Population of nonnative states of lysozyme variants drives amyloid fibril formation

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

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

Nanopore single-molecule biosensor in protein denaturation analysis

Unclear issues in protein studies include but not limited to the stability and denaturation mechanism in the presence of denaturants. Herein, we report a dynamic monitoring approach based on nanopore single-molecule biosensor, which can detect the protein's folding and unfolding transitions by recording a nanopore ionic current. When gradually increasing the concentration of denaturant guanidine hydrochloride (GdmCl), sensitive responses were observed with lysozyme unfolding. The emergence of the featured biphasic-pulse demonstrated the existence of a stable intermediate. It was the first time to experimentally confirm the dynamic equilibrium between the intermediate and the native states at single molecule level, therefore consolidating the standpoint of lysozyme denaturation process following the three-state model. Additionally, we got more insights into the conformation about the intermediate as globular-like structure, larger gyration radius, and enhanced positive charge density. We considered that the manner of denaturant toward lysozyme adopts the "direct" model based on stronger electrostatic and van der Waals forces. Nanopore biosensor exhibited excellent sensitivity with a low detection concentration of 280 pM and reproducibility in analysing the folding intermediate of lysozyme.

Analyses of Mutation Displacements from Homology Models

Evaluation of the structural perturbations introduced by a single amino acid mutation is the main issue for protein structural biology. We propose here to present some recent advances in methods, allowing the splitting of distortion between the actual substitution effect and the contribution of the local flexibility of the position where the mutation occurs. Its main drawback is the need of many structures with a single mutation in each of them. To bypass this difficulty, we propose to use molecular modeling tools, with several software enabling us to build a model from a template, given the sequence. As a proof of concept, we rely on a gold standard, the human lysozyme. Both wild-type and three mutant structures are available in the PDB. Two of these mutations result in amyloid fibril formation, and the last one is neutral. As a conclusion, irrespective of the algorithm used for modeling, side chain conformations at the site of mutation are reliable, although long-range effects are out of reach of these tools.

Generating Ensembles of Dynamic Misfolding Proteins

The early stages of protein misfolding and aggregation involve disordered and partially folded protein conformers that contain a high degree of dynamic disorder. These dynamic species may undergo large-scale intra-molecular motions of intrinsically disordered protein (IDP) precursors, or flexible, low affinity inter-molecular binding in oligomeric assemblies. In both cases, generating atomic level visualization of the interconverting species that captures the conformations explored and their physico-chemical properties remains hugely challenging. How specific sub-ensembles of conformers that are on-pathway to aggregation into amyloid can be identified from their aggregation-resilient counterparts within these large heterogenous pools of rapidly moving molecules represents an additional level of complexity. Here, we describe current experimental and computational approaches designed to capture the dynamic nature of the early stages of protein misfolding and aggregation, and discuss potential challenges in describing these species because of the ensemble averaging of experimental restraints that arise from motions on the millisecond timescale. We give a perspective of how machine learning methods can be used to extract aggregation-relevant sub-ensembles and provide two examples of such an approach in which specific interactions of defined species within the dynamic ensembles of α-synuclein (αSyn) and β2-microgloblulin (β2m) can be captured and investigated.

Man does not live by intrinsically unstructured proteins alone: The role of structured regions in aggregation

Protein misfolding is a topic that is of primary interest both in biology and medicine because of its impact on fundamental processes and disease. In this review, we revisit the concept of protein misfolding and discuss how the field has evolved from the study of globular folded proteins to focusing mainly on intrinsically unstructured and often disordered regions. We argue that this shift of paradigm reflects the more recent realisation that misfolding may not only be an adverse event, as originally considered, but also may fulfil a basic biological need to compartmentalise the cell with transient reversible granules. We nevertheless provide examples in which structure is an important component of a much more complex aggregation behaviour that involves both structured and unstructured regions of a protein. We thus suggest that a more comprehensive evaluation of the mechanisms that lead to aggregation might be necessary.

Structural Water Stabilizes Protein Motifs in Liquid Protein Phase: The Folding Mechanism of Short β-Sheets Coupled to Phase Transition

Macromolecular associates, such as membraneless organelles or lipid-protein assemblies, provide a hydrophobic environment, i.e., a liquid protein phase (LP), where folding preferences can be drastically altered. LP as well as the associated phase change from water (W) is an intriguing phenomenon related to numerous biological processes and also possesses potential in nanotechnological applications. However, the energetic effects of a hydrophobic yet water-containing environment on protein folding are poorly understood. Here, we focus on small β-sheets, the key motifs of proteins, undergoing structural changes in liquid–liquid phase separation (LLPS) and also model the mechanism of energy-coupled unfolding, e.g., in proteases, during W → LP transition. Due to the importance of the accurate description for hydrogen bonding patterns, the employed models were studied by using quantum mechanical calculations. The results demonstrate that unfolding is energetically less favored in LP by ~0.3–0.5 kcal·mol⁻¹ per residue in which the difference further increased by the presence of explicit structural water molecules, where the folded state was preferred by ~1.2–2.3 kcal·mol⁻¹ per residue relative to that in W. Energetics at the LP/W interfaces was also addressed by theoretical isodesmic reactions. While the models predict folded state preference in LP, the unfolding from LP to W renders the process highly favorable since the unfolded end state has >1 kcal·mol⁻¹ per residue excess stabilization.

