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Amyloids have special structural properties and are involved in many aspects of biological function. In particular, amyloids are the cause or hallmarks of a group of notorious and incurable neurodegenerative diseases. The extraordinary high molecular weight and aggregation states of amyloids have posed a challenge for researchers studying them. Solid-state NMR (SSNMR) has been extensively applied to study the structures and dynamics of amyloids for the past 20 or more years and brought us tremendous progress in understanding their structure and related diseases. These studies, at the same time, helped to push SSNMR technical developments in sensitivity and resolution. In this review, some interesting research studies and important technical developments are highlighted to give the reader an overview of the current state of this field. [Display omitted] Solid-state NMR is a very powerful method for studying amyloid fibrils. In this review, Liu et al. describe how solid-state NMR has been applied to elucidate the structures and dynamic properties of amyloids. They also discuss experimental strategies, technical developments, and current limitations in this field. [ABSTRACT FROM AUTHOR]

• TDP-43 aggregation is highly dependent on the protein domains. • Aggregation and morphological outcomes are influenced by triggers. • Polymorphism of TDP-43 is a promising drug target. Nuclear TAR DNA-binding protein 43 (TDP-43) mitigates cellular function, but the dynamic nucleus-cytoplasm shuttling of TDP-43 is disrupted in diseases, such as Amyotrophic Lateral Sclerosis (ALS). The polymorphic nature of the TDP-43 structures in vitro and in vivo is a result of environmental factors leading to the protein pathogenesis. Once the triggers which mitigate TDP-43 biochemistry are identified, new therapies can be developed. This review aims to illustrate recent discoveries in the diversity of TDP-43 structures (amyloidogenic and non-amyloidogenic) and highlight the triggers which result in their formation. [ABSTRACT FROM AUTHOR]

Structural biology of proteins emphasises that proteins ought to have an ordered structure to perform their biological role optimally. The over-reliance on the ordered structure of proteins is now slowly shifting towards a more comprehensive discussion platform. Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are gaining momentum in protein structural biology as we update ourselves with evolutionary traits and functional importance in various organisms. The evolution and functional significance of this diverse class of protein conformations are based on sequence exhibition, structural attainment, and interactions with their immediate surroundings. In this review, we emphasise the evolutionary status of disordered proteins and correlate their functional importance in the physiology of specific organisms. We aim to close this review by establishing a positive correlation between IDPs and their importance in human health and future medicine. Establishing firm roles of IDPs and IDPRs with extensive research will help expand the field of structural biology, helping us understand the fundamentals of protein folding and misfolding, associated diseases and drug design. [ABSTRACT FROM AUTHOR]

The morphology of supramolecular polymer aggregates evolved during normal aging from thin 25-nm-wide nanoribbons into 1-µm-wide nanoribbons and nanotubes thanks to hydrophobic interactions between phenylalanine residues exposed on the edges of nanoribbons. [Display omitted] • Benzene-1,3,5-tricarboxamide decorated with diphenylalanine self-assemble into micrometer-long nanoribbons immediately after dissolution. • Nanoribbons interact laterally via "sticky edges" and gradually merge over the entire length. • After reaching a critical width nanoribbons self-merge, irreversibly forming nanotubes. • Mechanical perturbations cause nanotube fracture and fragmentation similar to analogous inorganic materials. During the aging of supramolecular systems, new stable materials with different morphologies, molecular packing, and hierarchical organization may form from the initial assembly. Understanding the mechanisms and pathways accompanying age-related changes may allow for the controlled synthesis of multiple materials from a single molecule in a nature-inspired manner. Herein, we demonstrate the multi-stage evolution of a single solution of C3-symmetric peptide amphiphile containing diphenylalanine fragment and benzyl-1,3,5-tricarboxamide core. Transmission electron microscopy reveals the rapid formation of 20–40 nm wide nanoribbons in an aqueous solution within 60 s after preparation. The lateral edges of nanoribbons contain solvent-exposed aromatic residues that tend to merge via an unconventional edge-to-edge zipping mechanism, leading to the nanoribbon's growth in width. After reaching a critical width and flexibility, "sticky edges" on the same nanoribbon may merge via a self-zipping mechanism, forming rigid nanotubes. Eventually, mechanical perturbations cause buckling and fracture of nanotubes into shorter nanotubes via flexural or tensile failure. This work reports new evolution pathways in soft 2D assemblies and introduces solution ageing as a promising method to control morphology of peptide amphiphiles. [ABSTRACT FROM AUTHOR]

The fields of allostery and amyloid-related pathologies, such as Parkinson's disease (PD), have been extensively explored individually, but less is known about how amyloids control allostery. Recent advancements have revealed that amyloids can drive allosteric effects in both intrinsically disordered proteins, such as alpha-synuclein (αS), and multi-domain signaling proteins, such as protein kinase A (PKA). Amyloid-driven allostery plays a central role in explaining the mechanisms of gain-of-pathological-function mutations in αS (e.g. E46K, which causes early PD onset) and loss-of-physiological-function mutations in PKA (e.g. A211D, which predisposes to tumors). This review highlights allosteric effects of disease-related mutations and how they can cause exposure of amyloidogenic regions, leading to amyloids that are either toxic or cause aberrant signaling. We also discuss multiple potential modulators of these allosteric effects, such as MgATP and kinase substrates, opening future opportunities to improve current pharmacological interventions against αS and PKA-related pathologies. Overall, we show that amyloid-driven allosteric models are useful to explain the mechanisms underlying disease-related mutations. [Display omitted] • Amyloid-Driven Allostery (ADA) is the amplification of allosteric effects by amyloids. • ADA is observed for both intrinsically disordered and globular multi-domain proteins. • ADA explains the mechanism of action of disease-related inherited mutations. • ADA applies to gain-of-pathological / loss-of-physiological function mutations. • Metabolites and kinase substrates modulate ADA, opening pharmacological opportunities. [ABSTRACT FROM AUTHOR]

A modified lysine residue containing an environment-sensitive moiety was prepared through a straightforward synthesis, and its fluorescent properties were examined. The new fluorescent sensor, DMN-BocK, can monitor amyloid aggregation processes associated with neurodegenerative diseases such as Alzheimer's or Parkinson's. DMN-BocK offers advantages over classical amyloid-specific dyes like Thioflavins or Congo Red because it is (1) available to detect a broader range of amyloid structures; (2) useful both in vitro and in cellulo ; (3) capable of differentiating amyloid structures, providing information on the binding site microenvironment; and (4) a synthon than can be incorporated into protein sequences to gain further structural information. Our findings suggest that DMN-based amino-acid probes have a strong potential to become a sensor of choice for in vitro and in cellulo studies of amyloid aggregation in drug discovery assays. • The non-natural amino acid DMN-BocK acts as an environment-sensitive fluorescence probe. • DMN-BocK can become a sensor of choice to study amyloid proteins. • Unlike classical amyloid-specific dyes, DMN-BocK can differentiate amyloid proteins. [ABSTRACT FROM AUTHOR]

