Surface effects mediate self-assembly of amyloid-β peptides

Insights into the mechanism of peptide fibril growth on gold surface

Understanding the formation of β-fibrils over the gold surface is of paramount interest in nano-bio-medicinal Chemistry. The intricate mechanism of self-assembly of neurofibrillogenic peptides and their growth over the gold surface remains elusive, as experiments are limited in unveiling the microscopic dynamic details, in particular, at the early stage of the peptide aggregation. In this work, we carried out equilibrium molecular dynamics and enhanced sampling simulations to elucidate the underlying mechanism of the growth of an amyloid-forming sequence of tau fragments over the gold surface. Our results disclose that the collective intermolecular interactions between the peptide chains and peptides with the gold surface facilitate the peptide adsorption, followed by integration, finally leading to the fibril formation.

Impact of flexibility on the aggregation of polymeric macromolecules

Dependence of the dimerization probability and the aggregation behavior of polymeric macromolecules on their flexibility is studied using Langevin dynamics simulations. It is found that the dimerization probability is a non-monotonic function of the polymers persistence length. For a given value of inter-polymer attraction strength, semiflexible polymers have lower dimerization probability relative to flexible and rigid polymers of the same length. The threshold temperature of the formation of aggregates in a many-polymer system and its dependence on the polymers persistence length is also investigated. The simulation results of two- and many-polymer systems are in good agreement and show how the amount of flexibility affects the dimerization and the aggregation behaviors of polymeric macromolecules.

Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction

Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature. Because hierarchy gives rise to unique properties and functions, many have sought inspiration from nature when designing and fabricating hierarchical matter. More and more, however, nature's own high-information content building blocks, proteins, peptides, and peptidomimetics, are being coopted to build hierarchy because the information that determines structure, function, and interfacial interactions can be readily encoded in these versatile macromolecules. Here, we take stock of recent progress in the rational design and characterization of hierarchical materials produced from high-information content blocks with a focus on stimuli-responsive and "smart" architectures. We also review advances in the use of computational simulations and data-driven predictions to shed light on how the side chain chemistry and conformational flexibility of macromolecular blocks drive the emergence of order and the acquisition of hierarchy and also on how ionic, solvent, and surface effects influence the outcomes of assembly. Continued progress in the above areas will ultimately usher in an era where an understanding of designed interactions, surface effects, and solution conditions can be harnessed to achieve predictive materials synthesis across scale and drive emergent phenomena in the self-assembly and reconfiguration of high-information content building blocks.

Acquiring structural and mechanical information of a fibrous network through deep learning

Fibrous networks play an essential role in the structure and properties of a variety of biological and engineered materials, such as cytoskeletons, protein filament-based hydrogels, and entangled or crosslinked polymer chains. Therefore, insight into the structural features of these fibrous networks and their constituent filaments is critical for discovering the structure-property-function relationships of these material systems. In this paper, a fibrous network-deep learning system (FN-DLS) is established to extract fibrous network structure information from atomic force microscopy images. FN-DLS accurately assesses the structural and mechanical characteristics of fibrous networks, such as contour length, number of nodes, persistence length, mesh size and fractal dimension. As an open-source system, FN-DLS is expected to serve a vast community of scientists working on very diverse disciplines and pave the way for new approaches on the study of biological and synthetic polymer and filament networks found in current applied and fundamental sciences.

Effect of Surface-Chelated Cu2+ on Amyloid-β Peptide Fibrillation

Abnormal interactions of copper (Cu) ions with amyloid-β (Aβ) peptides are believed to play an important role in the pathogenesis of Alzheimer's disease (AD). However, there is still debate as to the exact role of Cu ions in Aβ amyloidosis despite extensive studies on Aβ-Cu interactions. Unlike previously reported works, we herein study the effect of surface-chelated Cu²⁺, rather than the more usual solution-phase dissolved Cu²⁺, on Aβ aggregation. Through the combination of single molecule fluorescent tracking, atomic force microscopy imaging experiments, and all-atom molecular dynamic simulations, we show that the surface-chelated Cu²⁺ dynamically interacts with Aβ chains, restricts their 2D-diffusivity on the surface, and retards their fibrillation, while the designated surfaces without Cu²⁺ facilitate the 2D-diffusivity of Aβ chains for better interpeptide interaction and promote Aβ fibrillation. We offer a microscopic molecular insight into the retardation mechanism of surface-chelated Cu²⁺ on Aβ fibrillation, suggesting that the surface-bound pools of metal ions are critical in AD progression and drug design.

