1
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Potapenko A, Davidson JM, Lee A, Laird AS. The deubiquitinase function of ataxin-3 and its role in the pathogenesis of Machado-Joseph disease and other diseases. Biochem J 2024; 481:461-480. [PMID: 38497605 PMCID: PMC11088879 DOI: 10.1042/bcj20240017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
Machado-Joseph disease (MJD) is a devastating and incurable neurodegenerative disease characterised by progressive ataxia, difficulty speaking and swallowing. Consequently, affected individuals ultimately become wheelchair dependent, require constant care, and face a shortened life expectancy. The monogenic cause of MJD is expansion of a trinucleotide (CAG) repeat region within the ATXN3 gene, which results in polyglutamine (polyQ) expansion within the resultant ataxin-3 protein. While it is well established that the ataxin-3 protein functions as a deubiquitinating (DUB) enzyme and is therefore critically involved in proteostasis, several unanswered questions remain regarding the impact of polyQ expansion in ataxin-3 on its DUB function. Here we review the current literature surrounding ataxin-3's DUB function, its DUB targets, and what is known regarding the impact of polyQ expansion on ataxin-3's DUB function. We also consider the potential neuroprotective effects of ataxin-3's DUB function, and the intersection of ataxin-3's role as a DUB enzyme and regulator of gene transcription. Ataxin-3 is the principal pathogenic protein in MJD and also appears to be involved in cancer. As aberrant deubiquitination has been linked to both neurodegeneration and cancer, a comprehensive understanding of ataxin-3's DUB function is important for elucidating potential therapeutic targets in these complex conditions. In this review, we aim to consolidate knowledge of ataxin-3 as a DUB and unveil areas for future research to aid therapeutic targeting of ataxin-3's DUB function for the treatment of MJD and other diseases.
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Affiliation(s)
- Anastasiya Potapenko
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Jennilee M. Davidson
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Albert Lee
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Angela S. Laird
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
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2
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Sciandrone B, Palmioli A, Ciaramelli C, Pensotti R, Colombo L, Regonesi ME, Airoldi C. Cell-Free and In Vivo Characterization of the Inhibitory Activity of Lavado Cocoa Flavanols on the Amyloid Protein Ataxin-3: Toward New Approaches against Spinocerebellar Ataxia Type 3. ACS Chem Neurosci 2024; 15:278-289. [PMID: 38154144 PMCID: PMC10797631 DOI: 10.1021/acschemneuro.3c00560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/30/2023] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3) is a neurodegenerative disorder characterized by ataxia and other neurological manifestations, with a poor prognosis and a lack of effective therapies. The amyloid aggregation of the ataxin-3 protein is a hallmark of SCA3 and one of the main biochemical events prompting its onset, making it a prominent target for the development of preventive and therapeutic interventions. Here, we tested the efficacy of an aqueous Lavado cocoa extract and its polyphenolic components against ataxin-3 aggregation and neurotoxicity. The combination of biochemical assays and atomic force microscopy morphological analysis provided clear evidence of cocoa flavanols' ability to hinder ATX3 amyloid aggregation through direct physical interaction, as assessed by NMR spectroscopy. The chemical identity of the flavanols was investigated by ultraperformance liquid chromatography-high-resolution mass spectrometry. The use of the preclinical model Caenorhabditis elegans allowed us to demonstrate cocoa flavanols' ability to ameliorate ataxic phenotypes in vivo. To the best of our knowledge, Lavado cocoa is the first natural source whose extract is able to directly interfere with ATX3 aggregation, leading to the formation of off-pathway species.