Neurodegenerative disorders such as Parkinson's (PD) and Alzheimer's diseases (AD) are linked with the assembly and accumulation of proteins into structured scaffold called amyloids. These diseases pose significant challenges due to their complex and multifaceted nature. While the primary focus has been on endogenous amyloids, recent evidence suggests that bacterial amyloids may contribute to the development and exacerbation of such disorders. The gut-brain axis is emerging as a communication pathway between bacterial and human amyloids. This review delves into the novel role and potential mechanism of bacterial amyloids in modulating human amyloid formation and the progression of AD and PD. [Display omitted] • Gut microbiota and its metabolites are an imperative part of our immune, digestive and metabolic pathways. • Microbial products such as amyloids in the gut of healthy and diseased individuals play a crucial role in the pathophysiology of many diseases. • Bacterial amyloids modulate human amyloid assembly and may contribute to the progression of neurodegenerative diseases. • The gut-brain axis serves as the main communication pathway between human and bacterial amyloids. [ABSTRACT FROM AUTHOR]

Parkinson's disease (PD) is one of many neurodegenerative diseases. The protein associated with PD is α-synuclein (AS). Aggregation of AS protein into oligomers, protofilaments, and finally to fibrils yields to the development of PD. The aggregation process of AS leads to the formation of polymorphic AS fibrils. Herein, we compared four polymorphic full-length AS 1 – 140 fibrils, using extensive computational tools. The main conclusion of this study emphasizes the role of the structurally packed non-amyloid component (NAC) core domain in AS fibrils. Polymorphic AS fibrils that presented a packed NAC core domain, exhibited more β-sheets and fewer fluctuations in the NAC domain. Hence, these AS fibrils are more stable and populated than the AS fibrils, by which the NAC domains are more exposed, more fluctuate and less packed in the fibrillary structure. Therefore, this study emphasizes the importance of the NAC domain packing in the morphology of AS fibrils. The results obtained in this study will initiate future studies to develop compounds to prevent and inhibit AS aggregation. [Display omitted] • Two new AS 1 – 140 fibrils were constructed by molecular modeling and previous cryo-EM data. • Polymorphic AS fibrils show distinct NAC shape domains. • The packing shape of NAC in AS fibrils is crucial for fibril stability. [ABSTRACT FROM AUTHOR]

The whey protein β-lactoglobulin (βLG) forms fibrils similar to the amyloid fibrils in the neurodegenerative diseases due to its higher predisposition of β-sheets. This study shed light on the understanding different inorganic Keggin polyoxometalates (POMs) interaction with the protein βLG fibrils. POMs such as Phosphomolybdic acid (PMA), silicomolybdic acid (SMA), tungstosilicic acid (TSA), and phosphotungstic acid (PTA) were used due to their inherent higher anionic charges. The interaction studies were monitored with fluorescence spectra and Thioflavin T assay for both the βLG monomers and the fibrils initially to elucidate the binding ability of the POMs. The binding of POMs and βLG is also demonstrated by molecular docking studies. Zeta potential studies showed the electrostatic mediated higher interactions of the POMs with the protein fibrils. Isothermal titration calorimetry (ITC) studies showed that the molybdenum containing POMs have higher affinity to the protein fibrils than the tungsten. This study could help understanding formation of food grade protein fibrils which have profound importance in food industries. [Display omitted] • Binding of POMs to beta lactoglobulin fibrils evaluated using biophysical techniques. • POMs disintegrated the protofibrils of beta lactoglobulin. • POMs can have applicability as functional ingredients in food industries. [ABSTRACT FROM AUTHOR]

Disruption of the neuronal membrane by toxic amyloid β oligomers is hypothesized to be the major event associated with Alzheimer's disease's neurotoxicity. Misfolding of amyloid β is followed by aggregation via different pathways in which structurally different amyloid β oligomers can be formed. The respective toxic actions of these structurally diverse oligomers can vary significantly. Linking a particular toxic action to a structurally unique kind of amyloid β oligomers and resolving their toxicity-determining feature remains challenging because of their transient stability and heterogeneity. Moreover, the lipids that make up the membrane affect amyloid β oligomers' behavior, thus adding to the problem's complexity. The present review compares and analyzes the latest results to improve understanding of amyloid β oligomers' interaction with lipid bilayers. [Display omitted] [ABSTRACT FROM AUTHOR]

Proteins and their aggregation is significant field of research due to their association with various conformational maladies including well-known neurodegenerative diseases like Alzheimer's (AD), Parkinson's (PD), and Huntington's (HD) diseases. Amyloids despite being given negative role for decades are also believed to play a functional role in bacteria to humans. In this review, we discuss both facets of amyloid. We have shed light on AD, which is one of the most common age-related neurodegenerative disease caused by accumulation of Aβ fibrils as extracellular senile plagues. We also discuss PD caused by the aggregation and deposition of α-synuclein in form of Lewy bodies and neurites. Other amyloid-associated diseases such as HD and amyotrophic lateral sclerosis (ALS) are also discussed. We have also reviewed functional amyloids that have various biological roles in both prokaryotes and eukaryotes that includes formation of biofilm and cell attachment in bacteria to hormone storage in humans, We discuss in detail the role of Curli fibrils' in biofilm formation, chaplins in cell attachment to peptide hormones, and Pre-Melansomal Protein (PMEL) roles. The disease-related and functional amyloids are compared with regard to their structural integrity, variation in regulation, and speed of forming aggregates and elucidate how amyloids have turned from foe to friend. [ABSTRACT FROM AUTHOR]

[Display omitted] • Importance of disaggregation mechanism and innate disaggregation in living systems. • Different types and mechanism of disaggregation reported in literature. • Structural details of the interactions and the disaggregation mechanisms. • Amyloid disaggregation in protein aggregation disorders as a potential treatment. • Proposed amyloid disaggregation mechanism of an ATP-independent chaperone (L-PGDS). Protein aggregation and deposition of uniformly arranged amyloid fibrils in the form of plaques or amorphous aggregates is characteristic of amyloid diseases. The accumulation and deposition of proteins result in toxicity and cause deleterious effects on affected individuals known as amyloidosis. There are about fifty different proteins and peptides involved in amyloidosis including neurodegenerative diseases and diseases affecting vital organs. Despite the strenuous effort to find a suitable treatment option for these amyloid disorders, very few compounds had made it to unsuccessful clinical trials. It has become a compelling challenge to understand and manage amyloidosis with the increased life expectancy and ageing population. While most of the currently available literature and knowledge base focus on the amyloid inhibitory mechanism as a treatment option, it is equally important to organize and understand amyloid disaggregation strategies. Disaggregation strategies are important and crucial as they are present innately functional in many living systems and dissolution of preformed amyloids may provide a direct benefit in many pathological conditions. In this review, we have compiled the known amyloid disaggregation mechanism, interactions, and possibilities of using disaggregases as a treatment option for amyloidosis. We have provided the structural details using protein-ligand docking models to visualize the interaction between these disaggregases with amyloid fibrils and their respective proposed amyloid disaggregation mechanisms. After reviewing and comparing the different amyloid disaggregase systems and their proposed mechanisms, we presented two different hypotheses for ATP independent disaggregases using L-PGDS as a model. Finally, we have highlighted the importance of understanding the underlying disaggregation mechanisms used by these chaperones and organic compounds before the implementation of these disaggregases as a potential treatment option for amyloidosis. [ABSTRACT FROM AUTHOR]