Near-Wall Aggregation of Amyloidogenic Aβ 1-40 Peptide: Direct Observation by the FRET

The formation of amyloid fibrils is one of the variants of the self-organization of polypeptide chains. For the amyloid aggregation, the solution must be oversaturated with proteins. The interface of the liquid (solution) and solid (vessel walls) phases can trigger the adsorption of protein molecules, and the resulting oversaturation can initiate conformational transitions in them. In any laboratory experiment, we cannot exclude the presence of surfaces such as the walls of vessels, cuvettes, etc. However, in many works devoted to the study of amyloid formation, this feature is not considered. In our work, we investigated the behavior of the Aβ 1-40 peptide at the water–glass, water–quartz, and water–plastic interface. We carried out a series of simple experiments and showed that the Aβ 1-40 peptide is actively adsorbed on these surfaces, which leads to a significant interaction and aggregation of peptides. This means that the interface can be the place where the first amyloid nucleus appears. We suggest that this effect may also be one of the reasons for the difficulty of reproducing kinetic data when studying the aggregation of the amyloid of the Aβ 1-40 peptide and other amyloidogenic proteins

Spatial organization of protein aggregates on red blood cells as physical biomarkers of Alzheimer's disease pathology

Quantifying physical differences of protein aggregates implicated in Alzheimer’s disease (AD), in blood, could provide crucial information on disease stages. Here, red blood cells (RBCs) from 50 patients with neurocognitive complaints and 16 healthy individuals were profiled using an atomic force microscope (AFM). AFM measurements revealed patient age– and stage of neurocognitive disorder–dependent differences in size, shape, morphology, assembly, and prevalence of protein aggregates on RBCs, referred to as physical biomarkers. Crystals composed of fibrils were exclusively detected on RBCs for AD patients aged above 80 years. Fibril prevalence was negatively correlated with the cerebrospinal fluid (CSF) β-amyloid (Aβ) 42/40 ratio and was observed to be higher in the Aβ-positive patient category. Using a cutoff of ≥40% fibril prevalence, the CSF Aβ status was classified with 88% accuracy (sensitivity 100%, specificity 73%). The merits and challenges in integrating physical biomarkers in AD diagnosis are discussed.

Elongation rate and average length of amyloid fibrils in solution using isotope-labelled small-angle neutron scattering

We demonstrate a solution method that allows both elongation rate and average fibril length of assembling amyloid fibrils to be estimated. The approach involves acquisition of real-time neutron scattering data during the initial stages of seeded growth, using contrast matched buffer to make the seeds effectively invisible to neutrons. As deuterated monomers add on to the seeds, the labelled growing ends give rise to scattering patterns that we model as cylinders whose increase in length with time gives an elongation rate. In addition, the absolute intensity of the signal can be used to determine the number of growing ends per unit volume, which in turn provides an estimate of seed length. The number of ends did not change significantly during elongation, demonstrating that any spontaneous or secondary nucleation was not significant compared with growth on the ends of pre-existing fibrils, and in addition providing a method of internal validation for the technique. Our experiments on initial growth of alpha synuclein fibrils using 1.2 mg ml-1 seeds in 2.5 mg ml-1 deuterated monomer at room temperature gave an elongation rate of 6.3 ± 0.5 Å min-1, and an average seed length estimate of 4.2 ± 1.3 μm.

Spin coating mediated morphology modulation in self assembly of peptides

Controlling the morphology and nanostructure of self-assembled peptide molecules is of fundamental importance to chemistry and material science due to their bioactivity in both in vivo and in vitro settings, ability to act as templates for conjugating bio-recognition elements, hybrid supramolecular assembly, possible detection and treatment of diseases and so on. In this article, we show that spin coating, a widely utilized method for obtaining ultra-thin polymer films, has been utilised to modulate the self-assembly of peptide molecules, which has traditionally been achieved by chemical functionalisation of the molecules. With the specific example of diphenylalanine-based peptide molecules, we show that a variety of self-assembled architectures such as long fibrils, short fibrils, globules, nanodots, and so on, spanning over large areas can be obtained by simultaneously varying the spinning speed (RPM) and the solution concentration (Cp) during spin coating. We correlate the variation in morphology to a transition from spin dewetting at very low Cp (or high RPM) to the formation of continuous films at high Cp (or low RPM) during the initial stage of spin coating. We further show the generality of the approach by achieving distinct self-assembled morphologies with diphenylalanine analogues with different C-terminal and N-terminal groups by modulation of spin coating parameters, though the exact morphology obtained under identical coating conditions depends on the chemical nature of the peptide molecules. The work opens up a new possible route for creating complex peptide assemblies on demand by simultaneous control of molecular functionalisation and spin coating parameters vis - a - vis the applied centrifugal force.

Aβ aggregation behavior at interfaces with switchable wettability: a bioinspired perspective to understand amyloid formation

An amphiphilic taurocholic acid (TCA) doped polypyrrole (PPy) film (PPy/TCA) was used as a dynamic mimic membrane model to explore how switchable surface wettability influences amyloid aggregation. Our results indicate that the hydrophobic surface, not the hydrophilic surface, plays important roles in Aβ40 adsorption and aggregation.

