1,008 results on '"Christopher M, Dobson"'
Search Results
2. Exogenous misfolded protein oligomers can cross the intestinal barrier and cause a disease phenotype in C. elegans
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Michele Perni, Benedetta Mannini, Catherine K. Xu, Janet R. Kumita, Christopher M. Dobson, Fabrizio Chiti, and Michele Vendruscolo
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Medicine ,Science - Abstract
Abstract Misfolded protein oligomers are increasingly recognized as highly cytotoxic agents in a wide range of human disorders associated with protein aggregation. In this study, we assessed the possible uptake and resulting toxic effects of model protein oligomers administered to C. elegans through the culture medium. We used an automated machine-vision, high-throughput screening procedure to monitor the phenotypic changes in the worms, in combination with confocal microscopy to monitor the diffusion of the oligomers, and oxidative stress assays to detect their toxic effects. Our results suggest that the oligomers can diffuse from the intestinal lumen to other tissues, resulting in a disease phenotype. We also observed that pre-incubation of the oligomers with a molecular chaperone (αB-crystallin) or a small molecule inhibitor of protein aggregation (squalamine), reduced the oligomer absorption. These results indicate that exogenous misfolded protein oligomers can be taken up by the worms from their environment and spread across tissues, giving rise to pathological effects in regions distant from their place of absorbance.
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- 2021
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3. Two human metabolites rescue a C. elegans model of Alzheimer’s disease via a cytosolic unfolded protein response
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Priyanka Joshi, Michele Perni, Ryan Limbocker, Benedetta Mannini, Sam Casford, Sean Chia, Johnny Habchi, Johnathan Labbadia, Christopher M. Dobson, and Michele Vendruscolo
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Biology (General) ,QH301-705.5 - Abstract
Joshi et al. identify two human metabolites, carnosine and kynurenic acid, that rescue a C. elegans model of Alzheimer’s disease by inhibiting the aggregation of the amyloid beta peptide in vivo. They find that these metabolites trigger a cytosolic unfolded protein response through the transcription factor HSF-1 and molecular chaperones DNJ-12 and DNJ-19, thus providing mechanistic links between metabolite homeostasis and protein homeostasis to further insights into interventions against neurodegenerative diseases.
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- 2021
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4. The role of structural dynamics in the thermal adaptation of hyperthermophilic enzymes
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Giuliana Fusco, Francesco Bemporad, Fabrizio Chiti, Christopher M. Dobson, and Alfonso De Simone
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thermophilic proteins ,protein dynamics ,NMR ,residual dipolar couplings ,restrained MD simulations ,Biology (General) ,QH301-705.5 - Abstract
Proteins from hyperthermophilic organisms are evolutionary optimised to adopt functional structures and dynamics under conditions in which their mesophilic homologues are generally inactive or unfolded. Understanding the nature of such adaptation is of crucial interest to clarify the underlying mechanisms of biological activity in proteins. Here we measured NMR residual dipolar couplings of a hyperthermophilic acylphosphatase enzyme at 80°C and used these data to generate an accurate structural ensemble representative of its native state. The resulting energy landscape was compared to that obtained for a human homologue at 37°C, and additional NMR experiments were carried out to probe fast (15N relaxation) and slow (H/D exchange) backbone dynamics, collectively sampling fluctuations of the two proteins ranging from the nanosecond to the millisecond timescale. The results identified key differences in the strategies for protein-protein and protein-ligand interactions of the two enzymes at the respective physiological temperatures. These include the dynamical behaviour of a β-strand involved in the protection against aberrant protein aggregation and concerted motions of loops involved in substrate binding and catalysis. Taken together these results elucidate the structure-dynamics-function relationship associated with the strategies of thermal adaptation of protein molecules.
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- 2022
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5. The release of toxic oligomers from α-synuclein fibrils induces dysfunction in neuronal cells
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Roberta Cascella, Serene W. Chen, Alessandra Bigi, José D. Camino, Catherine K. Xu, Christopher M. Dobson, Fabrizio Chiti, Nunilo Cremades, and Cristina Cecchi
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Science - Abstract
The self-assembly of α-synuclein (αS) is a pathological feature of Parkinson’s disease. The αS species responsible for neuronal damage are not well characterized. Here, the authors show that αS fibrils release soluble prefibrillar oligomeric species responsible for neurotoxicity in vitro.
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- 2021
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6. A dopamine metabolite stabilizes neurotoxic amyloid-β oligomers
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Rodrigo Cataldi, Sean Chia, Katarina Pisani, Francesco S. Ruggeri, Catherine K. Xu, Tomas Šneideris, Michele Perni, Sunehera Sarwat, Priyanka Joshi, Janet R. Kumita, Sara Linse, Johnny Habchi, Tuomas P. J. Knowles, Benedetta Mannini, Christopher M. Dobson, and Michele Vendruscolo
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Biology (General) ,QH301-705.5 - Abstract
Cataldi et al. investigates the impact of the dopamine derivative DOPAL on the Aβ peptide oligomer formation. They report that DOPAL promotes the formation of stable Aβ oligomers that exert toxicity on neuroblastoma cells by increasing cytosolic calcium levels and generating reactive oxygen species. This study connects Aβ aggregation with processes regulating cellular homeostasis in the brain.
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- 2021
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7. Screening of small molecules using the inhibition of oligomer formation in α-synuclein aggregation as a selection parameter
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Roxine Staats, Thomas C. T. Michaels, Patrick Flagmeier, Sean Chia, Robert I. Horne, Johnny Habchi, Sara Linse, Tuomas P. J. Knowles, Christopher M. Dobson, and Michele Vendruscolo
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Chemistry ,QD1-999 - Abstract
Promising treatments for neurogenerative disorders may involve targeting kinetic intermediates, including α-synuclein oligomers. Here a kinetic method for quantifying oligomer populations is used to screen small molecule inhibitors of oligomerisation and gain mechanistic insight into their modes of action.
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- 2020
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8. Cytosolic aggregation of mitochondrial proteins disrupts cellular homeostasis by stimulating the aggregation of other proteins
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Urszula Nowicka, Piotr Chroscicki, Karen Stroobants, Maria Sladowska, Michal Turek, Barbara Uszczynska-Ratajczak, Rishika Kundra, Tomasz Goral, Michele Perni, Christopher M Dobson, Michele Vendruscolo, and Agnieszka Chacinska
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mitochondria ,aggregation ,chaperones ,neurodegeneration ,homeostasis ,metastable proteins ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Mitochondria are organelles with their own genomes, but they rely on the import of nuclear-encoded proteins that are translated by cytosolic ribosomes. Therefore, it is important to understand whether failures in the mitochondrial uptake of these nuclear-encoded proteins can cause proteotoxic stress and identify response mechanisms that may counteract it. Here, we report that upon impairments in mitochondrial protein import, high-risk precursor and immature forms of mitochondrial proteins form aberrant deposits in the cytosol. These deposits then cause further cytosolic accumulation and consequently aggregation of other mitochondrial proteins and disease-related proteins, including α-synuclein and amyloid β. This aggregation triggers a cytosolic protein homeostasis imbalance that is accompanied by specific molecular chaperone responses at both the transcriptomic and protein levels. Altogether, our results provide evidence that mitochondrial dysfunction, specifically protein import defects, contributes to impairments in protein homeostasis, thus revealing a possible molecular mechanism by which mitochondria are involved in neurodegenerative diseases.
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- 2021
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9. A metastable subproteome underlies inclusion formation in muscle proteinopathies
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Prajwal Ciryam, Matthew Antalek, Fernando Cid, Gian Gaetano Tartaglia, Christopher M. Dobson, Anne-Katrin Guettsches, Britta Eggers, Matthias Vorgerd, Katrin Marcus, Rudolf A. Kley, Richard I. Morimoto, Michele Vendruscolo, and Conrad C. Weihl
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Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract Protein aggregation is a pathological feature of neurodegenerative disorders. We previously demonstrated that protein inclusions in the brain are composed of supersaturated proteins, which are abundant and aggregation-prone, and form a metastable subproteome. It is not yet clear, however, whether this phenomenon is also associated with non-neuronal protein conformational disorders. To respond to this question, we analyzed proteomic datasets from biopsies of patients with genetic and acquired protein aggregate myopathy (PAM) by quantifying the changes in composition, concentration and aggregation propensity of proteins in the fibers containing inclusions and those surrounding them. We found that a metastable subproteome is present in skeletal muscle from healthy patients. The expression of this subproteome escalate as proteomic samples are taken more proximal to the pathologic inclusion, eventually exceeding its solubility limits and aggregating. While most supersaturated proteins decrease or maintain steady abundance across healthy fibers and inclusion-containing fibers, proteins within the metastable subproteome rise in abundance, suggesting that they escape regulation. Taken together, our results show in the context of a human conformational disorder that the supersaturation of a metastable subproteome underlies widespread aggregation and correlates with the histopathological state of the tissue.
