Modulation of α-Synuclein Aggregation by Cytochrome c Binding and Hetero-dityrosine Adduct Formation

Order-to-Disorder and Disorder-to-Order Transitions of Proteins upon Binding to Phospholipid Membranes: Common Ground and Dissimilarities

Cytochrome c is one of the most prominent representatives of peripheral membrane proteins. Besides functioning as an electron transfer carrier in the mitochondrial respiratory chain, it can acquire peroxidase capability, promote the self-assembly of α-synuclein, and function as a scavenger of superoxide. An understanding of its function requires knowledge of how the protein interacts with the inner membrane of mitochondria. The first part of this article provides an overview of a variety of experiments that were aimed at exploring the details of cytochrome c binding to anionic lipid liposomes, which serve as a model system for the inner membrane. While cytochrome c binding involves a conformational change from a folded into a partially disordered state, α-synuclein is intrinsically disordered in solution and subjected to a partial coil -> helix transition on membranes. Depending on the solution conditions and the surface density of α-synuclein, the protein facilitates the self-assembly into oligomers and fibrils. As for cytochrome c, results of binding experiments are discussed. In addition, the article analyzes experiments that explored α-synuclein aggregation. Similarities and differences between cytochrome c and α-synuclein binding are highlighted. Finally, the article presents a brief account of the interplay between cytochrome c and α-synuclein and its biological relevance.

Dityrosine in food: A review of its occurrence, health effects, detection methods, and mitigation strategies

Protein and amino acid oxidation in food products produce many new compounds, of which the reactive and toxic compound dityrosine, derived from oxidized tyrosine, is the most widely studied. The high reactivity of dityrosine enables this compound to induce oxidative stress and disrupt thyroid hormone function, contributing to the pathological processes of several diseases, such as obesity, diabetes, cognitive dysfunction, aging, and age-related diseases. From the perspective of food safety and human health, protein-oxidation products in food are the main concern of consumers, health management departments, and the food industry. This review highlights the latest research on the formation pathways, toxicity, detection methods, occurrence in food, and mitigation strategies for dityrosine. Furthermore, the control of dityrosine in family cooking and food-processing industry has been discussed. Food-derived dityrosine primarily originates from high-protein foods, such as meat and dairy products. Considering its toxicity, combining rapid high sensitivity dityrosine detection techniques with feasible control methods could be an effective strategy to ensure food safety and maintain human health. However, the current dityrosine detection and mitigation strategies exhibit some inherent characteristics and limitations. Therefore, developing technologies for rapid and effective dityrosine detection and control at the industrial level is necessary.

Oxidative phosphorylation mediated pathogenesis of Parkinson's disease and its implication via Akt signaling

Substantia Nigra Pars-compacta (SNpc), in the basal ganglion region, is a primary source of dopamine release. These dopaminergic neurons require more energy than other neurons, as they are highly arborized and redundant. Neurons meet most of their energy demand (∼90%) from mitochondria. Oxidative phosphorylation (OxPhos) is the primary pathway for energy production. Many genes involved in Parkinson's disease (PD) have been associated with OxPhos, especially complex I. Abrogation in complex I leads to reduced ATP formation in these neurons, succumbing to death by inducing apoptosis. This review discusses the interconnection between complex I-associated PD genes and specific mitochondrial metabolic factors (MMFs) of OxPhos. Interestingly, all the complex I-associated PD genes discussed here have been linked to the Akt signaling pathway; thus, neuron survival is promoted and smooth mitochondrial function is ensured. Any changes in these genes disrupt the Akt pathway, which hampers the opening of the permeability transition pore (PTP) via GSK3β dephosphorylation; promotes destabilization of OxPhos; and triggers the release of pro-apoptotic factors.