Defining the Neuropathological Aggresome across in Silico, in Vitro, and ex Vivo Experiments

The loss of proteostasis over the life course is associated with a wide range of debilitating degenerative diseases and is a central hallmark of human aging. When left unchecked, proteins that are intrinsically disordered can pathologically aggregate into highly ordered fibrils, plaques, and tangles (termed amyloids), which are associated with countless disorders such as Alzheimer's disease, Parkinson's disease, type II diabetes, cancer, and even certain viral infections. However, despite significant advances in protein folding and solution biophysics techniques, determining the molecular cause of these conditions in humans has remained elusive. This has been due, in part, to recent discoveries showing that soluble protein oligomers, not insoluble fibrils or plaques, drive the majority of pathological processes. This has subsequently led researchers to focus instead on heterogeneous and often promiscuous protein oligomers. Unfortunately, significant gaps remain in how to prepare, model, experimentally corroborate, and extract amyloid oligomers relevant to human disease in a systematic manner. This Review will report on each of these techniques and their successes and shortcomings in an attempt to standardize comparisons between protein oligomers across disciplines, especially in the context of neurodegeneration. By standardizing multiple techniques and identifying their common overlap, a clearer picture of the soluble neuropathological aggresome can be constructed and used as a baseline for studying human disease and aging.

Modeling Effects of Surface Properties and Probe Density for Nanoscale Biosensor Design: A Case Study of DNA Hybridization near Surfaces

Electrochemical biosensors have extremely robust applications while offering ease of preparation, miniaturization, and tunability. By adjusting the arrangement and properties of immobilized probes on the sensor surface to optimize target-probe association, one can design highly sensitive and efficient sensors. In electrochemical nucleic acid biosensors, a self-assembled monolayer (SAM) is widely used as a tunable surface with inserted DNA or RNA probes to detect target sequences. The effects of inhomogeneous probe distribution across surfaces are difficult to study experimentally due to inadequate resolution. Regions of high probe density may inhibit hybridization with targets, and the magnitude of the effect may vary depending on the hybridization mechanism on a given surface. Another fundamental question concerns diffusion and hybridization of DNA taking place on surfaces and whether it speeds up or hinders molecular recognition. We used all-atom Brownian dynamics simulations to help answer these questions by simulating the hybridization process of single-stranded DNA (ssDNA) targets with a ssDNA probe on polar, nonpolar, and anionic SAMs at three different probe surface densities. Moreover, we simulated three tightly packed probe clusters by modeling clusters with different interprobe spacing on two different surfaces. Our results indicate that hybridization efficiency depends strongly on finding a balance that allows attractive forces to steer target DNA toward probes without anchoring it to the surface. Furthermore, we found that the hybridization rate becomes severely hindered when interprobe spacing is less than or equal to the target DNA length, proving the need for a careful design to both enhance target-probe association and avoid steric hindrance. We developed a general kinetic model to predict hybridization times and found that it works accurately for typical probe densities. These findings elucidate basic features of nanoscale biosensors, which can aid in rational design efforts and help explain trends in experimental hybridization rates at different probe densities.

Hyaluronan-carnosine conjugates inhibit Aβ aggregation and toxicity

Alzheimer’s disease is the most common neurodegenerative disorder. Finding a pharmacological approach that cures and/or prevents the onset of this devastating disease represents an important challenge for researchers. According to the amyloid cascade hypothesis, increases in extracellular amyloid-β (Aβ) levels give rise to different aggregated species, such as protofibrils, fibrils and oligomers, with oligomers being the more toxic species for cells. Many efforts have recently been focused on multi-target ligands to address the multiple events that occur concurrently with toxic aggregation at the onset of the disease. Moreover, investigating the effect of endogenous compounds or a combination thereof is a promising approach to prevent the side effects of entirely synthetic drugs. In this work, we report the synthesis, structural characterization and Aβ antiaggregant ability of new derivatives of hyaluronic acid (Hy, 200 and 700 kDa) functionalized with carnosine (Car), a multi-functional natural dipeptide. The bioactive substances (HyCar) inhibit the formation of amyloid-type aggregates of Aβ₄₂ more than the parent compounds; this effect is proportional to Car loading. Furthermore, the HyCar derivatives are able to dissolve the amyloid fibrils and to reduce Aβ-induced toxicity in vitro. The enzymatic degradation of Aβ is also affected by the interaction with HyCar.

