Misfolded Research Articles

DELE1 maintains muscle proteostasis to promote growth and survival in mitochondrial myopathy.

Mitochondrial dysfunction causes devastating disorders, including mitochondrial myopathy, but how muscle senses and adapts to mitochondrial dysfunction is not well understood. Here, we used diverse mouse models of mitochondrial myopathy to show that the signal for mitochondrial dysfunction originates within mitochondria. The mitochondrial proteins OMA1 and DELE1 sensed disruption of the inner mitochondrial membrane and, in response, activated the mitochondrial integrated stress response (mt-ISR) to increase the building blocks for protein synthesis. In the absence of the mt-ISR, protein synthesis in muscle was dysregulated causing protein misfolding, and mice with early-onset mitochondrial myopathy failed to grow and survive. The mt-ISR was similar following disruptions in mtDNA maintenance (Tfam knockout) and mitochondrial protein misfolding (CHCHD10 G58R and S59L knockin) but heterogenous among mitochondria-rich tissues, with broad gene expression changes observed in heart and skeletal muscle and limited changes observed in liver and brown adipose tissue. Taken together, our findings identify that the DELE1 mt-ISR mediates a similar response to diverse forms of mitochondrial stress and is critical for maintaining growth and survival in early-onset mitochondrial myopathy.

Protein aggregation is a consequence of the dormancy-inducing membrane toxin TisB in Escherichia coli.

Protein aggregates occur in all living cells due to misfolding of proteins. In bacteria, protein aggregation is associated with cellular inactivity, which is related to dormancy and tolerance to stressful conditions, including exposure to antibiotics. In Escherichia coli, the membrane toxin TisB is an important factor for dormancy and antibiotic tolerance upon DNA damage mediated by the fluoroquinolone antibiotic ciprofloxacin. Here, we show that TisB provokes protein aggregation, which, in turn, promotes an extended state of cellular dormancy. Our study suggests that protein aggregation is a consequence of membrane toxins with the potential to affect the duration of dormancy and the outcome of antibiotic therapy.

Unraveling the Molecular Jam: How Crowding Shapes Protein Aggregation in Neurodegenerative Disorders.

Protein misfolding and aggregation are the hallmarks of neurodegenerative diseases including Huntington's disease, Parkinson's disease, Alzheimer's disease, and prion diseases. A crowded cellular environment plays a crucial role in modulating protein aggregation processes in vivo and the pathological aggregation of proteins linked to different neurodegenerative disorders. Here, we review recent studies examining the effects of various crowding agents, such as polysaccharides, polyethylene glycol, and proteins like BSA and lysozyme on the behaviors of aggregation of several amyloidogenic peptides and proteins, including amylin, huntingtin, tau, α-synuclein, prion, and amyloid-β. We also summarize how the aggregation kinetics, thermodynamic stability, and morphology of amyloid fibrils are altered significantly in the presence of crowding agents. In addition, we also discuss the molecular basis underlying the modulation of amyloidogenic aggregation, focusing on changes in the protein conformation, and the nucleation mechanism. The molecular understanding of the effects of macromolecular crowding on amyloid aggregation is essential for revealing disease pathologies and identifying possible therapeutic targets. Thus, this review offers a perspective on the complex interplay between protein aggregation and the crowded cellular environment in vivo and explains the relevance of crowding in the context of neurodegenerative disorders.

Light Chain (AL) Amyloidosis for Nephrologists - Treatment Standard.

Amyloidosis is a group of complex diseases caused by the misfolding and aggregation of proteins into amyloid fibrils. AL amyloidosis is one of the most prevalent forms of amyloidosis, characterized by the gradual proliferation of light chains from plasma cell clones. A growing body of evidence has contributed to our understanding of its pathogenesis, presentation, and clinical course. Increased recognition of its clinical sequelae has increased the prevalence of AL amyloidosis. Renal involvement, seen in up to 70% of cases, is particularly challenging due to its impact on quality of life and access to treatment options. Thus, early recognition of its unique sequelae, appropriate staging, and a comprehensive understanding of treatment options balanced by their organ toxicities are crucial to managing this disease. We review the current treatment standards and discuss novel developments in the pathophysiology, diagnosis, outcome prediction, and management of AL amyloidosis for the Nephrologist.

