and Opportunities in the Characterization of Cellulose - An Important Regulator of Cell Wall Growth and Mechanics

The plant cell wall is a dynamic network of several biopolymers and structural proteins including cellulose, pectin, hemicellulose and lignin. Cellulose is one of the main load bearing components of this complex, heterogeneous structure, and in this way, is an important regulator of cell wall growth and mechanics. Glucan chains of cellulose aggregate via hydrogen bonds and van der Waals forces to form long thread-like crystalline structures called cellulose microfibrils. The shape, size, and crystallinity of these microfibrils are important structural parameters that influence mechanical properties of the cell wall and these parameters are likely important determinants of cell wall digestibility for biofuel conversion. Cellulose-cellulose and cellulose-matrix interactions also contribute to the regulation of the mechanics and growth of the cell wall. As a consequence, much emphasis has been placed on extracting valuable structural details about cell wall components from several techniques, either individually or in combination, including diffraction/scattering, microscopy, and spectroscopy. In this review, we describe efforts to characterize the organization of cellulose in plant cell walls. X-ray scattering reveals the size and orientation of microfibrils; diffraction reveals unit lattice parameters and crystallinity. The presence of different cell wall components, their physical and chemical states, and their alignment and orientation have been identified by Infrared, Raman, Nuclear Magnetic Resonance, and Sum Frequency Generation spectroscopy. Direct visualization of cell wall components, their network-like structure, and interactions between different components has also been made possible through a host of microscopic imaging techniques including scanning electron microscopy, transmission electron microscopy, and atomic force microscopy. This review highlights advantages and limitations of different analytical techniques for characterizing cellulose structure and its interaction with other wall polymers. We also delineate emerging opportunities for future developments of structural characterization tools and multi-modal analyses of cellulose and plant cell walls. Ultimately, elucidation of the structure of plant cell walls across multiple length scales will be imperative for establishing structure-property relationships to link cell wall structure to control of growth and mechanics.

Confinement-Induced Ordering and Self-Folding of Cellulose Nanofibrils

Cellulose is a pervasive polymer, displaying hierarchical lengthscales and exceptional strength and stiffness. Cellulose's complex organization, however, also hinders the detailed understanding of the assembly, mesoscopic properties, and structure of individual cellulose building blocks. This study combines nanolithography with atomic force microscopy to unveil the properties and structure of single cellulose nanofibrils under weak geometrical confinement. By statistical analysis of the fibril morphology, it emerges that confinement induces both orientational ordering and self-folding of the fibrils. Excluded volume simulations reveal that this effect does not arise from a fibril population bias applied by the confining slit, but rather that the fibril conformation itself changes under confinement, with self-folding favoring fibril's free volume entropy. Moreover, a nonstochastics angular bending probability of the fibril kinks is measured, ruling out alternating amorphous-crystalline regions. These findings push forward the understanding of cellulose nanofibrils and may inspire the design of functional materials based on fibrous templates.

Amyloid Fibrils Length Controls Shape and Structure of Nematic and Cholesteric Tactoids

Amyloid fibrils offer the possibility of controlling their contour length, aspect ratio, and length distribution, without affecting other structural parameters. Here we show that a fine control in the contour length distribution of β-lactoglobulin amyloid fibrils, achieved by mechanical shear stresses of different levels, translates into the organization of tactoids of different shapes and morphologies. While longer fibrils lead to highly elongated nematic tactoids in an isotropic continuous matrix, only sufficiently shortened amyloid fibrils lead to cholesteric droplets. The progressive decrease in amyloid fibrils length leads to a linear decrease of the anchoring strength and homogeneous tactoid → bipolar tactoid → cholesteric droplet transitions. Upon fibrils length increase, we first find experimentally and predict theoretically a decrease of the cholesteric pitch, before full disappearance of the cholesteric phase. The latter is understood to arise from the decrease of the energy barrier separating cholesteric and nematic phases over thermal energy for progressively longer, semiflexible fibrils.