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Affiliation(s)
- Barbara Sciandrone
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, P.zza Della Scienza 2, 20126 Milan, Italy
| | - Alessandro Palmioli
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, P.zza Della Scienza 2, 20126 Milan, Italy
- NeuroMI,
Milan Center for Neuroscience, University
of Milano-Bicocca, 20126 Milano, Italy
| | - Carlotta Ciaramelli
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, P.zza Della Scienza 2, 20126 Milan, Italy
- NeuroMI,
Milan Center for Neuroscience, University
of Milano-Bicocca, 20126 Milano, Italy
| | - Roberta Pensotti
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, P.zza Della Scienza 2, 20126 Milan, Italy
| | - Laura Colombo
- Department
of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via M. Negri 2, 20156 Milano, Italy
| | - Maria Elena Regonesi
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, P.zza Della Scienza 2, 20126 Milan, Italy
- NeuroMI,
Milan Center for Neuroscience, University
of Milano-Bicocca, 20126 Milano, Italy
| | - Cristina Airoldi
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, P.zza Della Scienza 2, 20126 Milan, Italy
- NeuroMI,
Milan Center for Neuroscience, University
of Milano-Bicocca, 20126 Milano, Italy
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3
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Haver HN, Wedemeyer M, Butcher E, Peterson FC, Volkman BF, Scaglione KM. Mechanistic Insight into the Suppression of Polyglutamine Aggregation by SRCP1. ACS Chem Biol 2023; 18:549-560. [PMID: 36791332 PMCID: PMC10023506 DOI: 10.1021/acschembio.2c00893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Protein aggregation is a hallmark of the polyglutamine diseases. One potential treatment for these diseases is suppression of polyglutamine aggregation. Previous work identified the cellular slime mold Dictyostelium discoideum as being naturally resistant to polyglutamine aggregation. Further work identified serine-rich chaperone protein 1 (SRCP1) as a protein that is both necessary in Dictyostelium and sufficient in human cells to suppress polyglutamine aggregation. Therefore, understanding how SRCP1 suppresses aggregation may be useful for developing therapeutics for the polyglutamine diseases. Here we utilized a de novo protein modeling approach to generate predictions of SRCP1's structure. Using our best-fit model, we generated mutants that were predicted to alter the stability of SRCP1 and tested these mutants' stability in cells. Using these data, we identified top models of SRCP1's structure that are consistent with the C-terminal region of SRCP1 forming a β-hairpin with a highly dynamic N-terminal region. We next generated a series of peptides that mimic the predicted β-hairpin and validated that they inhibit aggregation of a polyglutamine-expanded mutant huntingtin exon 1 fragment in vitro. To further assess mechanistic details of how SRCP1 inhibits polyglutamine aggregation, we utilized biochemical assays to determine that SRCP1 inhibits secondary nucleation in a manner dependent upon the regions flanking the polyglutamine tract. Finally, to determine if SRCP1 more could generally suppress protein aggregation, we confirmed that it was sufficient to inhibit aggregation of polyglutamine-expanded ataxin-3. Together these studies provide details into the structural and mechanistic basis of the inhibition of protein aggregation by SRCP1.
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Affiliation(s)
- Holly N. Haver
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27710 USA
| | - Michael Wedemeyer
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226 USA
| | - Erin Butcher
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27710 USA
| | - Francis C. Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226 USA
| | - Brian F. Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226 USA
| | - K. Matthew Scaglione
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27710 USA
- Department of Neurology, Duke University, Durham, NC, 27710 USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Durham, NC, 27710 USA
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4
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A Robust Assay to Monitor Ataxin-3 Amyloid Fibril Assembly. Cells 2022; 11:cells11121969. [PMID: 35741099 PMCID: PMC9222203 DOI: 10.3390/cells11121969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 02/05/2023] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3) is caused by the expansion of a glutamine repeat in the protein ataxin-3, which is deposited as intracellular aggregates in affected brain regions. Despite the controversial role of ataxin-3 amyloid structures in SCA3 pathology, the identification of molecules with the capacity to prevent aberrant self-assembly and stabilize functional conformation(s) of ataxin-3 is a key to the development of therapeutic solutions. Amyloid-specific kinetic assays are routinely used to measure rates of protein self-assembly in vitro and are employed during screening for fibrillation inhibitors. The high tendency of ataxin-3 to assemble into oligomeric structures implies that minor changes in experimental conditions can modify ataxin-3 amyloid assembly kinetics. Here, we determine the self-association rates of ataxin-3 and present a detailed study of the aggregation of normal and pathogenic ataxin-3, highlighting the experimental conditions that should be considered when implementing and validating ataxin-3 amyloid progress curves in different settings and in the presence of ataxin-3 interactors. This assay provides a unique and robust platform to screen for modulators of the first steps of ataxin-3 aggregation—a starting point for further studies with cell and animal models of SCA3.