Aptamer-engineered gold nanorod driven an absorbance enhanced strategy for sensitive biomacromolecule profiling

Gold nanorods (AuNRs)-based plasmonic biosensor offers new opportunity for quantification of biomacromolecules due to their high designability and low technical demands. However, existing methods for the optical detection of biomacromolecule require the targets to induce the aggregation or etching of AuNRs. This limits the range of targets that can be detected, because molecules at extremely low concentration are difficult to arouse aggregation or etching of AuNRs. Thus, it is still challenge to design a scheme for the biomacromolecules at extremely low concentration which can't arouse aggregation or etching of AuNRs based on their plasmonic property. This study proposes a universal absorbance enhanced strategy for biomacromolecule detection with aptamers engineered AuNRs. The biosensor assay (Apts/AuNRs) is designed through assembly of two aptamers on AuNRs to specified recognize the target biomacromolecules, forming closed-loop conformation based on the proximity-dependent ligation, producing absorbance enhancement in the plasmonic peak of AuNRs. It is interesting that the absorbance enhancement increases gradually with increasing protein concentration within a certain range, whereas no aggregation or etching of AuNRs was observed compared with the typical AuNRs based LSPR sensor. Taking advantage of the excellent near infrared light absorption of AuNRs, Apts/AuNRs could be utilized to detect red protein such as cytochrome C, which exhibited better performance than AuNPs based plasmonic sensor. On this basis, the selectivity detection of cytochrome C with the detection of limit down to picomole level was demonstrated. By changing the type of aptamers on AuNRs, the sensitive and credible method was also utilized for the analysis of telomerase activity in nerve cell lysate. Telomerase activity in 4 × 10⁴ neuroblastoma cell was determined to be about 3.575 U/L, which was close to the result of ELISA kit. Good recovery was achieved using standard samples recovery. This study broadens the scope of AuNRs based plasmonic ‬‬‬‬‬‬property ‬‬‬‬and offer a simple, sensitive and selective strategy for biomacromolecules detection in complexed biofluid.

Cholesterol in Synaptic Vesicle Membranes Regulates the Vesicle-Binding, Function, and Aggregation of α-Synuclein

Loss of function and aggregation of the neuronal protein α-Synuclein (A-Syn) underlies the pathogenesis of Parkinson's disease (PD), and both the function and aggregation of this protein happen to be mediated via its binding to the synaptic vesicles (SVs) at the presynaptic termini. An essential constituent of SV membranes is cholesterol, with which A-Syn directly interacts while binding to membranes. Thus, cholesterol content in SV membranes is likely to affect the binding of A-Syn to these vesicles and consequently its functional and pathogenic behaviors. Interestingly, the dyshomeostasis of cholesterol has often been associated with PD, with reports linking both high and low cholesterol levels to an increased risk of neurodegeneration. Herein, using SV-mimicking liposomes containing increasing percentages of membrane cholesterol, we show (with mathematical interpretation) that the binding of A-Syn to synaptic-like vesicles is strongest in the presence of an optimum cholesterol content, which correlates to its maximum function and minimum aggregation. This implicates a minimum risk of neurodegeneration at optimum cholesterol levels and rationalizes the existing controversial relationship between cholesterol levels and PD. Increased membrane cholesterol was, however, found to protect against damage caused by aggregated A-Syn, complementing previous reports and portraying one advantage of high cholesterol over low.

Conformational distortion in a fibril-forming oligomer arrests alpha-Synuclein fibrillation and minimizes its toxic effects

The fibrillation pathway of alpha-Synuclein, the causative protein of Parkinson's disease, encompasses transient, heterogeneous oligomeric forms whose structural understanding and link to toxicity are not yet understood. We report that the addition of the physiologically-available small molecule heme at a sub-stoichiometric ratio to either monomeric or aggregated α-Syn, targets a His50 residue critical for fibril-formation and stabilizes the structurally-heterogeneous populations of aggregates into a minimally-toxic oligomeric state. Cryo-EM 3D reconstruction revealed a 'mace'-shaped structure of this monodisperse population of oligomers, which is comparable to a solid-state NMR Greek key-like motif (where the core residues are arranged in parallel in-register sheets with a Greek key topology at the C terminus) that forms the fundamental unit/kernel of protofilaments. Further structural analyses suggest that heme binding induces a distortion in the Greek key-like architecture of the mace oligomers, which impairs their further appending into protofilaments and fibrils. Additionally, our study reports a novel mechanism of prevention as well as reclamation of amyloid fibril formation by blocking an inter-protofilament His50 residue using a small molecule.