The loss of crystallins solubility with aging and the formation of amyloid-like aggregates is considered the hallmark characteristic of cataract pathology. The present study was carried out to assess the effect of temperature on the soluble lens protein and the formation of protein aggregates with typical amyloid characteristics. The soluble fraction of lens proteins was subjected for heat treatment in the range of 40–60 °C, and the nature of protein aggregates was assessed by using Congo red (CR), thioflavin T (ThT), and 8-anilinonaphthalene-1-sulfonic acid (ANS) binding assays, circular dichroism (CD), Fourier-transform infrared (FT-IR) spectroscopy, and transmission electron microscopy (TEM). The heat-treated protein samples displayed a substantial bathochromic shift (≈15 nm) in the CR's absorption maximum (λ max) and increased ThT and ANS binding. The heat treatment of lens soluble proteins results in the formation of nontoxic, β-sheet rich, non-fibrillar, protein aggregates similar to the structures evident in the insoluble fraction of proteins isolated from the cataractous lens. The data obtained from the present study suggest that the exposure of soluble lens proteins to elevated temperature leads to the formation of non-fibrillar aggregates, establishing the role of amyloid in the heat-induced augmentation of cataracts pathology. Schematic model of heat-induced aggregation of the soluble fraction of lens proteins and their amyloid-like characteristics. The total proteins in an age-related cataract lens are partitioned into a soluble and insoluble fraction of proteins. The insoluble fraction contains large aggregates that might have formed through amyloid-like aggregation or sequestration of β-sheet rich crystallins, displaying typical amyloid characteristics. On the contrary, the soluble fraction of proteins might consist of soluble amyloid oligomers along with the native crystallins and other lens proteins, which upon heat treatment, sequestered as amyloids. Although both the aggregates display typical amyloid characteristics and identical morphology, they significantly differ in their stability in the presence of SDS. The heat-induced aggregated soluble fraction of protein gets disaggregated in the presence of SDS, whereas the insoluble fraction of protein remains stable. [Display omitted] [ABSTRACT FROM AUTHOR]

Alterations to the global levels of certain types of post-translational modifications (PTMs) are commonly observed in neurodegenerative diseases. The net influence of these PTM changes to the progression of these diseases can be deduced from cellular and animal studies. However, at the molecular level, how one PTM influences a given protein is not uniform and cannot be easily generalized from systemic observations, thus requiring protein-specific interrogations. Given that protein aggregation is a shared pathological hallmark in neurodegeneration, it is important to understand how these PTMs affect the behavior of amyloid-forming proteins. For this purpose, protein semisynthesis techniques, largely via native chemical and expressed protein ligation, have been widely used. These approaches have thus far led to our increased understanding of the site-specific consequences of certain PTMs to amyloidogenic proteins' endogenous function, their propensity for aggregation, and the structural variations these PTMs induce toward the aggregates formed. [Display omitted] [ABSTRACT FROM AUTHOR]

Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses. [Display omitted] • Aggregation-related disorders are caused by both amyloids and amorphous species. • Amyloids and amorphous aggregates show distinct characteristics upon aggregation. • Short peptides provide a valuable model in protein aggregation research. • LLPS might help understand the processes underlying amyloid fibrillation. [ABSTRACT FROM AUTHOR]

Understanding Aβ aggregation and inhibiting it at early stages is of utmost importance in treating Alzheimer's and other related amyloidogenic diseases. However, majority of the techniques to study Aβ aggregation mainly target the late stages; while those used to monitor early stages are either expensive, use extrinsic dyes, or do not provide information on molecular level interactions. Here, we investigate the early events of Aβ 16-22 (KLVFFAE) aggregation using Aβ 16-22 derived switch-peptides (SwPs) through a novel label-free approach employing Protein Charge Transfer Spectra (ProCharTS). When pH is increased from 2 to 7.2, the Aβ-derived switch peptides undergo controlled self-assembly, where the initial random coil peptides convert into β-sheet. We leveraged the intrinsic absorbance/luminescence arising from ProCharTS among growing peptide oligomers to observe the aggregation kinetics in real-time. In comparison to monomer, the lysine and glutamate headgroups in the peptide oligomer are expected to come in proximity enhancing ProCharTS intensity due to photoinduced electron transfer. With a combination of Aβ-derived switch-peptides and ProCharTS, we obtained structural insights on the early stages of Aβ-derived SwP aggregation in four unique peptides. Increase in scatter corrected ProCharTS absorbance (250–500 nm) and luminescence (320–720 nm) along with decreased mean luminescence lifetime (2.3–0.8 ns) characterize the initial stages of aggregation monitored for 1–96 h depending on the peptide. We correlated the results with Circular Dichroism (CD), 8-anilino-1-naphthalenesulfonic acid (ANS) and Thioflavin T (ThT) measurements. We demonstrate ProCharTS as an intrinsic analytical probe with following advantages over other conventional methods to track aggregation: it is a label-free probe; it's intensity can be measured using a UV–Vis spectrophotometer; it is more sensitive in detecting the early molecular events in aggregation compared to ANS and ThT; and it can provide information on specific contacts made between charged headgroups of Lysine/Glutamate in the oligomer. [Display omitted] • ProCharTS is sensitive to proximity between charged headgroups in protein. • This sensitivity was exploited to monitor formation of Abeta soluble oligomers. • ProCharTS can serve as label-free analytical probe to track peptide aggregation. • ProCharTS was more sensitive to oligomer formation compared to ANS or Thioflavin T. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) and cataract represent two common protein misfolding diseases closely associated with aging. Growing evidence suggests that these two diseases may be interrelated with each other through cross-sequence interactions between β-amyloid (Aβ) peptide and the short aggregating peptides derived from proteolytic breakdown of α-crystallin. αΑ(66–80) is one of several peptides produced by the proteolytic breakdown of α-crystallin in aged eye lens. Although it is evident that the Aβ(1–40) and αΑ(66–80) coexist in aged eye lenses and both the peptides are known to form macromolecular assemblies, their cross-sequence interaction and the seeding behavior are not known. In this study, the aggregation behavior of αΑ(66–80) has been examined in the presence of Aβ(1–40) on using thioflavin T (ThT) based aggregation kinetics. The presence of monomeric Aβ(1–40) augmented the aggregation kinetics of αΑ(66–80) and reduced the lag time of αΑ(66–80) aggregation. However, the addition of Aβ(1–40) or αΑ(66–80) fibrils (seeds) didn't result in any change in the rate of αΑ(66–80) aggregation. In this in vitro study, we could show that the presence Aβ(1–40) has substantial effect on the aggregation of αΑ(66–80), which suggests a possible interaction between AD and cataract pathologies. [ABSTRACT FROM AUTHOR]

Protein misfolding and aggregation are associated with human diseases and aging. However, microorganisms widely exploit the self-propagating properties of misfolded infectious protein particles, prions, as epigenetic information carriers that drive various phenotypic adaptations and encode molecular information. Microbial prion research has faced a paradigm shift in recent years, with breakthroughs that demonstrate the great functional and structural diversity of these agents. Here, we outline unorthodox examples of microbial prions in yeast and other microorganisms, focusing on their noncanonical functions. We discuss novel molecular mechanisms for the inheritance of conformationally-encoded epigenetic information and the evolutionary advantages they confer. Lastly, in light of recent advancements in the field of molecular self-assembly, we present a hypothesis regarding the existence of non-proteinaceous prion-like entities. This year marks the 55th anniversary of the discovery that prions, typically associated with human diseases, can function as information carriers in microorganisms, where they confer adaptive advantages to the cells that harbor them. Until very recently, microbial prion research has been primarily focused on yeast, and the canonical characteristics of these epigenetic moieties included a set of typical structural and functional traits. Recent studies have significantly expanded the definition of microbial prions; it is now clear that they are more structurally and functionally diverse than previously assumed and are widespread in the microbial world. Microbial prions can regulate a wide variety of cellular processes and confer various evolutionary advantages by intricate molecular mechanisms, and many more paradigm-shifting examples are yet to be discovered. [ABSTRACT FROM AUTHOR]