Seeding Aggregation Assays in Lewy Bodies Disorders: A Narrative State-of-the-Art Review

Multiple system atrophy and Lewy body diseases (LBDs) such as Parkinson’s disease, dementia with Lewy bodies, and Parkinson’s disease with dementia, known as synucleinopathies, are defined neuropathologically by the accumulation and deposition of aberrant protein aggregates, primarily in neuronal cells. Seeding aggregation assays (SAA) have significant potential as biomarkers for early diagnosis, monitoring disease progression, and evaluating treatment efficacy for these diseases. Real-time quaking-induced conversion (RT-QuIC) and Protein Misfolding Cyclic Amplification (PMCA) assays represent two ultrasensitive protein amplification techniques that were initially tested for the field of prion disorders. Although the fundamental idea behind the creation of these two methods is very similar, their technical differences resulted in different levels of diagnostic accuracy for the identification of prion proteins, making the RT-QuIC assay the most trustworthy and effective instrument for the detection of suspected cases of LBDs and prion-like diseases.

Unveiling fungal strategies: Mycoremediation in multi-metal pesticide environment using proteomics

Micropollutants, such as heavy metals and pesticides, inhibit microbial growth, threatening ecosystems. Yet, the mechanism behind mycoremediation of the pesticide lindane and multiple metals (Cd, Total Cr, Cu, Ni, Pb, Zn) remains poorly understood. In our study, we investigated cellular responses in Aspergillus fumigatus PD-18 using LC-MS/MS, identifying 2190 proteins, 1147 of which were consistently present under both stress conditions. Specifically, Cu-Zn superoxide dismutase and heat shock proteins were up-regulated to counter oxidative stress and protein misfolding. Proteins involved in intracellular trafficking, secretion, and vesicular transport; RNA processing and modification showed enhanced abundance and regulating stress response pathways. Additionally, haloalkane dehalogenase and homogentisate 1,2-dioxygenase played pivotal roles in lindane mineralization. Bioinformatics analysis highlighted enriched pathways such as Glyoxylate and dicarboxylate metabolism and Purine metabolism, that are crucial for combating adverse environments. We identified the hub protein 26 S proteasome regulatory subunit complex as potential biomarker and remedial targets for mycoremediation of wastewater, suggesting practical applications for environmental remediation.

Ankaflavin and Monascin Prevent Fibrillogenesis of Hen Egg White Lysozyme: Focus on Noncovalent and Covalent Interactions.

Misfolding and amyloid fibrillogenesis of proteins have close relationships with several neurodegenerative diseases. The present work investigates the inhibitive activities of ankaflavin (AK) and monascin (MS), two yellow pigments separated from Monascus-fermented rice, on hen egg white lysozyme (HEWL) fibrillation. The results demonstrated that AK/MS suppressed HEWL fibrillation through interfering with the nucleation period and AK was more potent. Fluorescence quenching and in silico docking studies revealed that AK/MS bond to HEWL by the formation of noncovalent forces with some critical amino acid residues that tend to form fibrils. Compared to those of AK, hydrogen bonding interactions between MS and Asn46, Trp62, and Trp63 residues in HEWL were slightly weaker. Besides, the covalent interaction between MS and HEWL with the binding site of Arg68 was found. These observations offered reasonable explanations for the difference in the mechanisms of AK and MS inhibiting HEWL fibrillogenesis. In a word, all data acquired herein indicated AK/MS as potent candidates for the improvement and treatment of neurological disorders.

Enzymatic Synthesis of Isotopically Labeled Hydrogen Peroxide for Mass Spectrometry-Based Applications.

Methionine oxidation is involved in multiple biological processes including protein misfolding and enzyme regulation. However, it is often challenging to measure levels of methionine oxidation by mass spectrometry, in part due to the prevalence of artifactual oxidation that occurs during the sample preparation and ionization steps of typical proteomic workflows. Isotopically labeled hydrogen peroxide (H218O2) can be used to block unoxidized methionines and enables accurate measurement of in vivo levels of methionine oxidation. However, H218O2 is an expensive reagent that can be difficult to obtain from commercial sources. Here, we report a method for synthesizing H218O2 in-house. Glucose oxidase catalyzes the oxidation of β-d-glucose and produces hydrogen peroxide in the process. We took advantage of this reaction to enzymatically synthesize H218O2 from 18O2 and assessed its concentration, purity, and utility in measuring methionine oxidation levels by mass spectrometry.