In Situ Observation of Alignment Templating by Seed Crystals in Highly Anisotropic Polymer Transistors

Due to the highly directional nature of transport in polymer-based organic field-effect transistors (OFETs), alignment of the polymer backbone can significantly affect device performance. While many methods of alignment have been detailed, the mechanism of alignment is rarely revealed-especially in cases of flow-induced alignment. Polymer aggregates are often observed in highly aligned systems, but their role is similarly unclear. Here, we present a comprehensive characterization of blade-coated P(NDI2OD-T2) (N2200) for OFET applications, including a rigorous, multimodal characterization of its in-plane alignment. Film thickness follows the expected power-law dependence on coating speed, while bulk polymer backbone orientation transitions from perpendicular to parallel to the coating direction as speed is increased. Charge carrier mobility >2 cm2/(V s) is achieved parallel to the coating direction for aligned N2200 coated at 5 mm/s and is found to be strongly correlated with the in-plane alignment of the fibrillar morphology at the film's surface, characterized with atomic force microscopy and near-edge X-ray absorption. We develop a model of N2200 crystal anisotropy through rotational scans of grazing incidence wide-angle X-ray scattering (GIWAXS) and use it to analyze simultaneous in situ GIWAXS and UV-vis reflectance data from polymer solutions coated at 5 mm/s. A small population of crystals align early in the drying process, but bulk alignment occurs very late in the drying process, likely mediated by a lyotropic liquid crystal phase transition templated by the aligned crystals. Our characterization also suggests that the majority of material in N2200 thin films is noncrystalline at these conditions.

Comparative study on foaming and emulsifying properties of different beta-lactoglobulin aggregates

Different beta-lactoglobulin aggregates have different foaming and emulsifying properties.

Adsorption and Interfacial Layer Structure of Unmodified Nanocrystalline Cellulose at Air/Water Interfaces

Nanocrystalline cellulose (NCC) is a promising biological nanoparticle for the stabilization of fluid interfaces.  However, the adsorption and interfacial layer structure of NCC are poorly understood as it is currently unknown how to form  NCC interfacial layers. Herein, we present parameters for the adsorption of unmodified NCC at the air-water (A/W) interface. Initial NCC adsorption is limited by diffusion, followed by monolayer saturation and decrease in surface tension at the time scale of hours. These results confirm the current hypothesis of a Pickering stabilization. NCC interfacial performance can be modulated by salt-induced charge screening, enhancing adsorption kinetics, surface load, and interfacial viscoelasticity. Adsorbed NCC layers were visualized by atomic force microscopy at planar Langmuir films and curved air bubbles, whereat NCC coverage was higher at curved interfaces. Structural analysis by neutron reflectometry revealed that NCC forms a discontinuous monolayer with crystallites oriented in the interfacial plane at a contact angle < 90°, favoring NCC desorption upon area compression. This provides the fundamental framework on the formation and structure of NCC layers at the A/W interface, paving the way for exploiting NCC interfacial stabilization for tailored colloidal materials.

Single-Molecule Study of Peptide Gel Dynamics Reveals States of Prestress

De novo peptide surfactant (I₃K) gels provide an ideal system to study the complex dynamics of lightly cross-linked semiflexible fibers because of their large contour lengths, simple chemistry, and slow dynamics. We used single-molecule fluorescence microscopy to record individual fibers and Fourier decomposition of the fiber dynamics to separate thermal contributions to the persistence length from compressive states of prestress (SPS). Our results show that SPS in the network depend strongly on peptide concentration, buffer, and pH and that the fibril energies in SPS follow a Lévy distribution. The presence of SPS in the network imply that collective states of self-stress are also present. Therefore, semiflexible polymer gels need to be considered as complex load-bearing structures and the mean field models for polymer gel elasticity and dynamics often applied to them will not be fully representative of the behavior at the nanoscale. We quantify the impact of cross-links on reptation tube dynamics, which provides a second population of tube fluctuations in addition to those expected for uncross-linked entangled solutions.