The aggregation of β-crystallins in the human eye lens constitutes a critical step during the development of cataract. We anticipated that the presence of Aggregation-Prone Regions (APRs) in their primary structure, which might be responsible for conformational change required for the self-assembly. To examine the presence of APRs, we systematically analyzed the primary structures of β-crystallins. Out of seven subtypes, the βB1-crystallin found to possess the highest aggregation score with 9 APRs in its primary structure. To confirm the amyloidogenic nature of these newly identified APRs, we further studied the aggregation behavior of one of the APRs spanning from 174 to 180 residues (174LWVYGFS180) of βB1-crystallin, which is referred as βB1 (174-180). Under in vitro conditions, the synthetic analogue of βB1 (174-180) peptide formed visible aggregates and displayed high Congo red (CR) bathochromic shift, Thioflavin T (ThT) binding and fibrilar morphology under transmission electron microscopy, which are the typical characteristics of amyloids. Further, the aggregated βB1 (174-180) was found to induce aggregation of the soluble fraction of proteins isolated from the human cataractous lens. This observation suggests that the presence of APRs in βB1-crystallin might be serving as one of the intrinsic supplementary factors responsible for constitutive aggregation behavior of βB1-crystallin and development of cataract. [ABSTRACT FROM AUTHOR]

Amyloids are proteins of a cross-β structure found as deposits in several diseases and also in normal tissues (nails, spider net, silk). Aromatic amino acids are frequently found in amyloid deposits. Although they are not indispensable, aromatic amino acids, phenylalanine, tyrosine and tryptophan, enhance significantly the kinetics of formation and thermodynamic stability, while tape or ribbon-like morphology is represented in systems with experimentally detected π - π interactions between aromatic rings. Analysis of geometries and energies of the amyloid PDB structures indicate the prevalence of aromatic-nonaromatic interactions and confirm that aromatic-aromatic interactions are not crucial for the amyloid formation. [ABSTRACT FROM AUTHOR]

• CS@Se inhibits Aβ aggregation and protects SH-SY5Y cells from Aβ 1–42 -induced cytotoxicity. • CS@Se protects the cytoskeleton structures and decreases the cytoskeleton instability that is induced by okadaic acid. • CS@Se suppresses the oxidative stress induced by Aβ 1–42 in SH-SY5Y cells. • CS@Se attenuates the hyperphosphorylation of tau at Ser396 and Ser404 sites by regulating the expression of GSK-3β. The purpose of this study was to ascertain the effect of selenium-chondroitin sulfate nanoparticles (CS@Se) on multi-target-directed therapy for the treatment of Alzheimer's disease (AD). CS@Se nanoparticles were successfully synthesized, and their therapeutic effects were studied in in vitro AD models. CS@Se effectively inhibited amyloid-β (Aβ) aggregation and protected SH-SY5Y cells from Aβ 1–42 -induced cytotoxicity. Moreover, CS@Se significantly decreased okadaic acid-induced actin cytoskeleton instability in SH-SY5Y cells. In addition, CS@Se decreased the levels of reactive oxygen species (ROS) and malondialdehyde (MDA) and increased the levels of glutathione peroxidase (GSH-Px). The Western blot results indicated that CS@Se attenuated the hyperphosphorylation of tau (Ser396/Ser404) by regulating the expression of GSK-3β. In summary, this study demonstrated that CS@Se could inhibit the aggregation of Aβ, reduce damage to the cytoskeleton, mitigate oxidative stress and attenuate the hyperphosphorylation of tau protein. CS@Se might be a potent multi-functional agent for the treatment of AD and thus warrants further research and evaluation. [ABSTRACT FROM AUTHOR]

Evolution of macromolecules could be considered as a milestone in the history of life. Nucleic acids are the long stretches of nucleotides that contain all the possible codes and information of life. On the other hand, proteins are their actual translated outcomes, or reflections of modifications in their structure that have occurred at a slow, but steady rate over a very long period of evolution. Over the years of research, biophysicists, biochemists, molecular and structural biologists have unfurled several layers of the structural convolutions in these chemical molecules; however evolutionists look over their structures through a different prism, which may or may not coincide with others. There remains a need to outline several well-known, but less discussed features of protein structures, like intrinsically disordered states, degron signals and different types of ubiquitin chains providing degradation signals, which help the cellular proteolytic machinery to identify and target the proteins towards degradation pathways. There are several important factors, which are critical for folding of proteins into their native three-dimensional conformations by the cytoplasmic chaperones; but in real time how the chaperones fold the newly synthesized polypeptide sequences into a particular three-dimensional shape within a fraction of second is still a mystery for biologists as well as mathematicians. Multiple similar unsolved or unaddressed questions need to be addressed in detail so that future line of research can dig deeper into the finer details of these structures of the proteins. [ABSTRACT FROM AUTHOR]

Severe coronavirus disease 2019 (COVID-19) infection leads to multifactorial acute respiratory distress syndrome (ARDS), with little therapeutic success. The pathophysiology associated with ARDS or post-ARDS is not yet well understood. We hypothesize that amyloid formation occurring due to protein homeostasis disruption can be one of the complications associated with COVID-19-induced-ARDS. [ABSTRACT FROM AUTHOR]

Abstract Background Carbamylation is a non-enzymatic post-translational modification (PTM), which involves the covalent modification of N-terminus of protein or ε-amino group of Lys. The role of carbamylation in several age-related disorders is well documented, however, the relationship between carbamylation and neurodegenerative disorders including Alzheimer's disease remains uncharted. Methods In the present study, using aggregation-prone tau-core hexapeptide fragments 306VQIVYK311 (PHF6) and 275VQIINK280 (PHF6*) as models, we have elucidated the effect of carbamylation on aggregation kinetics and the changes occurring in the 3-dimensional architecture of fibrils using biophysical assays and molecular dynamics simulations. Results We found that carbamylation aids in amyloid formation and can convert the unstructured off-pathway aggregates into robust amyloids, which were toxic to cells. Electron microscopy images and molecular dynamics simulations of PHF6 fibrils showed that carbamylated peptides can form excess hydrogen bonds and modulate the pitch length and twist of peptides fibrils. We have also compared N-terminal carbamylation to acetylation and further extended our finding to full length tau that exhibits aggregation upon carbamylation even in the absence of any external inducer. Conclusion Our in vitro and in silico results together suggest that carbamylation can modulate the aggregation pathway of the amyloidegenic sequences and cause structural changes in fibril assemblies. General significance Carbamylation acts as a switch, which triggers the aggregation in short amyloidogenic peptide fragments and modulate the structural changes in resulting amyloid fibrils. Graphical abstract Unlabelled Image Highlights • Carbamylation is a non-enzymatic PTM involving the covalent modification of Nα-NH 2 of protein or Nε-NH 2 of Lys • The effect of carbamylation on aggregation of short amyloidogenic peptides and tau protein in vitro and in silico • Carbamylation acts as a switch which triggers the amyloidogenesis and converts off-pathway aggregates into amyloids • Electron Microscopy & Molecular Dynamics studies revealed that carbamylation modulated structural changes in PHF6 fibrils [ABSTRACT FROM AUTHOR]