Bisdemethoxycurcumin, a novel potent polyphenolic compound, effectively inhibits the formation of amyloid aggregates in ALS-associated hSOD1 mutant (L38R)

Protein misfolding is a biological process that leads to protein aggregation. Anomalous misfolding and aggregation of human superoxide dismutase (hSOD1) into amyloid aggregates is a characteristic feature of amyotrophic lateral sclerosis (ALS), a neurodegenerative illness. Thus, focusing on the L38R mutant may be a wise decision to comprehend the SOD1 disease process in ALS. We suggest that Bisdemethoxycurcumin (BDMC) may be a strong anti-amyloidogenic polyphenol against L38R mutant aggregation. Protein stability, hydrophobicity, and flexibility were altered when BDMC was bound to the L38R mutant, as shown by molecular dynamic (MD) simulations and molecular docking. FTIR data shows α-Helix dominance in BDMC-containing samples, with reduced β-sheet and disordered peaks, indicating the decrease of aggregate species. ThT aggregation kinetics curves show BDMC reduces L38R mutant aggregation dose-dependently, with higher BDMC concentrations yielding greater reductions. TEM images showed various quantities of amorphous aggregates, but notably, 60 μM BDMC markedly reduced aggregate density, underscoring BDMC's inhibitory effect. Hemolysis tests revealed aggregate species in BDMC-treated samples were less toxic than in L38R mutant samples alone at the same concentrations and exposure times. Overall, BDMC has substantial potential to develop highly effective inhibitors that mitigate the risk of fatal ALS.

Computational Insights Into the Mechanism of EGCG's Binding and Inhibition of the TDP-43 Aggregation.

Misfolding and aggregation of TAR DNA-binding protein, TDP-43, is linked to devastating proteinopathies such as ALS. Therefore, targeting TDP-43's aggregation is significant for therapeutics. Recently, green tea polyphenol, EGCG, was observed to promote non-toxic TDP-43 oligomer formation disallowing TDP-43 aggregation. Here, we investigated if the anti-aggregation effect of EGCG is mediated via EGCG's binding to TDP-43. In silico molecular docking and molecular dynamics (MD) simulation suggest a strong binding of EGCG with TDP-43's aggregation-prone C-terminal domain (CTD). Three replicas, each having 800 ns MD simulation of the EGCG-TDP-43-CTD complex, yielded a high negative binding free energy (ΔG) inferring a stable complex formation. Simulation snapshots show that EGCG forms close and long-lasting contacts with TDP-43's Phe-313 and Ala-341 residues, which were previously identified for monomer recruitment in CTD's aggregation. Notably, stable physical interactions between TDP-43 and EGCG were also detected invitro using TTC staining and isothermal titration calorimetry which revealed a high-affinity binding site of EGCG on TDP-43 (Kd, 7.8 μM; ΔG, -6.9 kcal/mol). Additionally, TDP-43 co-incubated with EGCG was non-cytotoxic when added to HEK293 cells. In summary, EGCG's binding to TDP-43 and blocking of residues important for aggregation can be a possible mechanism of its anti-aggregation effects on TDP-43.

Amyloidosis

Amyloidosis are rare protein misfolding and deposition diseases which, with very few exceptions, are treatable easily nowadays. The prognosis depends on the form of amyloidosis, which is particularly unfavorable for heart involvement that is diagnosed too late. Patients die within months to a few years or suffer irreversible loss of function of the affected organs. Once the diagnosis has been made, treatment should be started without delay. Amyloidosis centers offer support in the diagnosis and development as well as clinical trials of an optimal therapy concept.