Mitochondrial CHCHD2: Disease-Associated Mutations, Physiological Functions, and Current Animal Models

Rare mutations in the mitochondrial protein coiled-coil-helix-coiled-coil-helix domain containing 2 (CHCHD2) are associated with Parkinson's disease (PD) and other Lewy body disorders. CHCHD2 is a bi-organellar mediator of oxidative phosphorylation, playing crucial roles in regulating electron flow in the mitochondrial electron transport chain and acting as a nuclear transcription factor for a cytochrome c oxidase subunit (COX4I2) and itself in response to hypoxic stress. CHCHD2 also regulates cell migration and differentiation, mitochondrial cristae structure, and apoptosis. In this review, we summarize the known disease-associated mutations of CHCHD2 in Asian and Caucasian populations, the physiological functions of CHCHD2, how CHCHD2 mutations contribute to α-synuclein pathology, and current animal models of CHCHD2. Further, we discuss the necessity of continued investigation into the divergent functions of CHCHD2 and CHCHD10 to determine how mutations in these similar mitochondrial proteins contribute to different neurodegenerative diseases.

Megadalton-sized Dityrosine Aggregates of α-Synuclein Retain High Degrees of Structural Disorder and Internal Dynamics

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Despite their large size, αSyn dityrosine aggregates are dynamic and disordered.

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αSyn dityrosine aggregates specifically form in complex environments.

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αSyn dityrosine aggregates retain residual membrane binding activity.

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Dityrosine aggregates inhibit amyloid formation of monomeric αSyn.

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αSyn dityrosine aggregates are not cytotoxic.

Heterogeneous aggregates of the human protein α-synuclein (αSyn) are abundantly found in Lewy body inclusions of Parkinson’s disease patients. While structural information on classical αSyn amyloid fibrils is available, little is known about the conformational properties of disease-relevant, non-canonical aggregates. Here, we analyze the structural and dynamic properties of megadalton-sized dityrosine adducts of αSyn that form in the presence of reactive oxygen species and cytochrome c, a proapoptotic peroxidase that is released from mitochondria during sustained oxidative stress. In contrast to canonical cross-β amyloids, these aggregates retain high degrees of internal dynamics, which enables their characterization by solution-state NMR spectroscopy. We find that intermolecular dityrosine crosslinks restrict αSyn motions only locally whereas large segments of concatenated molecules remain flexible and disordered. Indistinguishable aggregates form in crowded in vitro solutions and in complex environments of mammalian cell lysates, where relative amounts of free reactive oxygen species, rather than cytochrome c, are rate limiting. We further establish that dityrosine adducts inhibit classical amyloid formation by maintaining αSyn in its monomeric form and that they are non-cytotoxic despite retaining basic membrane-binding properties. Our results suggest that oxidative αSyn aggregation scavenges cytochrome c’s activity into the formation of amorphous, high molecular-weight structures that may contribute to the structural diversity of Lewy body deposits.