The Aβ42 aggregates with different structures and morphology was investigated through a single molecule label-free technique. To this end, the quartz nanopipettes were functionalized with polyethylene glycol. The set of Aβ42- epigallocatechin-3-gallate fibrils with length (from 85 nm to 250 nm) obtained by sonication was detected. The comparison of experimental and computed value of the amplitude of relative current blockade using a geometrical model show that for fibrils longer than 80 nm, the discriminating parameter is their diameter. Then, non-fibril oligomers obtain from Aβ42(Osaka) aggregation at different time seed was investigated. The analysis of the amplitude of relative current blockade shows that detected oligomers are smaller than 30 nm regardless the aggregation time. In addition, the wide distributions of the dwell time suggests the polymorph character of the sample. [Display omitted] • The Aβ42 aggregates size was investigated through a nanopipette. • For fibril, the discriminating parameter is their diameter as soon as the length is >80 nm. • Aβ42(Osaka) aggregates form for non-fibril oligomers smaller than 30 nm regardless the aggregation time. [ABSTRACT FROM AUTHOR]

Newly synthesized polypeptides must pass stringent quality controls in cells to ensure appropriate folding and function. However, mutations, environmental stresses and aging can reduce efficiencies of these controls, leading to accumulation of protein aggregates, amyloid fibrils and plaques. In-vitro experiments have shown that even single amino acid substitutions can drastically enhance or mitigate protein aggregation kinetics. In this work, we have collected a dataset of 220 unique mutations in 25 proteins and classified them as enhancers or mitigators on the basis of their effect on protein aggregation rate. The data were analyzed via machine learning to identify features capable of distinguishing between aggregation rate enhancers and mitigators. Our initial Support Vector Machine (SVM) model separated such mutations with an overall accuracy of 69%. When local secondary structures at the mutation sites were considered, the accuracies further improved by 13–15%. The machine-learnt features are distinct for each secondary structure class at mutation sites. Protein stability and flexibility changes are important features for mutations in α-helices. β-strand propensity, polarity and charge become important when mutations occur in β-strands and ability to form secondary structure, helical tendency and aggregation propensity are important for mutations lying in coils. These results have been incorporated into a sequence-based algorithm (available at http://www.iitm.ac.in/bioinfo/aggrerate-disc/ ) capable of predicting whether a mutation will enhance or mitigate a protein's aggregation rate. This algorithm will find several applications towards understanding protein aggregation in human diseases, enable in-silico optimization of biopharmaceuticals and enzymes for improved biophysical attributes and de novo design of bio-nanomaterials. [ABSTRACT FROM AUTHOR]

α-Synuclein protein, whose aggregation is associated with Parkinson’s disease, is detected using a compact, label-free, localized surface plasmon resonance (LSPR) based optical sensor. U-shaped fiber optic probe immobilized with gold nanoparticles (GNP), and subsequently functionalized using a film of chitosan was used as a sensing platform. The chitosan film acts as a sensitive and selective polysaccharide bioreceptor for detection of α-Synuclein. Binding of amyloid proteins to this film causes a localized change of dielectric constant surrounding the nanoparticles, leading to a change in the spectrum at the output end of the fiber. The combination of binding rate kinetics and intensity change was measured to develop a robust sensing platform. The sensor could detect the presence of monomers & amyloid fibrils independently up to 70 nM and could differentiate them in mixtures having fibril to monomer ratio from 0.1 to 10, within 15 min. The present study introduces a new platform for sensitive detection of amyloid fibrils and monomer of α-Synuclein (independently as well as in mixtures) for potential applications in inhibition and aggregation based studies. [ABSTRACT FROM AUTHOR]

Understanding Aβ amyloid oligomers associated with neuro-degenerative diseases is needed due to their toxic characteristics and mediation of amyloid fibril growth. Depending on various physiological circumstances such as ionic strength, metal ion, and point-residue mutation, oligomeric amyloids exhibit polymorphic behavior and structural stabilities, i.e. showing different conformation and stabilities. Specifically, experimental and computational researchers have found that the capping modulates the physical and chemical properties of amyloids by preserving electrostatic energy interactions, which is one of the dominant factors for amyloid stability. Still, there is no detailed knowledge for the polymorphic amyloids with reflecting the terminal capping effects. In the present study, we investigated the role of terminal capping (i.e. N-terminal acetylation and C-terminal amidation) on polymorphic Aβ 16–21 amyloid oligomer and protofibrils via molecular dynamics (MD) simulations. We found that the capping effects have differently altered the conformation of polymorphic antiparallel-homo and –hetero Aβ 16–21 amyloid oligomer, but not Aβ 16–21 amyloid protofibrils. However, regardless of polymorphic composition of the amyloids, the capping induces the thermodynamic instabilities of Aβ 16–21 amyloid oligomers, but does not show any distinct affect on Aβ 16–21 amyloid protofibrils. Specifically, among the molecular mechanic factors, electrostatic energy dominantly contributes the thermodynamic stability of the Aβ 16–21 amyloids. We hope that our computation study about the role of the capping effects on the polymorphic amyloids will facilitate additional efforts to enhance degradation of amyloids and to design a selective drug in the future. [ABSTRACT FROM AUTHOR]

After decades of research and clinical trials there is still no cure for Alzheimer’s disease (AD). While impaired clearance of amyloid beta (Aβ) peptides is considered as one of the major causes of AD, it was recently complemented by a potential role of other toxic amyloidogenic species. Insulin-degrading enzyme (IDE) is the proteolytic culprit of various β-forming peptides, both extracellular and intracellular. On the basis of demonstrated allosteric activation of IDE against Aβ, it is possible to propose a new strategy for the targeted IDE-based cleansing of different toxic aggregation-prone peptides. Consequently, specific allosteric activation of IDE coupled with state-of-the-art compound delivery and CRISP-Cas9 technique of transgene insertion can be instrumental in the fight against AD and related neurodegenerative maladies. [ABSTRACT FROM AUTHOR]

Increasing evidence proposed that amyloid deposition by proteins play a crucial role in an array of neurotoxic and degenerative disorders like Parkinson’s disease, systemic amyloidosis etc, that could be controlled by anti-aggregation methodologies which either inhibit or disaggregate such toxic aggregates. The present work targets the amyloid inhibiting and disaggregating potential of promethazine (PRM) against human insulin (HI) and human lysozyme (HL) fibrillogenesis. Biophysical techniques like Rayleigh scattering measurements (RLS), Thioflavin T (ThT) and 8-Anilinonaphthalene-1-sulfonic acid (ANS) fluorescence measurement, circular dichroism (CD) and dynamic light scattering (DLS) measurements illustrated the inhibitory action of PRM. The half maximal inhibitory concentration (IC 50 ) of PRM for HI and HL was estimated to be 114.81 ± 1.21 μM and 186.20 ± 1.03 μM, respectively. Microscopic techniques revealed the absence of fibrillar structures when HI and HL was co-incubated with PRM. Cytoprotective behavior of PRM was investigated by cell based cytotoxicity assay performed on SH-SY5Y neuronal cell lines. The half maximal disaggregation concentration (DC 50 ) was calculated as 21.37 ± 0.89 μM and 45.70 ± 0.76 μM, signifying that PRM is much potent to disaggregate pre formed fibrils rather than to inhibit fibrillation. Thus, PRM could be beneficial as therapeutic agent that can aid in the cure of amyloid related diseases. [ABSTRACT FROM AUTHOR]