Amyloid-β (Aβ42) Peptide Aggregation Rate and Mechanism on Surfaces with Widely Varied Properties: Insights from Brownian Dynamics Simulations

Amyloid-β (Aβ) plaques, which form by aggregation of harmless Aβ peptide monomers into larger fibrils, are characteristic of neurodegenerative disorders such as Alzheimer's disease. Efforts to treat Alzheimer's disease focus on stopping or reversing the aggregation process that leads to fibril formation. However, effective treatments are elusive due to certain unknown aspects of the process. Many hypotheses point to disruption of cell membranes by adsorbed Aβ monomers or oligomers, but how Aβ behaves and aggregates on surfaces of widely varying properties, such as those present in a cell, is unclear. Elucidating the effects of various surfaces on the dynamics of Aβ and the kinetics of the aggregation process from bulk solution to a surface-adsorbed multimer can help identify what drives aggregation, leading to new methods of intervention by inhibitory drugs or other means. In this work, we used all-atom Brownian dynamics simulations to study the association of two distinct Aβ42 monomer conformations with a surface-adsorbed or free-floating Aβ42 dimer. We calculated the association time, surface interaction energy, surface diffusion coefficient, surface residence time, and the mechanism of association on four different surfaces and two different bulk solution scenarios. In the presence of a surface, the majority of monomers underwent a two-dimensional surface-mediated association that depended primarily on an Aβ42 electrostatic interaction with the self-assembled monolayer (SAM) surfaces. Moreover, aggregation could be inhibited greatly by surfaces with high affinity for Aβ42 and heterogeneous charge distribution. Our results can be used to identify new opportunities for disrupting or reversing the Aβ42 aggregation process.

Complete aggregation pathway of amyloid β (1-40) and (1-42) resolved on an atomically clean interface

To visualize amyloid β (Aβ) aggregates requires an uncontaminated and artifact-free interface. This paper demonstrates the interface between graphene and pure water (verified to be atomically clean using tunneling microscopy) as an ideal platform for resolving size, shape, and morphology (measured by atomic force microscopy) of Aβ-40 and Aβ-42 peptide assemblies from 0.5 to 150 hours at a 5-hour time interval with single-particle resolution. After confirming faster aggregation of Aβ-42 in comparison to Aβ-40, a stable set of oligomers with a diameter distribution of ~7 to 9 nm was prevalently observed uniquely for Aβ-42 even after fibril appearance. The interaction energies between a distinct class of amyloid aggregates (dodecamers) and graphene was then quantified using molecular dynamics simulations. Last, differences in Aβ-40 and Aβ-42 networks were resolved, wherein only Aβ-42 fibrils were aligned through lateral interactions over micrometer-scale lengths, a property that could be exploited in the design of biofunctional materials.

Near-Infrared Light-Powered Janus Nanomotor Significantly Facilitates Inhibition of Amyloid-β Fibrillogenesis

Inspired by the natural motors, artificial nanomotors (NMs) have emerged as intelligent, advanced, and multifunctional nanoplatforms that can perform complex tasks in living environments. However, the functionalization of these fantastic materials is in its infancy, hindering the success of this booming field. Herein, an inhibitor-conjugated near-infrared (NIR) laser-propelled Janus nanomotor (JNM-I) was constructed and first applied in the modulation of amyloid-β protein (Aβ) aggregation which is highly associated with Alzheimer's disease (AD). Under NIR light illumination, JNM-I exhibited efficient propulsion through the "self-thermophoresis" effect, and the active motion of JNM-I increased the opportunity of the contacts between the immobilized inhibitors and Aβ species, leading to an intensification of JNM-I on modulating the on-pathway Aβ aggregation, as evidenced by the distinct changes of the amyloid morphology, conformation, and cytotoxicity. For example, with a NIR irradiation, 200 μg/mL of JNM-I increased the cultured SH-SY5Y cell viability from 68% to nearly 100%, but it only protected the cells to 89% viability without an NIR irradiation. Meanwhile, the NIR irradiation effectively improved the blood-brain barrier (BBB) penetration of JNM-I. Such a JNM-I has connected artificial nanomotors with protein aggregation and provided new insight into the potential applications of various nanomotors in the prevention and treatment of AD.

Functionalized DNA-spider silk nanohydrogels for controlled protein binding and release

Hydrogels are excellent scaffolds to accommodate sensitive enzymes in a protective environment. However, the lack of suitable immobilization techniques on substrates and the lack of selectivity to anchor a biocatalyst are major drawbacks preventing the use of hydrogels in bioanalytical devices. Here, nanofilm coatings on surfaces were made of a recombinant spider silk protein (rssp) to induce rssp self-assembly and thus the formation of fibril-based nanohydrogels. To functionalize spider silk nanohydrogels for bioselective binding of proteins, two different antithrombin aptamers were chemically conjugated with the rssp, thereby integrating the target-binding function into the nanohydrogel network. Human thrombin was selected as a sensitive model target, in which the structural integrity determines its activity. The chosen aptamers, which bind various exosites of thrombin, enabled selective and cooperative embedding of the protein into the nanohydrogels. The change of the aptamer secondary structure using complementary DNA sequences led to the release of active thrombin and confirmed the addressable functionalization of spider silk nanohydrogels.