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- 2019
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10. Enhancement of the Anti-Aggregation Activity of a Molecular Chaperone Using a Rationally Designed Post-Translational Modification
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Philip R. Lindstedt, Francesco A. Aprile, Maria J. Matos, Michele Perni, Jean B. Bertoldo, Barbara Bernardim, Quentin Peter, Gonzalo Jiménez-Osés, Tuomas P. J. Knowles, Christopher M. Dobson, Francisco Corzana, Michele Vendruscolo, and Gonçalo J. L. Bernardes
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Chemistry ,QD1-999 - Published
- 2019
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11. Different soluble aggregates of Aβ42 can give rise to cellular toxicity through different mechanisms
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Suman De, David C. Wirthensohn, Patrick Flagmeier, Craig Hughes, Francesco A. Aprile, Francesco S. Ruggeri, Daniel R. Whiten, Derya Emin, Zengjie Xia, Juan A. Varela, Pietro Sormanni, Franziska Kundel, Tuomas P. J. Knowles, Christopher M. Dobson, Clare Bryant, Michele Vendruscolo, and David Klenerman
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Science - Abstract
Amyloid beta (Aβ42) peptides form heterogeneous mixtures of aggregates, which are closely linked to Alzheimer’s disease. This study shows how different types of Aβ42 aggregates are associated with distinct mechanisms of toxicity
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- 2019
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12. Trodusquemine enhances Aβ42 aggregation but suppresses its toxicity by displacing oligomers from cell membranes
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Ryan Limbocker, Sean Chia, Francesco S. Ruggeri, Michele Perni, Roberta Cascella, Gabriella T. Heller, Georg Meisl, Benedetta Mannini, Johnny Habchi, Thomas C. T. Michaels, Pavan K. Challa, Minkoo Ahn, Samuel T. Casford, Nilumi Fernando, Catherine K. Xu, Nina D. Kloss, Samuel I. A. Cohen, Janet R. Kumita, Cristina Cecchi, Michael Zasloff, Sara Linse, Tuomas P. J. Knowles, Fabrizio Chiti, Michele Vendruscolo, and Christopher M. Dobson
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Science - Abstract
Transient oligomeric species of the amyloid-β peptide (Aβ42) have been identified as key pathogenic agents in Alzheimer’s disease. Here the authors find that the aminosterol trodusquemine enhances Aβ42 aggregation and suppresses Aβ42-induced toxicity by displacing oligomers from cell membranes.
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- 2019
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13. Squalamine and Its Derivatives Modulate the Aggregation of Amyloid-β and α-Synuclein and Suppress the Toxicity of Their Oligomers
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Ryan Limbocker, Roxine Staats, Sean Chia, Francesco S. Ruggeri, Benedetta Mannini, Catherine K. Xu, Michele Perni, Roberta Cascella, Alessandra Bigi, Liam R. Sasser, Natalie R. Block, Aidan K. Wright, Ryan P. Kreiser, Edward T. Custy, Georg Meisl, Silvia Errico, Johnny Habchi, Patrick Flagmeier, Tadas Kartanas, Jared E. Hollows, Lam T. Nguyen, Kathleen LeForte, Denise Barbut, Janet R. Kumita, Cristina Cecchi, Michael Zasloff, Tuomas P. J. Knowles, Christopher M. Dobson, Fabrizio Chiti, and Michele Vendruscolo
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protein misfolding diseases ,amyloid-β ,Alzheimer’s disease ,α-synuclein ,Parkinson’s disease ,oligomers ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
The aberrant aggregation of proteins is a key molecular event in the development and progression of a wide range of neurodegenerative disorders. We have shown previously that squalamine and trodusquemine, two natural products in the aminosterol class, can modulate the aggregation of the amyloid-β peptide (Aβ) and of α-synuclein (αS), which are associated with Alzheimer’s and Parkinson’s diseases. In this work, we expand our previous analyses to two squalamine derivatives, des-squalamine and α-squalamine, obtaining further insights into the mechanism by which aminosterols modulate Aβ and αS aggregation. We then characterize the ability of these small molecules to alter the physicochemical properties of stabilized oligomeric species in vitro and to suppress the toxicity of these aggregates to varying degrees toward human neuroblastoma cells. We found that, despite the fact that these aminosterols exert opposing effects on Aβ and αS aggregation under the conditions that we tested, the modifications that they induced to the toxicity of oligomers were similar. Our results indicate that the suppression of toxicity is mediated by the displacement of toxic oligomeric species from cellular membranes by the aminosterols. This study, thus, provides evidence that aminosterols could be rationally optimized in drug discovery programs to target oligomer toxicity in Alzheimer’s and Parkinson’s diseases.
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- 2021
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14. Comparative Studies in the A30P and A53T α-Synuclein C. elegans Strains to Investigate the Molecular Origins of Parkinson's Disease
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Michele Perni, Annemieke van der Goot, Ryan Limbocker, Tjakko J. van Ham, Francesco A. Aprile, Catherine K. Xu, Patrick Flagmeier, Karen Thijssen, Pietro Sormanni, Giuliana Fusco, Serene W. Chen, Pavan K. Challa, Julius B. Kirkegaard, Romain F. Laine, Kai Yu Ma, Martin B. D. Müller, Tessa Sinnige, Janet R. Kumita, Samuel I. A. Cohen, Renée Seinstra, Gabriele S. Kaminski Schierle, Clemens F. Kaminski, Denise Barbut, Alfonso De Simone, Tuomas P. J. Knowles, Michael Zasloff, Ellen A. A. Nollen, Michele Vendruscolo, and Christopher M. Dobson
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C. elegans ,Parkinson's disease ,alpha-synuclein ,drug discovery ,protein aggregation ,protein misfolding ,Biology (General) ,QH301-705.5 - Abstract
The aggregation of α-synuclein is a hallmark of Parkinson's disease (PD) and a variety of related neurological disorders. A number of mutations in this protein, including A30P and A53T, are associated with familial forms of the disease. Patients carrying the A30P mutation typically exhibit a similar age of onset and symptoms as sporadic PD, while those carrying the A53T mutation generally have an earlier age of onset and an accelerated progression. We report two C. elegans models of PD (PDA30P and PDA53T), which express these mutational variants in the muscle cells, and probed their behavior relative to animals expressing the wild-type protein (PDWT). PDA30P worms showed a reduced speed of movement and an increased paralysis rate, control worms, but no change in the frequency of body bends. By contrast, in PDA53T worms both speed and frequency of body bends were significantly decreased, and paralysis rate was increased. α-Synuclein was also observed to be less well localized into aggregates in PDA30P worms compared to PDA53T and PDWT worms, and amyloid-like features were evident later in the life of the animals, despite comparable levels of expression of α-synuclein. Furthermore, squalamine, a natural product currently in clinical trials for treating symptomatic aspects of PD, was found to reduce significantly the aggregation of α-synuclein and its associated toxicity in PDA53T and PDWT worms, but had less marked effects in PDA30P. In addition, using an antibody that targets the N-terminal region of α-synuclein, we observed a suppression of toxicity in PDA30P, PDA53T and PDWT worms. These results illustrate the use of these two C. elegans models in fundamental and applied PD research.
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- 2021
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15. Publisher Correction: Two human metabolites rescue a C. elegans model of Alzheimer’s disease via a cytosolic unfolded protein response
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Priyanka Joshi, Michele Perni, Ryan Limbocker, Benedetta Mannini, Sam Casford, Sean Chia, Johnny Habchi, Johnathan Labbadia, Christopher M. Dobson, and Michele Vendruscolo
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Biology (General) ,QH301-705.5 - Published
- 2021
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16. A Cell- and Tissue-Specific Weakness of the Protein Homeostasis System Underlies Brain Vulnerability to Protein Aggregation
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Rishika Kundra, Christopher M. Dobson, and Michele Vendruscolo
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Science - Abstract
Summary: The phenomenon of protein misfolding and aggregation is associated with a wide range of neurodegenerative conditions that cause progressive loss of function in specific regions of the human brain. To understand the causes of the selective cell and tissue vulnerability to the formation of these deposits, we analyzed the ability of different cell and tissue types to respond, in the absence of disease, to the presence of high levels of aggregation-prone proteins. By performing a transcriptional analysis, we found that the protein homeostasis system that regulates protein aggregation is weaker in neurons than in other cell types and in brain tissues than in other body tissues. These results suggest that the intrinsic level of regulation of protein aggregation in the healthy state is correlated with the selective vulnerability of cells and tissues to protein misfolding diseases. : Molecular Physiology; Neuroscience; Transcriptomics Subject Areas: Molecular Physiology, Neuroscience, Transcriptomics
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- 2020
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17. A Role of Cholesterol in Modulating the Binding of α-Synuclein to Synaptic-Like Vesicles
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Wing K. Man, Alfonso De Simone, Joseph D. Barritt, Michele Vendruscolo, Christopher M. Dobson, and Giuliana Fusco
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α-synuclein ,synaptic vesicles ,membrane interaction ,cholesterol ,nuclear magnetic resonance ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
α-Synuclein (αS) is a presynaptic protein whose aggregation is associated with Parkinson’s disease (PD). Although the physiological function of αS is still unclear, several lines of evidence indicate that this protein may play a role in the trafficking of synaptic vesicles (SVs) during neurotransmitter release, a task associated with its ability to bind SVs and promote their clustering. It is therefore crucial to identify the cellular factors that modulate this process. To address this question, using nuclear magnetic resonance (NMR) spectroscopy we have characterized the role of cholesterol, a major component of the membrane of SVs, in the binding of αS with synaptic-like vesicles. Our results indicate that cholesterol can act as a modulator of the overall affinity of αS for SVs by reducing the local affinity of the region spanning residues 65–97 in the non-amyloid-β component (NAC) of the protein. The increased population of bound states that expose the region 65–97 to the solvent was found to induce stronger vesicle-vesicle interactions by αS. These results provide evidence that cholesterol modulates the clustering of synaptic vesicles induced by (α)S, and supports the role of the disorder-to-order equilibrium of the NAC region in the modulation of the biological properties of the membrane-bound state of αS.