Protein aggregation and misfolding have been allied with numerous human disorders and thus inhibition of such occurrence has been center for intense research efforts against these diseases. Here, we investigated anti-fibrillation activity of cysteine and its effect on kinetics of stem bromelain amyloid fibril formation. We established the anti-fibrillation and anti aggregation activities of cysteine by using multiple approaches like turbidity measurements, dye binding assays (ThT and ANS) and structural changes were monitored by circular dichroism (CD) followed by electron microscopy. Our experimental study inferred that cysteine inhibits temperature induced fibrillation of protein in a concentration dependent way. In addition, MDA-MB-231 cell viability of pre-formed amyloid was increased in presence of cysteine as compared to the fibrils alone. Furthermore, dynamic light scattering studies of native, aggregated as well as incubated (amyloids in presence of cysteine) samples indicates that cysteine restores native like structures of stem bromelain. Isothermal titration calorimetric results revealed that hydrogen bonding between cysteine and stem bromelain plays a significant role during inhibition of stem bromelain aggregation. However, thiophilic interaction between thiol group of cysteine and aromatic amino acid residue of stem bromelain may also have noteworthy role in inhibition of amyloid formation. [ABSTRACT FROM AUTHOR]

Peptide–lipid interactions play an important role in defining the mode of action of drugs and the molecular mechanism associated with many diseases. Model membranes consisting of simple lipid mixtures mimicking real cell membranes can provide insight into the structural and dynamic aspects associated with these interactions. Small-angle scattering techniques based on X-rays and neutrons (SAXS/SANS) allow in situ determination of peptide partition and structural changes in lipid bilayers in vesicles with relatively high resolution between 1-100 nm. With advanced instrumentation, time-resolved SANS/SAXS can be used to track equilibrium and nonequilibrium processes such as lipid transport and morphological transitions to time scales down to a millisecond. In this review, we provide an overview of recent advances in the understanding of complex peptide–lipid membrane interactions using SAXS/SANS methods and model lipid membrane unilamellar vesicles. Particular attention will be given to the data analysis, possible pitfalls, and how to extract quantitative information using these techniques. [Display omitted] [ABSTRACT FROM AUTHOR]

The aggregation of specific proteins is hypothesized to cause several pathological conditions, which are collectively known as amyloid disorders. The aggregation of peptides and proteins is mainly associated with the perturbation of cellular function, ageing and various human disorders. Mounting evidence suggests that protein aggregation is often caused by mutation, environmental stress or the cellular response to an imbalanced protein homeostasis. This review summarizes the background information on the protein folding, misfolding, cellular strategies against protein aggregation, factors affecting protein aggregation and mechanism of protein aggregation. We then focus on various inhibitors for protein aggregation both in vitro and in vivo . We conclude with a perspective that better therapeutics could be developed by using cocktail of small molecule inhibitors for the treatment of amyloid diseases. [ABSTRACT FROM AUTHOR]

In spite of the fact that amyloid related neurodegenerative illnesses and non-neuropathic systemic amyloidosis have allured the research endeavors, as no cure has been announced yet apart from symptomatic treatment. Therapeutic agents which can reduce or disaggregate those toxic oligomers and fibrillar species have been studied with more compounds are on their way. The current research work describes comprehensive biophysical, computational and microscopic studies which reveal that L-3, 4-dihydroxyphenylalanine (L-Dopa) have indisputable efficacy to hinder the heat induced amyloid fibrillation of the human lysozyme (HL) and also preserve the fibril disaggregating potential. The IC 50 value of L-Dopa is calculated to be 63.0 ± 0.09 μM. L-Dopa intervenes in the process of amyloid fibrillogenesis through hydrophobic interaction and hydrogen bond formation with the amino acid residues found in the amyloid fibril forming prone region of HL as clarified by molecular simulation data. L-Dopa also disaggregates the mature amyloid fibrils into some unorganized species and the DC 50 value was estimated to be 19.95 ± 0.063 μM. Hence, L-Dopa and related compounds can act as effective inhibitors in the therapeutic development to combat systemic amyloidosis. [ABSTRACT FROM AUTHOR]

Protein misfolding and aggregation has been implicated as the cause of more than 20 diseases in humans such as Alzheimer’s and Parkinson’s and systemic amyloidosis. Retardation of Aβ- 42 aggregation is considered as a promising and challenging strategy for developing effective therapeutics against Alzheimer’s disease. Herein, we demonstrated the effect of vitamin B12 (VB) on inhibiting amyloid formation by employing ThT fluorescence assay, circular dichroism, ANS fluorescence assay, dynamic light scattering measurements and transmission electron microscopy and cell viability assay. Our results demonstrate that vitamin B12 (VB), inhibits Aβ- 42 aggregation in a concentration dependent manner. Further VB also provide protection against amyloid induced cytotoxicity in human neuronal cell line. This study points towards a promising strategy to combat Aβ- 42 aggregation and may have broader implication for targeting other neurological disorders whose distinct hallmark is also amyloid formation. [ABSTRACT FROM AUTHOR]

Background Alkaptonuria (AKU) is an ultra-rare disease associated to the lack of an enzyme involved in tyrosine catabolism. This deficiency results in the accumulation of homogentisic acid (HGA) in the form of ochronotic pigment in joint cartilage, leading to a severe arthropathy. Secondary amyloidosis has been also unequivocally assessed as a comorbidity of AKU arthropathy. Composition of ochronotic pigment and how it is structurally related to amyloid is still unknown. Methods We exploited Synchrotron Radiation Infrared and X-Ray Fluorescence microscopies in combination with conventional bio-assays and analytical tools to characterize chemical composition and morphology of AKU cartilage. Results We evinced that AKU cartilage is characterized by proteoglycans depletion, increased Sodium levels, accumulation of lipids in the peri-lacunar regions and amyloid formation. We also highlighted an increase of aromatic compounds and oxygen-containing species, depletion in overall Magnesium content (although localized in the peri-lacunar region) and the presence of calcium carbonate fragments in proximity of cartilage lacunae. Conclusions We highlighted common features between AKU and arthropathy, but also specific signatures of the disease, like presence of amyloids and peculiar calcifications. Our analyses provide a unified picture of AKU cartilage, shedding a new light on the disease and opening new perspectives. General significance Ochronotic pigment is a hallmark of AKU and responsible of tissue degeneration. Conventional bio-assays have not yet clarified its composition and its structural relationship with amyloids. The present work proposes new strategies for filling the aforementioned gap that encompass the integration of new analytical approaches with standardized analyses. [ABSTRACT FROM AUTHOR]

Summary Self-perpetuating ordered protein aggregates (amyloids and prions) are associated with a variety of neurodegenerative disorders. Although environmental agents have been linked to certain amyloid diseases, the molecular basis of their action remains unclear. We have employed endogenous yeast prions as a model system to study environmental control of amyloid formation. A short-lived actin-associated yeast protein Lsb2 can trigger prion formation by other proteins in a mode regulated by the cytoskeleton and ubiquitin-dependent processes. Here, we show that such a heterologous prion induction is due to the ability of Lsb2 to form a transient prion state, generated in response to thermal stress. Evolutionary acquisition of prion-inducing activity by Lsb2 is traced to a single amino acid change, coinciding with the acquisition of thermotolerance in the Saccharomyces yeast lineage. This raises the intriguing possibility that the transient prion formation could aid in functioning of Lsb2 at higher temperatures. [ABSTRACT FROM AUTHOR]