Physical and Toxicological Profiles of Human IAPP Amyloids and Plaques

Although much has been learned about the fibrillization kinetics, structure and toxicity of amyloid proteins, the properties of amyloid fibrils beyond the saturation phase are often perceived as chemically and biologically inert, despite evidence suggesting otherwise. To fill this knowledge gap, we examined the physical and biological characteristics of human islet amyloid polypeptide (IAPP) fibrils that were aged up to two months. Not only did aging decrease the toxicity of IAPP fibrils, but the fibrils also sequestered fresh IAPP and suppressed their toxicity in an embryonic zebrafish model. The mechanical properties of IAPP fibrils in different aging stages were probed by atomic force microscopy and sonication, which displayed comparable stiffness but age-dependent fragmentation, followed by self-assembly of such fragments into the largest lamellar amyloid structures reported to date. The dynamic structural and toxicity profiles of amyloid fibrils and plaques suggest that they play active, long-term roles in cell degeneration and may be a therapeutic target for amyloid diseases.

Quenched Stochastic Optical Reconstruction Microscopy (qSTORM) with Graphene Oxide

Quenched Stochastic Optical Reconstruction Microscopy (qSTORM) was demonstrated with graphene oxide sheets, peptides and bacteria; a method of contrast enhancement with super-resolution fluorescence microscopy. Individual sheets of graphene oxide (GO) were imaged with a resolution of 16 nm using the quenching of fluorescence emission by GO via its large Resonant Energy Transfer (RET) efficiency. The method was then extended to image self-assembled peptide aggregates (resolution 19 nm) and live bacterial cells (resolution 55 nm, the capsular structure of E. coli from urinary tract infections) with extremely low backgrounds and high contrasts (between one and two orders of magnitude contrast factor improvements that depended on the thickness of the graphene oxide layer used). Graphene oxide films combined with STORM imaging thus provide an extremely convenient method to image samples with large backgrounds due to non-specifically bound fluorophores (either due to excess labelling or autofluorescent molecules), which is a common occurrence in studies of both biological cells and soft-condensed matter. The GO quenches the fluorescence across a thin layer at distances of less than 15 nm. Graphene oxide films coated with thin layers (≤15 nm) of polystyrene, polymethylmethacrylate and polylysine are shown to be effective in producing high contrast qSTORM images, providing a convenient modulation of sample/substrate interactions. The GO coatings can also provide an increased image resolution and a factor of 2.3 improvement was observed with the peptide fibres using a feature of interest metric,when there was a large non-specifically bound background.

Programming Protein Polymerization with DNA

A strategy that utilizes DNA for controlling the association pathway of proteins is described. This strategy uses sequence-specific DNA interactions to program energy barriers for polymerization, allowing for either step-growth or chain-growth pathways to be accessed. Two sets of mutant green fluorescent protein (mGFP)-DNA monomers with single DNA modifications have been synthesized and characterized. Depending on the deliberately controlled sequence and conformation of the appended DNA, these monomers can be polymerized through either a step-growth or chain-growth pathway. Cryo-electron microscopy with Volta phase plate technology enables the visualization of the distribution of the oligomer and polymer products, and even the small mGFP-DNA monomers. Whereas cyclic and linear polymer distributions were observed for the step-growth DNA design, in the case of the chain-growth system linear chains exclusively were observed, and a dependence of the chain length on the concentration of the initiator strand was noted. Importantly, the chain-growth system possesses a living character whereby chains can be extended with the addition of fresh monomer. This work represents an important and early example of mechanistic control over protein assembly, thereby establishing a robust methodology for synthesizing oligomeric and polymeric protein-based materials with exceptional control over architecture.

Mitigating Human IAPP Amyloidogenesis In Vivo with Chiral Silica Nanoribbons

Amyloid fibrils generally display chirality, a feature which has rarely been exploited in the development of therapeutics against amyloid diseases. This study reports, for the first time, the use of mesoscopic chiral silica nanoribbons against the in vivo amyloidogenesis of human islet amyloid polypeptide (IAPP), the peptide whose aggregation is implicated in type 2 diabetes. The thioflavin T assay and transmission electron microscopy show accelerated IAPP fibrillization through elimination of the nucleation phase and shortening of the elongation phase by the nanostructures. Coarse-grained simulations offer complementary molecular insights into the acceleration of amyloid aggregation through their nonspecific binding and directional seeding with the nanostructures. This accelerated IAPP fibrillization translates to reduced toxicity, especially for the right-handed silica nanoribbons, as revealed by cell viability, helium ion microscopy, as well as zebrafish embryo survival, developmental, and behavioral assays. This study has implicated the potential of employing chiral nanotechnologies against the mesoscopic enantioselectivity of amyloid proteins and their associated diseases.