Molecular Model for the Surface-Catalyzed Protein Self-Assembly

The importance of cell surfaces in the self-assembly of proteins is widely accepted. One biologically significant event is the assembly of amyloidogenic proteins into aggregates, which leads to neurodegenerative disorders like Alzheimer's and Parkinson's diseases. The interaction of amyloidogenic proteins with cellular membranes appears to dramatically facilitate the aggregation process. Recent findings indicate that, in the presence of surfaces, aggregation occurs at physiologically low concentrations, suggesting that interaction with surfaces plays a critical role in the disease-prone aggregation process. However, the molecular mechanisms behind the on-surface aggregation process remain unclear. Here, we provide a theoretical model that offers a molecular explanation. According to this model, monomers transiently immobilized to surfaces increase the local monomer protein concentration and thus work as nuclei to dramatically accelerate the entire aggregation process. This physical-chemical theory was verified by experimental studies, using mica surfaces, to examine the aggregation kinetics of amyloidogenic α-synuclein protein and non-amyloidogenic cytosine deaminase APOBEC3G.

A Novel Method to Measure the Effective Change of the Interfacial Energy due to Kinetic Self-Assembly of Amyloid Fibrils

Adsorbates growing a self-assembled layer on a solid-liquid interface can significantly change the effective interfacial energy at the solid surface. However, measuring the changes in the effective surface energy while these adsorbates accumulate is challenging, as static contact angle measurements can be affected by the motion and accumulation of these adsorbates at the droplet's boundary (coffee stain effects). In this report, we utilize a novel method that takes advantage of spin-induced dewetting to measure the change in the effective surface energy as the self-assembly progresses. We use a previously well-studied model system of self-assembled fibrils of amyloid-β (Aβ) peptides on the mica substrate to demonstrate the feasibility of this method. Using variations of terminal spin speeds and acceleration rates, we measure the terminal spin speed at which a wetting-dewetting transition (WDT) occurs on a surface that hosts self-assembled Aβ_12-28 fibrils. By comparing this speed with the WDT speed on the bare mica substrate, we can quantify the spreading coefficient and thus the effective change of the substrate's interfacial energy due to the adsorption of mobile peptides at various stages of the self-assembly. These measurements show that the surface becomes more hydrophilic as the self-assembly progresses and thus can explain previous observations that the self-assembly of this particular peptide system is self-limiting and stops before full surface coverage.

Steady, Symmetric, and Reversible Growth and Dissolution of Individual Amyloid-β Fibrils

Oligomers and fibrils of the amyloid-β (Aβ) peptide are implicated in the pathology of Alzheimer's disease. Here, we monitor the growth of individual Aβ40 fibrils by time-resolved in situ atomic force microscopy and thereby directly measure fibril growth rates. The measured growth rates in a population of fibrils that includes both single protofilaments and bundles of filaments are independent of the fibril thickness, indicating that cooperation between adjacent protofilaments does not affect incorporation of monomers. The opposite ends of individual fibrils grow at similar rates. In contrast to the "stop-and-go" kinetics that has previously been observed for amyloid-forming peptides, growth and dissolution of the Aβ40 fibrils are relatively steady for peptide concentration of 0-10 μM. The fibrils readily dissolve in quiescent peptide-free solutions at a rate that is consistent with the microscopic reversibility of growth and dissolution. Importantly, the bimolecular rate coefficient for the association of a monomer to the fibril end is significantly smaller than the diffusion limit, implying that the transition state for incorporation of a monomer into a fibril is associated with a relatively high free energy.

Effect of Terminal Modifications on the Adsorption and Assembly of hIAPP(20-29)

The assembly of peptides and proteins into nanoscale amyloid fibrils via formation of intermolecular β-sheets not only plays an important role in the development of degenerative diseases but also represents a promising approach for the synthesis of functional nanomaterials. In many biological and technological settings, peptide assembly occurs in the presence of organic and inorganic interfaces with different physicochemical properties. In an attempt to dissect the relative contributions of the different molecular interactions governing amyloid assembly at interfaces, we here present a systematic study of the effects of terminal modifications on the adsorption and assembly of the human islet amyloid polypeptide fragment hIAPP(20-29) at organic self-assembled monolayers (SAMs) presenting different functional groups (cationic, anionic, polar, or hydrophobic). Using a selection of complementary in situ and ex situ analytical techniques, we find that even this well-defined and comparatively simple model system is governed by a rather complex interplay of electrostatic interactions, hydrophobic interactions, and hydrogen bonding, resulting in a plethora of observations and dependencies, some of which are rather counterintuitive. In particular, our results demonstrate that terminal modifications can have tremendous effects on peptide adsorption and assembly dynamics, as well as aggregate morphology and molecular structure. The effects exerted by the terminal modifications can furthermore be modulated in nontrivial ways by the physicochemical properties of the SAM surface. Therefore, terminal modifications are an important factor to consider when conducting and comparing peptide adsorption and aggregation studies and may represent an additional parameter for guiding the assembly of peptide-based nanomaterials.