Modification with N-benzylisatin restricts stress-induced aggregation of hen egg white lysozyme: Anti-amyloidogenic property of isatin derivative with possible clinical implications

Hen egg white lysozyme (HEWL) is a structural homolog of human lysozyme and is widely used as a model protein to investigate protein aggregation. The effect of N-benzylisatin on stress-induced aggregation of HEWL has been investigated in the present study. Interaction of the isatin derivative with HEWL induced changes in protein secondary and tertiary structural conformation as evident from different biophysical and spectroscopic studies. In addition, modification with N-benzylisatin was found to increase the conformational stability of HEWL and afford considerable resistance to the protein to stress-induced aggregation as indicated from subsequent experimental studies, including thioflavin T fluorescence, microscopic imaging and dynamic light scattering analysis. Protein modification was analysed and confirmed by MALDI-TOF and ESI-MS studies. The results highlight possible clinical implications of isatin derivative in the treatment of protein misfolding and conformational disorders.

α-Synuclein Responses in the Laterodorsal Tegmentum, the Pedunculopontine Tegmentum, and the Substantia Nigra: Implications for Early Appearance of Sleep Disorders in Parkinson's Disease

BACKGROUND

Parkinson's disease (PD) is a neurodegenerative disorder associated with insoluble pathological aggregates of the protein α-synuclein. While PD is diagnosed by motor symptoms putatively due to aggregated α-synuclein-mediated damage to substantia nigra (SN) neurons, up to a decade before motor symptom appearance, patients exhibit sleep disorders (SDs). Therefore, we hypothesized that α-synuclein, which can be present in monomeric, fibril, and other forms, has deleterious cellular actions on sleep-control nuclei.

OBJECTIVE

We investigated whether native monomer and fibril forms of α-synuclein have effects on neuronal function, calcium dynamics, and cell-death-induction in two sleep-controlling nuclei: the laterodorsal tegmentum (LDT), and the pedunculopontine tegmentum (PPT), as well as the motor-controlling SN.

METHODS

Size exclusion chromatography, Thioflavin T emission, and circular dichroism spectroscopy were used to isolate structurally defined forms of recombinant, human α-synuclein. Neuronal and viability effects of characterized monomeric and fibril forms of α-synuclein were determined on LDT, PPT, and SN neurons using electrophysiology, calcium imaging, and neurotoxicity assays.

RESULTS

In LDT and PPT, both forms of α-synuclein induced excitation and increased calcium, and the monomeric form heightened putatively excitotoxic neuronal death, whereas, in the SN we saw inhibition, decreased intracellular calcium, and monomeric α-synuclein was not associated with heightened cell death.

CONCLUSION

Nucleus-specific differential effects suggest mechanistic underpinnings of SDs' prodromal appearance in PD. While speculative, we hypothesize that the monomeric form of α-synuclein compromises functionality of sleep-control neurons, leading to the presence of SDs decades prior to motor dysfunction.

Elevated temperatures accelerate the formation of toxic amyloid fibrils of hen egg-white lysozyme

The formation of amyloid fibrils is critical for neurodegenerative diseases. Some physiochemical conditions can promote the conversion of proteins from soluble globular shapes into insoluble well‐organized amyloid fibrils. The aim of this study was to investigate the effect of temperatures on amyloid fibrils formation in vitro using the protein model of hen egg‐white lysozyme (HEWL). The HEWL fibrils were prepared at temperatures of 37, 45, 50 and 57°C in glycine solution of pH 2.2. Under transmission electron microscopy, we found the well‐organized HEWL amyloid fibrils at temperatures of 45, 50 and 57°C after 10 days of incubation. Thioflavin T and Congo red florescence assays confirmed that the formation and growth of HEWL fibrils displayed a temperature‐dependent increase, and 57°C produced the most amounts. Meanwhile, the surface hydrophobicity of aggregates was greatly increased by ANS binding assay, and β‐sheet contents by circular dichroism analysis were increased by 17.8%, 22.0% and 34.9%, respectively. Furthermore, the HEWL fibrils formed at 57°C caused significant cytotoxicity in SH‐SY5Y cells after 48 hr exposure, and the cell viability determined by MTT assay was decreased, with 81.35 ± 0.29% for 1 μM, 61.45 ± 2.62% for 2 μM, and 11.58 ± 0.39% (p < .01) for 3 μM. Nuclear staining results also confirmed the apoptosis features. These results suggest that the elevated temperatures could accelerate protein unfolding of the native structure and formation of toxic amyloid fibrils, which can improve understanding the mechanisms of the unfolding and misfolding process of prion protein.

Protein-Based Nano-Vessels Facilitates the Victoria Blue B Mediated Inhibition of Amyloid Fibrillation

Amyloid fibrils are associated with a number of serious and incurable diseases. The understanding of the pathogenic formation of amyloid proteins is progressing. Nonetheless, no treatment is available to deal with amyloid diseases. It is reported here that victoria blue B (VBB) contains an intrinsic marginal inhibitory activity toward protein fibrillation. Moreover, when VBB is co-assembled with scaffold proteins to form fluorescent protein nano-vessels (VBB-FPNs), these complexes show much improved fibrillation inhibitory effects. VBB-FPNs can effectively inhibit lysozyme fibrils formation likely through delaying the nucleation and elongation in a concentration-dependent manner as shown by fluorescent assay, circular dichroism, transmission electron microscopy, and atomic force microscopy. This work describes a new inhibitor of protein fibrillation and provides a new means to enhance the inhibition efficiency of given inhibitors, thus affording a fresh angle to modulate protein fibrillation.