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- 2020
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18. The Pathological G51D Mutation in Alpha-Synuclein Oligomers Confers Distinct Structural Attributes and Cellular Toxicity
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Catherine K. Xu, Marta Castellana-Cruz, Serene W. Chen, Zhen Du, Georg Meisl, Aviad Levin, Benedetta Mannini, Laura S. Itzhaki, Tuomas P. J. Knowles, Christopher M. Dobson, Nunilo Cremades, and Janet R. Kumita
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α-synuclein ,toxic oligomers ,Parkinson’s disease ,familial mutations ,α-helical structure ,Organic chemistry ,QD241-441 - Abstract
A wide variety of oligomeric structures are formed during the aggregation of proteins associated with neurodegenerative diseases. Such soluble oligomers are believed to be key toxic species in the related disorders; therefore, identification of the structural determinants of toxicity is of upmost importance. Here, we analysed toxic oligomers of α-synuclein and its pathological variants in order to identify structural features that could be related to toxicity and found a novel structural polymorphism within G51D oligomers. These G51D oligomers can adopt a variety of β-sheet-rich structures with differing degrees of α-helical content, and the helical structural content of these oligomers correlates with the level of induced cellular dysfunction in SH-SY5Y cells. This structure–function relationship observed in α-synuclein oligomers thus presents the α-helical structure as another potential structural determinant that may be linked with cellular toxicity in amyloid-related proteins.
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- 2022
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19. Microfluidic deposition for resolving single-molecule protein architecture and heterogeneity
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Francesco Simone Ruggeri, Jerome Charmet, Tadas Kartanas, Quentin Peter, Sean Chia, Johnny Habchi, Christopher M. Dobson, Michele Vendruscolo, and Tuomas P. J. Knowles
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Science - Abstract
Manual sample deposition on a substrate can introduce artifacts in quantitative AFM measurements. Here the authors present a microfluidic spray device for reliable deposition of subpicoliter droplets which dry out in milliseconds after landing on the surface, thereby avoiding protein self-assembly.
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- 2018
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20. The contribution of biophysical and structural studies of protein self-assembly to the design of therapeutic strategies for amyloid diseases
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Nunilo Cremades and Christopher M. Dobson
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Amyloid aggregation ,Fibril ,Oligomer ,Neurodegenerative diseases ,Therapeutic approaches ,Structure ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Many neurodegenerative disorders, including Alzheimer's, Parkinson's and the prion diseases, are characterized by a conformational conversion of normally soluble proteins or peptides into pathological species, by a process of misfolding and self-assembly that leads ultimately to the formation of amyloid fibrils. Recent studies support the idea that multiple intermediate species with a wide variety of degrees of neuronal toxicity are generated during such processes. The development of a high level of knowledge of the nature and structure of the pathogenic amyloid species would significantly enhance efforts to underline the molecular origins of these disorders and also to develop both accurate diagnoses and effective therapeutic interventions for these types of conditions. In this review, we discuss recent biophysical and structural information concerning different types of amyloid aggregates and the way in which such information can guide rational therapeutic approaches designed to target specific pathogenic events that occur during the development of these highly debilitating and increasingly common diseases.
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- 2018
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21. The Amyloid Fibril-Forming β-Sheet Regions of Amyloid β and α-Synuclein Preferentially Interact with the Molecular Chaperone 14-3-3ζ
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Danielle M. Williams, David C. Thorn, Christopher M. Dobson, Sarah Meehan, Sophie E. Jackson, Joanna M. Woodcock, and John A. Carver
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14-3-3 proteins ,molecular chaperone ,amyloid β ,α-synuclein ,NMR spectroscopy ,amyloid fibril ,Organic chemistry ,QD241-441 - Abstract
14-3-3 proteins are abundant, intramolecular proteins that play a pivotal role in cellular signal transduction by interacting with phosphorylated ligands. In addition, they are molecular chaperones that prevent protein unfolding and aggregation under cellular stress conditions in a similar manner to the unrelated small heat-shock proteins. In vivo, amyloid β (Aβ) and α-synuclein (α-syn) form amyloid fibrils in Alzheimer’s and Parkinson’s diseases, respectively, a process that is intimately linked to the diseases’ progression. The 14-3-3ζ isoform potently inhibited in vitro fibril formation of the 40-amino acid form of Aβ (Aβ40) but had little effect on α-syn aggregation. Solution-phase NMR spectroscopy of 15N-labeled Aβ40 and A53T α-syn determined that unlabeled 14-3-3ζ interacted preferentially with hydrophobic regions of Aβ40 (L11-H21 and G29-V40) and α-syn (V3-K10 and V40-K60). In both proteins, these regions adopt β-strands within the core of the amyloid fibrils prepared in vitro as well as those isolated from the inclusions of diseased individuals. The interaction with 14-3-3ζ is transient and occurs at the early stages of the fibrillar aggregation pathway to maintain the native, monomeric, and unfolded structure of Aβ40 and α-syn. The N-terminal regions of α-syn interacting with 14-3-3ζ correspond with those that interact with other molecular chaperones as monitored by in-cell NMR spectroscopy.
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- 2021
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22. Inhibiting the Ca2+ Influx Induced by Human CSF
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Anna Drews, Suman De, Patrick Flagmeier, David C. Wirthensohn, Wei-Hsin Chen, Daniel R. Whiten, Margarida Rodrigues, Cécile Vincke, Serge Muyldermans, Ross W. Paterson, Catherine F. Slattery, Nick C. Fox, Jonathan M. Schott, Henrik Zetterberg, Christopher M. Dobson, Sonia Gandhi, and David Klenerman
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neurodegenerative conditions ,Alzheimer’s disease ,cerebrospinal fluid ,beta amyloid ,oligomers ,clusterin ,antibodies ,single molecule imaging ,fluorescence measurements ,calcium influx ,Biology (General) ,QH301-705.5 - Abstract
One potential therapeutic strategy for Alzheimer’s disease (AD) is to use antibodies that bind to small soluble protein aggregates to reduce their toxic effects. However, these therapies are rarely tested in human CSF before clinical trials because of the lack of sensitive methods that enable the measurement of aggregate-induced toxicity at low concentrations. We have developed highly sensitive single vesicle and single-cell-based assays that detect the Ca2+ influx caused by the CSF of individuals affected with AD and healthy controls, and we have found comparable effects for both types of samples. We also show that an extracellular chaperone clusterin; a nanobody specific to the amyloid-β peptide (Aβ); and bapineuzumab, a humanized monoclonal antibody raised against Aβ, could all reduce the Ca2+ influx caused by synthetic Aβ oligomers but are less effective in CSF. These assays could be used to characterize potential therapeutic agents in CSF before clinical trials.
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- 2017
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23. Clusterin protects neurons against intracellular proteotoxicity
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Jenna M. Gregory, Daniel R. Whiten, Rebecca A. Brown, Teresa P. Barros, Janet R. Kumita, Justin J. Yerbury, Sandeep Satapathy, Karina McDade, Colin Smith, Leila M. Luheshi, Christopher M. Dobson, and Mark R. Wilson
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TDP-43 ,Cytoplasmic inclusions ,Proteotoxicity ,Chaperone translocation ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract It is now widely accepted in the field that the normally secreted chaperone clusterin is redirected to the cytosol during endoplasmic reticulum (ER) stress, although the physiological function(s) of this physical relocation remain unknown. We have examined in this study whether or not increased expression of clusterin is able to protect neuronal cells against intracellular protein aggregation and cytotoxicity, characteristics that are strongly implicated in a range of neurodegenerative diseases. We used the amyotrophic lateral sclerosis-associated protein TDP-43 as a primary model to investigate the effects of clusterin on protein aggregation and neurotoxicity in complementary in vitro, neuronal cell and Drosophila systems. We have shown that clusterin directly interacts with TDP-43 in vitro and potently inhibits its aggregation, and observed that in ER stressed neuronal cells, clusterin co-localized with TDP-43 and specifically reduced the numbers of cytoplasmic inclusions. We further showed that the expression of TDP-43 in transgenic Drosophila neurons induced ER stress and that co-expression of clusterin resulted in a dramatic clearance of mislocalized TDP-43 from motor neuron axons, partially rescued locomotor activity and significantly extended lifespan. We also showed that in Drosophila photoreceptor cells, clusterin co-expression gave ER stress-dependent protection against proteotoxicity arising from both Huntingtin-Q128 and mutant (R406W) human tau. We therefore conclude that increased expression of clusterin can provide an important defense against intracellular proteotoxicity under conditions that mimic specific features of neurodegenerative disease.