Dynamic protein hydration water mediates the aggregation kinetics of amyloid β peptides at interfaces

Protein hydration water is essential for protein misfolding and amyloid formation, but how it directs the course of amyloid formation has yet to be elucidated. Here, we experimentally demonstrated that femtosecond sum frequency generation vibrational spectroscopy (SFG–VS) and the femtosecond IR pump–SFG probe technique can serve as powerful tools for addressing this issue. Using amyloid β(1–42) peptide as a model, we determined the transient misfolding intermediates by probing the amide band spectral features and the local hydration water changes by measuring the ultrafast vibrational dynamics of the amide I band. For the first time, we established a correlation between the dynamic change in protein hydration water and aggregation propensity. The aggregation propensity depends on the dynamic change in the hydration water, rather than the static hydration water content of the initial protein state. Water expulsion enhances the aggregation propensity and promotes amyloid formation, while protein hydration attenuates the aggregation propensity and inhibits amyloid formation. The suppression of water expulsion and protein hydration can prevent protein aggregation and stabilize proteins. These findings contribute to a better understanding of the underlying effect of hydration water on amyloid formation and protein structural stability and provide a strategy for maintaining long–term stabilization of biomolecules.

Discovery of Novel Inhibitors against ALS-Related SOD1(A4V) Aggregation through the Screening of a Chemical Library Using Differential Scanning Fluorimetry (DSF)

Background: Cu/Zn Superoxide Dismutase 1 (SOD1) is a 32 kDa cytosolic dimeric metalloenzyme that neutralizes superoxide anions into oxygen and hydrogen peroxide. Mutations in SOD1 are associated with ALS, a disease causing motor neuron atrophy and subsequent mortality. These mutations exert their harmful effects through a gain of function mechanism, rather than a loss of function. Despite extensive research, the mechanism causing selective motor neuron death still remains unclear. A defining feature of ALS pathogenesis is protein misfolding and aggregation, evidenced by ubiquitinated protein inclusions containing SOD1 in affected motor neurons. This work aims to identify compounds countering SOD1(A4V) misfolding and aggregation, which could potentially aid in ALS treatment. Methods: The approach employed was in vitro screening of a library comprising 1280 pharmacologically active compounds (LOPAC®) in the context of drug repurposing. Using differential scanning fluorimetry (DSF), these compounds were tested for their impact on SOD1(A4V) thermal stability. Results and Conclusions: Dimer stability was the parameter chosen as the criterion for screening, since the dissociation of the native SOD1 dimer is the step prior to its in vitro aggregation. The screening revealed one compound raising protein-ligand Tm by 6 °C, eleven inducing a higher second Tm, suggesting a stabilization effect, and fourteen reducing Tm from 10 up to 26 °C, suggesting possible interactions or non-specific binding.

Effects of treadmill exercise on endoplasmic reticulum protein folding and endoplasmic reticulum-associated protein degradation pathways in APP/PS1 mice

A hallmark of Alzheimer's disease (AD) is the disruption of protein homeostasis (proteostasis), manifested by the misfolding and aggregation of proteins. Molecular chaperones and the endoplasmic reticulum (ER)-associated protein degradation (ERAD) pathway in the ER are essential for correct protein folding and degradation of misfolded proteins respectively, thus contributing to the maintenance of proteostasis. The present study aimed to investigate whether the beneficial effects of exercise in an AD mice model is associated with changes in ER protein folding and ERAD. APP/PS1 transgenic and wild-type mice were subjected to treadmill exercise for three months. The levels of molecular chaperones, specifically protein disulfide isomerases (PDIs) and heat shock proteins (HSPs), as well as ERAD-associated molecules were analyzed in the hippocampus. The result revealed a decrease in mRNA levels of PDIA2, PDIA3, PDIA4, PDIA5, PDIA6, HSPA1B, HSPA8, HSP90B1, DNAJB2, CRYAB, and CNX, an increase in mRNA levels of HSPA5 and HSPH1, an increase in protein levels of HERPUD1, and a decrease in protein levels of VCP in APP/PS1 mice. However, following a 3-month treadmill exercise regimen, an increase in mRNA levels of PDIA2, PDIA4, PDIA6, HSPA1A, HSPA8, HSP90AB1, and DNAJB2, as well as an increase in protein levels of VCP and DERL2, and a decrease in protein levels of HERPUD1 were noted. Overall, our findings indicate that disruptions in hippocampal ER protein folding and ERAD pathways may be implicated in AD, with exercise serving as a regulator of these pathways.