Summary Formation of amyloids is the hallmark of several neurodegenerative pathologies. Structural investigation of these complex transformation processes poses significant experimental challenges due to the co-existence of multiple species. The additive nature of small-angle X-ray scattering (SAXS) data allows for probing the evolution of these mixtures of oligomeric states, but the decomposition of SAXS data into species-specific spectra and relative concentrations is burdened by ambiguity. We present an objective SAXS data decomposition method by adapting the multivariate curve resolution alternating least squares (MCR-ALS) chemometric method. The approach enables rigorous and robust decomposition of synchrotron SAXS data by simultaneously introducing these data in different representations that emphasize molecular changes at different time and structural resolution ranges. The approach has allowed the study of fibrillogenic forms of insulin and the familial mutant E46K of α-synuclein, and is generally applicable to any macromolecular mixture that can be probed by SAXS. [ABSTRACT FROM AUTHOR]

Transmissive spongiform encephalopathies (TSE) are a group of neurodegenerative diseases caused by infectious protein particles, known as prions. Prions are formed from cellular prion proteins (PrP) and can be transmitted between different mammalian species. Subsequently, the host's PrPs are then converted to prions, followed by the onset of TSE. Interspecies prion infectivity is governed by the amino acid sequence differences of PrPs and prions' inability to replicate in a host is termed a species barrier. Here, we investigated the amino acid sequence determinants of species barrier between recombinant human (rHuPrP) and hamster (rShaPrP) prion protein amyloid fibrils. We discovered that a unidirectional species barrier between rShaPrP and rHuPrP amyloid fibrils exists. This barrier stems from the difference of amino acid sequences in the conserved β2-α2 loop region. Our results revealed that individual amino acids in the β2-α2 loop region are critical for overcoming the barrier between human and hamster prion protein amyloid fibrils in vitro. Furthermore, the barrier was only possible to observe through aggregation kinetics, as the secondary structure rHuPrP fibrils was not affected by the cross-seeding. Overall, we demonstrated the mechanistic pathway behind this interspecies barrier phenomenon, which increases our understanding of prion-related disease development. [ABSTRACT FROM AUTHOR]

The p53 protein plays a critical role in the prevention of genome mutations in the body, however, this protein is frequently mutated in cancer and almost all cancers exhibit malfunction along the p53 pathway. In addition to a loss of activity, mutant p53 protein is prone to unfolding and aggregation, eventually forming amyloid aggregates. There continues to be a considerable effort to develop strategies to restore normal p53 expression and activity and this review details recent advances in small-molecule stabilization of mutant p53 protein and the design of p53 aggregation inhibitors. [ABSTRACT FROM AUTHOR]

Liquid-liquid phase separation (LLPS) is currently recognized as a common mechanism involved in the regulation of a number of cellular functions. On the other hand, aberrant phase separation has been linked to the biogenesis of several neurodegenerative disorders since many proteins that undergo LLPS are also found in pathological aggregates. The formation of mixed protein coacervates may constitute a risk factor in overlapping neuropathologies, such as Parkinson's (PD) and Alzheimer's (AD) diseases. In this work, we evaluated the homotypic and heterotypic phase behaviour of the PD-related protein α-synuclein (AS) in the presence of the biologically relevant molecules ATP, polyamines, and the AD-related protein Tau. We found that AS exhibits a low propensity to form homotypic liquid droplets, yet phase separates into liquid-like or solid-like phases depending on the interacting biomolecule. We further demonstrated the synergistic droplet formation of AS and Tau providing support for a mechanism in which mixed condensates might contribute to the biogenesis of AS/Tau pathologies. [Display omitted] • α-synuclein has a low propensity to form liquid droplets at physiological pH and temperature. • Spermine induces α-synuclein liquid droplets that evolve into non-amyloid protein aggregates. • Spermidine and ATP induce rapid formation of non-amyloid α-synuclein aggregates. • Tau and α-synuclein synergically interact to form heterotypic condensates. [ABSTRACT FROM AUTHOR]

This manuscript examines influences of differently functionalized surfaces on the formation of solution-dispersed polydopamine (pDA). Glass vials functionalized with different functional groups provided a set of conditions with which the relationship between the area of active surface and the rate of pDA formation could be systematically studied. The results suggest that charged and polar surfaces accelerate pDA formation in solution, with the effect of -NH 2 surfaces being exceptionally strong. In the vials, pDA formed as both forms of dispersions in solution and films at solid-liquid interface. Further analyses confirmed that both forms of pDA formed with -NH 2 surfaces were chemically similar to conventional pDA synthesized without help of functional surfaces. Among short peptide-based amyloid fibers with defined surface functional groups, and those displaying lysines (-NH 2) greatly accelerated the formation of pDA, consistent with the results of -NH 2 -functionalized vials. The results suggest that pDA formation may be facilitated by surface functional groups of solid-liquid interfaces, and have implications for the overlooked roles of amyloid fibers in biological melanogenesis. [Display omitted] • Solution-phase polydopamine formation is accelerated by polar and charged surfaces. • The roles of amine groups differ critically between those in solution and at surface. • Amyloid fibers are similarly active to charged surfaces in polydopamine formation. [ABSTRACT FROM AUTHOR]

Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed phases associated with diseases such as amyloid fibrils. Although seemingly different, these assemblies all originate from fundamental protein interactions and are driven by similar thermodynamic and kinetic factors. Here we review recent advances in understanding protein self-assembly through a soft condensed matter perspective with an emphasis on three specific systems: globular proteins, viruses, and amyloid fibrils. We conclude with a discussion of unanswered questions in the field. [ABSTRACT FROM AUTHOR]

Summary Although transcription factors are prevalent among yeast prion proteins, the role of prion-mediated transcriptional regulation remains elusive. Here, we show that the yeast prion [ SWI + ] abolishes flocculin ( FLO ) gene expression and results in a complete loss of multicellularity. Further investigation demonstrates that besides Swi1, multiple other proteins essential for FLO expression, including Mss11, Sap30, and Msn1 also undergo conformational changes and become inactivated in [ SWI + ] cells. Moreover, the asparagine-rich region of Mss11 can exist as prion-like aggregates specifically in [ SWI + ] cells, which are SDS resistant, heritable, and curable, but become metastable after separation from [ SWI + ]. Our findings thus reveal a prion-mediated mechanism through which multiple regulators in a biological pathway can be inactivated. In combination with the partial loss-of-function phenotypes of [ SWI + ] cells on non-glucose sugar utilization, our data therefore demonstrate that a prion can influence distinct traits differently through multi-level regulations, providing insights into the biological roles of prions. [ABSTRACT FROM AUTHOR]

Amyloid oligomers and fibrils are protein aggregates that cause an onset and progression of many neurodegenerative diseases, diabetes type 2 and systemic amyloidosis. Although a growing body of evidence shows that oligomers and fibrils trigger mitochondrial dysfunction simultaneously enhancing production of reactive oxygen species, exact mechanisms by which these protein aggregates exert their toxicities remain unclear. In this study, we used advanced microscopic and spectroscopic methods to examine topography and structure of insulin aggregates grown in the lipid-free environment, as well as in the presence of major classes of phospho- and sphingolipids. We also employed a set of molecular markers to determine the extent to which insulin aggregates induce a damage of cell endoplasmic reticulum (ER), an important cell organelle used for calcium storage, protein synthesis and folding. Our results show that insulin aggregates activate the expression of Activating Transcription Factor 6 (ATF6), a transmembrane protein that is involved in unfolded protein response (UPR) of the stressed ER. At the same time, two other ER transmembrane proteins, Inositol Requiring 1 (IRE1α) and eLF2a, the product of PKR-like ER kinase (PERK), exhibited very low expression levels. Furthermore, amyloid aggregates trigger an expression of the 78-kDa glucose-regulated protein GRP78, which is also involved in the UPR. We also observed UPR-induced expression of a proapoptotic transcription factor CHOP, which, in turn, regulates expression of caspase 3 kinase and BCL2 protein family members, including the ER localized Bax. These findings show that insulin oligomers and fibrils induce UPR-associated ER stress and ultimately fatal changes in cell homeostasis. • Insulin aggregates induce unfolded protein response (UPR) in cells and ultimately fatal changes in cell homeostasis. • Amyloid-stress engages Activating Transcription Factor 6 (ATF6), a transmembrane protein that is involved in UPR. • Inositol Requiring 1 (IRE1α) and eLF2a exhibit low expression levels upon the ER stress exerted by insulin aggregates. • Amyloid aggregates trigger an expression of the 78-kDa glucose-regulated protein GRP78, which is also involved in the UPR. [ABSTRACT FROM AUTHOR]

