Structural and functional diversity among amyloid proteins: Agents of disease, building blocks of biology, and implications for molecular engineering

CryoEM reveals the complex self-assembly of a chemically driven disulfide hydrogel

Inspired by the adaptability of biological materials, a variety of synthetic, chemically driven self-assembly processes have been developed that result in the transient formation of supramolecular structures. These structures form through two simultaneous reactions, forward and backward, which generate and consume a molecule that undergoes self-assembly. The dynamics of these assembly processes have been shown to differ from conventional thermodynamically stable molecular assemblies. However, the evolution of nanoscale morphologies in chemically driven self-assembly and how they compare to conventional assemblies has not been resolved. Here, we use a chemically driven redox system to separately carry out the forward and backward reactions. We analyze the forward and backward reactions both sequentially and synchronously with time-resolved cryogenic transmission electron microscopy (cryoEM). Quantitative image analysis shows that the synchronous process is more complex and heterogeneous than the sequential process. Our key finding is that a thermodynamically unstable stacked nanorod phase, briefly observed in the backward reaction, is sustained for ∼6 hours in the synchronous process. Kinetic Monte Carlo modeling show that the synchronous process is driven by multiple cycles of assembly and disassembly. The collective data suggest that chemically driven self-assembly can create sustained morphologies not seen in thermodynamically stable assemblies by kinetically stabilizing transient intermediates. This finding provides plausible design principles to develop and optimize supramolecular materials with novel properties.

ECAmyloid: An amyloid predictor based on ensemble learning and comprehensive sequence-derived features

Amyloid fibrils formed by the mis-aggregation of amyloid proteins can lead to neuronal degenerations in the Alzheimer's disease. Predicting amyloid proteins not only contributes to understanding physicochemical properties and formation mechanism of amyloid proteins, but also has significant implications in the amyloid disease treatment and the development of a new purpose for amyloid materials. In this study, an ensemble learning model with sequence-derived features, ECAmyloid, is proposed to identify amyloids. The sequence-derived features including Pseudo Position Specificity Score Matrix (Pse-PSSM), Split Amino Acid Composition (SAAC), Solvent Accessibility (SA), and Secondary Structure Information (SSI) are employed to incorporate sequence composition, evolutionary and structural information. The individual learners of the ensemble learning model are selected by an increment classifier selection strategy. The final prediction results are determined by voting of prediction results of multiple individual learners. In view of the imbalanced benchmark dataset, the Synthetic Minority Over-sampling Technique (SMOTE) is adopted to generate positive samples. To eliminate irrelevant features and redundant features, correlation-based feature subset (CFS) selection combined with a heuristic search strategy is performed to obtain the optimal feature subset. Experimental results indicate that the ensemble classifier achieves an accuracy of 98.29%, a sensitivity of 0.992, a specificity of 0.974 on the training dataset using the 10-fold cross validation, far higher than the results obtained by its individual learners. Compared with the original feature set, the accuracy, sensitivity, specificity, MCC, F1-score, G-Mean of the ensemble method trained by the optimal feature subset are improved by 1.05%, 0.012, 0.01, 0.021, 0.011 and 0.011, respectively. Moreover, the comparison results with existing methods on two same independent test datasets demonstrate that the proposed method is an effective and promising predictor for large-scale determination of amyloid proteins. The data and code used to develop ECAmyloid has been shared to Github, and can be freely downloaded at https://github.com/KOALA-L/ECAmyloid.git.

Developments in Trapped Ion Mobility Mass Spectrometry to Probe the Early Stages of Peptide Aggregation

