Salt-induced formations of partially folded intermediates and amyloid fibrils suggests a common underlying mechanism

Unraveling the Effects of Hexametaphosphate: Insights into Trypsin Aggregation and Structural Reversal

Elevated serum phosphate levels have been linked to increased mortality rates. This study investigated the effect of millimolar (mM) concentrations of sodium hexametaphosphate (SHMP) on trypsin's aggregation and structural stability at intestinal pH levels. We used various spectroscopic and microscopic techniques to investigate the structural changes of trypsin aggregates. Turbidity and light scattering results revealed that trypsin aggregates began to solubilize at SHMP concentrations above 1 mM, with maximum solubilization observed at 6 mM SHMP. Intrinsic, thioflavin T (ThT) fluorescence, and far-UV CD spectra indicated that trypsin amorphous aggregates turn into native-like structures in the presence of 6 mM SHMP. Transmission electron microscope (TEM) imaging also showed the disappearance of amorphous aggregates at higher SHMP concentrations. This study showed that higher SHMP concentrations solubilized the trypsin aggregates and induced a native-like conformation. These findings highlighted that SHMP could be a good protein aggregate solubilizer, with future applications in inclusion body solubilization and protein refolding.

Fibrillization of lentil proteins is impacted by the protein extraction conditions and co-extracted phenolics

Legume proteins can be induced to form amyloid-like fibrils upon heating at low pH, with the exact conditions greatly impacting the fibril characteristics. The protein extraction method may also impact the resulting fibrils, although this effect has not been carefully examined. Here, the fibrillization of lentil protein prepared using various extraction methods and the corresponding fibril morphology were characterized. It was found that an acidic, rather than alkaline, protein extraction method was better suited for producing homogeneous, long, and straight fibrils from lentil proteins. During alkaline extraction, co-extracted phenolic compounds bound proteins through covalent and non-covalent interactions, contributing to the formation of heterogeneous, curly, and tangled fibrils. Recombination of isolated phenolics and proteins (from acidic extracts) at alkaline pH resulted in a distinct morphology, implicating a role for polyphenol oxidase also in modifying proteins during alkaline extraction. These results help disentangle the complex factors affecting legume protein fibrillization.

Electrostatics Choreographs the Aggregation Dynamics of Full-Length TDP-43 via a Monomeric Amyloid Precursor

TDP-43 is a ubiquitously expressed, multidomain functional protein that is distinctively known to form aggregates in many fatal neurodegenerative disorders. However, the information for arresting TDP-43 aggregation is missing due to a lack of understanding of the molecular mechanism of the aggregation and structural properties of TDP-43. TDP-43 is inherently prone to aggregation and has minimal protein solubility. Multiple studies have been performed on the smaller parts of TDP-43 or the full-length protein attached to a large solubilization tag. However, the presence of co-solutes or solubilization tags is observed to interfere with the molecular properties and aggregation mechanism of full-length TDP-43. Notably, this study populated and characterized the native, dimeric state of TDP-43 without the interference of co-solutes or protein modifications. We observed that the electrostatics of the local environment is capable of the partial unfolding and monomerization of the native dimeric state of TDP-43 into an amyloidogenic molten globule. By employing the tools of thermodynamics and kinetics, we reveal the structural characteristics and temporal order of the early intermediates and transition states during the transition of the molten globule to β-rich, amyloid-like aggregates of TDP-43, which is governed by the electrostatics of the environment. The current advanced understanding of the nature of native and early aggregation-prone intermediates, early steps, and the influence of electrostatics in TDP-43 aggregation is essential for drug design.

Probing the interaction mechanisms between sunset yellow dye and trypsin protein leading to amorphous aggregation under low pH conditions

Protein aggregation poses a significant concern in the field of food sciences, and various factors, such as synthetic food dyes, can contribute to protein aggregation. One such dye, Sunset Yellow (SY), is commonly employed in the food industry. Trypsin was used as a model protein to assess the impact of SY. We employed several biophysical techniques to examine the binding and aggregation mechanisms between SY and trypsin at different pHs. Results from intrinsic fluorescence measurements indicate a stronger interaction between SY and trypsin at pH 2.0 compared to pH 6.0. Turbidity data reveal trypsin aggregation in the presence of 0.05-3.0 mM SY at pH 2.0, while no aggregation was observed at pH 6.0. Kinetic data demonstrate a rapid, lag-phase-free SY-induced aggregation of trypsin. Circular dichroism analysis reveals that trypsin adopts a secondary structure in the presence of SY at pH 6.0, whereas at pH 2.0, the secondary structure was nearly lost with increasing SY concentrations. Furthermore, turbidity and kinetics data suggest that trypsin aggregation depends on trypsin concentrations and pH. Our study highlights potential health risks associated with the consumption of SY, providing insights into its impact on human health and emphasizing the necessity for further research in this field.