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5
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Coelho P, Fão L, Mota S, Rego AC. Mitochondrial function and dynamics in neural stem cells and neurogenesis: Implications for neurodegenerative diseases. Ageing Res Rev 2022; 80:101667. [PMID: 35714855 DOI: 10.1016/j.arr.2022.101667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/21/2022] [Accepted: 06/09/2022] [Indexed: 11/28/2022]
Abstract
Mitochondria have been largely described as the powerhouse of the cell and recent findings demonstrate that this organelle is fundamental for neurogenesis. The mechanisms underlying neural stem cells (NSCs) maintenance and differentiation are highly regulated by both intrinsic and extrinsic factors. Mitochondrial-mediated switch from glycolysis to oxidative phosphorylation, accompanied by mitochondrial remodeling and dynamics are vital to NSCs fate. Deregulation of mitochondrial proteins, mitochondrial DNA, function, fission/fusion and metabolism underly several neurodegenerative diseases; data show that these impairments are already present in early developmental stages and NSC fate decisions. However, little is known about mitochondrial role in neurogenesis. In this Review, we describe the recent evidence covering mitochondrial role in neurogenesis, its impact in selected neurodegenerative diseases, for which aging is the major risk factor, and the recent advances in stem cell-based therapies that may alleviate neurodegenerative disorders-related neuronal deregulation through improvement of mitochondrial function and dynamics.
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Affiliation(s)
- Patrícia Coelho
- CNC, Center for Neuroscience and Cell Biology, University of Coimbra Polo 1, Coimbra, Portugal.
| | - Lígia Fão
- CNC, Center for Neuroscience and Cell Biology, University of Coimbra Polo 1, Coimbra, Portugal; FMUC- Faculty of Medicine, University of Coimbra Polo 3, Coimbra, Portugal.
| | - Sandra Mota
- CNC, Center for Neuroscience and Cell Biology, University of Coimbra Polo 1, Coimbra, Portugal; III, Institute of Interdisciplinary Research, University of Coimbra, Coimbra, Portugal.
| | - A Cristina Rego
- CNC, Center for Neuroscience and Cell Biology, University of Coimbra Polo 1, Coimbra, Portugal; FMUC- Faculty of Medicine, University of Coimbra Polo 3, Coimbra, Portugal.
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6
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Johnson SL, Libohova K, Blount JR, Sujkowski AL, Prifti MV, Tsou WL, Todi SV. Targeting the VCP-binding motif of ataxin-3 improves phenotypes in Drosophila models of Spinocerebellar Ataxia Type 3. Neurobiol Dis 2021; 160:105516. [PMID: 34563642 PMCID: PMC8693084 DOI: 10.1016/j.nbd.2021.105516] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/23/2021] [Accepted: 09/21/2021] [Indexed: 11/28/2022] Open
Abstract
Of the family of polyglutamine (polyQ) neurodegenerative diseases, Spinocerebellar Ataxia Type 3 (SCA3) is the most common. Like other polyQ diseases, SCA3 stems from abnormal expansions in the CAG triplet repeat of its disease gene resulting in elongated polyQ repeats within its protein, ataxin-3. Various ataxin-3 protein domains contribute to its toxicity, including the valosin-containing protein (VCP)-binding motif (VBM). We previously reported that VCP, a homo-hexameric protein, enhances pathogenic ataxin-3 aggregation and exacerbates its toxicity. These findings led us to explore the impact of targeting the SCA3 protein by utilizing a decoy protein comprising the N-terminus of VCP (N-VCP) that binds ataxin-3's VBM. The notion was that N-VCP would reduce binding of ataxin-3 to VCP, decreasing its aggregation and toxicity. We found that expression of N-VCP in Drosophila melanogaster models of SCA3 ameliorated various phenotypes, coincident with reduced ataxin-3 aggregation. This protective effect was specific to pathogenic ataxin-3 and depended on its VBM. Increasing the amount of N-VCP resulted in further phenotype improvement. Our work highlights the protective potential of targeting the VCP-ataxin-3 interaction in SCA3, a key finding in the search for therapeutic opportunities for this incurable disorder.
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Affiliation(s)
- Sean L Johnson
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jessica R Blount
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Alyson L Sujkowski
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Matthew V Prifti
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Department of Neurology, Wayne State University School of Medicine, Detroit, MI 48201, USA.
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7
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Pathological ATX3 Expression Induces Cell Perturbations in E. coli as Revealed by Biochemical and Biophysical Investigations. Int J Mol Sci 2021; 22:ijms22020943. [PMID: 33477953 PMCID: PMC7835732 DOI: 10.3390/ijms22020943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 02/06/2023] Open
Abstract
Amyloid aggregation of human ataxin-3 (ATX3) is responsible for spinocerebellar ataxia type 3, which belongs to the class of polyglutamine neurodegenerative disorders. It is widely accepted that the formation of toxic oligomeric species is primarily involved in the onset of the disease. For this reason, to understand the mechanisms underlying toxicity, we expressed both a physiological (ATX3-Q24) and a pathological ATX3 variant (ATX3-Q55) in a simplified cellular model, Escherichia coli. It has been observed that ATX3-Q55 expression induces a higher reduction of the cell growth compared to ATX3-Q24, due to the bacteriostatic effect of the toxic oligomeric species. Furthermore, the Fourier transform infrared microspectroscopy investigation, supported by multivariate analysis, made it possible to monitor protein aggregation and the induced cell perturbations in intact cells. In particular, it has been found that the toxic oligomeric species associated with the expression of ATX3-Q55 are responsible for the main spectral changes, ascribable mainly to the cell envelope modifications. A structural alteration of the membrane detected through electron microscopy analysis in the strain expressing the pathological form supports the spectroscopic results.