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- 2017
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24. Silk micrococoons for protein stabilisation and molecular encapsulation
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Ulyana Shimanovich, Francesco S. Ruggeri, Erwin De Genst, Jozef Adamcik, Teresa P. Barros, David Porter, Thomas Müller, Raffaele Mezzenga, Christopher M. Dobson, Fritz Vollrath, Chris Holland, and Tuomas P. J. Knowles
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Science - Abstract
Silk fibres currently used in biotechnology are chemically reconstituted silk fibroins (RSF), which are more stable than native silk fibroin (NSF) but possess different biophysical properties. Here, the authors use microfluidic droplets to encapsulate and store NSF, preserving their native structure.
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- 2017
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25. Nanobodies raised against monomeric ɑ-synuclein inhibit fibril formation and destabilize toxic oligomeric species
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Marija Iljina, Liu Hong, Mathew H. Horrocks, Marthe H. Ludtmann, Minee L. Choi, Craig D. Hughes, Francesco S. Ruggeri, Tim Guilliams, Alexander K. Buell, Ji-Eun Lee, Sonia Gandhi, Steven F. Lee, Clare E. Bryant, Michele Vendruscolo, Tuomas P. J. Knowles, Christopher M. Dobson, Erwin De Genst, and David Klenerman
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Protein aggregation ,Amyloid toxicity ,Neurodegeneration ,Aggregation inhibitors ,Antibody ,Single-molecule fluorescence ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background The aggregation of the protein ɑ-synuclein (ɑS) underlies a range of increasingly common neurodegenerative disorders including Parkinson’s disease. One widely explored therapeutic strategy for these conditions is the use of antibodies to target aggregated ɑS, although a detailed molecular-level mechanism of the action of such species remains elusive. Here, we characterize ɑS aggregation in vitro in the presence of two ɑS-specific single-domain antibodies (nanobodies), NbSyn2 and NbSyn87, which bind to the highly accessible C-terminal region of ɑS. Results We show that both nanobodies inhibit the formation of ɑS fibrils. Furthermore, using single-molecule fluorescence techniques, we demonstrate that nanobody binding promotes a rapid conformational conversion from more stable oligomers to less stable oligomers of ɑS, leading to a dramatic reduction in oligomer-induced cellular toxicity. Conclusions The results indicate a novel mechanism by which diseases associated with protein aggregation can be inhibited, and suggest that NbSyn2 and NbSyn87 could have significant therapeutic potential.
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- 2017
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26. Supersaturated proteins are enriched at synapses and underlie cell and tissue vulnerability in Alzheimer's disease
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Rosie Freer, Pietro Sormanni, Prajwal Ciryam, Burkhard Rammner, Silvio O. Rizzoli, Christopher M. Dobson, and Michele Vendruscolo
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Biophysics ,Neuroscience ,Alzheimer's disease ,Protein supersaturation ,Neuronal vulnerability ,Protein homeostasis ,Science (General) ,Q1-390 ,Social sciences (General) ,H1-99 - Abstract
Neurodegenerative disorders progress across the brain in characteristic spatio-temporal patterns. A better understanding of the factors underlying the specific cell and tissue vulnerability responsible for such patterns could help identify the molecular origins of these conditions. To investigate these factors, based on the observation that neurodegenerative disorders are closely associated with the presence of aberrant protein deposits, we made the hypothesis that the vulnerability of cells and tissues is associated to the overall levels of supersaturated proteins, which are those most metastable against aggregation. By analyzing single-cell transcriptomic and subcellular proteomics data on healthy brains of ages much younger than those typical of disease onset, we found that the most supersaturated proteins are enriched in cells and tissues that succumb first to neurodegeneration. Then, by focusing the analysis on a metastable subproteome specific to Alzheimer's disease, we show that it is possible to recapitulate the pattern of disease progression using data from healthy brains. We found that this metastable subproteome is significantly enriched for synaptic processes and mitochondrial energy metabolism, thus rendering the synaptic environment dangerous for aggregation. The present identification of protein supersaturation as a signature of cell and tissue vulnerability in neurodegenerative disorders could facilitate the search for effective treatments by providing clearer points of intervention.
- Published
- 2019
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27. An engineered monomer binding-protein for α-synuclein efficiently inhibits the proliferation of amyloid fibrils
- Author
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Emil Dandanell Agerschou, Patrick Flagmeier, Theodora Saridaki, Céline Galvagnion, Daniel Komnig, Laetitia Heid, Vibha Prasad, Hamed Shaykhalishahi, Dieter Willbold, Christopher M Dobson, Aaron Voigt, Bjoern Falkenburger, Wolfgang Hoyer, and Alexander K Buell
- Subjects
amyloid ,inhibtion ,nucleation ,β-wrapin ,AS69 ,Parkinson's disease ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Removing or preventing the formation of [Formula: see text]-synuclein aggregates is a plausible strategy against Parkinson’s disease. To this end, we have engineered the [Formula: see text]-wrapin AS69 to bind monomeric [Formula: see text]-synuclein with high affinity. In cultured cells, AS69 reduced the self-interaction of [Formula: see text]-synuclein and formation of visible [Formula: see text]-synuclein aggregates. In flies, AS69 reduced [Formula: see text]-synuclein aggregates and the locomotor deficit resulting from [Formula: see text]-synuclein expression in neuronal cells. In biophysical experiments in vitro, AS69 highly sub-stoichiometrically inhibited both primary and autocatalytic secondary nucleation processes, even in the presence of a large excess of monomer. We present evidence that the AS69-[Formula: see text]-synuclein complex, rather than the free AS69, is the inhibitory species responsible for sub-stoichiometric inhibition of secondary nucleation. These results represent a new paradigm that high affinity monomer binders can lead to strongly sub-stoichiometric inhibition of nucleation processes.
- Published
- 2019
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- View/download PDF
28. Physical Determinants of Amyloid Assembly in Biofilm Formation
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Maria Andreasen, Georg Meisl, Jonathan D. Taylor, Thomas C. T. Michaels, Aviad Levin, Daniel E. Otzen, Matthew R. Chapman, Christopher M. Dobson, Steve J. Matthews, and Tuomas P. J. Knowles
- Subjects
biofilms ,functional bacterial amyloids ,protein aggregation ,Microbiology ,QR1-502 - Abstract
ABSTRACT A wide range of bacterial pathogens have been shown to form biofilms, which significantly increase their resistance to environmental stresses, such as antibiotics, and are thus of central importance in the context of bacterial diseases. One of the major structural components of these bacterial biofilms are amyloid fibrils, yet the mechanism of fibril assembly and its importance for biofilm formation are currently not fully understood. By studying fibril formation in vitro, in a model system of two common but unrelated biofilm-forming proteins, FapC from Pseudomonas fluorescens and CsgA from Escherichia coli, we found that the two proteins have a common aggregation mechanism. In both systems, fibril formation proceeds via nucleated growth of linear fibrils exhibiting similar measured rates of elongation, with negligible fibril self-replication. These similarities between two unrelated systems suggest that convergent evolution plays a key role in tuning the assembly kinetics of functional amyloid fibrils and indicates that only a narrow window of mechanisms and assembly rates allows for successful biofilm formation. Thus, the amyloid assembly reaction is likely to represent a means for controlling biofilm formation, both by the organism and by possible inhibitory drugs. IMPORTANCE Biofilms are generated by bacteria, embedded in the formed extracellular matrix. The biofilm's function is to improve the survival of a bacterial colony through, for example, increased resistance to antibiotics or other environmental stresses. Proteins secreted by the bacteria act as a major structural component of this extracellular matrix, as they self-assemble into highly stable amyloid fibrils, making the biofilm very difficult to degrade by physical and chemical means once formed. By studying the self-assembly mechanism of the fibrils from their monomeric precursors in two unrelated bacteria, our experimental and theoretical approaches shed light on the mechanism of functional amyloid assembly in the context of biofilm formation. Our results suggest that fibril formation may be a rate-limiting step in biofilm formation, which in turn has implications on the protein self-assembly reaction as a target for potential antibiotic drugs.
- Published
- 2019
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29. Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response.