Microwave-induced formation of oligomeric amyloid aggregates

Amyloid aggregates have emerged as a significant hallmark of neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Although it has been recently reported that microwave heating induces amyloid aggregation compared with conventional heating methods, the mechanism of amyloid aggregate induction has remained unclear. In this study, we investigated the formation of oligomeric amyloid aggregates (OAAs) by microwave irradiation at microscale volumes of solution. Microwave irradiation of protein monomer solution triggered rapid formation of OAAs within 7 min. We characterized the formation of OAAs using atomic force microscopy, thioflavin T fluorescent assay and circular dichroism. In the microwave system, we also investigated the inhibitory effect on the formation of amyloid aggregates by L-ascorbic acid as well as enhanced amyloid aggregation by silver nanomaterials such as nanoparticles and nanowires. We believe that microwave technology has the potential to facilitate the study of amyloid aggregation in the presence of chemical agents or nanomaterials.

Kinetics of Surface-Mediated Fibrillization of Amyloid-β (12-28) Peptides

Surfaces or interfaces are considered to be key factors in facilitating the formation of amyloid fibrils under physiological conditions. In this report, we study the kinetics of the surface-mediated fibrillization (SMF) of an amyloid-β fragment (Aβ_12-28) on mica. We employ a spin-coating-based drying procedure to control the exposure time of the substrate to a low-concentration peptide solution and then monitor the fibril growth as a function of time via atomic force microscopy (AFM). The evolution of surface-mediated fibril growth is quantitatively characterized in terms of the length histogram of imaged fibrils and their surface concentration. A two-dimensional (2D) kinetic model is proposed to numerically simulate the length evolution of surface-mediated fibrils by assuming a diffusion-limited aggregation (DLA) process along with size-dependent rate constants. We find that both monomer and fibril diffusion on the surface are required to obtain length histograms as a function of time that resemble those observed in experiments. The best-fit simulated data can accurately describe the key features of experimental length histograms and suggests that the mobility of loosely bound amyloid species is crucial in regulating the kinetics of SMF. We determine that the mobility exponent for the size dependence of the DLA rate constants is α = 0.55 ± 0.05, which suggests that the diffusion of loosely bound surface fibrils roughly depends on the inverse of the square root of their size. These studies elucidate the influence of deposition rate and surface diffusion on the formation of amyloid fibrils through SMF. The method used here can be broadly adopted to study the diffusion and aggregation of peptides or proteins on various surfaces to investigate the role of chemical interactions in two-dimensional fibril formation and diffusion.

Adsorption and Fibrillization of Islet Amyloid Polypeptide at Self-Assembled Monolayers Studied by QCM-D, AFM, and PM-IRRAS

Aggregation and fibrillization of human islet amyloid polypeptide (hIAPP) plays an important role in the development of type 2 diabetes mellitus. Understanding the interaction of hIAPP with interfaces such as cell membranes at a molecular level therefore represents an important step toward new therapies. Here, we investigate the fibrillization of hIAPP at different self-assembled alkanethiol monolayers (SAMs) by quartz crystal microbalance with dissipation monitoring (QCM-D), atomic force microscopy (AFM), and polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS). We find that hydrophobic interactions with the CH₃-terminated SAM tend to retard hIAPP fibrillization compared to the carboxylic acid-terminated SAM where attractive electrostatic interactions lead to the formation of a three-dimensional network of interwoven fibrils. At the hydroxyl- and amino-terminated SAMs, fibrillization appears to be governed by hydrogen bonding between the peptide and the terminating groups which may even overcome electrostatic repulsion. These results thus provide fundamental insights into the molecular mechanisms governing amyloid assembly at interfaces.

Self-assembly of two hydrophobins from marine fungi affected by interaction with surfaces

Hydrophobins are amphiphilic fungal proteins endowed with peculiar characteristics, such as a high surface activity and an interface triggered self-assembly. Several applications of these proteins have been proposed in the food, cosmetics and biomedical fields. Moreover, their use as proteinaceous coatings can be effective for materials and nanomaterials applications. The discovery of novel hydrophobins with diverse properties may be advantageous from both the scientific and industrial points of view. Stressful environmental conditions of fungal growth may induce the production of proteins with peculiar features. Two Class I hydrophobins from fungi isolated from marine environment have been recently purified. Herein, their propensity to aggregate forming nanometric fibrillar structures has been compared, using different techniques, such as circular dichroism, dynamic light scattering and Thioflavin T fluorescence assay. Furthermore, TEM and AFM images indicate that the interaction of these proteins with specific surfaces, are crucial in the formation of amyloid fibrils and in the assembly morphologies. These self-assembling proteins show promising properties as bio-coating for different materials via a green process. Biotechnol. Bioeng. 2017;114: 2173-2186. © 2017 Wiley Periodicals, Inc.