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8
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Johnson SL, Ranxhi B, Libohova K, Tsou WL, Todi SV. Ubiquitin-interacting motifs of ataxin-3 regulate its polyglutamine toxicity through Hsc70-4-dependent aggregation. eLife 2020; 9:60742. [PMID: 32955441 PMCID: PMC7505662 DOI: 10.7554/elife.60742] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/30/2020] [Indexed: 12/17/2022] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3) belongs to the family of polyglutamine neurodegenerations. Each disorder stems from the abnormal lengthening of a glutamine repeat in a different protein. Although caused by a similar mutation, polyglutamine disorders are distinct, implicating non-polyglutamine regions of disease proteins as regulators of pathogenesis. SCA3 is caused by polyglutamine expansion in ataxin-3. To determine the role of ataxin-3’s non-polyglutamine domains in disease, we utilized a new, allelic series of Drosophila melanogaster. We found that ataxin-3 pathogenicity is saliently controlled by polyglutamine-adjacent ubiquitin-interacting motifs (UIMs) that enhance aggregation and toxicity. UIMs function by interacting with the heat shock protein, Hsc70-4, whose reduction diminishes ataxin-3 toxicity in a UIM-dependent manner. Hsc70-4 also enhances pathogenicity of other polyglutamine proteins. Our studies provide a unique insight into the impact of ataxin-3 domains in SCA3, identify Hsc70-4 as a SCA3 enhancer, and indicate pleiotropic effects from HSP70 chaperones, which are generally thought to suppress polyglutamine degeneration.
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Affiliation(s)
- Sean L Johnson
- Department of Pharmacology, Wayne State University, Detroit, United States
| | - Bedri Ranxhi
- Department of Pharmacology, Wayne State University, Detroit, United States
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University, Detroit, United States
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University, Detroit, United States
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University, Detroit, United States.,Department of Neurology, Wayne State University, Detroit, United States
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9
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Vendredy L, Adriaenssens E, Timmerman V. Small heat shock proteins in neurodegenerative diseases. Cell Stress Chaperones 2020; 25:679-699. [PMID: 32323160 PMCID: PMC7332613 DOI: 10.1007/s12192-020-01101-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Small heat shock proteins are ubiquitously expressed chaperones, yet mutations in some of them cause tissue-specific diseases. Here, we will discuss how small heat shock proteins give rise to neurodegenerative disorders themselves while we will also highlight how these proteins can fulfil protective functions in neurodegenerative disorders caused by protein aggregation. The first half of this paper will be focused on how mutations in HSPB1, HSPB3, and HSPB8 are linked to inherited peripheral neuropathies like Charcot-Marie-Tooth (CMT) disease and distal hereditary motor neuropathy (dHMN). The second part of the paper will discuss how small heat shock proteins are linked to neurodegenerative disorders like Alzheimer's, Parkinson's, and Huntington's disease.
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Affiliation(s)
- Leen Vendredy
- Department of Biomedical Sciences and Institute Born Bunge, Peripheral Neuropathy Research Group, University of Antwerp, Antwerp, Belgium
| | - Elias Adriaenssens
- Department of Biomedical Sciences and Institute Born Bunge, Peripheral Neuropathy Research Group, University of Antwerp, Antwerp, Belgium
| | - Vincent Timmerman
- Department of Biomedical Sciences and Institute Born Bunge, Peripheral Neuropathy Research Group, University of Antwerp, Antwerp, Belgium.