Membrane protein chaperone and sodium chloride modulate the kinetics and morphology of amyloid beta aggregation

Protein aggregation is a biological phenomenon caused by the accumulation of misfolded proteins. Amyloid beta (Aβ) peptides are derived from the cleavage of a larger membrane protein molecule and accumulate to form plaques extracellularly. According to the amyloid hypothesis, accumulation of Aβ aggregates in the brain is primarily responsible for the pathogenesis of Alzheimer's disease (AD). Therefore, the disassembly of Aβ aggregates may provide opportunities for alleviating or treating AD. Here, we show that the novel protein targeting machinery from chloroplast, chloroplast signal recognition particle 43 (cpSRP43), is an ATP-independent membrane protein chaperone that can both prevent and reverse Aβ aggregation effectively. Using of thioflavin T dye, we obtained the aggregation kinetics of Aβ aggregation and determined that the chaperone prevents Aβ aggregation in a concentration-dependent manner. Size exclusion chromatography and sedimentation assays showed that 10-fold excess of cpSRP43 can keep Aβ in the soluble monomeric form. Electron microscopy showed that the fibril structure was disrupted in the presence of this chaperone. Importantly, cpSRP43 utilizes the binding energy to actively remodel the preformed Aβ aggregates without assistance by a co-chaperone and ATP, emphasizing its unique function among protein chaperones. Moreover, when sodium chloride concentration is higher than 25 mm, the Aβ aggregation rate increases drastically to form tightly associated aggregates and generate more oligomers. Our results demonstrate that the presence of cpSRP43 and low NaCl levels inhibit or retard Aβ peptide aggregation, potentially opening new avenues to strategically develop an effective treatment for AD.

Monovalent cations have different effects on the assembly kinetics and morphology of α-synuclein amyloid fibrils

Formation of α-synuclein amyloid fibrils is a pathological hallmark of Parkinson's disease and a phenomenon that is strongly modulated by environmental factors. Here, we compared effects of different monovalent cations (Li+, Na+, K+) on the formation and properties of α-synuclein amyloid fibrils. Na+ > Li+ were found to have concentration-dependent catalytic effects on primary nucleation whereas K+ ions acted inhibitory. We discuss this discrepancy in terms of a superior affinity of Na+ and Li+ to carboxylic protein groups, resulting in reduced Columbic repulsion and by considering K+ as an ion with poor protein binding and slight chaotropic character, which could promote random coil protein structure. K+ ions, furthermore, appeared to lower the β-sheet content of the fibrils and increase their persistence lengths, the latter we interpret as a consequence of lesser ion binding and hence higher line charge of the fibrils. The finding that Na+ and K+ have opposite effects on α-synuclein aggregation is intriguing in relation to the significant transient gradients of these ions across axonal membranes, but also important for the design and interpretation of biophysical assays where buffers containing these monovalent cations have been intermixedly used.

Investigating the Effects of NaCl on the Formation of AFs from Gluten in Cooked Wheat Noodles

To clarify the effect of NaCl concentration (0-2.0%) on the formation of amyloid fibrils (AFs) in cooked wheat noodles, the morphology, surface hydrophobicity, secondary structure, molecular weight distribution, microstructure, and crystal structure of AFs were investigated in this paper. Fluorescence data and Congo red stain images confirmed the presence of AFs and revealed that the 0.4% NaCl concentration promoted the production of AFs. The surface hydrophobicity results showed that the hydrophobicity of AFs increased significantly from 3942.05 to 6117.57 when the salt concentration increased from 0 to 0.4%, indicating that hydrophobic interactions were critical for the formation of AFs. Size exclusion chromatography combined with gel electrophoresis plots showed that the effect of NaCl on the molecular weight of AFs was small and mainly distributed in the range of 5-7.1 KDa (equivalent to 40-56 amino acid residues). X-ray diffraction and AFM images showed that the 0.4% NaCl concentration promoted the formation and longitudinal growth of AFs, while higher NaCl concentrations inhibited the formation and expansion of AFs. This study contributes to the understanding of the mechanism of AF formation in wheat flour processing and provides new insight into wheat gluten aggregation behavior.