Cross-Species and Cross-Polymorph Seeding of Lysozyme Amyloid Reveals a Dominant Polymorph

The ability to self-propagate is one of the most intriguing characteristics of amyloid fibrils, and is a feature of great interest both to stopping unwanted pathological amyloid, and for engineering functional amyloid as a useful nanomaterial. The sequence and structural tolerances for amyloid seeding are not well understood, particularly concerning the propagation of distinct fibril morphologies (polymorphs) across species. This study examined the seeding and cross-seeding reactions between two unique fibril polymorphs, one long and flexible (formed at pH 2) and the other short and rigid (formed at pH 6.3), of human lysozyme and hen egg-white lysozyme. Both polymorphs could cross-seed aggregation across species, but this reaction was markedly reduced under physiological conditions. For both species, the pH 6.3 fibril polymorph was dominant, seeding fibril growth with a faster growth rate constant at pH 2 than the pH 2 polymorph. Based on fibrillation kinetics and fibril morphology, we found that the pH 2 polymorph was not able to faithfully replicate itself at pH 6.3. These results show that two distinct amyloid polymorphs are both capable of heterologous seeding across two species (human and hen) of lysozyme, but that the pH 6.3 polymorph is favored, regardless of the species, likely due to a lower energy barrier, or faster configurational diffusion, to accessing this particular misfolded form. These findings contribute to our better understanding of amyloid strain propagation across species barriers.

Analyses of displacements resulting from a point mutation in proteins

The effects of a single residue substitution on the protein backbone are frequently quite small and there are many other potential sources of structural variation for protein. We present here a methodology considering different sources of distortions in order to isolate the very effect of the mutation. To validate our methodology, we consider a well-studied family with many single mutants: the human lysozyme. Most of the perturbations are expected to be at the very localisation of the mutation, but in many cases the effects are propagated at long range. We show that the distances between the mutated residue and the 5% most disturbed residues exponentially decreases. One third of the affected residues are in direct contact with the mutated position; the remaining two thirds are potential allosteric effects. We confirm the reliability of the residues identified as significantly perturbed by comparing our results to experimental studies. We confirm with the present method all the previously identified perturbations. This study shows that mutations have long-range impact on protein backbone that can be detected, although the displacement of the affected atoms is small.

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

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

Reflections on professor Sir Christopher M. Dobson (1949-2019)

I have been invited to summarize my career with an emphasis on the time I spent in the laboratory of Prof Christopher M. Dobson, who sadly passed away on September 8th 2019, and to describe his role as a mentor. I accepted this slightly unusual request as it constitutes a unique way for me to express my deep gratitude and admiration for Chris.

Methylglyoxal modification reduces the sensitivity of hen egg white lysozyme to stress-induced aggregation: Insight into the anti-amyloidogenic property of α-dicarbonyl compound

The reactive α-oxoaldehyde, methylglyoxal reacts with different proteins to form Advanced Glycation End Products (AGEs) through Maillard reaction. Its level increases significantly in diabetic condition. Here, we have investigated the effect of different concentrations of methylglyoxal (200-400 µM) on the monomeric protein, hen egg white lysozyme (HEWL) following incubation for 3 weeks. Reaction of methylglyoxal with HEWL induced considerable changes in tertiary structure of the protein, but no significant alteration in secondary structure, as evident from different spectroscopic and biophysical studies. Interestingly, methylglyoxal modification was found to enhance the thermal stability of the protein and reduce its sensitivity to stress-induced aggregation. Finally, peptide mass fingerprinting revealed modification of arginine (Arg-45, Arg-14, Arg-68 or Arg-72) and lysine (Lys-116) residues of the protein to AGE adducts, namely, hydroimidazolone, tetrahydropyrimidine, and carboxyethyllysine. Methylglyoxal-derived AGE adducts (MAGE) appear to be responsible for the observed changes in protein. As demonstrated in the present study, the findings may highlight a possible therapeutic potential of the α-oxoaldehyde against protein misfolding and conformational disorder.Communicated by Ramaswamy H. Sarma.

The growth of amyloid fibrils: rates and mechanisms

Amyloid fibrils are β-sheet-rich linear protein polymers that can be formed by a large variety of different proteins. These assemblies have received much interest in recent decades, due to their role in a range of human disorders. However, amyloid fibrils are also found in a functional context, whereby their structural, mechanical and thermodynamic properties are exploited by biological systems. Amyloid fibrils form through a nucleated polymerisation mechanism with secondary processes acting in many cases to amplify the number of fibrils. The filamentous nature of amyloid fibrils implies that the fibril growth rate is, by several orders of magnitude, the fastest step of the overall aggregation reaction. This article focusses specifically on in vitro experimental studies of the process of amyloid fibril growth, or elongation, and summarises the state of knowledge of its kinetics and mechanisms. This work attempts to provide the most comprehensive summary, to date, of the available experimental data on amyloid fibril elongation rate constants and the temperature and concentration dependence of amyloid fibril elongation rates. These data are compared with those from other types of protein polymers. This comparison with data from other polymerising proteins is interesting and relevant because many of the basic ideas and concepts discussed here were first introduced for non-amyloid protein polymers, most notably by the Japanese school of Oosawa and co-workers for cytoskeletal filaments.

Unfolding Pathways of Hen Egg-White Lysozyme in Ethanol

The aggregation of amyloid fibrils can lead to various diseases including Alzheimer's, Parkinson's disease, and transmissible spongiform encephalopathy. Amyloid fibrils can develop from a variety of proteins in the body as they misfold into a primarily β-sheet structure and aggregate. Human lysozyme has been shown to have far reaching effects in the human health-a homologous enzyme, hen egg-white lysozyme, has been shown to denature to a primarily β-sheet structure at low pH and high alcohol content solution. We have studied these systems in atomic-level detail with a combination of constant pH and microsecond long molecular dynamics simulation in explicit solvent, which cumulatively total over 10 μs of simulation time. These studies have allowed us to determine two potential unfolding pathways depending on the protonation state of a key glutamic acid residue as well as the effect of solution dynamics and pH on the unfolding process.