Christopher Martin Dobson. 8 October 1949 — 8 September 2019

Christopher Martin Dobson was a distinguished biophysical chemist who earned an international reputation for his work on protein folding, misfolding and aggregation. Protein folding is a crucial process in biochemistry where a protein transitions from a disordered state to a structured, three-dimensional form after being synthesized by a ribosome. This transformation is essential for the protein to attain its biological functionality. The intricate folding pathway is guided by various interactions between amino acids within the protein chain. When protein folding goes awry, it can lead to misfolded proteins, which are associated with various disorders such as Alzheimer's and Parkinson's disease. The study of protein folding and misfolding has significant implications for both basic science and medical research. Chris's career spanned almost five decades, resulted in more than 870 publications and established a legacy that will influence the lives of many for decades to come. His outstanding mentorship resulted in some 100 of his former students and post-docs taking up independent positions at academic institutions in all parts of the world, while his research work has left a lasting imprint on the biophysical sciences and inspired an entire generation of research scientists.

Metabolic perturbations associated with hIAPP-induced insulin resistance in skeletal muscles: Implications to the development of type 2 diabetes

The human islet amyloid polypeptide (hIAPP) tends to misfold and self-assemble to form amyloid fibrils, which has been associated with the loss of function and viability of pancreatic β-cells in type 2 diabetes mellitus (T2DM). The role of hIAPP in the development of insulin resistance (a hallmark of T2DM) in skeletal muscles – the major sites for glucose utilization – needs further investigation. Even though, insulin-resistant conditions have been known to stimulate hIAPP aggregation, the events that lead to the development of insulin resistance due to hIAPP aggregation in skeletal muscles remain unidentified. Here, we have attempted to identify metabolic perturbations in L6 myotubes that were exposed to increasing concentrations of recombinant hIAPP for different time durations. It was observed that hIAPP exposure was associated with increased mitochondrial and cellular ROS levels, loss in mitochondrial membrane potential and viability of the myotubes. Metabolomic investigations of hIAPP-treated myotubes revealed significant perturbations in o-phosphocholine, sn-glycero-3-phosphocholine and dimethylamine levels (p < 0.05). Therefore, we anticipate that defects in glycerophospholipid metabolism and the associated oxidative stress and membrane damage may play key roles in the development of insulin resistance due to protein misfolding in skeletal muscles. In summary, the perturbed metabolites and their pathways have not only the potential to be used as early biomarkers to predict the onset of insulin resistance and T2DM but also as therapeutic targets for the effective management of the same.

Proteases: Role in Various Human Diseases.

Proteases, a group of hydrolytic enzymes catalyzing the hydrolysis of peptide bonds, play pivotal roles in various physiological processes and have emerged as key contributors to the pathogenesis of diverse diseases. This work provides an insight into the impact of protease activity on different disease contexts, highlighting their involvement in cancer, inflammatory disorders, cardiovascular diseases, infectious diseases, and neurodegenerative conditions. In cancer, proteases facilitate tumor growth, invasion, and metastasis, while in inflammatory diseases, dysregulated protease activity exacerbates tissue damage and inflammation. Cardiovascular diseases involve proteases in extracellular matrix remodeling, affecting arterial structure. In infectious diseases, proteases play crucial roles in pathogen invasion and immune evasion. Neurodegenerative diseases are characterized by protease dysregulation, contributing to protein misfolding and aggregation. As research progresses, understanding the intricate relationships between proteases and diseases becomes essential for developing targeted therapeutic strategies. This review aims to provide a comprehensive glimpse into the diverse impact of protease activities on various diseases, emphasizing their potential as crucial players in the landscape of disease pathology and potential therapeutic interventions.

Use of the Novel Site-Directed Enzyme Enhancement Therapy (SEE-Tx) Drug Discovery Platform to Identify Pharmacological Chaperones for Glutaric Acidemia Type 1.