Graphene quantum dots against human IAPP aggregation and toxicity in vivo

The development of biocompatible nanomaterials has become a new frontier in the detection, treatment and prevention of human amyloid diseases. Here we demonstrated the use of graphene quantum dots (GQDs) as a potent inhibitor against the in vivo aggregation and toxicity of human islet amyloid polypeptide (IAPP), a hallmark of type 2 diabetes. GQDs initiated contact with IAPP through electrostatic and hydrophobic interactions as well as hydrogen bonding, which subsequently drove the peptide fibrillization off-pathway to eliminate the toxic intermediates. Such interactions, probed in vitro by a thioflavin T kinetic assay, fluorescence quenching, circular dichroism spectroscopy, a cell viability assay and in silico by discrete molecular dynamics simulations, translated to a significant recovery of embryonic zebrafish from the damage elicited by IAPP in vivo, as indicated by improved hatching as well as alleviated reactive oxygen species production, abnormality and mortality of the organism. This study points to the potential of using zero-dimensional nanomaterials for in vivo mitigation of a range of amyloidosis.

Environmentally Controlled Curvature of Single Collagen Proteins

The predominant structural protein in vertebrates is collagen, which plays a key role in extracellular matrix and connective tissue mechanics. Despite its prevalence and physical importance in biology, the mechanical properties of molecular collagen are far from established. The flexibility of its triple helix is unresolved, with descriptions from different experimental techniques ranging from flexible to semirigid. Furthermore, it is unknown how collagen type (homo- versus heterotrimeric) and source (tissue derived versus recombinant) influence flexibility. Using SmarTrace, a chain-tracing algorithm we devised, we performed statistical analysis of collagen conformations collected with atomic force microscopy to determine the protein's mechanical properties. Our results show that types I, II, and III collagens-the key fibrillar varieties-exhibit similar molecular flexibilities. However, collagen conformations are strongly modulated by salt, transitioning from compact to extended as KCl concentration increases in both neutral and acidic pH. Although analysis with a standard worm-like chain model suggests that the persistence length of collagen can attain a wide range of values within the literature range, closer inspection reveals that this modulation of collagen's conformational behavior is not due to changes in flexibility but rather arises from the induction of curvature (either intrinsic or induced by interactions with the mica surface). By modifying standard polymer theory to include innate curvature, we show that collagen behaves as an equilibrated curved worm-like chain in two dimensions. Analysis within the curved worm-like chain model shows that collagen's curvature depends strongly on pH and salt, whereas its persistence length does not. Thus, we find that triple-helical collagen is well described as semiflexible irrespective of source, type, pH, and salt environment. These results demonstrate that collagen is more flexible than its conventional description as a rigid rod, which may have implications for its cellular processing and secretion.

High-performance nanomaterials formed by rigid yet extensible cyclic β-peptide polymers

Organisms have evolved biomaterials with an extraordinary convergence of high mechanical strength, toughness, and elasticity. In contrast, synthetic materials excel in stiffness or extensibility, and a combination of the two is necessary to exceed the performance of natural biomaterials. We bridge this materials property gap through the side-chain-to-side-chain polymerization of cyclic β-peptide rings. Due to their strong dipole moments, the rings self-assemble into rigid nanorods, stabilized by hydrogen bonds. Displayed amines serve as functionalization sites, or, if protonated, force the polymer to adopt an unfolded conformation. This molecular design enhances the processability and extensibility of the biopolymer. Molecular dynamics simulations predict stick-slip deformations dissipate energy at large strains, thereby, yielding toughness values greater than natural silks. Moreover, the synthesis route can be adapted to alter the dimensions and displayed chemistries of nanomaterials with mechanical properties that rival nature.