Role of Disulfide Bonds and Topological Frustration in the Kinetic Partitioning of Lysozyme Folding Pathways

Disulfide bonds in proteins can strongly influence the folding pathways by constraining the conformational space. Lysozyme has four disulfide bonds and is widely studied for its antibacterial properties. Experiments on lysozyme infer that the protein folds through a fast and a slow pathway. However, the reasons for the kinetic partitioning in the folding pathways are not completely clear. Using a coarse-grained protein model and simulations, we show that two out of the four disulfide bonds, which are present in the α-domain of lysozyme, are responsible for the slow folding pathway. In this pathway, a kinetically trapped intermediate state, which is close to the native state, is populated. In this state, the orientations of α-helices present in the α-domain are misaligned relative to each other. The protein in this state has to partially unfold by breaking down the interhelical contacts between the misaligned helices to fold to the native state. However, the topological constraints due to the two disulfide bonds present in the α-domain make the protein less flexible, and it is trapped in this conformation for hundreds of milliseconds. On disabling these disulfide bonds, we find that the kinetically trapped intermediate state and the slow folding pathway disappear. Simulations mimicking the folding of protein without disulfide bonds under oxidative conditions show that the native disulfide bonds are formed as the protein folds, indicating that folding guides the formation of disulfide bonds. The sequence of formation of the disulfide bonds is Cys64-Cys80 → Cys76-Cys94 → Cys30-Cys115 → Cys6-Cys127. Any disulfide bond that forms before its precursor in the sequence has to break and follow the sequence for the protein to fold. These results show that lysozyme also serves as a very good model system to probe the role of disulfide bonds and topological frustration in protein folding. The predictions from the simulations can be verified by single-molecule fluorescence resonance energy transfer or single-molecule pulling experiments, which can probe heterogeneity in the folding pathways.

Studies on lysozyme modifications induced by substituted p-benzoquinones

Protein misfolding can facilitate a protein damaging process and makes it susceptible to a series of events such as unfolding, adduct formation, oligomerization, or aggregation. Loss of a protein's native structure may result in its biological malfunction and/or cellular toxicity that could cause associated diseases. Several factors were identified for causing structural changes of a protein, however quinone-induced protein modifications received very little attention whether for amyloidal or non-amyloidal proteins. In this paper, we report our investigation on lysozyme modifications upon treatment with selected benzoquinones (BQs), utilizing fluorescence spectroscopy including anisotropy determination, UV-Vis spectroscopy, and SDS-PAGE. Lysozyme was reacted with substituted BQs in order to examine substituent effects on protein modifications. In addition, we evaluated lysozyme modifications induced by 1,4-benzoquinone in concentration-, pH-, temperature-, and time-dependent studies. Our study shows that all BQs can readily modify lysozyme in a complex manner through adduct formation, oligomerization, polymeric aggregation, and/or fibrilization. Electrochemical properties of selected BQs were monitored using cyclic voltammetry in phosphate buffered aqueous solution, and it was found that quinone reduction potentials correlate well with their reactivity trend toward lysozyme.

Insight into the specificity and severity of pathogenic mechanisms associated with missense mutations through experimental and structural perturbation analyses

Most pathogenic missense mutations cause specific molecular phenotypes through protein destabilization. However, how protein destabilization is manifested as a given molecular phenotype is not well understood. We develop here a structural and energetic approach to describe mutational effects on specific traits such as function, regulation, stability, subcellular targeting or aggregation propensity. This approach is tested using large-scale experimental and structural perturbation analyses in over thirty mutations in three different proteins (cancer-associated NQO1, transthyretin related with amyloidosis and AGT linked to primary hyperoxaluria type I) and comprising five very common pathogenic mechanisms (loss-of-function and gain-of-toxic function aggregation, enzyme inactivation, protein mistargeting and accelerated degradation). Our results revealed that the magnitude of destabilizing effects and, particularly, their propagation through the structure to promote disease-associated conformational states largely determine the severity and molecular mechanisms of disease-associated missense mutations. Modulation of the structural perturbation at a mutated site is also shown to cause switches between different molecular phenotypes. When very common disease-associated missense mutations were investigated, we also found that they were not among the most deleterious possible missense mutations at those sites, and required additional contributions from codon bias and effects of CpG sites to explain their high frequency in patients. Our work sheds light on the molecular basis of pathogenic mechanisms and genotype–phenotype relationships, with implications for discriminating between pathogenic and neutral changes within human genome variability from whole genome sequencing studies.

In silico prediction of novel residues involved in amyloid primary nucleation of human I56T and D67H lysozyme

Background

Amyloidogenic proteins are most often associated with neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease, but there are more than two dozen human proteins known to form amyloid fibrils associated with disease. Lysozyme is an antimicrobial protein that is used as a general model to study amyloid fibril formation. Studies aimed at elucidating the process of amyloid formation of lysozyme tend to focus on partial unfolding of the native state due to the relative instability of mutant amyloidogenic variants. While this is well supported, the data presented here suggest the native structure of the variants may also play a role in primary nucleation.

Results

Three-dimensional structural analysis identified lysozyme residues 21, 62, 104, and 122 as displaced in both amyloidogenic variants compared to wild type lysozyme. Residue interaction network (RIN) analysis found greater clustering of residues 112–117 in amyloidogenic variants of lysozyme compared to wild type. An analysis of the most energetically favored predicted dimers and trimers provided further evidence for a role for residues 21, 62, 104, 122, and 112–117 in amyloid formation.