Allosteric regulators acting as pharmacological chaperones hold promise for innovative therapeutics since they target noncatalytic sites and stabilize the folded protein without competing with the natural substrate, resulting in a net gain of function. Exogenous allosteric regulators are typically more selective than active site inhibitors and can be more potent than competitive inhibitors when the natural substrate levels are high. To identify novel structure-targeted allosteric regulators (STARs) that bind to and stabilize the mitochondrial enzyme glutaryl-CoA dehydrogenase (GCDH), the computational site-directed enzyme enhancement therapy (SEE-Tx) technology was applied. SEE-Tx is an innovative drug discovery platform with the potential to identify drugs for treating protein misfolding disorders, such as glutaric acidemia type 1 (GA1) disease. Putative allosteric regulators were discovered using structure- and ligand-based virtual screening methods and validated using orthogonal biophysical and biochemical assays. The computational approach presented here could be used to discover allosteric regulators of other protein misfolding disorders.

An antireductant approach ameliorates misfolded proinsulin-induced hyperglycemia and glucose intolerance in male Akita mice.

Protein folding in the endoplasmic reticulum (ER) requires a high ratio of oxidized to reduced glutathione (GSSG/rGSH). Since the GSSG/rGSH depends on total glutathione (tGSH = GSSG + rGSH) levels, we hypothesized that limiting GSH biosynthesis will ameliorate protein misfolding by enhancing the ER oxidative milieu. As a proof-of-concept, we used DL-buthionine-(S,R)-sulfoximine (BSO) to inhibit GSH biosynthesis in Akita mice, which are prone to proinsulin misfolding. We conducted a 2-week intervention to investigate if BSO was safe and a 6-week intervention to find its effect on glucose intolerance. In both cohorts, male heterozygous Akita (AK) and wild-type (WT) mice were continuously administered 15mM BSO. No adverse effects were observed on body weight, food intake, and water intake in either cohort. Unaltered levels of plasma aspartate and alanine aminotransferases, and cystatin-C, indicate that BSO was safe. BSO-induced decreases in tGSH were tissue-dependent with maximal effects in the kidneys, where it altered the expression of genes associated with GSH biosynthesis, redox status, and proteostasis. BSO treatment decreased random blood glucose levels to 80% and 67%of levels in untreated mice in short-term and long-term cohorts, respectively, and 6-h fasting blood glucose to 82% and 74%of levels in untreated mice, respectively. BSO also improved glucose tolerance by 37% in AK mice in the long-term cohort, without affecting insulin tolerance. Neither glucose tolerance nor insulin tolerance were affected in WT. Data indicate that BSO might treat misfolded proinsulin-induced glucose intolerance. Future studies should investigate the effect of BSO on proinsulin misfolding and if it improves glucose intolerance in individuals with Mutant Insulin Diabetes of Youth.

Unraveling the Molecular Pathogenesis of Protein C Deficiency-Associated VTE: Insights from Protein C Mutations C238G and R189W in Thai Patients.

Protein C (PC) deficiency is a well-established risk factor for thromboembolism (TE), commonly manifesting in pediatric patients. This study aimed to elucidate the pathogenic mechanisms of two novel PC mutations, C238G and R189W, identified in Thai children with both venous and arterial TE. The effects of wild-type (WT), C238G, and R189W PC variants were investigated through transient transfection of HEK293T cells. PC secretion levels were measured, and immunofluorescence analysis was performed to assess intracellular localization. ER stress-related gene expression and UPR activation were evaluated. Structural analysis was conducted to explore the significance of the C238 and R189W residue in PC functionality. The C238G mutation led to a severe 95% reduction in PC secretion, while R189W showed a 30% decrease compared with WT. Immunofluorescence revealed that C238G-PC was predominantly retained in the ER, indicating protein misfolding. C238G-expressing cells exhibited significant upregulation of ER stress-related genes and UPR activation. In contrast, R189W resulted in only a modest increase in UPR gene expression, suggesting a less pronounced impact on protein folding and secretion. Structural analysis demonstrated the critical role of the C238 residue in maintaining PC's disulfide bond and overall conformation. This study reveals distinct molecular mechanisms by which the C238G and R189W mutations contribute to PC deficiency and increased thrombotic risk. The findings emphasize the essential role of the C238 residue in preserving PC structure and secretion, enhancing the understanding of PC deficiency-associated TE in pediatric patients.