Amyloid-Based Albumin Hydrogels

Amyloid fibrils may serve as building blocks for the preparation of novel hydrogel materials from abundant, low-cost, and biocompatible polypeptides. This work presents the formation of physically cross-linked, self-healing hydrogels based on bovine serum albumin at room temperature through a straightforward disulfide reduction step induced by tris (2-carboxyethyl) phosphine hydrochloride. The structure and surface charge of the amyloid-like fibrils is determined by the pH of the solution during self-assembly, giving rise to hydrogels with distinct physicochemical properties. The hydrogel surface can be readily functionalized with the extracellular matrix protein fibronectin and supports cell adhesion, spreading, and long-term culture. This study offers a simple, versatile, and inexpensive method to prepare amyloid-based albumin hydrogels with potential applications in the biomedical field.

Multivariate effects of pH, salt, and Zn2+ ions on Aβ40 fibrillation

Amyloid-β (Aβ) peptide aggregation plays a central role in the progress of Alzheimer's disease (AD), of which Aβ-deposited extracellular amyloid plaques are a major hallmark. The brain micro-environmental variation in AD patients, like local acidification, increased ionic strength, or changed metal ion levels, cooperatively modulates the aggregation of the Aβ peptides. Here, we investigate the multivariate effects of varied pH, ionic strength and Zn²⁺ on Aβ₄₀ fibrillation kinetics. Our results reveal that Aβ fibrillation kinetics are strongly affected by pH and ionic strength suggesting the importance of electrostatic interactions in regulating Aβ₄₀ fibrillation. More interestingly, the presence of Zn²⁺ ions can further alter or even reserve the role of pH and ionic strength on the amyloid fibril kinetics, suggesting the importance of amino acids like Histidine that can interact with Zn²⁺ ions. Both pH and ionic strength regulate the secondary nucleation processes, however regardless of pH and Zn²⁺ ions, ionic strength can also modulate the morphology of Aβ₄₀ aggregates. These multivariate effects in bulk solution provide insights into the correlation of pH-, ionic strength- or Zn²⁺ ions changes with amyloid deposits in AD brain and will deepen our understanding of the molecular pathology in the local brain microenvironment.

Salt-Inducing Assembly Polymorphism Strategy for Cytotoxicity Differentiation of Phenol-Soluble Modulin α3 Assemblies

Phenol-soluble modulin α3 (PSMα3) can self-assemble into fibrous assemblies with a unique "cross-α" sheet structure, which serves as a key virulence factor in the infection of Staphylococcus aureus. However, the structure-cytotoxicity relationships of PSMα3 still remain elusive. Herein, we utilized the strategy of salt-inducing assembly polymorphism to controllably prepare three PSMα3 assemblies with morphological and structural distinctions, including amorphous aggregates (AAs), rigid fibrils (RFs), and oligomers/curvilinear fibrils (OCFs), which provided a convincing method to facilitate the structure-cytotoxicity investigation of PSMα3 assemblies. Our results affirmed that amyloid fibrillation was essential for the enhancement of PSMα3 cytotoxicity, which was proved based on the evidence that RFs and OCFs both triggered more obvious cytotoxicity than AAs. Furthermore, our study also demonstrated that the cytotoxicity was severely dependent on the size and structure of PSMα3 fibrils. In detail, smaller OCFs rich in α-helices exhibited stronger virulence than RFs with larger sizes and low α-helical contents. The cytotoxicity caused by such fibrils was achieved via a membrane-disrupting mechanism, in which RFs and OCFs might be prone to membrane thinning and perforation, respectively. This strategy of salt-inducing PSMα3 assembly polymorphism facilitated the comprehension of the relationship between the characteristics of PSMα3 assemblies and their cytotoxicity and was also helpful to understanding the intrinsic assembly mechanism of the PSMα3.

Insights into Cerebral Amyloid Angiopathy Type 1 and Type 2 from Comparisons of the Fibrillar Assembly and Stability of the Aβ40-Iowa and Aβ40-Dutch Peptides

Two distinct diseases are associated with the deposition of fibrillar amyloid-β (Aβ) peptides in the human brain in an age-dependent fashion. Alzheimer's disease is primarily associated with parenchymal plaque deposition of Aβ42, while cerebral amyloid angiopathy (CAA) is associated with amyloid formation of predominantly Aβ40 in the cerebral vasculature. In addition, familial mutations at positions 22 and 23 of the Aβ sequence can enhance vascular deposition in the two major subtypes of CAA. The E22Q (Dutch) mutation is associated with CAA type 2, while the D23N (Iowa) mutation is associated with CAA type 1. Here we investigate differences in the formation and structure of fibrils of these mutant Aβ peptides in vitro to gain insights into their biochemical and physiological differences in the brain. Using Fourier transform infrared and nuclear magnetic resonance spectroscopy, we measure the relative propensities of Aβ40-Dutch and Aβ40-Iowa to form antiparallel structure and compare these propensities to those of the wild-type Aβ40 and Aβ42 isoforms. We find that both Aβ40-Dutch and Aβ40-Iowa have strong propensities to form antiparallel β-hairpins in the first step of the fibrillization process. However, there is a marked difference in the ability of these peptides to form elongated antiparallel structures. Importantly, we find marked differences in the stability of the protofibril or fibril states formed by the four Aβ peptides. We discuss these differences with respect to the mechanisms of Aβ fibril formation in CAA.