Conclusions

This study used lysozyme as a model to demonstrate the utility of combining 3D structural analysis with RIN analysis for studying the general process of amyloidogenesis. Results indicated that binding of two or more amyloidogenic lysozyme mutants may be involved in amyloid nucleation by placing key residues (21, 62, 104, 122, and 112–117) in proximity before partial unfolding occurs. Identifying residues in the native state that may be involved in amyloid formation could provide novel drug targets to prevent a range of amyloidoses.

Minimalist Prion-Inspired Polar Self-Assembling Peptides

Nature provides copious examples of self-assembling supramolecular nanofibers. Among them, amyloid structures have found amazing applications as advanced materials in fields such as biomedicine and nanotechnology. Prions are a singular subset of proteins able to switch between a soluble conformation and an amyloid state. The ability to transit between these two conformations is encoded in the so-called prion domains (PrDs), which are long and disordered regions of low complexity, enriched in polar and uncharged amino acids such as Gln, Asn, Tyr, Ser, and Gly. The polar nature of PrDs results in slow amyloid formation, which allows kinetic control of fiber assembly. This approach has been exploited for fabrication of multifunctional materials because in contrast to most amyloids, PrDs lack hydrophobic stretches that can nucleate their aggregation, their assembly depends on the establishment of a large number of weak interactions along the complete domain. The length and low complexity of PrDs make their chemical synthesis for applied purposed hardly affordable. Here, we designed four minimalist polar binary patterned peptides inspired in PrDs, which include the [Q/N/G/S]-Y-[Q/N/G/S] motif frequently observed in these domains: NYNYNYN, QYQYQYQ, SYSYSYS, and GYGYGYG. Despite their small size, they all recapitulate the properties of full-length PrDs, self-assembling into nontoxic amyloids under physiological conditions. Thus, they constitute small building blocks for the construction of tailored prion-inspired nanostructures. We exploited Tyr residues in these peptides to generate highly stable dityrosine cross-linked assemblies for the immobilization of metal nanoparticles in the fibrils surface and to develop an electrocatalytic amyloid scaffold. Moreover, we show that the shorter and more polar NYNNYN, QYQQYQ, and SYSSYS hexapeptides also self-assemble into amyloid-like structures, consistent with the presence of these tandem motifs in human prion-like proteins.

A sticky situation: Aberrant protein-protein interactions in Parkinson's disease

The aberrant aggregation of normally soluble proteins into amyloid fibrils is the pathological hallmark of several neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Understanding this process will be key to developing both diagnostic and therapeutic approaches for neurodegenerative diseases. Recent advances in biophysical techniques, coupled with kinetic analyses have enabled a thorough description of the key molecular steps involved in protein aggregation. In this review, we discuss these advances and how they have been applied to study the ability of one such protein, α-Synuclein, to form neurotoxic oligomers.

Application of Lysine-specific Labeling to Detect Transient Interactions Present During Human Lysozyme Amyloid Fibril Formation

Populating transient and partially unfolded species is a crucial step in the formation and accumulation of amyloid fibrils formed from pathogenic variants of human lysozyme linked with a rare but fatal hereditary systemic amyloidosis. The partially unfolded species possess an unstructured β-domain and C-helix with the rest of the α-domain remaining native-like. Here we use paramagnetic relaxation enhancement (PRE) measured by NMR spectroscopy to study the transient intermolecular interactions between such intermediate species. Nitroxide spin labels, introduced specifically at three individual lysine residues, generate distinct PRE profiles, indicating the presence of intermolecular interactions between residues within the unfolded β-domain. This study describes the applicability to PRE NMR measurements of selective lysine labeling, at different sites within a protein, as an alternative to the introduction of spin labels via engineered cysteine residues. These results reveal the importance of the β-sheet region of lysozyme for initiating self-assembly into amyloid fibrils.

Factors affecting the physical stability (aggregation) of peptide therapeutics

The number of biological therapeutic agents in the clinic and development pipeline has increased dramatically over the last decade and the number will undoubtedly continue to increase in the coming years. Despite this fact, there are considerable challenges in the development, production and formulation of such biologics particularly with respect to their physical stabilities. There are many cases where self-association to form either amorphous aggregates or highly structured fibrillar species limits their use. Here, we review the numerous factors that influence the physical stability of peptides including both intrinsic and external factors, wherever possible illustrating these with examples that are of therapeutic interest. The effects of sequence, concentration, pH, net charge, excipients, chemical degradation and modification, surfaces and interfaces, and impurities are all discussed. In addition, the effects of physical parameters such as pressure, temperature, agitation and lyophilization are described. We provide an overview of the structures of aggregates formed, as well as our current knowledge of the mechanisms for their formation.

Self-assembling peptide and protein amyloids: from structure to tailored function in nanotechnology

Self-assembled peptide and protein amyloid nanostructures have traditionally been considered only as pathological aggregates implicated in human neurodegenerative diseases. In more recent times, these nanostructures have found interesting applications as advanced materials in biomedicine, tissue engineering, renewable energy, environmental science, nanotechnology and material science, to name only a few fields. In all these applications, the final function depends on: (i) the specific mechanisms of protein aggregation, (ii) the hierarchical structure of the protein and peptide amyloids from the atomistic to mesoscopic length scales and (iii) the physical properties of the amyloids in the context of their surrounding environment (biological or artificial). In this review, we will discuss recent progress made in the field of functional and artificial amyloids and highlight connections between protein/peptide folding, unfolding and aggregation mechanisms, with the resulting amyloid structure and functionality. We also highlight current advances in the design and synthesis of amyloid-based biological and functional materials and identify new potential fields in which amyloid-based structures promise new breakthroughs.