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10
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Rosselli-Murai LK, Joseph JG, Lopes-Cendes I, Liu AP, Murai MJ. The Machado-Joseph disease-associated form of ataxin-3 impacts dynamics of clathrin-coated pits. Cell Biol Int 2020; 44:1252-1259. [PMID: 31970864 DOI: 10.1002/cbin.11312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/22/2020] [Indexed: 12/14/2022]
Abstract
Expansion above a certain threshold in the polyglutamine (polyQ) tract of ataxin-3 is the main cause of neurodegeneration in Machado-Joseph disease. Ataxin-3 contains an N-terminal catalytic domain, called Josephin domain, and a highly aggregation-prone C-terminal domain containing the polyQ tract. Recent work has shown that protein aggregation inhibits clathrin-mediated endocytosis (CME). However, the effects of polyQ expansion in ataxin-3 on CME have not been investigated. We hypothesize that the expansion of the polyQ tract in ataxin-3 could impact CME. Here, we report that both the wild-type and the expanded ataxin-3 reduce transferrin internalization and expanded ataxin-3 impacts dynamics of clathrin-coated pits (CCPs) by reducing CCP nucleation and increasing short-lived abortive CCPs. Since endocytosis plays a central role in regulating receptor uptake and cargo release, our work highlights a potential mechanism linking protein aggregation to cellular dysregulation.
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Affiliation(s)
- Luciana K Rosselli-Murai
- Department of Pharmacology, University of Michigan Medical School, 2301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, Michigan, 48109, USA.,Department of Mechanical Engineering, University of Michigan, 2674 GGB, 2350 Hayward, Ann Arbor, Michigan, 48109, USA
| | - Jophin G Joseph
- Department of Mechanical Engineering, University of Michigan, 2674 GGB, 2350 Hayward, Ann Arbor, Michigan, 48109, USA
| | - Iscia Lopes-Cendes
- Department of Medical Genetics, School of Medical Sciences, University of Campinas, R. Tessália Vieira de Camargo, 126, Campinas, São Paulo, 13083-970, Brazil.,The Brazilian Institute of Neuroscience and Neurotechnology, R. Vital Brasil, 251, Campinas, São Paulo, 13083-888, Brazil
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, 2674 GGB, 2350 Hayward, Ann Arbor, Michigan, 48109, USA
| | - Marcelo J Murai
- Department of Pharmacology, University of Michigan Medical School, 2301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, Michigan, 48109, USA.,Department of Medical Genetics, School of Medical Sciences, University of Campinas, R. Tessália Vieira de Camargo, 126, Campinas, São Paulo, 13083-970, Brazil
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11
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Moldovean SN, Chiş V. Molecular Dynamics Simulations Applied to Structural and Dynamical Transitions of the Huntingtin Protein: A Review. ACS Chem Neurosci 2020; 11:105-120. [PMID: 31841621 DOI: 10.1021/acschemneuro.9b00561] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Over the recent years, Huntington's disease (HD) has become widely discussed in the scientific literature especially because at the mutant level there are several contradictions regarding the aggregation mechanism. The specific role of the physiological huntingtin protein remains unknown, due to the lack of characterization of its entire crystallographic structure, making the experimental and theoretical research even harder when taking into consideration its involvement in multiple biological functions and its high affinity for different interacting partners. Different types of models, containing fewer (not more than 35 Qs) polyglutamine residues for the WT structure and above 35 Qs for the mutants, were subjected to classical or advanced MD simulations to establish the proteins' structural stability by evaluating their conformational changes. Outside the polyQ tract, there are two other regions of interest (the N17 domain and the polyP rich domain) considered to be essential for the aggregation kinetics at the mutant level. The polymerization process is considered to be dependent on the polyQ length. As the polyQ tract's dimension increases, the structures present more β-sheet conformations. Contrarily, it is also considered that the aggregation stability is not necessarily dependent on the number of Qs, while the initial stage of the aggregation seed might play the decisive role. A general assumption regarding the polyP domain is that it might preserve the polyQ structures soluble by acting as an antagonist for β-sheet formation.
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Affiliation(s)
| | - Vasile Chiş
- Babeş-Bolyai University, Faculty of Physics, Kogălniceanu 1, RO-400084 Cluj-Napoca, Romania
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12
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Computational prediction and redesign of aberrant protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:43-83. [DOI: 10.1016/bs.pmbts.2019.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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13
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Orlando G, Silva A, Macedo-Ribeiro S, Raimondi D, Vranken W. Accurate prediction of protein beta-aggregation with generalized statistical potentials. Bioinformatics 2019; 36:2076-2081. [DOI: 10.1093/bioinformatics/btz912] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/27/2019] [Accepted: 12/03/2019] [Indexed: 01/04/2023] Open
Abstract
Abstract
Motivation
Protein beta-aggregation is an important but poorly understood phenomena involved in diseases as well as in beneficial physiological processes. However, while this task has been investigated for over 50 years, very little is known about its mechanisms of action. Moreover, the identification of regions involved in aggregation is still an open problem and the state-of-the-art methods are often inadequate in real case applications.