- Author
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Tessa Sinnige, Prashanth Ciryam, Samuel Casford, Christopher M Dobson, Mario de Bono, and Michele Vendruscolo
- Subjects
Medicine ,Science - Abstract
Although the aggregation of the amyloid-β peptide (Aβ) into amyloid fibrils is a well-established hallmark of Alzheimer's disease, the complex mechanisms linking this process to neurodegeneration are still incompletely understood. The nematode worm C. elegans is a valuable model organism through which to study these mechanisms because of its simple nervous system and its relatively short lifespan. Standard Aβ-based C. elegans models of Alzheimer's disease are designed to study the toxic effects of the overexpression of Aβ in the muscle or nervous systems. However, the wide variety of effects associated with the tissue-level overexpression of Aβ makes it difficult to single out and study specific cellular mechanisms related to the onset of Alzheimer's disease. Here, to better understand how to investigate the early events affecting neuronal signalling, we created a C. elegans model expressing Aβ42, the 42-residue form of Aβ, from a single-copy gene insertion in just one pair of glutamatergic sensory neurons, the BAG neurons. In behavioural assays, we found that the Aβ42-expressing animals displayed a subtle modulation of the response to CO2, compared to controls. Ca2+ imaging revealed that the BAG neurons in young Aβ42-expressing nematodes were activated more strongly than in control animals, and that neuronal activation remained intact until old age. Taken together, our results suggest that Aβ42-expression in this very subtle model of AD is sufficient to modulate the behavioural response but not strong enough to generate significant neurotoxicity, suggesting that slightly more aggressive perturbations will enable effectively studies of the links between the modulation of a physiological response and its associated neurotoxicity.
- Published
- 2019
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30. Parallel and Sequential Pathways of Molecular Recognition of a Tandem-Repeat Protein and Its Intrinsically Disordered Binding Partner
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Ben M. Smith, Pamela J. E. Rowling, Christopher M. Dobson, and Laura S. Itzhaki
- Subjects
repeat protein ,tandem-repeat protein ,intrinsic disorder ,intrinsically disordered protein ,fuzzy complex ,protein-protein interactions ,Microbiology ,QR1-502 - Abstract
The Wnt signalling pathway plays an important role in cell proliferation, differentiation, and fate decisions in embryonic development and the maintenance of adult tissues. The twelve armadillo (ARM) repeat-containing protein β-catenin acts as the signal transducer in this pathway. Here, we investigated the interaction between β-catenin and the intrinsically disordered transcription factor TCF7L2, comprising a very long nanomolar-affinity interface of approximately 4800 Å2 that spans ten of the twelve ARM repeats of β-catenin. First, a fluorescence reporter system for the interaction was engineered and used to determine the kinetic rate constants for the association and dissociation. The association kinetics of TCF7L2 and β-catenin were monophasic and rapid (7.3 ± 0.1 × 107 M−1·s−1), whereas dissociation was biphasic and slow (5.7 ± 0.4 × 10−4 s−1, 15.2 ± 2.8 × 10−4 s−1). This reporter system was then combined with site-directed mutagenesis to investigate the striking variability in the conformation adopted by TCF7L2 in the three different crystal structures of the TCF7L2–β-catenin complex. We found that the mutation had very little effect on the association kinetics, indicating that most interactions form after the rate-limiting barrier for association. Mutations of the N- and C-terminal subdomains of TCF7L2 that adopt relatively fixed conformations in the crystal structures had large effects on the dissociation kinetics, whereas the mutation of the labile sub-domain connecting them had negligible effect. These results point to a two-site avidity mechanism of binding with the linker region forming a “fuzzy” complex involving transient contacts that are not site-specific. Strikingly, the two mutations in the N-terminal subdomain that had the largest effects on the dissociation kinetics showed two additional phases, indicating partial flux through an alternative dissociation pathway that is inaccessible to the wild type. The results presented here provide insights into the kinetics of the molecular recognition of a long intrinsically disordered region with an elongated repeat-protein surface, a process found to involve parallel routes with sequential steps in each.
- Published
- 2021
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31. Publisher Correction: A dopamine metabolite stabilizes neurotoxic amyloid-β oligomers
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Rodrigo Cataldi, Sean Chia, Katarina Pisani, Francesco S. Ruggeri, Catherine K. Xu, Tomas Šneideris, Michele Perni, Sunehera Sarwat, Priyanka Joshi, Janet R. Kumita, Sara Linse, Johnny Habchi, Tuomas P. J. Knowles, Benedetta Mannini, Christopher M. Dobson, and Michele Vendruscolo
- Subjects
Biology (General) ,QH301-705.5 - Abstract
A Correction to this paper has been published: https://doi.org/10.1038/s42003-021-01680-7
- Published
- 2021
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32. Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping
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Marie N. Bongiovanni, Julien Godet, Mathew H. Horrocks, Laura Tosatto, Alexander R. Carr, David C. Wirthensohn, Rohan T. Ranasinghe, Ji-Eun Lee, Aleks Ponjavic, Joelle V. Fritz, Christopher M. Dobson, David Klenerman, and Steven F. Lee
- Subjects
Science - Abstract
Many super-resolution imaging techniques use fluorescence emission intensity to obtain precise positional information, but other spectral information is ignored. Here, the authors develop a method that records the spectrum and position of single dye molecules to map the hydrophobicity of a surface.
- Published
- 2016
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33. Structural basis of synaptic vesicle assembly promoted by α-synuclein
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Giuliana Fusco, Tillmann Pape, Amberley D. Stephens, Pierre Mahou, Ana Rita Costa, Clemens F. Kaminski, Gabriele S. Kaminski Schierle, Michele Vendruscolo, Gianluigi Veglia, Christopher M. Dobson, and Alfonso De Simone
- Subjects
Science - Abstract
α-synuclein, a protein associated to Parkinson's disease, is involved in synaptic vesicle interaction and assembly. Here, the authors use NMR spectroscopy and super-resolution microscopy to unveil the nature and molecular mechanism of α-synuclein-mediated synaptic vesicle clustering.
- Published
- 2016
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34. Kinetic analysis reveals the diversity of microscopic mechanisms through which molecular chaperones suppress amyloid formation
- Author
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Paolo Arosio, Thomas C. T. Michaels, Sara Linse, Cecilia Månsson, Cecilia Emanuelsson, Jenny Presto, Jan Johansson, Michele Vendruscolo, Christopher M. Dobson, and Tuomas P. J. Knowles
- Subjects
Science - Abstract
Molecular chaperones are recognized to interfere with protein aggregation, yet the underlying mechanisms are largely unknown. Here, the authors develop a kinetic model that reveals the variety of distinct microscopic mechanisms through which molecular chaperones act to suppress amyloid formation.
- Published
- 2016
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35. Formation of amyloid loops in brain tissues is controlled by the flexibility of protofibril chains
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Alyssa Miller, Jiapeng Wei, Sarah Meehan, Christopher M. Dobson, Mark E. Welland, David Klenerman, Michele Vendruscolo, Francesco Simone Ruggeri, Tuomas P. J. Knowles, Miller, Alyssa [0000-0002-6980-9794], Wei, Jiapeng [0000-0003-4146-0604], Meehan, Sarah [0000-0002-2778-4373], Welland, Mark E [0000-0002-4157-5826], Klenerman, David [0000-0001-7116-6954], Vendruscolo, Michele [0000-0002-3616-1610], Ruggeri, Francesco Simone [0000-0002-1232-1907], and Apollo - University of Cambridge Repository
- Subjects
Amyloid ,atomic force microscopy ,Amyloid beta-Peptides ,Multidisciplinary ,Organic Chemistry ,Brain ,Amyloidogenic Proteins ,Microscopy, Atomic Force ,Organische Chemie ,protein aggregation ,Departement Agrotechnologie en Voedingswetenschappen ,amyloid pore ,Alzheimer Disease ,Humans ,Life Science ,Department of Agrotechnology and Food Sciences ,Physical Chemistry and Soft Matter - Abstract
Neurodegenerative diseases, such as Alzheimer’s disease (AD), are associated with protein misfolding and aggregation into amyloid fibrils. Increasing evidence suggests that soluble, low-molecular-weight aggregates play a key role in disease-associated toxicity. Within this population of aggregates, closed-loop pore-like structures have been observed for a variety of amyloid systems, and their presence in brain tissues is associated with high levels of neuropathology. However, their mechanism of formation and relationship with mature fibrils have largely remained challenging to elucidate. Here, we use atomic force microscopy and statistical theory of biopolymers to characterize amyloid ring structures derived from the brains of AD patients. We analyze the bending fluctuations of protofibrils and show that the process of loop formation is governed by the mechanical properties of their chains. We conclude that ex vivo protofibril chains possess greater flexibility than that imparted by hydrogen-bonded networks characteristic of mature amyloid fibrils, such that they are able to form end-to-end connections. These results explain the diversity in the structures formed from protein aggregation and shed light on the links between early forms of flexible ring-forming aggregates and their role in disease.