The Significance of the Location of Mutations for the Native-State Dynamics of Human Lysozyme

The conversion of human lysozyme into amyloid fibrils is associated with a rare but fatal hereditary form of nonneuropathic systemic amyloidosis. The accumulation of large amounts of aggregated protein is thought to be initiated by the formation of transient intermediate species of disease-related lysozyme variants, essentially due to the loss of global cooperativity under physiologically relevant conditions. Interestingly, all five naturally occurring, amyloidogenic, single-point mutations are located in the β-domain of lysozyme, the region that is predominantly unfolded during the formation of the transient intermediate species. Given the lack of known naturally occurring, amyloidogenic, single-point mutations in the α-domain, we chose three specific mutations to address the effects that location may have on native-state dynamics, as studied by hydrogen-deuterium (HD) exchange experiments analyzed by NMR spectroscopy, and mass spectrometry. We compared the effect of a destabilizing α-domain mutation (I23A) with that of the well-characterized I59T β-domain variant. We also investigated the effect of a mutation that has minor effects on native-state stability at the domain interface (I56V) and compared it with that of a variant with similar stability within the C-helix (I89V). We show that when variants have similar reduced native-state stabilities, the location of the mutation (I23A versus I59T) is crucial to the native-state dynamics, with the α-domain mutation having a significantly lower ability to populate transient intermediate species under physiologically relevant conditions. Interestingly, the mutation at the interface (I56V) has a greater effect in facilitating the formation of transient intermediate species at elevated temperatures compared with the variants containing α-domain mutations, even though this mutation results in only minor changes to the native-state stability of lysozyme. These findings reveal that the location of specific mutations is an important factor in determining the native-state dynamical properties of human lysozyme in the context of its propensity to populate the aggregation-prone transient intermediate species associated with pathogenic amyloid formation.

The native state of prion protein (PrP) directly inhibits formation of PrP-amyloid fibrils in vitro

The conversion of globular proteins into amyloid fibrils is associated with a wide variety of human diseases. One example is the prion protein (PrP), which adopts an α-helical structure in the native state but its amyloid form is implicated in the pathogenesis of prion diseases. Previous evidence has suggested that destabilization of the native state promotes amyloid formation, but the underlying mechanism remains unknown. In this study, we report that the native state of PrP serves as a potent inhibitor in the formation of PrP amyloid fibrils. By monitoring the time courses of thioflavin T fluorescence, the kinetics of amyloid formation was studied in vitro under various concentrations of pre-formed amyloid, monomer, and denaturant. Quantitative analysis of the kinetic data using various models of enzyme kinetics suggested that the native state of PrP is either an uncompetitive or noncompetitive inhibitor of amyloid formation. This study highlights the significant role of the native state in inhibiting amyloid formation, which provides new insights into the pathogenesis of misfolding diseases.

Molecular Insight into Human Lysozyme and Its Ability to Form Amyloid Fibrils in High Concentrations of Sodium Dodecyl Sulfate: A View from Molecular Dynamics Simulations

Changes in the tertiary structure of proteins and the resultant fibrillary aggregation could result in fatal heredity diseases, such as lysozyme systemic amyloidosis. Human lysozyme is a globular protein with antimicrobial properties with tendencies to fibrillate and hence is known as a fibril-forming protein. Therefore, its behavior under different ambient conditions is of great importance. In this study, we conducted two 500000 ps molecular dynamics (MD) simulations of human lysozyme in sodium dodecyl sulfate (SDS) at two ambient temperatures. To achieve comparative results, we also performed two 500000 ps human lysozyme MD simulations in pure water as controls. The aim of this study was to provide further molecular insight into all interactions in the lysozyme-SDS complexes and to provide a perspective on the ability of human lysozyme to form amyloid fibrils in the presence of SDS surfactant molecules. SDS, which is an anionic detergent, contains a hydrophobic tail with 12 carbon atoms and a negatively charged head group. The SDS surfactant is known to be a stabilizer for helical structures above the critical micelle concentration (CMC) [1]. During the 500000 ps MD simulations, the helical structures were maintained by the SDS surfactant above its CMC at 300 K, while at 370 K, human lysozyme lost most of its helices and gained β-sheets. Therefore, we suggest that future studies investigate the β-amyloid formation of human lysozyme at SDS concentrations above the CMC and at high temperatures.

A Population Shift between Sparsely Populated Folding Intermediates Determines Amyloidogenicity

The balance between protein folding and misfolding is a crucial determinant of amyloid assembly. Transient intermediates that are sparsely populated during protein folding have been identified as key players in amyloid aggregation. However, due to their ephemeral nature, structural characterization of these species remains challenging. Here, using the power of nonuniformly sampled NMR methods we investigate the folding pathway of amyloidogenic and nonamyloidogenic variants of β2-microglobulin (β2m) in atomic detail. Despite folding via common intermediate states, we show that the decreased population of the aggregation-prone ITrans state and population of a less stable, more dynamic species ablate amyloid formation by increasing the energy barrier for amyloid assembly. The results show that subtle changes in conformational dynamics can have a dramatic effect in determining whether a protein is amyloidogenic, without perturbation of the mechanism of protein folding.