Results
In this article we present AgMata, an unsupervised tool for the identification of such regions from amino acidic sequence based on a generalized definition of statistical potentials that includes biophysical information. The tool outperforms the state-of-the-art methods on two different benchmarks. As case-study, we applied our tool to human ataxin-3, a protein involved in Machado–Joseph disease. Interestingly, AgMata identifies aggregation-prone residues that share the very same structural environment. Additionally, it successfully predicts the outcome of in vitro mutagenesis experiments, identifying point mutations that lead to an alteration of the aggregation propensity of the wild-type ataxin-3.
Availability and implementation
A python implementation of the tool is available at https://bitbucket.org/bio2byte/agmata.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gabriele Orlando
- Interuniversity Institute of Bioinformatics in Brussels, ULB/VUB, Triomflaan, Brussels 1050, Belgium
- Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Alexandra Silva
- IBMC-Instituto de Biologia Molecular e Celular
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC-Instituto de Biologia Molecular e Celular
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal
| | | | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB/VUB, Triomflaan, Brussels 1050, Belgium
- Structural Biology, Vrije Universiteit Brussel, Brussels 1050, Belgium
- Centre for Structural Biology, VIB, Brussels 1050, Belgium
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14
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Contessotto MG, Rosselli-Murai LK, Garcia MCC, Oliveira CL, Torriani IL, Lopes-Cendes I, Murai MJ. The Machado-Joseph disease-associated expanded form of ataxin-3: Overexpression, purification, and preliminary biophysical and structural characterization. Protein Expr Purif 2018; 152:40-45. [DOI: 10.1016/j.pep.2018.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/15/2018] [Accepted: 07/14/2018] [Indexed: 01/14/2023]
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15
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Visentin C, Navarro S, Grasso G, Regonesi ME, Deriu MA, Tortora P, Ventura S. Protein Environment: A Crucial Triggering Factor in Josephin Domain Aggregation: The Role of 2,2,2-Trifluoroethanol. Int J Mol Sci 2018; 19:ijms19082151. [PMID: 30042316 PMCID: PMC6121581 DOI: 10.3390/ijms19082151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 11/28/2022] Open
Abstract
The protein ataxin-3 contains a polyglutamine stretch that triggers amyloid aggregation when it is expanded beyond a critical threshold. This results in the onset of the spinocerebellar ataxia type 3. The protein consists of the globular N-terminal Josephin domain and a disordered C-terminal tail where the polyglutamine stretch is located. Expanded ataxin-3 aggregates via a two-stage mechanism: first, Josephin domain self-association, then polyQ fibrillation. This highlights the intrinsic amyloidogenic potential of Josephin domain. Therefore, much effort has been put into investigating its aggregation mechanism(s). A key issue regards the conformational requirements for triggering amyloid aggregation, as it is believed that, generally, misfolding should precede aggregation. Here, we have assayed the effect of 2,2,2-trifluoroethanol, a co-solvent capable of stabilizing secondary structures, especially α-helices. By combining biophysical methods and molecular dynamics, we demonstrated that both secondary and tertiary JD structures are virtually unchanged in the presence of up to 5% 2,2,2-trifluoroethanol. Despite the preservation of JD structure, 1% of 2,2,2-trifluoroethanol suffices to exacerbate the intrinsic aggregation propensity of this domain, by slightly decreasing its conformational stability. These results indicate that in the case of JD, conformational fluctuations might suffice to promote a transition towards an aggregated state without the need for extensive unfolding, and highlights the important role played by the environment on the aggregation of this globular domain.
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Affiliation(s)
- Cristina Visentin
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
| | - Gianvito Grasso
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), CH-6928 Manno, Switzerland.
| | - Maria Elena Regonesi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy.
- Centro di Neuroscienze di Milano (Neuro-MI), 20126 Milano, Italy.
| | - Marco Agostino Deriu
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), CH-6928 Manno, Switzerland.
| | - Paolo Tortora
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy.