Synthetic materials tend to excel in either stiffness or extensibility, whereas a combination of the two is necessary to exceed the performance of natural biomaterials. Here the authors present a bioinspired polymer consisting of cyclic β-peptide rings that is capable of transitioning between rigid and unfolded conformations on demand.

Heparin assisted assembly of somatostatin amyloid nanofibrils results in disordered precipitates by hindrance of protofilaments interactions

Amyloid nanofibrils are β-sheet rich protein or peptide assemblies that have pathological roles in over 20 neurodegenerative diseases, but also can have essential physiological roles. This wide variety of functions is likely to be due to subtle differences in amyloid structure and assembly mechanisms. Glycosaminoglycans (GAGs), like heparin, are frequently used in vitro to increase the kinetics of assembly of amyloid fibrils. However, little is known about the effects of adding large polymeric sugars on assembly mechanisms and amyloid nanostructures. Here, we provide insights into the kinetics, assembly mechanisms and structural effects of heparin on the self-assembly of a functional-amyloid forming neuropeptide hormone, somatostatin-14. We show that pure somatostatin-14 self-assembles into amyloid fibrils via the formation of antiparallel β-sheet networks, in a typical amyloid aggregation process. These fibrils then laterally assemble into ordered liquid crystalline structures through the generation of further parallel β-sheet networks. If heparin molecules are present, they intercalate between the peptide assemblies during the initial stages of aggregation. This intercalation screens electrostatic repulsions hindering the lateral association of protofilaments, preventing liquid crystal formation and resulting in the rapid formation of disordered micron scale precipitates. Our results show that aggregation promotors like heparin can have large effects not just on the kinetics of aggregation but also on assembly mechanisms, and the architecture of amyloid assemblies. Thus highlighting the dangers of using such polymeric sugars in fundamental studies of amyloid aggregation, especially when drawing conclusions on structure-function relationships or when investigating amyloid-based nanostructures as bionanomaterials.

Structure of DNA obtained during the ab initio synthesis by Bst DNA polymerase in the presence of the nicking endonuclease from Bacillus stearothermophilus (Nt.BstNBI)

Communicated by Ramaswamy H. Sarma.

Nanoscale inhibition of polymorphic and ambidextrous IAPP amyloid aggregation with small molecules

Understanding how small molecules interface amyloid fibrils on the nanoscale is of importance for developing therapeutic treatment against amyloid-based diseases. Here we show, for the first time, that human islet amyloid polypeptide (IAPP) in the fibrillar form is polymorphic and ambidextrous possessing multiple periodicities. Upon interfacing with small molecule epigallocatechin gallate (EGCG), IAPP aggregation was rendered off pathway assuming the form of soft and disordered clusters, while mature IAPP fibrils displayed kinks and branching but conserved the twisted fibril morphology. These nanoscale phenomena resulted from competitive interactions between EGCG and the IAPP amyloidogenic region, as well as end capping of the fibrils by the small molecule. This information is crucial to delineating IAPP toxicity implicated in type 2 diabetes and developing new inhibitors against amyloidogenesis.

Nanocellulose Fragmentation Mechanisms and Inversion of Chirality from the Single Particle to the Cholesteric Phase

Understanding how nanostructure and nanomechanics influence physical material properties on the micro- and macroscale is an essential goal in soft condensed matter research. Mechanisms governing fragmentation and chirality inversion of filamentous colloids are of specific interest because of their critical role in load-bearing and self-organizing functionalities of soft nanomaterials. Here we provide a fundamental insight into the self-organization across several length scales of nanocellulose, an important biocolloid system with wide-ranging applications as structural, insulating, and functional material. Through a combined microscopic and statistical analysis of nanocellulose fibrils at the single particle level, we show how mechanically and chemically induced fragmentations proceed in this system. Moreover, by studying the bottom-up self-assembly of fragmented carboxylated cellulose nanofibrils into cholesteric liquid crystals, we show via direct microscopic observations that the chirality is inverted from right-handed at the nanofibril level to left-handed at the level of the liquid crystal phase. These results improve our fundamental understanding of nanocellulose and provide an important rationale for its application in colloidal systems, liquid crystals, and nanomaterials.