Influence of ion specificity and concentration on the conformational transition of intrinsically disordered sheep prion peptide

The structural sensitivity of the IDPs with the ions has been observed experimentally; however, it is still unclear how the presence of different metal ions affects structural stability. We performed atomistic molecular dynamics simulation of sheep prion peptide (142-167) in presence of different monovalent, divalent ions at various concentrations to find out the effect of the size, charge, and ionic concentration on the structure of the peptide. It is found that Li + ions have a higher survival probability compared to Na + , K + and Mg2 + affecting the solvation structure of the protein leading to the alpha-helix structure. At high concentration, due to the increase in the ion-solvent and ion-counter interactions, the effect of the ions is screened on the surface of the protein and hence no ion specificity is observed. This study demonstrates how ions can be used to regulate the protein structure and function that can help in designing drugs.

Ion-Mediated Morphological Diversity in Protein Amyloid Systems

Salt ions are considered among the major determinants ruling protein folding, stability, and self-assembly in the context of amyloid-related diseases, protein drug development, and functional biomaterials. Here, we report that Hofmeister ions not only determine the rate constants of the aggregation reaction for human insulin and hen egg white lysozyme but also control the generation of a plethora of amyloid-like morphologies ranging from the nanoscale to the microscale. We anticipate that the latter is a result of a balance between colloidal and conformational stability combined with an ion-specific effect and highlight the importance of salt ions in controlling the biological functions of protein aggregates.

Development of HANABI, an ultrasonication-forced amyloid fibril inducer

Amyloid fibrils involved in amyloidoses are crystal-like aggregates, which are formed by breaking supersaturation of denatured proteins. Ultrasonication is an efficient method of agitation for breaking supersaturation and thus inducing amyloid fibrils. By combining an ultrasonicator and a microplate reader, we developed the HANABI (HANdai Amyloid Burst Inducer) system that enables high-throughput analysis of amyloid fibril formation. Among high-throughput approaches of amyloid fibril assays, the HANABI system has advantages in accelerating and detecting spontaneous amyloid fibril formation. HANABI is also powerful for amplifying a tiny amount of preformed amyloid fibrils by seeding. Thus, HANABI will contribute to creating therapeutic strategies against amyloidoses by identifying their biomarkers.

Strong acids induce amyloid fibril formation of β2-microglobulin via an anion-binding mechanism

Amyloid fibrils, crystal-like fibrillar aggregates of proteins associated with various amyloidoses, have the potential to propagate via a prion-like mechanism. Among known methodologies to dissolve preformed amyloid fibrils, acid treatment has been used with the expectation that the acids will degrade amyloid fibrils similar to acid inactivation of protein functions. Contrary to our expectation, treatment with strong acids, such as HCl or H₂SO₄, of β₂-microglobulin (β2m) or insulin actually promoted amyloid fibril formation, proportionally to the concentration of acid used. A similar promotion was observed at pH 2.0 upon the addition of salts, such as NaCl or Na₂SO₄. Although trichloroacetic acid, another strong acid, promoted amyloid fibril formation of β2m, formic acid, a weak acid, did not, suggesting the dominant role of anions in promoting fibril formation of this protein. Comparison of the effects of acids and salts confirmed the critical role of anions, indicating that strong acids likely induce amyloid fibril formation via an anion-binding mechanism. The results suggest that although the addition of strong acids decreases pH, it is not useful for degrading amyloid fibrils, but rather induces or stabilizes amyloid fibrils via an anion-binding mechanism.