Background Homocysteine (Hcy) is a sulfur containing non-protein amino acid that occupies a central role in metabolism of thiol compounds. The past decade had noticed an explosion in interests of Hcy and this very interest came primarily from the fact that increased Hcy level is related to various neurodegenerative and vascular complications. Scope of review Several factors responsible for the Hcy-associated neurotoxicity have been proposed and well documented in literature, including oxidative stress and apoptosis. In addition, protein covalent modification by the metabolite of Hcy, Hcy thiolactone (HTL), has now been shown to be another cause of cellular Hcy toxicity. This mechanism, termed as “protein N-homocysteinylation”, is known to result in protein denaturation, enzyme inactivation and even amyloid formation. The role of protein N-homocysteinylation and the resulting consequences with regard to neurodegeneration have not yet been extensively discussed. The present review describes major advances in understanding protein N-homocysteinylation and their role in neurodegeneration. Major conclusions Formation of protein aggregates/amyloids are crucial events in various human pathologies including neurodegenerative diseases. Since elevated Hcy has been closely linked to neurodegeneration, N-homocysteinylation-induced protein modification and aggregates/amyloids formation could be one possible mechanism for the neurodegenerative conditions. General significance The information highlighted here provides us an understanding of the role protein modification by N-homocysteinylation in neurodegenerative diseases. [ABSTRACT FROM AUTHOR]

Assembly of amyloid proteins into aggregates requires the ordering of the monomers in oligomers and especially in such highly organized structures as fibrils. This ordering is accompanied by structural transitions leading to the formation of ordered β-structural motifs in proteins and peptides lacking secondary structures. To characterize the effect of the monomer arrangements on the aggregation process at various stages, we performed comparative studies of the yeast prion protein Sup35 heptapeptide (GNNQQNY) along with its dimeric form CGNNQQNY-(d-Pro)-G-GNNQQNY. The (d-Pro)-G linker in this construct is capable of adopting a β-turn, facilitating the assembly of the dimer into the dimeric antiparallel hairpin structure (AP-hairpin). We applied Atomic Force Microscopy (AFM) techniques to follow peptide–peptide interactions at the single molecule level, to visualize the morphology of aggregates formed by both constructs, thioflavin T (ThT) fluorescence to follow the aggregation kinetics, and circular dichroism (CD) spectroscopy to characterize the secondary structure of the constructs. The ThT fluorescence data showed that the AP-hairpin aggregation kinetics is insensitive to the external environment such as ionic strength and pH contrary to the monomers the kinetics of which depends dramatically on the ionic strength and pH. The AFM topographic imaging revealed that AP-hairpins primarily assemble into globular aggregates, whereas linear fibrils are primary assemblies of the monomers suggesting that both constructs follow different aggregation pathways during the self-assembly. These morphological differences are in line with the AFM force spectroscopy experiments and CD spectroscopy measurements, suggesting that the AP-hairpin is structurally rigid regardless of changes of environmental factors. [ABSTRACT FROM AUTHOR]

In Alzheimer's disease (AD), the initial stages of the aggregation process of the β-amyloid peptide (Aβ) present a particular interest to understand the origin of the development of this disease. In this work, we present a sensor with the property of solvatofluorochromism that allows a fluorophore to undergo a shift in its emission wavelengths when placed in environments of different polarity. We used the natural adsorption binding of the dye 2-Me-4-OMe-TM, a silicon-modified xanthene derivative, to macrostructures and its solvatofluorochromic behavior to detect, in real time, modifications in the environment polarity around the dye during the initial stages of Aβ aggregation process, using steady-state, time resolved fluorescence spectroscopy and advanced fluorescence imaging techniques as fluorescence lifetime imaging microscopy (FLIM). During this progression, formation of pre-amyloid aggregates produces strong local changes in hydrophobicity that can be monitored by the fluorescent dye 2-Me-4-OMe-TM. In particular, this dye has two different emission bands and by establishing a polarity scale based on the ratiometric value of the average fluorescence lifetimes between both bands, we were able to quantify the hydrophobicity of the detected aggregates and established a method for distinguishing between aggregates of different types. • A silicon-modified xanthene derivative capable of marking amyloid aggregates. • The solvatochromism of the dye allows establishing a microenvironment polarity scale. • FLIM microscopy of Aβ aggregates shows different stages of the aggregation process. [ABSTRACT FROM AUTHOR]

Hemocytes of Heliothis virescens (F.) (Lepidoptera, Noctuidae) larvae produce a protein, P102, with a putative endoribonuclease-U domain. In previous works we have shown that P102 is involved in Lepidopteran immune response by forming amyloid fibrils, which catalyze and localize melanin deposition around non-self intruders during encapsulation, preventing harmful systemic spreading. Here we demonstrate that P102 belongs to a new class of proteins that, at least in Lepidoptera, has a diminished endoribonuclease-U activity probably due to the lack of two out of five catalytically essential residues. We show that the P102 homolog from Trichoplusia ni (Lepidoptera, Noctuidae) displays catalytic site residues identical to P102, a residual endoribonuclease-U activity and the ability to form functional amyloids. On the basis of these results as well as sequence and structural analyses, we hypothesize that all the Lepidoptera endoribonuclease-U orthologs with catalytic site residues identical to P102 form a subfamily with similar function. [ABSTRACT FROM AUTHOR]

• The production of cottage cheese involves heat treatment and acidification of milk. • The cottage cheese contains amyloid-like protein aggregates. • These milk derived protein aggregates (MAPA) are found to be non-toxic. Cottage cheese, extensively consumed worldwide, contains coagulated milk protein (casein), produced through boiling and acidification of milk. Casein forms amyloid or amyloid-like structures at high temperatures and low pH. Due to the similarities in the preparation of casein amyloids and cottage cheese, we hypothesized the presence of amyloid or amyloid-like protein aggregates in cottage cheese. To examine this hypothesis, cottage cheese was prepared from cow (Bos indicus) milk and isolated amyloids through a water extraction method. The isolated protein aggregates displayed typical characteristics of amyloids, such as a bathochromic shift in the wavelength of maximum absorption (λ max) of Congo red (CR), high thioflavin T (ThT) binding, increased surface hydrophobicity, and high β-sheet structure. However, they did not show antibacterial activity and toxic properties against erythrocytes. Our study revealed that the heat-treatment and subsequent acidification during cottage cheese preparation lead to the formation of non-toxic amyloid-like aggregates. [ABSTRACT FROM AUTHOR]