Construction of a Holliday Junction in Small Circular DNA Molecules for Stable Motifs and Two-Dimensional Lattices

Design rules for DNA nanotechnology have been mostly learnt from using linear single-stranded (ss) DNA as the source material. For example, the core structure of a typical DAO (double crossover, antiparallel, odd half-turns) tile for assembling 2D lattices is constructed from only two linear ss-oligonucleotide scaffold strands, similar to two ropes making a square knot. Herein, a new type of coupled DAO (cDAO) tile and 2D lattices of small circular ss-oligonucleotides as scaffold strands and linear ss-oligonucleotides as staple strands are reported. A cDAO tile of cDAO-c64nt (c64nt: circular 64 nucleotides), shaped as a solid parallelogram, is constructed with a Holliday junction (HJ) at the center and two HJs at both poles of a c64nt; similarly, cDAO-c84nt, shaped as a crossed quadrilateral composed of two congruent triangles, is formed with a HJ at the center and four three-way junctions at the corners of a c84nt. Perfect 2D lattices were assembled from cDAO tiles: infinite nanostructures of nanoribbons, nanotubes, and nanorings, and finite nanostructures. The structural relationship between the visible lattices imaged by AFM and the corresponding invisible secondary and tertiary molecular structures of HJs, inclination angle of hydrogen bonds against the double-helix axis, and the chirality of the tile can be interpreted very well. This work could shed new light on DNA nanotechnology with unique circular tiles.

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 β-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 β-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.

Confinement-induced liquid crystalline transitions in amyloid fibril cholesteric tactoids

Chirality is ubiquitous in nature and plays crucial roles in biology, medicine, physics and materials science. Understanding and controlling chirality is therefore an important research challenge with broad implications. Unlike other chiral colloids, such as nanocellulose or filamentous viruses, amyloid fibrils form nematic phases but appear to miss their twisted form, the cholesteric or chiral nematic phases, despite a well-defined chirality at the single fibril level. Here we report the discovery of cholesteric phases in amyloids, using β-lactoglobulin fibrils shortened by shear stresses. The physical behaviour of these new cholesteric materials exhibits unprecedented structural complexity, with confinement-driven ordering transitions between at least three types of nematic and cholesteric tactoids. We use energy functional theory to rationalize these results and observe a chirality inversion from the left-handed amyloids to right-handed cholesteric droplets. These findings deepen our understanding of cholesteric phases, advancing their use in soft nanotechnology, nanomaterial templating and self-assembly.

Differential effects of silver and iron oxide nanoparticles on IAPP amyloid aggregation

Recent studies have shown promise on the use of small molecules and nanoparticles (NPs) for the inhibition of protein aggregation, a hallmark of neurodegenerative diseases and type 2 diabetes (T2D). Towards this end here we show the differential effects of silver and iron oxide nanoparticles (AgNPs and IONPs) on the mesoscopic properties of human islet amyloid polypeptide (IAPP) aggregation associated with T2D. Both citrate- and branched polyethyleneimine-coated AgNPs (c-AgNPs, bPEI-AgNPs) inhibited IAPP aggregation at 500 μg mL^-1, likely through electrostatic attraction and sequestering of IAPP monomers from fibrillation. In comparison, bare, brushed polyethylene glycol- and phosphorylcholine-grafted IONPs (bPEG-IONPs, bPC-IONPs) at 500 μg mL^-1 elicited no major effect on IAPP fibril contour length, while bPC-IONPs induced significant fibril softening and looping likely mediated by dipolar interactions. While monovalent Ag⁺ up to 50 μg mL^-1 showed no effect on the contour length or stiffness of IAPP fibrils, multivalent Fe³⁺ at 5 μg mL^-1 halted IAPP fibrillation likely through ion-peptide crosslinking. Except bPEI-AgNPs, all three types of IONPs and c-AgNPs at 100 μg mL^-1 alleviated IAPP toxicity in HEK293 cells indicating no clear correlation between protein aggregation and their induced cytotoxicity. This study demonstrates the complexity of protein aggregation intervened by NPs of different physicochemical properties and - together with existing literature - facilitates nanotechnological applications for mitigating amyloid-mediated pathologies.