Nicking and fragmentation are responsible for α-lactalbumin amyloid fibril formation at acidic pH and elevated temperature

Amyloid fibrils are ordered aggregates that may be formed from disordered, partially unfolded, and fragments of proteins and peptides. There are several diseases, which are due to the formation and deposition of insoluble β-sheet protein aggregates in various tissue, collectively known as amyloidosis. Here, we have used bovine α-lactalbumin as a model protein to understand the mechanism of amyloid fibril formation at pH 1.6 and 65°C under non-reducing conditions. Amyloid fibril formation is confirmed by Thioflavin T fluorescence and atomic force microscopy (AFM). Our finding demonstrates that hydrolysis of peptide bonds occurs under these conditions, which results in nicking and fragmentation. The nicking and fragmentation have been confirmed on non-reducing and reducing gel. We have identified the fragments by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. The fragmentation may initiate nucleation as it coincides with AFM images. Conformational changes associated with monomer resulting in fibrillation are shown by circular dichroism and Raman spectroscopy. The current study highlights the importance of nicking and fragmentation in amyloid fibril formation, which may help understand the role of acidic pH and proteolysis under in vivo conditions in the initiation of amyloid fibril formation.

Polyphenol-solubility alters amyloid fibril formation of α-synuclein

Amyloid fibril formation is associated with various amyloidoses, including neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Amyloid fibrils form above the solubility of amyloidogenic proteins or peptides upon breaking supersaturation, followed by a nucleation and elongation mechanism, which is similar to the crystallization of solutes. Many additives, including salts, detergents, and natural compounds, promote or inhibit amyloid formation. However, the underlying mechanisms of the opposing effects are unclear. We examined the effects of two polyphenols, that is, epigallocatechin gallate (EGCG) and kaempferol-7─O─glycoside (KG), with high and low solubilities, respectively, on the amyloid formation of α-synuclein (αSN). EGCG and KG inhibited and promoted amyloid formation of αSN, respectively, when monitored by thioflavin T (ThT) fluorescence or transmission electron microscopy (TEM). Nuclear magnetic resonance (NMR) analysis revealed that, although interactions of αSN with soluble EGCG increased the solubility of αSN, thus inhibiting amyloid formation, interactions of αSN with insoluble KG reduced the solubility of αSN, thereby promoting amyloid formation. Our study suggests that opposing effects of polyphenols on amyloid formation of proteins and peptides can be interpreted based on the solubility of polyphenols.

Unraveling the NaCl Concentration Effect on the First Stages of α-Synuclein Aggregation

Intraneuronal aggregation of the intrinsically disordered protein α-synuclein is at the core of Parkinson's disease and related neurodegenerative disorders. Several reports show that the concentration of salts in the medium heavily affects its aggregation rate and fibril morphology, but a characterization of the individual monomeric conformations underlying these effects is still lacking. In this work, we have applied our α-synuclein-optimized coarse-grained molecular dynamics approach to decipher the structural features of the protein monomer under a range of NaCl concentrations (0.0-1.0 M). The results show that key intramolecular contacts between the terminal domains are lost at intermediate concentrations (leading to extended conformations likely to fibrillate), but recovered at high concentrations (leading to compact conformations likely to evolve toward amorphous aggregates). The pattern of direct interactions of the terminal α-synuclein domains with Na⁺ and Cl^- ions plays a key role in explaining this effect. Our results are consistent with a recent study reporting a fibrillation enhancement at moderate NaCl concentrations but an inhibition at higher concentrations. The present work will contribute to improving our understanding of the structural features of monomeric α-synuclein, determining its NaCl-induced fibrillation propensity and the molecular basis of synucleinopathies, necessary for the future development of disease-halting therapies.

The protein-surfactant stoichiometry governs the conformational switching and amyloid nucleation kinetics of tau K18

Amyloids are pathological hallmarks of a number of debilitating neurodegenerative diseases. Understanding the molecular mechanism of protein amyloid assembly with an emphasis on structural characterization of early, key prefibrillar species is important for targeted drug design and clinical interventions. Tau is an intrinsically disordered, microtubule-binding protein which is also implicated in various neurodegenerative disorders such as frontotemporal dementia, Down's syndrome, Alzheimer's disease, etc. Earlier reports have demonstrated that tau aggregation in vitro is triggered by anionic inducers, presumably due to charge compensation which facilitates intermolecular association between the tau polypeptide chains. However, the molecular mechanism of tau amyloid aggregation, involving the structural characterization of amyloidogenic intermediates formed especially during early key steps, remains elusive. In this work, we have employed a spectroscopic toolbox to elucidate the mechanism of anionic surfactant-induced disorder-to-order amyloid transition of a tau segment. This study revealed that the amyloid assembly is mediated via binding-induced conformational switching into an early partially helical amyloid-competent intermediate. Additionally, protein and inducer concentration-dependent studies indicated that at the higher protein and/or inducer concentrations, competing off-pathway intermediates dampen the amyloid assembly which implies that the stoichiometry of protein and inducer plays a key regulatory role in the amyloid nucleation and fibril elongation kinetics.