Potential Artifacts in Sample Preparation Methods Used for Imaging Amyloid Oligomers and Protofibrils due to Surface-Mediated Fibril Formation

Accurate imaging of nanometer-sized structures and morphologies is essential to characterizing amyloid species formed at various stages of amyloid aggregation. In this article, we examine the effect of different drying procedures on the final morphology of surface-mediated fibrils formed during the incubation period, which may then be mistaken as oligomers or protofibrils intentionally formed in solution for a particular study. Atomic force microscopy results show that some artifacts, such as globules, flakelike structures, and even micrometer-long fibrils, can be produced under various drying conditions. We also demonstrate that one can prevent drying artifacts by using an appropriate spin-coating procedure to dry amyloid samples. This procedure can bypass the wetting/dewetting transition of the liquid layer during the drying process and preserve the structure of interest on the substrate without generating drying artifacts.

Self-Assembly, Dynamics, and Polymorphism of hIAPP(20-29) Aggregates at Solid-Liquid Interfaces

The misfolding and subsequent assembly of proteins and peptides into insoluble amyloid structures play important roles in the development of numerous diseases. The dynamics of self-assembly and the morphology of the resulting aggregates critically depend on various environmental factors and especially on the presence of interfaces. Here, we show in detail how the presence of surfaces with different physicochemical properties influences the assembly dynamics and especially the aggregate morphology of hIAPP(20-29), an amyloidogenic fragment of the peptide hormone human islet amyloid polypeptide (hIAPP), which is involved in the development of type 2 diabetes. Time-lapse atomic force microscopy is employed to study the assembly dynamics of hIAPP(20-29) and the morphology of the resulting aggregates in bulk solution as well as at hydrophilic and hydrophobic model surfaces. We find that the presence of hydrophilic mica surfaces promotes fibrillation when compared with the assembly in bulk solution and results in a more pronounced polymorphism. Three fibrillar species are found to coexist on the mica surface, that is, straight, coiled, and ribbon-like fibrils, whereas only the straight and coiled fibrils are observed in bulk solution after comparable incubation times. In addition, the straight and coiled fibrils assembled at the mica surface have significantly different dimensions compared with those assembled in bulk solution. The three fibrillar species found on the mica surface most likely form independently by lateral association of arbitrary numbers of protofibrils with about 2 nm height. On hydrophobic hydrocarbon surfaces, fibrillation is retarded but not completely suppressed, in contrast to previous observations for full-length hIAPP(1-37). Our results show that peptide-surface interactions may induce diverse, peptide-specific alterations of amyloid assembly dynamics and fibrillar polymorphism. They may therefore contribute to a deeper understanding of the molecular processes that govern amyloid aggregation at different surfaces.

Surface-induced assembly of sophorolipids

The surface self-assembly properties of acidic sophorolipids, a bolaform microbial glycolipid with pH-responsive properties, were studied based on the chemical nature of the support and pH of the solution.

Characterizing the Effect of Multivalent Conjugates Composed of Aβ-Specific Ligands and Metal Nanoparticles on Neurotoxic Fibrillar Aggregation

Therapeutically active small molecules represent promising nonimmunogenic alternatives to antibodies for specifically targeting disease-relevant receptors. However, a potential drawback compared to antibody-antigen interactions may be the lower affinity of small molecules toward receptors. Here, we overcome this low-affinity problem by coating the surface of nanoparticles (NPs) with multiple ligands. Specifically, we explored the use of gold and platinum nanoparticles to increase the binding affinity of Aβ-specific small molecules to inhibit Aβ peptide aggregation into fibrils in vitro. The interactions of bare NPs, free ligands, and NP-bound ligands with Aβ are comprehensively studied via physicochemical methods (spectroscopy, microscopy, immunologic tests) and cell assays. Reduction of thioflavin T fluorescence, as an indicator for β-sheet content, and inhibition of cellular Aβ excretion are even more effective with NP-bound ligands than with the free ligands. The results from this study may have implications in the development of therapeutics for treating Alzheimer's disease.

Self-assembly mechanisms of nanofibers from peptide amphiphiles in solution and on substrate surfaces

We report the investigation of the self-assembly mechanism of nanofibers, using a small peptide amphiphile (NapFFKYp) as a model. Combining experimental and simulation methods, we identify the self-assembly pathways in the solution and on the substrates, respectively. In the solution, peptide amphiphiles undergo the nucleation process to grow into nanofibers. The nanofibers can further twist into high-ordered nanofibers with aging. On the substrates, peptide amphiphiles form nanofibers and nanosheet structures simultaneously. This surface-induced nanosheet consists of rod-like structures, and its thickness is substrate-dependent. Most intriguingly, water can transform the nanosheet into the nanofiber. Molecular dynamic simulation suggests that hydrophobic and ion-ion interactions are dominant forces during the self-assembly process.