- Published
- 2023
36. Correction to ‘Bifunctional fluorescent probes for detection of amyloid aggregates and reactive oxygen species’
- Author
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Lisa-Maria Needham, Judith Weber, James W. B. Fyfe, Omaru M. Kabia, Dung T. Do, Ewa Klimont, Yu Zhang, Margarida Rodrigues, Christopher M. Dobson, Sonia Gandhi, Sarah E. Bohndiek, Thomas N. Snaddon, and Steven F. Lee
- Subjects
Science - Published
- 2018
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37. Basosquamous Carcinoma: A Single Centre Clinicopathological Evaluation and Proposal of an Evidence-Based Protocol
- Author
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Jordan W. Oldbury, Richard A. J. Wain, Sameera Abas, Christopher M. Dobson, and Srinivasan S. Iyer
- Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Basosquamous carcinoma (BSC) is an uncommon skin malignancy with significant invasive and metastatic potential. There are currently no clear management guidelines. This study evaluates the management and outcomes of patients diagnosed with BSC over a 7-year period. We present an evidence-based unit protocol for the management of BSC. All patients treated for BSC between 2009 and 2015 were reviewed. Data collected included patient demographics, tumour-specific information, management strategy, presence of recurrence or metastasis, and details of follow-up. 74 patients were identified, making this one of the largest cohorts of BSC patients reported. Mean age at diagnosis was 75.4 years, with a male:female ratio of 1.6:1. The most common tumour site was the head and neck (n=43, 58.1%). All tumours were graded at pT1 (n=51) or pT2 (n=23). Inadequate excision occurred in 17 patients (23%). Mean excision margins were >4mm peripherally and deep. Inadequately excised BSCs were further treated with wide local excision (n=6) or radiotherapy (n=5), or both (n=1). There were no cases of local recurrence or metastatic disease. This study demonstrates a cohort of patients with BSCs that appear less aggressive than previously reported. Current management with surgical excision appears to produce adequate results. However, an evidence-based guideline is still lacking.
- Published
- 2018
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38. Bifunctional fluorescent probes for detection of amyloid aggregates and reactive oxygen species
- Author
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Lisa-Maria Needham, Judith Weber, James W. B. Fyfe, Omaru M. Kabia, Dung T. Do, Ewa Klimont, Yu Zhang, Margarida Rodrigues, Christopher M. Dobson, Sonia Ghandi, Sarah E. Bohndiek, Thomas N. Snaddon, and Steven F. Lee
- Subjects
fluorophores ,ros ,sensors ,protein aggregation ,single-molecule imaging ,thioflavin t ,Science - Abstract
Protein aggregation into amyloid deposits and oxidative stress are key features of many neurodegenerative disorders including Parkinson's and Alzheimer's disease. We report here the creation of four highly sensitive bifunctional fluorescent probes, capable of H2O2 and/or amyloid aggregate detection. These bifunctional sensors use a benzothiazole core for amyloid localization and boronic ester oxidation to specifically detect H2O2. We characterized the optical properties of these probes using both bulk fluorescence measurements and single-aggregate fluorescence imaging, and quantify changes in their fluorescence properties upon addition of amyloid aggregates of α-synuclein and pathophysiological H2O2 concentrations. Our results indicate these new probes will be useful to detect and monitor neurodegenerative disease.
- Published
- 2018
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39. The Hsc70 disaggregation machinery removes monomer units directly from α-synuclein fibril ends
- Author
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Tuomas P. J. Knowles, Christopher M. Dobson, Quentin Peter, Ewa Andrzejewska, Michele Vendruscolo, Matthias Schneider, Georg Krainer, F. Ulrich Hartl, Therese W. Herling, Francesco Simone Ruggeri, Andreas Bracher, Alyssa M. Miller, Victoria A. Trinkaus, Saurabh Gautam, Schneider, Matthias M [0000-0002-1894-1859], Gautam, Saurabh [0000-0003-0366-6169], Krainer, Georg [0000-0002-9626-7636], Peter, Quentin AE [0000-0002-8018-3059], Ruggeri, Francesco Simone [0000-0002-1232-1907], Vendruscolo, Michele [0000-0002-3616-1610], Bracher, Andreas [0000-0001-8530-7594], Hartl, F Ulrich [0000-0002-7941-135X], Knowles, Tuomas PJ [0000-0002-7879-0140], Apollo - University of Cambridge Repository, Schneider, Matthias M. [0000-0002-1894-1859], Peter, Quentin A. E. [0000-0002-8018-3059], Hartl, F. Ulrich [0000-0002-7941-135X], Knowles, Tuomas P. J. [0000-0002-7879-0140], Peter, Quentin A E [0000-0002-8018-3059], and Knowles, Tuomas P J [0000-0002-7879-0140]
- Subjects
Amyloid ,631/45/470/2284 ,147/3 ,123 ,Science ,Kinetics ,General Physics and Astronomy ,macromolecular substances ,Fibril ,General Biochemistry, Genetics and Molecular Biology ,101/62 ,639/638/440/56 ,chemistry.chemical_compound ,Single-molecule biophysics ,Biophysical chemistry ,Chaperones ,Escherichia coli ,Life Science ,Humans ,HSP70 Heat-Shock Proteins ,Fragmentation (cell biology) ,82/62 ,Synucleinopathies ,Multidisciplinary ,'de novo' protein folding ,HSC70 Heat-Shock Proteins ,article ,Parkinson Disease ,General Chemistry ,HSP40 Heat-Shock Proteins ,humanities ,Monomer ,631/57/2272/1590 ,chemistry ,alpha-Synuclein ,Biophysics ,631/57/2265 ,α synuclein ,631/45/470/1981 ,Protein aggregation ,Molecular Chaperones - Abstract
Funder: EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013)); doi: https://doi.org/10.13039/100011199, Funder: EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council); doi: https://doi.org/10.13039/100010663, Molecular chaperones contribute to the maintenance of cellular protein homoeostasis through assisting de novo protein folding and preventing amyloid formation. Chaperones of the Hsp70 family can further disaggregate otherwise irreversible aggregate species such as α-synuclein fibrils, which accumulate in Parkinson’s disease. However, the mechanisms and kinetics of this key functionality are only partially understood. Here, we combine microfluidic measurements with chemical kinetics to study α-synuclein disaggregation. We show that Hsc70 together with its co-chaperones DnaJB1 and Apg2 can completely reverse α-synuclein aggregation back to its soluble monomeric state. This reaction proceeds through first-order kinetics where monomer units are removed directly from the fibril ends with little contribution from intermediate fibril fragmentation steps. These findings extend our mechanistic understanding of the role of chaperones in the suppression of amyloid proliferation and in aggregate clearance, and inform on possibilities and limitations of this strategy in the development of therapeutics against synucleinopathies.
- Published
- 2021
40. Formation of amyloid loops in brain tissues is controlled by the flexibility of protofibril chains
- Author
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Alyssa M. Miller, Sarah Meehan, Christopher M. Dobson, Mark E. Welland, David Klenerman, Michele Vendruscolo, Francesco Simone Ruggeri, and Tuomas P. J. Knowles
- Abstract
Neurodegenerative diseases, such as Alzheimer’s Disease (AD), are associated with protein misfolding and aggregation into amyloid fibrils. Increasing evidence suggests that soluble, low molecular weight aggregates play a key role in disease-associated toxicity. Within these aggregates, protofibrillar loop-like structures have been observed for a variety of amyloid systems and their presence in brain tissues is associated with high levels of neuropathology. However, their mechanism of formation and relationship with mature fibrils has largely remained challenging to elucidate. Here, we use atomic force microscopy and statistical theory of biopolymers to characterise amyloid ring structures derived from the brains of AD patients. We analyse the bending fluctuations of protofibrils and show that the process of loop formation is governed by the mechanical properties of their chains. We conclude that ex vivo protofibril chains possess greater flexibility than that imparted by hydrogen-bonded networks characteristic of mature amyloid fibrils, such that they are able to form end-to-end connections. Furthermore, we show that these findings can be extended to several amyloid systems, giving a general framework relating the mechanical properties of assemblies and the conditions in which they can form loop structures. These results explain the diversity in the structures formed from protein aggregation and sheds light on the links between early forms of flexible ring-forming aggregates and their role in disease.