Ion mobility mass spectrometry (IM-MS) has proven to be an excellent method to characterize the structure of amyloidogenic protein and peptide aggregates, which are formed in coincidence with the development of neurodegenerative diseases. However, it remains a challenge to obtain detailed structural information on all conformational intermediates, originating from the early onset of those pathologies, due to their complex and heterogeneous environment. One way to enhance the insights and the identification of these early stage oligomers is by employing high resolution ion mobility mass spectrometry experiments. This would allow us to enhance the mobility separation and MS characterization. Trapped ion mobility spectrometry (TIMS) is an ion mobility technique known for its inherently high resolution and has successfully been applied to the analysis of protein conformations among others. To obtain conformational information on fragile peptide aggregates, the instrumental parameters of the TIMS-Quadrupole-Time-of-Flight mass spectrometer (TIMS-qToF-MS) have to be optimized to allow the study of intact aggregates and ensure their transmission toward the detector. Here, we investigate the suitability and application of TIMS to probe the aggregation process, targeting the well-characterized M307-N319 peptide segment of the TDP-43 protein, which is involved in the development of amyotrophic lateral sclerosis. By studying the influence of key parameters over the full mass spectrometer, such as source temperature, applied voltages or RFs among others, we demonstrate that by using an optimized instrumental method TIMS can be used to probe peptide aggregation.

The anti-platelet drug ticlopidine inhibits FapC fibrillation and biofilm production: Highlighting its antibiotic activity

Multidrug resistance of bacteria and persistent infections related to biofilms, as well as the low availability of new antibacterial drugs, make it urgent to develop new antibiotics. Here, we evaluate the antibacterial and anti-biofilm properties of ticlopidine (TP), an anti-platelet aggregation drug, TP showed antibacterial activity against both gram-positive (MRSA) and gram-negative (E. coli, and P. aeruginosa) bacteria over a long treatment period. TP significantly reduced the survival of gram-negative bacteria in human blood though impact on gram-positives was more limited. TP may cause death in MRSA by inhibiting staphyloxanthin pigment synthesis, leading to oxidative stress, while scanning electron microscopy imaging indicate a loss of membrane integrity, damage, and consequent death due to lysis in gram-negative bacteria. TP showed good anti-biofilm activity against P. aeruginosa and MRSA, and a stronger biofilm degradation activity on P. aeruginosa compared to MRSA. Measuring fluorescence of the amyloid-reporter Thioflavin T (ThT) in biofilm implicated inhibition of amyloid formation as part of TP activity. This was confirmed by assays on the purified protein in P. aeruginosa, FapC, whose fibrillation kinetics was inhibited by TP. TP prolonged the lag phase of aggregation and reduced the subsequent growth rate and prolonging the lag phase to very long times provides ample opportunity to exert TP's antibacterial effect. We conclude that TP shows activity as an antibiotic against both gram-positive and gram-negative bacteria thanks to a broad range of activities, targeting bacterial metabolic processes, cellular structures and the biofilm matrix.

The role of α-sheet structure in amyloidogenesis: characterization and implications

Amyloid diseases are linked to protein misfolding whereby the amyloidogenic protein undergoes a conformational change, aggregates and eventually forms amyloid fibrils. While the amyloid fibrils and plaques are hallmarks of these diseases, they typically form late in the disease process and do not correlate with disease. Instead, there is growing evidence that smaller, soluble toxic oligomers form prior and appear to be early triggers of the molecular pathology underlying these diseases. Nearly 20 years ago, we proposed the α-sheet hypothesis after discovering that the early conformational changes observed during atomistic molecular dynamics simulations involve the formation of a non-standard protein structure, α-sheet. Furthermore, we proposed that toxic oligomers contain α-sheet structure and that preferentially targeting this structure could neutralize the toxicity, prevent further aggregation and serve as the basis for early detection of disease. Here, we present the origin of the α-sheet hypothesis and describe α-sheet structure and the corresponding mechanisms of conversion. We discuss experimental studies demonstrating that both mammalian and bacterial amyloid systems form α-sheet oligomers before converting to conventional β-sheet fibrils. Furthermore, we show that the process can be inhibited with de novo designed α-sheet peptides complementary to the structure in the toxic oligomers.

Molecular dynamics study on the effects of charged amino acid distribution under low pH condition to the unfolding of hen egg white lysozyme and formation of beta strands

Aggregation of unfolded or misfolded proteins into amyloid fibrils can cause various diseases in humans. However, the fibrils synthesized in vitro can be developed toward useful biomaterials under some physicochemical conditions. In this study, atomistic molecular dynamics simulations were performed to address the mechanism of beta-sheet formation of the unfolded hen egg-white lysozyme (HEWL) under a high temperature and low pH. Simulations of the protonated HEWL at pH 2 and the non-protonated HEWL at pH 7 were performed at the highly elevated temperature of 450 K to accelerate the unfolding, followed by the 333 K temperature to emulate some previous in vitro studies. The simulations showed that HEWL unfolded faster, and higher beta-strand contents were observed at pH 2. In addition, one of the simulation replicas at pH 2 showed that the beta-strand forming sequence was consistent with the ‘K-peptide’, proposed as the core region for amyloidosis in previous experimental studies. Beta-strand formation mechanisms at the earlier stage of amyloidosis were explained in terms of the radial distribution of the amino acids. The separation between groups of positively charged sidechains from the hydrophobic core corresponded to the clustering of the hydrophobic residues and beta-strand formation.