Characterization of heat induced spherulites of lysozyme reveals new insight on amyloid initiation

Here, we report results obtained during our experiments to visualize how heat transforms globular protein, lysozyme into building block of β-amyloids. Light scattering experiments showed formation of lower order associated species around 50-70 °C followed by rapid cooperativity to β-amyloid fibrils. Interestingly, crystallization drops set at higher temperatures either led to aggregates or spherulites. The latter possess an amorphous β-fibril rich core with thin crystalline needles projecting outwards. Diffraction of the crystalline outgrowths revealed novel dimers and trimers of lysozyme where individual chains were similar to monomer with marginal gain in β-sheet content. Importantly, analysis of Amide I stretching frequencies showed that protein loses its secondary structure at temperatures higher than where we obtained crystals followed by rapid gain in β-sheet content. Interestingly, attempts to use the needles as seeds for more crystals led to "broom-like" fibril formations at the ends. Further, aggregation inhibitors like arginine and benzyl alcohol completely obliterated spherulites formation during crystallization. Refinement of crystals of lysozyme in presence of these molecules showed these small molecules bind to the interfaces of heat associated dimers and trimers. Overall our work concludes that heat induced weakly associated structures of lysozyme are the first step towards its amyloid formation.

Insights into Kinetics of Agitation-Induced Aggregation of Hen Lysozyme under Heat and Acidic Conditions from Various Spectroscopic Methods

Protein misfolding and amyloid formation are an underlying pathological hallmark in a number of prevalent diseases of protein aggregation ranging from Alzheimer’s and Parkinson’s diseases to systemic lysozyme amyloidosis. In this context, we have used complementary spectroscopic methods to undertake a systematic study of the self-assembly of hen egg-white lysozyme under agitation during a prolonged heating in acidic pH. The kinetics of lysozyme aggregation, monitored by Thioflavin T fluorescence, dynamic light scattering and the quenching of tryptophan fluorescence by acrylamide, is described by a sigmoid curve typical of a nucleation-dependent polymerization process. Nevertheless, we observe significant differences between the values deduced for the kinetic parameters (lag time and aggregation rate). The fibrillation process of lysozyme, as assessed by the attenuated total reflection-Fourier transform infrared spectroscopy, is accompanied by an increase in the β-sheet conformation at the expense of the α-helical conformation but the time-dependent variation of the content of these secondary structures does not evolve as a gradual transition. Moreover, the tryptophan fluorescence-monitored kinetics of lysozyme aggregation is described by three phases in which the temporal decrease of the tryptophan fluorescence quantum yield is of quasilinear nature. Finally, the generated lysozyme fibrils exhibit a typical amyloid morphology with various lengths (observed by atomic force microscopy) and contain exclusively the full-length protein (analyzed by highly performance liquid chromatography). Compared to the data obtained by other groups for the formation of lysozyme fibrils in acidic pH without agitation, this work provides new insights into the structural changes (local, secondary, oligomeric/fibrillar structures) undergone by the lysozyme during the agitation-induced formation of fibrils.

Amyloid Fibres: Inert End-Stage Aggregates or Key Players in Disease?

The formation of amyloid fibres is a hallmark of amyloid disorders. Nevertheless, the lack of correlation between fibre load and disease as observed, for example, in Alzheimer's disease, means that fibres are considered secondary contributors to the onset of cellular dysfunction. Instead, soluble intermediates of amyloid assembly are often described as the agents of toxicity. Here, we discuss recent experimental discoveries which suggest that amyloid fibres should be considered as disease-relevant species that can mediate a range of pathological processes. These include disruption of biological membranes, secondary nucleation, amyloid aggregate transmission, and the disruption of protein homeostasis (proteostasis). Thus, a greater understanding of amyloid fibre biology could enhance prospects of developing therapeutic interventions against this devastating class of protein-misfolding disorders.

Accelerated insulin aggregation under alternating current electric fields: Relevance to amyloid kinetics

The time-dependent nucleation phase is critical to amyloid fibrillation and related to many pathologies, in which the conversion from natively folded amyloidogenic proteins to oligomers via nucleation is often hypothesized as a possible underlying mechanism. In this work, non-uniform AC-electric fields across two asymmetric electrodes were explored to control and examine the aggregation of insulin, a model amyloid protein, in aqueous buffer solution at constant temperature (20 °C) by fluorescence correlation spectroscopy and fluorescence microscopy. Insulin was rapidly concentrated in a strong AC-field by imposed AC-electroosmosis flow over an optimal frequency range of 0.5-2 kHz. In the presence of an AC-field, direct fibrillation from insulin monomers without the formation of oligomer precursors was observed. Once the insulin concentration had nearly doubled its initial concentration, insulin aggregates were observed in solution. The measured lag time for the onset of insulin aggregation, determined from the abrupt reduction in insulin concentration in solution, was significantly shortened from months or years in the absence of AC-fields to 1 min-3 h under AC-fields. The ability of external fields to alter amyloid nucleation kinetics provides insights into the onset of amyloid fibrillation.

pH-induced molecular shedding drives the formation of amyloid fibril-derived oligomers

Amyloid disorders cause debilitating illnesses through the formation of toxic protein aggregates. The mechanisms of amyloid toxicity and the nature of species responsible for mediating cellular dysfunction remain unclear. Here, using β2-microglobulin (β2m) as a model system, we show that the disruption of membranes by amyloid fibrils is caused by the molecular shedding of membrane-active oligomers in a process that is dependent on pH. Using thioflavin T (ThT) fluorescence, NMR, EM and fluorescence correlation spectroscopy (FCS), we show that fibril disassembly at pH 6.4 results in the formation of nonnative spherical oligomers that disrupt synthetic membranes. By contrast, fibril dissociation at pH 7.4 results in the formation of nontoxic, native monomers. Chemical cross-linking or interaction with hsp70 increases the kinetic stability of fibrils and decreases their capacity to cause membrane disruption and cellular dysfunction. The results demonstrate how pH can modulate the deleterious effects of preformed amyloid aggregates and suggest why endocytic trafficking through acidic compartments may be a key factor in amyloid disease.