- Published
- 2022
- Full Text
- View/download PDF
41. Observation of an α-synuclein liquid droplet state and its maturation into Lewy body-like assemblies
- Author
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Christopher M. Dobson, Samuel T. Dada, Maarten C. Hardenberg, Elizabeth A Robinson, Monika Fuxreiter, Sam Casford, Gabriele S. Kaminski Schierle, Clemens F Kaminksi, Tessa Sinnige, Michele Vendruscolo, Ellen A. A. Nollen, Chetan Poudel, Vendruscolo, Michele [0000-0002-3616-1610], Apollo - University of Cambridge Repository, and Molecular Neuroscience and Ageing Research (MOLAR)
- Subjects
0301 basic medicine ,Parkinson's disease ,Arrested maturation ,Amyloid ,Synaptic vesicle ,Animals, Genetically Modified ,03 medical and health sciences ,0302 clinical medicine ,α-synuclein ,liquid‒liquid phase separation ,mental disorders ,Genetics ,medicine ,Animals ,Humans ,Maturation process ,Caenorhabditis elegans ,Caenorhabditis elegans Proteins ,Molecular Biology ,Medicine(all) ,biology ,Lewy body ,Chemistry ,Parkinson Disease ,Cell Biology ,General Medicine ,Articles ,biology.organism_classification ,medicine.disease ,Amyloid fibril ,In vitro ,nervous system diseases ,Disease Models, Animal ,030104 developmental biology ,030220 oncology & carcinogenesis ,Biophysics ,alpha-Synuclein ,α synuclein ,Lewy Bodies - Abstract
Misfolded α-synuclein is a major component of Lewy bodies, which are a hallmark of Parkinson’s disease. A large body of evidence shows that α-synuclein can self-assemble into amyloid fibrils, but the relationship between amyloid formation and Lewy body formation still remains unclear. Here we show, both in vitro and in a C. elegans model of Parkinson’s disease, that α-synuclein undergoes liquid-liquid phase separation by forming a liquid droplet state, which converts into an amyloid-rich hydrogel. This maturation process towards the amyloid state is delayed in the presence of model synaptic vesicles in vitro. Taken together, these results suggest that the formation of Lewy bodies is linked to the arrested maturation of α-synuclein condensates in the presence of lipids and other cellular components.
- Published
- 2021
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42. Microfluidic antibody affinity profiling of alloantibody-HLA interactions in human serum
- Author
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Matthias M. Schneider, Tom Scheidt, Ashley J. Priddey, Catherine K. Xu, Mengsha Hu, Georg Meisl, Sean R.A. Devenish, Christopher M. Dobson, Vasilis Kosmoliaptsis, Tuomas P.J. Knowles, Schneider, Matthias M [0000-0002-1894-1859], Scheidt, Tom [0000-0002-0185-7730], Xu, Catherine K [0000-0003-4726-636X], Meisl, Georg [0000-0002-6562-7715], Kosmoliaptsis, Vasilis [0000-0001-7298-1387], Knowles, TuomasP J [0000-0002-7879-0140], and Apollo - University of Cambridge Repository
- Subjects
Isoantibodies ,HLA Antigens ,Microfluidics ,Antibody Affinity ,Electrochemistry ,Biomedical Engineering ,Biophysics ,Humans ,Biosensing Techniques ,General Medicine ,Kidney Transplantation ,Biotechnology - Abstract
Antibody profiling is a fundamental component of understanding the humoral response in a wide range of disease areas. Most currently used approaches operate by capturing antibodies onto functionalised surfaces. Such measurements of surface binding are governed by an overall antibody titre, while the two fundamental molecular parameters, antibody affinity and antibody concentration, are challenging to determine individually from such approaches. Here, by applying microfluidic diffusional sizing (MDS), we show how we can overcome this challenge and demonstrate reliable quantification of alloantibody binding affinity and concentration of alloantibodies binding to Human Leukocyte Antigens (HLA), an extensively used clinical biomarker in organ transplantation, both in buffer and in crude human serum. Capitalising on the ability to vary both serum and HLA concentrations during MDS, we show that both affinity and concentration of HLA-specific antibodies can be determined directly in serum when neither of these parameters is known. Finally, we provide proof of principle in clinical transplant patient sera that our assay enables differentiation of alloantibody reactivity against HLA proteins of highly similar structure, providing information not attainable through currently available techniques. These results outline a path towards detection and in-depth profiling of humoral immunity and may enable further insights into the clinical relevance of antibody reactivity in clinical transplantation and beyond.
- Published
- 2023
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43. Aβ Oligomers Dysregulate Calcium Homeostasis by Mechanosensitive Activation of AMPA and NMDA Receptors
- Author
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Giulia Vecchi, Christopher M. Dobson, Roberta Cascella, Michele Vendruscolo, Cristina Cecchi, Benedetta Mannini, Fabrizio Chiti, and Giulia Fani
- Subjects
Physiology ,Cognitive Neuroscience ,Excitotoxicity ,chemistry.chemical_element ,AMPA receptor ,Calcium ,medicine.disease_cause ,Biochemistry ,Receptors, N-Methyl-D-Aspartate ,Cell membrane ,03 medical and health sciences ,0302 clinical medicine ,Alzheimer Disease ,medicine ,Homeostasis ,Humans ,neurodegenerative diseases ,Lipid bilayer ,Receptor ,senile plaques ,alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid ,030304 developmental biology ,Neurons ,0303 health sciences ,Amyloid beta-Peptides ,calcium homeostasis ,Chemistry ,membrane destabilization ,Memantine ,Cell Biology ,General Medicine ,Peptide Fragments ,medicine.anatomical_structure ,Biophysics ,Mechanosensitive channels ,memantine ,030217 neurology & neurosurgery ,medicine.drug ,Research Article ,Protein misfolding - Abstract
Alzheimer's disease, which is the most common form of dementia, is characterized by the aggregation of the amyloid β peptide (Aβ) and by an impairment of calcium homeostasis caused by excessive activation of glutamatergic receptors (excitotoxicity). Here, we studied the effects on calcium homeostasis caused by the formation of Aβ oligomeric assemblies. We found that Aβ oligomers cause a rapid influx of calcium ions (Ca2+) across the cell membrane by rapidly activating extrasynaptic N-methyl-d-aspartate (NMDA) receptors and, to a lower extent, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. We also observed, however, that misfolded oligomers do not interact directly with these receptors. Further experiments with lysophosphatidylcholine and arachidonic acid, which cause membrane compression and stretch, respectively, indicated that these receptors are activated through a change in membrane tension induced by the oligomers and transmitted mechanically to the receptors via the lipid bilayer. Indeed, lysophosphatidylcholine is able to neutralize the oligomer-induced activation of the NMDA receptors, whereas arachidonic acid activates the receptors similarly to the oligomers with no additive effects. An increased rotational freedom observed for a fluorescent probe embedded within the membrane in the presence of the oligomers also indicates a membrane stretch. These results reveal a mechanism of toxicity of Aβ oligomers in Alzheimer's disease through the perturbation of the mechanical properties of lipid membranes sensed by NMDA and AMPA receptors.
- Published
- 2021
44. Machine learning-aided protein identification from multidimensional signatures
- Author
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Christopher M. Dobson, Tuomas P. J. Knowles, Sean R. A. Devenish, Alexey S. Morgunov, Yuewen Zhang, Quentin Peter, Pavan K. Challa, Maya A. Wright, and Kadi L. Saar
- Subjects
Profiling (computer programming) ,Medical diagnostic ,Computer science ,business.industry ,Fingerprint (computing) ,Biomedical Engineering ,Bioengineering ,General Chemistry ,Machine learning ,computer.software_genre ,Biochemistry ,Machine Learning ,Set (abstract data type) ,Chemistry ,Amino acid composition ,Identity (object-oriented programming) ,Protein identification ,Artificial intelligence ,Amino acid content ,business ,computer - Abstract
The ability to determine the identity of specific proteins is a critical challenge in many areas of cellular and molecular biology, and in medical diagnostics. Here, we present a macine learning aided microfluidic protein characterisation strategy that within a few minutes generates a three-dimensional fingerprint of a protein sample indicative of its amino acid composition and size and, thereby, creates a unique signature for the protein. By acquiring such multidimensional fingerprints for a set of ten proteins and using machine learning approaches to classify the fingerprints, we demonstrate that this strategy allows proteins to be classified at a high accuracy, even though classification using a single dimension is not possible. Moreover, we show that the acquired fingerprints correlate with the amino acid content of the samples, which makes it is possible to identify proteins directly from their sequence without requiring any prior knowledge about the fingerprints. These findings suggest that such a multidimensional profiling strategy can lead to the development of a novel method for protein identification in a microfluidic format., Protein classification and identification from their multidimensional fingerprints obtained on a microfluidic chip.
- Published
- 2021
- Full Text
- View/download PDF
45. Widespread Aggregation and Neurodegenerative Diseases Are Associated with Supersaturated Proteins
- Author
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Prajwal Ciryam, Gian Gaetano Tartaglia, Richard I. Morimoto, Christopher M. Dobson, and Michele Vendruscolo
- Subjects
Biology (General) ,QH301-705.5 - Abstract
The maintenance of protein solubility is a fundamental aspect of cellular homeostasis because protein aggregation is associated with a wide variety of human diseases. Numerous proteins unrelated in sequence and structure, however, can misfold and aggregate, and widespread aggregation can occur in living systems under stress or aging. A crucial question in this context is why only certain proteins appear to aggregate readily in vivo, whereas others do not. We identify here the proteins most vulnerable to aggregation as those whose cellular concentrations are high relative to their solubilities. We find that these supersaturated proteins represent a metastable subproteome involved in pathological aggregation during stress and aging and are overrepresented in biochemical processes associated with neurodegenerative disorders. Consequently, such cellular processes become dysfunctional when the ability to keep intrinsically supersaturated proteins soluble is compromised. Thus, the simultaneous analysis of abundance and solubility can rationalize the diverse cellular pathologies linked to neurodegenerative diseases and aging.