The growth of marine fungi on seaweed polysaccharides produces cerato-platanin and hydrophobin self-assembling proteins

The marine fungi Paradendryphiela salina and Talaromyces pinophilus degrade and assimilate complex substrates from plants and seaweed. Additionally, these fungi secrete surface-active proteins, identified as cerato-platanins and hydrophobins. These hydrophobic proteins have the ability to self-assemble forming amyloid-like aggregates and play an essential role in the growth and development of the filamentous fungi. It is the first time that one cerato-platanin (CP) is identified and isolated from P. salina (PsCP) and two Class I hydrophobins (HFBs) from T. pinophilus (TpHYD1 and TpHYD2). Furthermore, it is possible to extract cerato-platanins and hydrophobins using marine fungi that can feed on seaweed biomass, and through a submerged liquid fermentation process. The propensity to aggregate of these proteins has been analyzed using different techniques such as Thioflavin T fluorescence assay, Fourier-transform Infrared Spectroscopy, and Atomic Force Microscopy. Here, we show that the formation of aggregates of PsCP and TpHYD, was influenced by the carbon source from seaweed. This study highlighted the potential of these self-assembling proteins generated from a fermentation process with marine fungi and with promising properties such as conformational plasticity with extensive applications in biotechnology, pharmacy, nanotechnology, and biomedicine.

Recent developments in sustainably sourced protein-based biomaterials

Research into the development of sustainable biomaterials is increasing in both interest and global importance due to the increasing demand for materials with decreased environmental impact. This research field utilises natural, renewable resources to develop innovative biomaterials. The development of sustainable biomaterials encompasses the entire material life cycle, from desirable traits, and environmental impact from production through to recycling or disposal. The main objective of this review is to provide a comprehensive definition of sustainable biomaterials and to give an overview of the use of natural proteins in biomaterial development. Proteins such as collagen, gelatin, keratin, and silk, are biocompatible, biodegradable, and may form materials with varying properties. Proteins, therefore, provide an intriguing source of biomaterials for numerous applications, including additive manufacturing, nanotechnology, and tissue engineering. We give an insight into current research and future directions in each of these areas, to expand knowledge on the capabilities of sustainably sourced proteins as advanced biomaterials.

Edge Strand Dissociation and Conformational Changes in Transthyretin under Amyloidogenic Conditions

During amyloidogenesis, proteins undergo conformational changes that allow them to aggregate and assemble into insoluble, fibrillar structures. Soluble oligomers that form during this process typically contain 2-24 monomeric subunits and are cytotoxic. Before the formation of these soluble oligomers, monomeric species first adopt aggregation-competent conformations. Knowledge of the structures of these intermediate states is invaluable to the development of molecular strategies to arrest pathological amyloid aggregation. However, the highly dynamic and interconverting nature of amyloidogenic species limits biophysical characterization of their structures during amyloidogenesis. Here, we use molecular dynamics simulations to probe conformations sampled by monomeric transthyretin under amyloidogenic conditions. We show that certain β-strands in transthyretin tend to unfold and sample nonnative conformations and that the edge strands in one β-sheet (the DAGH sheet) are particularly susceptible to conformational changes in the monomeric state. We also find that changes in the tertiary structure of transthyretin can be associated with disruptions to the secondary structure. We evaluated the conformations produced by molecular dynamics by calculating how well molecular-dynamics-derived structures reproduced NMR-derived interatomic distances. Finally, we leverage our computational results to produce experimentally testable hypotheses that may aid experimental explorations of pathological conformations of transthyretin.