- Centro di Neuroscienze di Milano (Neuro-MI), 20126 Milano, Italy.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
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16
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Blount JR, Libohova K, Marsh GB, Sutton JR, Todi SV. Expression and Regulation of Deubiquitinase-Resistant, Unanchored Ubiquitin Chains in Drosophila. Sci Rep 2018; 8:8513. [PMID: 29855490 PMCID: PMC5981470 DOI: 10.1038/s41598-018-26364-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/10/2018] [Indexed: 01/03/2023] Open
Abstract
The modifier protein, ubiquitin (Ub) regulates various cellular pathways by controlling the fate of substrates to which it is conjugated. Ub moieties are also conjugated to each other, forming chains of various topologies. In cells, poly-Ub is attached to proteins and also exists in unanchored form. Accumulation of unanchored poly-Ub is thought to be harmful and quickly dispersed through dismantling by deubiquitinases (DUBs). We wondered whether disassembly by DUBs is necessary to control unanchored Ub chains in vivo. We generated Drosophila melanogaster lines that express Ub chains non-cleavable into mono-Ub by DUBs. These chains are rapidly modified with different linkages and represent various types of unanchored species. We found that unanchored poly-Ub is not devastating in Drosophila, under normal conditions or during stress. The DUB-resistant, free Ub chains are degraded by the proteasome, at least in part through the assistance of VCP and its cofactor, p47. Also, unanchored poly-Ub that cannot be cleaved by DUBs can be conjugated en bloc, in vivo. Our results indicate that unanchored poly-Ub species need not be intrinsically toxic; they can be controlled independently of DUB-based disassembly by being degraded, or through conjugation onto other proteins.
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Affiliation(s)
- Jessica R Blount
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Gregory B Marsh
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Joanna R Sutton
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA. .,Department of Neurology, Wayne State University School of Medicine, Detroit, MI, USA.
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17
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Ristic G, Sutton JR, Libohova K, Todi SV. Toxicity and aggregation of the polyglutamine disease protein, ataxin-3 is regulated by its binding to VCP/p97 in Drosophila melanogaster. Neurobiol Dis 2018; 116:78-92. [PMID: 29704548 DOI: 10.1016/j.nbd.2018.04.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/26/2018] [Accepted: 04/22/2018] [Indexed: 01/01/2023] Open
Abstract
Among the nine dominantly inherited, age-dependent neurodegenerative diseases caused by abnormal expansion in the polyglutamine (polyQ) repeat of otherwise unrelated proteins is Spinocerebellar Ataxia Type 3 (SCA3). SCA3 is caused by polyQ expansion in the deubiquitinase (DUB), ataxin-3. Molecular sequelae related to SCA3 remain unclear. Here, we sought to understand the role of protein context in SCA3 by focusing on the interaction between this DUB and Valosin-Containing Protein (VCP). VCP is bound directly by ataxin-3 through an arginine-rich area preceding the polyQ repeat. We examined the importance of this interaction in ataxin-3-dependent degeneration in Drosophila melanogaster. Our assays with new isogenic fly lines expressing pathogenic ataxin-3 with an intact or mutated VCP-binding site show that disrupting the ataxin-3-VCP interaction delays the aggregation of the toxic protein in vivo. Importantly, early on flies that express pathogenic ataxin-3 with a mutated VCP-binding site are indistinguishable from flies that do not express any SCA3 protein. Also, reducing levels of VCP through RNA-interference has a similar, protective effect to mutating the VCP-binding site of pathogenic ataxin-3. Based on in vivo pulse-chases, aggregated species of ataxin-3 are highly stable, in a manner independent of VCP-binding. Collectively, our results highlight an important role for the ataxin-3-VCP interaction in SCA3, based on a model that posits a seeding effect from VCP on pathogenic ataxin-3 aggregation and subsequent toxicity.
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Affiliation(s)
- Gorica Ristic
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Joanna R Sutton
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA; Department of Neurology, Wayne State University School of Medicine, Detroit, MI, USA.
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18
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Polyglutamine-Independent Features in Ataxin-3 Aggregation and Pathogenesis of Machado-Joseph Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1049:275-288. [PMID: 29427109 DOI: 10.1007/978-3-319-71779-1_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The expansion of a trinucleotide (CAG) repeat, translated into a polyglutamine expanded sequence in the protein encoded by the MJD gene, was identified over 20 years ago as the causative mutation in a severe neurodegenerative disorder originally diagnosed in individuals of Portuguese ancestry. This incapacitating disease, called Machado-Joseph disease or spinocebellar ataxia type 3, is integrated into a larger group of neurodegenerative disorders-the polyglutamine expansion disorders-caused by extension of a CAG repeat in the coding sequence of otherwise unrelated genes. These diseases are generally linked with the appearance of intracellular inclusions , which despite having a controversial role in disease appearance and development represent a characteristic common fingerprint in all polyglutamine-related disorders. Although polyglutamine expansion is an obvious trigger for neuronal dysfunction, the role of the different domains of these complex proteins in the function and aggregation properties of the carrier proteins is being uncovered in recent studies. In this review the current knowledge about the structural and functional features of full-length ataxin-3 protein will be discussed. The intrinsic conformational dynamics and interplay between the globular and intrinsically disordered regions of ataxin-3 will be highlighted, and a perspective picture of the role of known ataxin-3 post-translational modifications on regulating ataxin-3 aggregation and function will be drawn.