- Published
- 2013
- Full Text
- View/download PDF
46. Bifunctional Anti-Non-Amyloid Component α-Synuclein Nanobodies Are Protective In Situ.
- Author
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David C Butler, Shubhada N Joshi, Erwin De Genst, Ankit S Baghel, Christopher M Dobson, and Anne Messer
- Subjects
Medicine ,Science - Abstract
Misfolding, abnormal accumulation, and secretion of α-Synuclein (α-Syn) are closely associated with synucleinopathies, including Parkinson's disease (PD). VH14 is a human single domain intrabody selected against the non-amyloid component (NAC) hydrophobic interaction region of α-Syn, which is critical for initial aggregation. Using neuronal cell lines, we show that as a bifunctional nanobody fused to a proteasome targeting signal, VH14PEST can counteract heterologous proteostatic effects of mutant α-Syn on mutant huntingtin Exon1 and protect against α-Syn toxicity using propidium iodide or Annexin V readouts. We compared this anti-NAC candidate to NbSyn87, which binds to the C-terminus of α-Syn. NbSyn87PEST degrades α-Syn as well or better than VH14PEST. However, while both candidates reduced toxicity, VH14PEST appears more effective in both proteostatic stress and toxicity assays. These results show that the approach of reducing intracellular monomeric targets with novel antibody engineering technology should allow in vivo modulation of proteostatic pathologies.
- Published
- 2016
- Full Text
- View/download PDF
47. Kinetic fingerprints differentiate the mechanisms of action of anti-Aβ antibodies
- Author
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Catherine K. Xu, Sean R. A. Devenish, Fang Qian, Samuel I. A. Cohen, Oskar Hansson, Thierry Bussiere, Georg Meisl, Sara Linse, Tiernan T. O'Malley, Katja Bernfur, Tuomas P. J. Knowles, Michele Vendruscolo, Eimantas Sileikis, Paul H. Weinreb, Tom Scheidt, Christopher M. Dobson, and Martin Lundqvist
- Subjects
chemistry.chemical_classification ,0303 health sciences ,biology ,Chemistry ,Peptide ,03 medical and health sciences ,0302 clinical medicine ,Mechanism of action ,Structural Biology ,biology.protein ,medicine ,Biophysics ,Structure–activity relationship ,Bapineuzumab ,Solanezumab ,Aducanumab ,Antibody ,medicine.symptom ,Gantenerumab ,Molecular Biology ,030217 neurology & neurosurgery ,030304 developmental biology ,medicine.drug - Abstract
The amyloid cascade hypothesis, according to which the self-assembly of amyloid-β peptide (Aβ) is a causative process in Alzheimer’s disease, has driven many therapeutic efforts for the past 20 years. Failures of clinical trials investigating Aβ-targeted therapies have been interpreted as evidence against this hypothesis, irrespective of the characteristics and mechanisms of action of the therapeutic agents, which are highly challenging to assess. Here, we combine kinetic analyses with quantitative binding measurements to address the mechanism of action of four clinical stage anti-Aβ antibodies, aducanumab, gantenerumab, bapineuzumab and solanezumab. We quantify the influence of these antibodies on the aggregation kinetics and on the production of oligomeric aggregates and link these effects to the affinity and stoichiometry of each antibody for monomeric and fibrillar forms of Aβ. Our results reveal that, uniquely among these four antibodies, aducanumab dramatically reduces the flux of Aβ oligomers. The effects of four antibodies on the aggregation pathway of Aβ are examined via an in-depth kinetics approach, revealing the specific molecular steps affected by each antibody.
- Published
- 2020
- Full Text
- View/download PDF
48. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors
- Author
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Paolo Arosio, Sara Linse, Gabriella T. Heller, Andela Saric, Michele Vendruscolo, Christopher M. Dobson, Tuomas P. J. Knowles, Thomas C. T. Michaels, Samo Curk, and Georg Meisl
- Subjects
Amyloid ,Multidisciplinary ,Drug discovery ,Chemistry ,Design elements and principles ,Biological Sciences ,Protein Aggregation, Pathological ,Kinetics ,Models, Chemical ,Computational chemistry ,Drug Design ,Amyloid aggregation ,Molecular mechanism ,Thermodynamics ,Molecular Targeted Therapy - Abstract
Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril formation is critical to the development of potential therapeutics against protein-misfolding diseases. A fundamental challenge for progress is the range of possible target species and the disparate timescales involved, since the aggregating proteins are simultaneously the reactants, products, intermediates, and catalysts of the reaction. It is a complex problem, therefore, to choose the states of the aggregating proteins that should be bound by the compounds to achieve the most potent inhibition. We present here a comprehensive kinetic theory of amyloid-aggregation inhibition that reveals the fundamental thermodynamic and kinetic signatures characterizing effective inhibitors by identifying quantitative relationships between the aggregation and binding rate constants. These results provide general physical laws to guide the design and optimization of inhibitors of amyloid-fibril formation, revealing in particular the important role of on-rates in the binding of the inhibitors.
- Published
- 2020
- Full Text
- View/download PDF
49. Direct measurement of lipid membrane disruption connects kinetics and toxicity of Aβ42 aggregation
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Patrick Flagmeier, Thomas C. T. Michaels, David Klenerman, Xiaoting Yang, Sara Linse, Alexander J. Dear, Suman De, Cecilia Emanuelsson, Christopher M. Dobson, Tuomas P. J. Knowles, and Michele Vendruscolo
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chemistry.chemical_classification ,Amyloid ,Structural Biology ,Chemistry ,Vesicle ,Toxicity ,Kinetics ,Fluorescence microscope ,Biophysics ,Peptide ,Protein aggregation ,Lipid bilayer ,Molecular Biology - Abstract
The formation of amyloid deposits in human tissues is a defining feature of more than 50 medical disorders, including Alzheimer’s disease. Strong genetic and histological evidence links these conditions to the process of protein aggregation, yet it has remained challenging to identify a definitive connection between aggregation and pathogenicity. Using time-resolved fluorescence microscopy of individual synthetic vesicles, we show for the Aβ42 peptide implicated in Alzheimer’s disease that the disruption of lipid bilayers correlates linearly with the time course of the levels of transient oligomers generated through secondary nucleation. These findings indicate a specific role of oligomers generated through the catalytic action of fibrillar species during the protein aggregation process in driving deleterious biological function and establish a direct causative connection between amyloid formation and its pathological effects.
- Published
- 2020
- Full Text
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50. Assessing motor-related phenotypes of Caenorhabditis elegans with the wide field-of-view nematode tracking platform
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Quentin Peter, Tuomas P. J. Knowles, Michele Vendruscolo, Renée I. Seinstra, Christopher M. Dobson, Mandy Koopman, Ellen A. A. Nollen, Michele Perni, and Molecular Neuroscience and Ageing Research (MOLAR)
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GENES ,Computer science ,ved/biology.organism_classification_rank.species ,Computational biology ,General Biochemistry, Genetics and Molecular Biology ,THRESHOLD ,03 medical and health sciences ,0302 clinical medicine ,High spatial resolution ,ADAPTATION ,Model organism ,Throughput (business) ,Caenorhabditis elegans ,030304 developmental biology ,Protocol (science) ,0303 health sciences ,IDENTIFICATION ,biology ,ved/biology ,AGGREGATION ,biology.organism_classification ,Phenotype ,Wide field ,MODEL ,Identification (information) ,SYNAPTIC-TRANSMISSION ,C-ELEGANS ,GAIT ,BEHAVIOR ,030217 neurology & neurosurgery - Abstract
Caenorhabditis elegans is a valuable model organism in biomedical research that has led to major discoveries in the fields of neurodegeneration, cancer and aging. Because movement phenotypes are commonly used and represent strong indicators of C. elegans fitness, there is an increasing need to replace manual assessments of worm motility with automated measurements to increase throughput and minimize observer biases. Here, we provide a protocol for the implementation of the improved wide field-of-view nematode tracking platform (WF-NTP), which enables the simultaneous analysis of hundreds of worms with respect to multiple behavioral parameters. The protocol takes only a few hours to complete, excluding the time spent culturing C. elegans, and includes (i) experimental design and preparation of samples, (ii) data recording, (iii) software management with appropriate parameter choices and (iv) post-experimental data analysis. We compare the WF-NTP with other existing worm trackers, including those having high spatial resolution. The main benefits of WF-NTP relate to the high number of worms that can be assessed at the same time on a whole-plate basis and the number of phenotypes that can be screened for simultaneously.
- Published
- 2020
- Full Text
- View/download PDF
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