Salt Dependence Conformational Stability of the Dimeric SAM Domain of MAPKKK Ste11 from Budding Yeast: A Native-State H/D Exchange NMR Study

The sterile α motif, also called the SAM domain, is known to form homo or heterocomplexes that modulate diverse biological functions through the regulation of specific protein-protein interactions. The MAPK pathway of budding yeast Saccharomyces cerevisiae is comprised of a three-tier kinase system akin to mammals. The MAPKKK Ste11 protein of yeast contains a homodimer SAM domain, which is critical for transmitting cues to the downstream kinases. The structural stability of the dimeric Ste11 SAM is maintained by hydrophobic and ionic interactions at the interfacial amino acids. The urea-induced equilibrium-unfolding process of the Ste11 SAM domain is cooperative without evidence of any intermediate states. The native-state H/D exchange under subdenaturing conditions is a useful method for the detection of intermediate states of proteins. In the present study, we investigated the effect of ionic strength on the conformational stability of the dimer using the H/D exchange experiments. The hydrogen exchange behavior of the Ste11 dimer under physiological salt concentrations reveals two partially unfolded metastable intermediate states, which may be generated by a sequential and cooperative unfolding of the five helices present in the domain. These intermediates appear to be significant for the reversible unfolding kinetics via hydrophobic collapse. In contrast, higher ionic concentrations eliminate this cooperative interactions that stabilize the pairs of helices.

Amyloid Formation of α-Synuclein Based on the Solubility- and Supersaturation-Dependent Mechanism

Amyloid fibrils are formed by denatured proteins when the supersaturation of denatured proteins is broken by agitation, such as ultrasonication, or by seeding, although the detailed mechanism of how solubility and supersaturation regulate amyloid formation remains unclear. To further understand the mechanism of amyloid formation, we examined α-synuclein (α-syn) amyloid formation at varying concentrations of SDS, LPA, heparin, or NaCl at pH 7.5. Amyloid fibrils were formed below or around the critical micelle concentrations (CMCs) of SDS (2.75 mM) and LPA (0.24 mM), although no fibrils were formed above the CMCs. On the other hand, amyloid fibrils were formed with 0.01-2.5 mg/mL of heparin and 0.5-1.0 M NaCl, and amyloid formation was gradually suppressed at higher concentrations of heparin and NaCl. To reproduce these concentration-dependent effects of additives, we constructed two models: (i) the ligand-binding-dependent solubility-modulation model and (ii) the cosolute-dependent direct solubility-modulation model, both of which were used by Tanford and colleagues to analyze the additive-dependent conformational transitions of proteins. The solubility of α-syn was assumed to vary depending on the concentration of additives either by the decreased solubility of the additive-α-syn complex (model i) or by the direct regulation of α-syn solubility (model ii). Both models well reproduced additive-dependent bell-shaped profiles of acceleration and inhibition observed for SDS and LPA. As for heparin and NaCl, participation of amorphous aggregates at high concentrations of additives was suggested. The models confirmed that solubility and supersaturation play major roles in driving amyloid formation in vitro, furthering our understanding of the pathogenesis of amyloidosis in vivo.

Exploration of Insulin Amyloid Polymorphism Using Raman Spectroscopy and Imaging

We aimed to investigate insulin amyloid fibril polymorphism caused by salt effects and heating temperature and to visualize the structural differences of the polymorphisms in situ using Raman imaging without labeling. The time course monitoring for amyloid formation was carried out in an acidic condition without any salts and with two species of salts (NaCl and Na₂SO₄) by heating at 60, 70, 80, and 90°C. The intensity ratio of two Raman bands at 1672 and 1657 cm^-1 due to antiparallel β-sheet and α-helix structures, respectively, was revealed to be an indicator of amyloid fibril formation, and the relative proportion of the β-sheet structure was higher in the case with salts, especially at a higher temperature with Na₂SO₄. In conjunction with the secondary structural changes of proteins, the S-S stretching vibrational mode of a disulfide bond (∼514 cm^-1) and the ratio of the tyrosine doublet I₈₅₀/I₈₂₆ were also found to be markers distinguishing polymorphisms of insulin amyloid fibrils by principal component analysis. Especially, amyloid fibrils with Na₂SO₄ media formed the gauche-gauche-gauche conformation of disulfide bond at a higher rate, but without any salts, the gauche-gauche-gauche conformation was partially transformed into the gauche-gauche-trans conformation at higher temperatures. The different environments of the hydroxyl groups of the tyrosine residue were assumed to be caused by fibril polymorphism. Raman imaging using these marker bands also successfully visualized the two- and three- dimensional structural differences of amyloid polymorphisms. These results demonstrate the potential of Raman imaging as a diagnostic tool for polymorphisms in tissues of amyloid-related diseases.

FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin and Trypsin under Neutral Salts

The effect of neutral salts on protein conformation was first analyzed by Hofmeister in 1888, however, even today this phenomenon is not completely understood. To clarify this effect, we studied changes in the secondary structure of two proteins: human serum albumin with predominantly α-helical structure and porcine pancreas β-trypsin with the typical β-structural arrangement in aqueous solutions of neutral salts (KSCN, KCl, (NH₄)₂SO₄). The changes in the secondary structure were studied at 23 °C and 80 °C by using the second derivative deconvolution method of the IR spectra. Our results demonstrated that the ability of the salts to stabilize/destabilize these two proteins correlates with the Hofmeister series of ions. At the same time, some exceptions were also observed. The destabilization of the native structures of both α-helical albumin and β-structural trypsin upon interaction with neutral salts leads to the formation of intermolecular β-sheets typical for amyloid fibrils or amorphous aggregates. Thus, our quantitative FTIR-spectroscopy analysis allowed us to further clarify the mechanisms and complexity of the neutral salt actions on protein structures which may lead to strategies preventing unwelcome misfolding of proteins.

Isoelectric point-amyloid formation of α-synuclein extends the generality of the solubility and supersaturation-limited mechanism

Proteins in either a native or denatured conformation often aggregate at an isoelectric point (pI), a phenomenon known as pI precipitation. However, only a few studies have addressed the role of pI precipitation in amyloid formation, the crystal-like aggregation of denatured proteins. We found that α-synuclein, an intrinsically disordered protein of 140 amino acid residues associated with Parkinson's disease, formed amyloid fibrils at pI (= 4.7) under the low-sodium phosphate conditions. Although α-synuclein also formed amyloid fibrils at a wide pH range under high concentrations of sodium phosphate, the pI-amyloid formation was characterized by marked amyloid-specific thioflavin T fluorescence and clear fibrillar morphology, indicating highly ordered structures. Analysis by heteronuclear NMR in combination with principal component analysis suggested that amyloid formation under low and high phosphate conditions occurred by distinct mechanisms. The former was likely to be caused by the intermolecular attractive charge-charge interactions, where α-synuclein has +17 and −17 charges even with the zero net charge. On the other hand, the latter was caused by the phosphate-dependent salting-out effects. pI-amyloid formation may play a role in the membrane-dependent amyloid formation of α-synuclein, where the negatively charged membrane surface reduces the local pH to pI and the membrane hydrophobic environment enhances electrostatic interactions. The results extend the supersaturation-limited mechanism of amyloid formation: Amyloid fibrils are formed under a variety of conditions of decreased solubility of denatured proteins triggered by the breakdown of supersaturation.

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pI precipitation of α-synuclein led to the formation of amyloid fibrils.

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Fibrils formed at pI were more organized than those formed under other conditions.

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Attractive charge-charge interactions are responsible for the pI-amyloid formation.

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pI-amyloid formation may lead to the amyloid formation upon phospholipid membranes.

Using protein engineering to understand and modulate aggregation

Protein aggregation occurs through a variety of mechanisms, initiated by the unfolded, non-native, or even the native state itself. Understanding the molecular mechanisms of protein aggregation is challenging, given the array of competing interactions that control solubility, stability, cooperativity and aggregation propensity. An array of methods have been developed to interrogate protein aggregation, spanning computational algorithms able to identify aggregation-prone regions, to deep mutational scanning to define the entire mutational landscape of a protein's sequence. Here, we review recent advances in this exciting and emerging field, focussing on protein engineering approaches that, together with improved computational methods, hold promise to predict and control protein aggregation linked to human disease, as well as facilitating the manufacture of protein-based therapeutics.

Early mechanisms of amyloid fibril nucleation in model and disease-related proteins

Protein amyloid aggregation is a hallmark in neuropathologies and other diseases of tremendous impact such as Alzheimer's or Parkinson's diseases. During the last decade, it has become increasingly evident that neuronal death is mainly induced by proteinaceous oligomers rather than the mature amyloid fibrils. Therefore, the earliest molecular events occurring during the amyloid aggregation cascade represent a growing interest of study. Important breakthroughs have been achieved using experimental data from different proteins, used as models, as well as systems related to diseases. Here, we summarize the structural properties of amyloid oligomeric and fibrillar aggregates and review the recent advances on how biophysical techniques can be combined with quantitative kinetic analysis and theoretical models to study the detailed mechanism of oligomer formation and nucleation of fibrils. These insights into the mechanism of early oligomerization and amyloid nucleation are of relevant interest in drug discovery and in the design of preventive strategies against neurodegenerative diseases.