The Division of Amyloid Fibrils: Systematic Comparison of Fibril Fragmentation Stability by Linking Theory with Experiments

The division of amyloid protein fibrils is required for the propagation of the amyloid state and is an important contributor to their stability, pathogenicity, and normal function. Here, we combine kinetic nanoscale imaging experiments with analysis of a mathematical model to resolve and compare the division stability of amyloid fibrils. Our theoretical results show that the division of any type of filament results in self-similar length distributions distinct to each fibril type and the conditions applied. By applying these theoretical results to profile the dynamical stability toward breakage for four different amyloid types, we reveal particular differences in the division properties of disease-related amyloid formed from α-synuclein when compared with non-disease associated model amyloid, the former showing lowered intrinsic stability toward breakage and increased likelihood of shedding smaller particles. Our results enable the comparison of protein filaments' intrinsic dynamic stabilities, which are key to unraveling their toxic and infectious potentials.

Protein Microgels from Amyloid Fibril Networks

Nanofibrillar forms of amyloidogenic proteins were initially discovered in the context of protein misfolding and disease but have more recently been found at the origin of key biological functionality in many naturally occurring functional materials, such as adhesives and biofilm coatings. Their physiological roles in nature reflect their great strength and stability, which has led to the exploration of their use as the basis of artificial protein-based functional materials. Particularly for biomedical applications, they represent attractive building blocks for the development of, for instance, drug carrier agents due to their inherent biocompatibility and biodegradability. Furthermore, the propensity of proteins to self-assemble into amyloid fibrils can be exploited under microconfinement, afforded by droplet microfluidic techniques. This approach allows the generation of multi-scale functional microgels that can host biological additives and can be designed to incorporate additional functionality, such as to aid targeted drug delivery.

Ultrasensitive Fluorescence Detection of Alzheimer's Disease Based on Polyvalent Directed Peptide Polymer Coupled to a Nanoporous ZnO Nanoplatform

Amyloid-beta 42 (Aβ₄₂), the key biomarker of Alzheimer's disease (AD), aggregates to form neurotoxic amyloid plaques. In this work, we modified two fluorescein isothiocyanate-labeled Aβ₄₂-targeting peptides and designed an Aβ₄₂-specific ultrasensitive polyvalent-directed peptide polymer (PDPP) to enhance AD diagnosis sensitivity. The dissociation constant of Aβ₄₂ by PDPP was 10³-fold higher than the single-site-directed peptide. The improved binding was due to the ability of PDPP to detect multiple receptors on the target. The power of the PDPP diagnostic probe was verified in its application to detect Aβ₄₂ in cerebrospinal fluid (CSF), which showed a lower limit of detection (LOD) in the fg mL^-1 range that is more sensitive than detection by antibodies or single peptides. In addition, we present a novel ultrasensitive diagnostic system using an array of nanoporous ZnO nanoparticles, which play a role in fluorescence signal amplification, to further improve AD diagnosis sensitivity. We enhanced the signal on the basis of the properties of nanoporous ZnO nanoparticles and measured and quantified an ultralow concentration (ag mL^-1 range) of Aβ₄₂. This PDPP coupled to the nanoporous ZnO-based system is a novel approach to AD diagnosis that might also be useful for the detection of other target biomarkers and clinical applications.

New clues into the self-assembly of Vmh2, a basidiomycota class I hydrophobin

Hydrophobins are fungal proteins that can self-assemble into amphiphilic films at hydrophobic-hydrophilic interfaces. Class I hydrophobin aggregates resemble amyloid fibrils, sharing some features with them. Here, five site-directed mutants of Vmh2, a member of basidiomycota class I hydrophobins, were designed and characterized to elucidate the molecular determinants playing a key role in class I hydrophobin self-assembly. The mechanism of fibril formation proposed for Vmh2 foresees that the triggering event is the destabilization of a specific loop (L1), leading to the formation of a β-hairpin, which in turn generates the β-spine of the amyloid fibril.

Interactions of aggregating peptides probed by IR-UV action spectroscopy

The interplay between intramolecular and formed inter-sheet hydrogen bonds and the effect of dispersion interactions on the formation of peptide dimers is studied using IR-UV action spectroscopy.