Modulation of α-Synuclein Fibrillation by Ultrasmall and Biocompatible Gold Nanoclusters

Parkinson's disease (PD) is the second most common neurodegenerative disorder, the pathogenesis of which is closely linked to the misfolding and aggregation of the neuronal protein α-Synuclein (A-Syn). Numerous molecules that inhibit/modulate the pathogenic aggregation of A-Syn in an effort to tackle PD pathogenesis have been reported, but none so far have been successful in treating the disease at the clinic. One major reason for this is the poor blood-brain barrier (BBB) permeability of most of the molecules being used. Therefore, using BBB-permeable (and biocompatible) nanomaterials as fibrillation modulators is gaining importance. In the present work, we show how nontoxic and ultrasmall gold nanoclusters (AuNCs) can systematically modulate the pathogenic fibrillation of A-Syn in vitro, based on the chemical nature of their capping agents, using two reported easily synthesizable AuNCs as models. In addition, we detect the BBB permeability in mice of one of these AuNCs solely by making use of its intrinsic fluorescence. Thus, our work exemplifies how AuNCs can be potential therapeutics against PD; while also acting as fluorescent probes for their own BBB permeability.

A Novel Tool to Investigate the Early and Late Stages of α-Synuclein Aggregation

The accumulation of an inherently disordered protein α-synuclein (α-syn) aggregates in brain tissue play a pivotal role in the pathology and etiology of Parkinson's disease. Aggregation of α-syn has been found to be complex and heterogeneous, occurring through multitudes of early- and late-stage intermediates. Because of the inherent complexity and large dynamic range (between a few microseconds to several days under in vitro measurement conditions), it is difficult for the conventional biophysical and biochemical techniques to sample the entire time window of α-syn aggregation. Here, for the first time, we introduced the Z-scan technique as a novel tool to investigate different conformations formed in the early and late stage of temperature and mechanical stress-induced α-syn aggregation, in which different species showed its characteristic nonlinear characteristics. A power-dependent study was also performed to observe the changes in the protein nonlinearity. The perceived nonlinearity was accredited to the thermal-lensing effect. A switch in the sign of the refractive nonlinearity was observed for the first time as a signature of the late oligomeric conformation, a prime suspect that triggers cell death associated with neurodegeneration. We validate Z-scan results using a combination of different techniques, like thioflavin-T fluorescence assay, fluorescence correlation spectroscopy, Fourier-transform infrared spectroscopy, and atomic force microscopy. We believe that this simple, inexpensive, and sensitive method can have potential future applications in detecting/monitoring conformations in other essential peptides/proteins related to different neurodegenerative and other human diseases.

Simultaneous Study of Anti-Ferroptosis and Antioxidant Mechanisms of Butein and (S)-Butin

To elucidate the mechanism of anti-ferroptosis and examine structural optimization in natural phenolics, cellular and chemical assays were performed with 2'-hydroxy chalcone butein and dihydroflavone (S)-butin. C11-BODIPY staining and flow cytometric assays suggest that butein more effectively inhibits ferroptosis in erastin-treated bone marrow-derived mesenchymal stem cells than (S)-butin. Butein also exhibited higher antioxidant percentages than (S)-butin in five antioxidant assays: linoleic acid emulsion assay, Fe3+-reducing antioxidant power assay, Cu2+-reducing antioxidant power assay, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide radical (PTIO•)-trapping assay, and α,α-diphenyl-β-picrylhydrazyl radical (DPPH•)-trapping assay. Their reaction products with DPPH• were further analyzed using ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UPLC-ESI-Q-TOF-MS). Butein and (S)-butin produced a butein 5,5-dimer (m/z 542, 271, 253, 225, 135, and 91) and a (S)-butin 5',5'-dimer (m/z 542, 389, 269, 253, and 151), respectively. Interestingly, butein forms a cross dimer with (S)-butin (m/z 542, 523, 433, 419, 415, 406, and 375). Therefore, we conclude that butein and (S)-butin exert anti-ferroptotic action via an antioxidant pathway (especially the hydrogen atom transfer pathway). Following this pathway, butein and (S)-butin yield both self-dimers and cross dimers. Butein displays superior antioxidant or anti-ferroptosis action to (S)-butin. This can be attributed the decrease in π-π conjugation in butein due to saturation of its α,β-double bond and loss of its 2'-hydroxy group upon biocatalytical isomerization.