Tuning self-assembled morphology of the Aβ(16-22) peptide by substitution of phenylalanine residues

The effects of the two phenylalanine (Phe) residues in the blocked Aβ(16-22) peptide on its self-assembly have been investigated by replacing both of them with two cyclohexylalanines (Chas) or two phenylglycines (Phgs). TEM and SANS studies revealed that the flat and wide nanoribbons of Aβ(16-22) were transformed into thin nanotubes when replaced with Chas, and thinner and twisted nanofibrils when replaced with Phgs. The red-shifting degree of characteristic CD peaks suggested an increased twisting in the self-assembly of the derivative peptides, especially in the case of Ac-KLV(Phg)(Phg)AE-NH2. Furthermore, molecular dynamics (MD) simulations also indicated the increasing trend in twisting when Chas or Phgs were substituted for Phes. These results demonstrated that the hydrophobic interactions and spatial conformation between Cha residues were sufficient to cause lateral association of β-sheets to twisted/helical nanoribbons, which finally developed into nanotubes, while for Phg residue, the loss of the rotational freedom of the aromatic ring induced much stronger steric hindrance for the lateral stacking of Ac-KLV(Phg)(Phg)AE-NH2 β-sheets, eventually leading to the nanofibril formation. This study thus demonstrates that both the aromatic structure and the steric conformation of Phe residues are crucial in Aβ(16-22) self-assembly, especially in the significant lateral association of β-sheets.

Self-assembled nanomaterials based on beta (β(3)) tetrapeptides

β(3)-amino acid based polypeptides offer a unique starting material for the design of self-assembled nanostructures such as fibres and hierarchical dendritic assemblies, due to their well-defined helical geometry in which the peptide side chains align at 120° due to the 3.0-3.1 residue pitch of the helix. In a previous work we have described the head-to-tail self-assembly of N-terminal acetylated β(3)-peptides into infinite helical nanorods that was achieved by designing a bioinspired supramolecular self-assembly motif. Here we describe the effect of consecutively more polar side chains on the self-assembly characteristics of β(3)-tetrapeptides Ac-β (3)Ala-β(3)Leu-β(3)Ile-β(3)Ala (Ac-β(3)[ALIA]), Ac-β(3)Ser-β(3)Leu-β(3)Ile-β(3)Ala (Ac-β(3)[SLIA]) and Ac-β (3)Lys-β (3)Leu-β(3)Ile-β (3)Glu (Ac-β(3)[KLIE]). β(3)-tetrapeptides complete 1 1/3 turns of the helix: thus in the oligomeric form the side chain positions shift 120° with each added monomer, forming a regular periodic pattern along the nanorod. Dynamic light scattering (DLS) measurements confirmed that these peptides self-assemble even in highly polar solvents such as water and DMSO, while diffusion-ordered NMR spectroscopy revealed the presence of a substantial monomeric population. Temperature dependence of the size distribution in DLS measurements suggests a dynamic equilibrium between monomers and oligomers. Solution casting produced distinct fibrillar deposits after evaporating the solvent. In the case of the apolar Ac-β(3)[ALIA] the longitudinal helix morphology gives rise to geometrically defined (∼70°) junctions between fibres, forming a mesh that opens up possibilities for applications e.g. in tissue scaffolding. The deposits of polar Ac-β(3)[SLIA] and Ac-β(3)[KLIE] exhibit fibres in regular parallel alignment over surface areas in the order of 10 μm.

Quantitative analysis of amyloid polymorphism using height histograms to correct for tip convolution effects in atomic force microscopy imaging

Development of a statistical height analysis method to study amyloid polymorphism.

Cell-Membrane-Mimicking Lipid-Coated Nanoparticles Confer Raman Enhancement to Membrane Proteins and Reveal Membrane-Attached Amyloid-β Conformation

Identifying the structures of membrane bound proteins is critical to understanding their function in healthy and diseased states. We introduce a surface enhanced Raman spectroscopy technique which can determine the conformation of membrane-bound proteins, at low micromolar concentrations, and also in the presence of a substantial membrane-free fraction. Unlike conventional surface enhanced Raman spectroscopy, our approach does not require immobilization of molecules, as it uses spontaneous binding of proteins to lipid bilayer-encapsulated Ag nanoparticles. We apply this technique to probe membrane-attached oligomers of Amyloid-β40 (Aβ40), whose conformation is keenly sought in the context of Alzheimer's disease. Isotope-shifts in the Raman spectra help us obtain secondary structure information at the level of individual residues. Our results show the presence of a β-turn, flanked by two β-sheet regions. We use solid-state NMR data to confirm the presence of the β-sheets in these regions. In the membrane-attached oligomer, we find a strongly contrasting and near-orthogonal orientation of the backbone H-bonds compared to what is found in the mature, less-toxic Aβ fibrils. Significantly, this allows a "porin" like β-barrel structure, providing a structural basis for proposed mechanisms of Aβ oligomer toxicity.