Amyloid properties of the yeast cell wall protein Toh1 and its interaction with prion proteins Rnq1 and Sup35

Amyloids are non-branching fibrils that are composed of stacked monomers stabilized by intermolecular β-sheets. Some amyloids are associated with incurable diseases, whereas others, functional amyloids, regulate different vital processes. The prevalence and significance of functional amyloids in wildlife are still poorly understood. In recent years, by applying new approach of large-scale proteome screening, a number of novel candidate amyloids were identified in the yeast Saccharomyces cerevisiae, many of which are localized in the yeast cell wall. In this work, we showed that one of these proteins, Toh1, possess amyloid properties. The Toh1-YFP hybrid protein forms detergent-resistant aggregates in the yeast cells while being expressed under its own P_TOH1 or inducible P_CUP1 promoter. Using bacterial system for generation of extracellular amyloid aggregates C-DAG, we demonstrated that the N-terminal Toh1 fragment, containing amyloidogenic regions predicted in silico, binds Congo Red dye, manifests ‘apple-green’ birefringence when examined between crossed polarizers, and forms amyloid-like fibrillar aggregates visualized by TEM. We have established that the Toh1(20–365)-YFP hybrid protein fluorescent aggregates are co-localized with a high frequency with Rnq1C-CFP and Sup35NM-CFP aggregates in the yeast cells containing [PIN⁺] and [PSI⁺] prions, and physical interaction of these aggregated proteins was confirmed by FRET. This is one of a few known cases of physical interaction of non-Q/N-rich amyloid-like protein and Q/N-rich amyloids, suggesting that interaction of different amyloid proteins may be determined not only by similarity of their primary structures but also by similarity of their secondary structures and of conformational folds.

Prions and Non-infectious Amyloids of Mammals - Similarities and Differences

Amyloids are highly ordered aggregates of protein fibrils exhibiting cross-β structure formed by intermolecular hydrogen bonds. Pathological amyloid deposition is associated with the development of several socially significant incurable human diseases. Of particular interest are infectious amyloids, or prions, that cause several lethal neurodegenerative diseases in humans and can be transmitted from one organism to another. Because of almost complete absence of criteria for infectious and non-infectious amyloids, there is a lack of consensus, especially, in the definition of similarities and differences between prions and non-infectious amyloids. In this review, we formulated contemporary molecular-biological criteria for identification of prions and non-infectious amyloids and focused on explaining the differences between these two types of molecules.

Protein Engineering Reveals Mechanisms of Functional Amyloid Formation in Pseudomonas aeruginosa Biofilms

Amyloids are typically associated with neurodegenerative diseases, but recent research demonstrates that several bacteria utilize functional amyloid fibrils to fortify the biofilm extracellular matrix and thereby resist antibiotic treatments. In Pseudomonas aeruginosa, these fibrils are composed predominantly of FapC, a protein with high-sequence conservation among the genera. Previous studies established FapC as the major amyloid subunit, but its mechanism of fibril formation in P. aeruginosa remained largely unexplored. Here, we examine the FapC sequence in greater detail through a combination of bioinformatics and protein engineering, and we identify specific motifs that are implicated in amyloid formation. Sequence regions of high evolutionary conservation tend to coincide with regions of high amyloid propensity, and mutation of amyloidogenic motifs to a designed, non-amyloidogenic motif suppresses fibril formation in a pH-dependent manner. We establish the particular significance of the third repeat motif in promoting fibril formation and also demonstrate emergence of soluble oligomer species early in the aggregation pathway. The insights reported here expand our understanding of the mechanism of amyloid polymerization in P. aeruginosa, laying the foundation for development of new amyloid inhibitors to combat recalcitrant biofilm infections.

Mapping Amyloid Regions in Gad m 1 with Peptide Arrays

Amyloid formation is basically featured by a protein-protein interaction in which the reacting regions are the segments assembling into cross β-sheets. To identify these segments both theoretical and experimental tools have been developed. Here, we focus on the use of peptide arrays to probe the binding of several amyloid-specific probes such as the OC and A11 anti-amyloid conformation-selective antibodies and of monomers and preformed fibrils. These arrays use libraries containing partly overlapping peptides derived from the sequence of Gad m 1, the major allergen from Atlantic cod, which forms amyloids under gastrointestinal relevant conditions.

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.