Possible mechanisms of polyphosphate-induced amyloid fibril formation of β2-microglobulin

Polyphosphate (polyP), which is found in various microorganisms and human cells, is an anionic biopolymer consisting of inorganic phosphates linked by high-energy phosphate bonds. Previous studies revealed that polyPs strongly promoted the amyloid formation of several amyloidogenic proteins; however, the mechanism of polyP-induced amyloid formation remains unclear. In the present study using β₂-microglobulin (β2m), a protein responsible for dialysis-related amyloidosis, we investigated amyloid formation in the presence of various chain lengths of polyPs at different concentrations under both acidic (pH 2.0 to 2.5) and neutral pH (pH 7.0 to 7.5) conditions. We found that the amyloid formation of β2m at acidic pH was significantly accelerated by the addition of polyPs at an optimal polyP concentration, which decreased with an increase in chain length. The results obtained indicated that electrostatic interactions between positively charged β2m and negatively charged polyPs play a major role in amyloid formation. Under neutral pH conditions, long polyP with 60 to 70 phosphates induced the amyloid formation of β2m at several micromoles per liter, a similar concentration range to that in vivo. Since β2m with an isoelectric point of 6.4 has a slightly negative net charge at pH 7, polyPs were unlikely to interact with β2m electrostatically. PolyPs appear to dehydrate water molecules around β2m under the unfolded conformation, leading to the preferential stabilization of less water-exposed amyloid fibrils. These results not only revealed the pH-dependent mechanism of the amyloid formation of β2m but also suggested that polyPs play an important role in the development of dialysis-related amyloidosis.

Cu/Zn-superoxide dismutase forms fibrillar hydrogels in a pH-dependent manner via a water-rich extended intermediate state

Under certain conditions, amyloid-like fibrils can develop into three-dimensional networks and form hydrogels by a self-assembly process. When Cu/Zn superoxide dismutase (SOD1), an anti-oxidative enzyme, undergoes misfolding, fibrillar aggregates are formed, which are a hallmark of a certain form of familial amyotrophic lateral sclerosis (ALS). However, the issue of whether SOD1 fibrils can be assembled into hydrogels remains to be tested. Here, we show that the SOD1 polypeptides undergo hydrogelation accompanied by the formation of thioflavin T-positive fibrils at pH 3.0 and 4.0, but not at pH 5.0 where precipitates are formed. The results of viscoelastic analyses indicate that the properties of SOD1 hydrogels (2%) were similar to and slightly more fragile than a 0.25% agarose gel. In addition, monitoring by a quartz crystal microbalance with admittance analysis showed that the denaturing of immobilized SOD1 on a sensor under the hydrogelation conditions at pH 3.0 and 4.0 resulted in an increase in the effective acoustic thickness from ~3.3 nm (a folded rigid form) to ~50 and ~100 nm (an extended water-rich state), respectively. In contrast, when SOD1 was denatured under the same conditions at pH 5.0, a compact water-poor state with an effective acoustic thickness of ~10 nm was formed. The addition of physiological concentrations of NaCl to the pH 4.0 sample induced a further extension of the SOD1 with larger amounts of water molecules (with an effective acoustic thickness of ~200 nm) but suppressed hydrogel formation. These results suggest that different denatured intermediate states of the protein before self-assembly play a major role in determining the characteristics of the resulting aggregates and that a conformational change to a suitable level of extended water-rich intermediate state before and/or during intermolecular assembling is required for fibrillation and hydrogelation in the case of globular proteins.

Foreword to 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', a special issue in Honour of Fumio Arisaka's 70th birthday

This issue of Biophysical Reviews, titled 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', is a collection of articles dedicated in honour of Professor Fumio Arisaka's 70th birthday. Initially, working in the fields of haemocyanin and actin filament assembly, Fumio went on to publish important work on the elucidation of structural and functional aspects of T4 phage biology. As his career has transitioned levels of complexity from proteins (hemocyanin) to large protein complexes (actin) to even more massive bio-nanomachinery (phage), it is fitting that the subject of this special issue is similarly reflective of his multiscale approach to structural biology. This festschrift contains articles spanning biophysical structure and function from the bio-molecular through to the bio-nanomachine level.