Engineering amyloid fibrils from β-solenoid proteins for biomaterials applications

Nature provides numerous examples of self-assembly that can potentially be implemented for materials applications. Considerable attention has been given to one-dimensional cross-β or amyloid structures that can serve as templates for wire growth or strengthen materials such as glue or cement. Here, we demonstrate controlled amyloid self-assembly based on modifications of β-solenoid proteins. They occur naturally in several contexts (e.g., antifreeze proteins, drug resistance proteins) but do not aggregate in vivo due to capping structures or distortions at their ends. Removal of these capping structures and regularization of the ends of the spruce budworm and rye grass antifreeze proteins yield micron length amyloid fibrils with predictable heights, which can be a platform for biomaterial-based self-assembly. The design process, including all-atom molecular dynamics simulations, purification, and self-assembly procedures are described. Fibril formation with the predicted characteristics is supported by evidence from thioflavin-T fluorescence, circular dichroism, dynamic light scattering, and atomic force microscopy. Additionally, we find evidence for lateral assembly of the modified spruce budworm antifreeze fibrils with sufficient incubation time. The kinetics of polymerization are consistent with those for other amyloid formation reactions and are relatively fast due to the preformed nature of the polymerization nucleus.

Oligomers, protofibrils and amyloid fibrils from recombinant human lysozyme (rHL): fibrillation process and cytotoxicity evaluation for ARPE-19 cell line

Amyloid-associated diseases, such Alzheimer's, Huntington's, Parkinson's, and type II diabetes, are related to protein misfolding and aggregation. Herein, the time evolution of scattered light intensity, hydrophobic properties, and conformational changes during fibrillation processes of rHL solutions at 55 °C and pH 2.0 were used to monitor the aggregation process of recombinant human lysozyme (rHL). Dynamic light scattering (DLS), thioflavin T (ThT) fluorescence, and surface tension (ST) at the air-water interface were used to analyze the hydrophobic properties of pre-amyloid aggregates involved in the fibrillation process of rHL to find a correlation between the hydrophobic character of oligomers, protofibrils and amyloid aggregates with the gain in cross-β-sheet structure, depending on the increase in the incubation periods. The ability of the different aggregates of rHL isolated during the fibrillation process to be adsorbed at the air-water interface can provide important information about the hydrophobic properties of the protein, which can be related to changes in the secondary structure of rHL, resulting in cytotoxic or non-cytotoxic species. Thus, we evaluated the cytotoxic effect of oligomers, protofibrils and amyloid fibrils on the cell line ARPE-19 using the MTT reduction test. The more cytotoxic protein species arose after a 600-min incubation time, suggesting that the hydrophobic character of pre-amyloid fibrils, in addition to the high prevalence of the cross-β-sheet conformation, can become toxic for the cell line ARPE-19.

Influence of the protein context on the polyglutamine length-dependent elongation of amyloid fibrils

Polyglutamine (polyQ) diseases, including Huntington's disease, are neurodegenerative disorders associated with the abnormal expansion of a polyQ tract within nine proteins. The polyQ expansion is thought to be a major determinant in the development of neurotoxicity, triggering protein aggregation into amyloid fibrils, although non-polyQ regions play a modulating role. In this work, we investigate the relative importance of the polyQ length, its location within a host protein, and the conformational state of the latter in the amyloid fibril elongation. Model polyQ proteins made of the β-lactamase BlaP containing up to 79Q inserted at two different positions, and quartz crystal microbalance and atomic force microscopy were used for this purpose. We demonstrate that, independently of the polyQ tract location and the conformational state of the host protein, the relative elongation rate of fibrils increases linearly with the polyQ length. The slope of the linear fit is similar for both sets of chimeras (i.e., the elongation rate increases by ~1.9% for each additional glutamine), and is also similar to that previously observed for polyQ peptides. The elongation rate is, however, strongly influenced by the location of the polyQ tract within BlaP and the conformational state of BlaP. Moreover, comparison of our results with those previously reported for aggregation in solution indicates that these two parameters also modulate the ability of BlaP-polyQ chimeras to form the aggregation nucleus. Altogether our results suggest that non-polyQ regions are valuable targets in order to interfere with the process of amyloid fibril formation associated with polyQ diseases.

Differential effects of ionic and non-ionic surfactants on lysozyme fibrillation

Fibril formation is a common property of many proteins, though not all are associated with diseases. Protein surface charges and the added co-solvents play vital roles in determining fibrillation pathways and kinetics. In order to understand these phenomena, the effects of anionic, cationic and non-ionic surfactants on lysozyme fibrillation were studied. Lysozyme forms fibrils in 2 M and 4 M urea solutions following nucleation-dependent and nucleation-independent pathways, respectively, at neutral pH. Under these conditions, the effects of sodium dodecyl sulfate (SDS), cetyltrimethylammonium bromide (CTAB), and triton X-100 (Tx) were investigated on the lysozyme structure and fibrillation. The results indicate that there are differential effects of ionic and non-ionic surfactants on fibrillation. In the presence of SDS and CTAB, above their critical micelle concentrations (CMC), lysozyme could not form fibrils. However, non-ionic Tx does not inhibit fibril formation at all concentrations. Note that the time for complete fibril formation is increased by Tx. All of the surfactants are found to increase the initial nucleation phase; however, the extent of increase is less at near the CMC of the ionic surfactants and at above the CMC of Tx. The rates of fibril elongation show varying effects in the presence of different surfactants. The results suggest that the nucleation phase of lysozyme fibrillation is primarily controlled by charge interactions and micellation of the surfactants, but multiple factors might influence the fibril elongation. Furthermore, the surfactants do not alter the fibrillation pathway from nucleation-dependent to nucleation-independent or vice versa in the studied conditions.