Zinc-coordination and C-peptide complexation: a potential mechanism for the endogenous inhibition of IAPP aggregation

Aggregation of the highly amyloidogenic IAPP is endogenously inhibited inside beta-cell granules at millimolar concentrations. Combining in vitro experiments and computer simulations, we demonstrated that the stabilization of IAPP upon the formation of zinc-coordinated ion molecular complex with C-peptide might be important for the endogenous inhibition of IAPP aggregation.

Characterization of Amyloid Fibril Networks by Atomic Force Microscopy

Dense networks of amyloid nanofibrils fabricated from common globular proteins adsorbed to solid supports can improve cell adhesion, spreading and differentiation compared to traditional flat, stiff 2D cell culture substrates like Tissue Culture Polystyrene (TCPS). This is due to the fibrous, nanotopographic nature of the amyloid fibril networks and the fact that they closely mimic the mechanical properties and architecture of the extracellular matrix (ECM). However, precise cell responses are strongly dependent on the nanostructure of the network at the cell culture interface, thus accurate characterization of the immobilized network is important. Due to its exquisite lateral resolution and simple sample preparation techniques, Atomic Force Microscopy (AFM) is an ideal technique to characterize the fibril network morphology. Thus, here we describe a detailed protocol, for the characterization of amyloid fibril networks by tapping mode AFM.

Lysophosphatidylcholine modulates the aggregation of human islet amyloid polypeptide

Amyloid aggregation of human islet amyloid polypeptide (IAPP) is a hallmark of type 2 diabetes (T2D), a metabolic disease and a global epidemic. Although IAPP is synthesized in pancreatic β-cells, its fibrils and plaques are found in the extracellular space indicating a causative transmembrane process. Numerous biophysical studies have revealed that cell membranes as well as model lipid vesicles promote the aggregation of amyloid-β (associated with Alzheimer's), α-synuclein (associated with Parkinson's) and IAPP, through electrostatic and hydrophobic interactions between the proteins/peptides and lipid membranes. Using a thioflavin T kinetic assay, transmission electron microscopy, circular dichroism spectroscopy, discrete molecular dynamics simulations as well as free energy calculations here we show that micellar lysophosphatidylcholine (LPC), the most abundant lysophospholipid in the blood, inhibited the amyloid aggregation of IAPP through nonspecific interactions while elevating the α-helical peptide secondary structure. This surprising finding suggests a native protective mechanism against IAPP aggregation in vivo.

Methods to Characterize the Nanostructure and Molecular Organization of Amphiphilic Peptide Assemblies

Methods to characterize the nanostructure and molecular organization of aggregates of peptides such as amyloid or amphiphilic peptide assemblies are reviewed. We discuss techniques to characterize conformation and secondary structure including circular and linear dichroism and FTIR and Raman spectroscopies, as well as fluorescence methods to detect aggregation. NMR spectroscopy methods, especially solid-state NMR measurements to probe beta-sheet packing motifs, are also briefly outlined. Also discussed are scattering methods including X-ray diffraction and small-angle scattering techniques including SAXS (small-angle X-ray scattering) and SANS (small-angle neutron scattering) and dynamic light scattering. Imaging methods are direct methods to uncover features of peptide nanostructures, and we provide a summary of electron microscopy and atomic force microscopy techniques. Selected examples are highlighted showing data obtained using these techniques, which provide a powerful suite of methods to probe ordering from the molecular scale to the aggregate superstructure.

Characterization of Structural and Configurational Properties of DNA by Atomic Force Microscopy

We describe a method to extract quantitative information on DNA structural and configurational properties from high-resolution topographic maps recorded by atomic force microscopy (AFM). DNA molecules are deposited on mica surfaces from an aqueous solution, carefully dehydrated, and imaged in air in Tapping Mode. Upon extraction of the spatial coordinates of the DNA backbones from AFM images, several parameters characterizing DNA structure and configuration can be calculated. Here, we explain how to obtain the distribution of contour lengths, end-to-end distances, and gyration radii. This modular protocol can be also used to characterize other statistical parameters from AFM topographies.