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19
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Polyglutamine expansion diseases: More than simple repeats. J Struct Biol 2017; 201:139-154. [PMID: 28928079 DOI: 10.1016/j.jsb.2017.09.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/24/2017] [Accepted: 09/15/2017] [Indexed: 12/27/2022]
Abstract
Polyglutamine (polyQ) repeat-containing proteins are widespread in the human proteome but only nine of them are associated with highly incapacitating neurodegenerative disorders. The genetic expansion of the polyQ tract in disease-related proteins triggers a series of events resulting in neurodegeneration. The polyQ tract plays the leading role in the aggregation mechanism, but other elements modulate the aggregation propensity in the context of the full-length proteins, as implied by variations in the length of the polyQ tract required to trigger the onset of a given polyQ disease. Intrinsic features such as the presence of aggregation-prone regions (APRs) outside the polyQ segments and polyQ-flanking sequences, which synergistically participate in the aggregation process, are emerging for several disease-related proteins. The inherent polymorphic structure of polyQ stretches places the polyQ proteins in a central position in protein-protein interaction networks, where interacting partners may additionally shield APRs or reshape the aggregation course. Expansion of the polyQ tract perturbs the cellular homeostasis and contributes to neuronal failure by modulating protein-protein interactions and enhancing toxic oligomerization. Post-translational modifications further regulate self-assembly either by directly altering the intrinsic aggregation propensity of polyQ proteins, by modulating their interaction with different macromolecules or by modifying their withdrawal by the cell quality control machinery. Here we review the recent data on the multifaceted aggregation pathways of disease-related polyQ proteins, focusing on ataxin-3, the protein mutated in Machado-Joseph disease. Further mechanistic understanding of this network of events is crucial for the development of effective therapies for polyQ diseases.
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20
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Ahmed R, VanSchouwen B, Jafari N, Ni X, Ortega J, Melacini G. Molecular Mechanism for the (-)-Epigallocatechin Gallate-Induced Toxic to Nontoxic Remodeling of Aβ Oligomers. J Am Chem Soc 2017; 139:13720-13734. [PMID: 28841302 DOI: 10.1021/jacs.7b05012] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
(-)-Epigallocatechin gallate (EGCG) effectively reduces the cytotoxicity of the Alzheimer's disease β-amyloid peptide (Aβ) by remodeling seeding-competent Aβ oligomers into off-pathway seeding-incompetent Aβ assemblies. However, the mechanism of EGCG-induced remodeling is not fully understood. Here we combine 15N and 1H dark-state exchange saturation transfer (DEST), relaxation, and chemical shift projection NMR analyses with fluorescence, dynamic light scattering, and electron microscopy to elucidate how EGCG remodels Aβ oligomers. We show that the remodeling adheres to a Hill-Scatchard model whereby the Aβ(1-40) self-association occurs cooperatively and generates Aβ(1-40) oligomers with multiple independent binding sites for EGCG with a Kd ∼10-fold lower than that for the Aβ(1-40) monomers. Upon binding to EGCG, the Aβ(1-40) oligomers become less solvent exposed, and the β-regions, which are involved in direct monomer-protofibril contacts in the absence of EGCG, undergo a direct-to-tethered contact shift. This switch toward less engaged monomer-protofibril contacts explains the seeding incompetency observed upon EGCG remodeling and suggests that EGCG interferes with secondary nucleation events known to generate toxic Aβ assemblies. Unexpectedly, the N-terminal residues experience an opposite EGCG-induced shift from tethered to direct contacts, explaining why EGCG remodeling occurs without release of Aβ(1-40) monomers. We also show that upon binding Aβ(1-40) oligomers the relative positions of the EGCG B and D rings change with respect to that of ring A. These distinct structural changes occurring in both Aβ(1-40) oligomers and EGCG during remodeling offer a foundation for understanding the molecular mechanism of EGCG as a neurotoxicity inhibitor. Furthermore, the results reported here illustrate the effectiveness of DEST-based NMR approaches in investigating the mechanism of low-molecular-weight amyloid inhibitors.
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Affiliation(s)
- Rashik Ahmed
- Department of Biochemistry and Biomedical Sciences and ‡Department of Chemistry and Chemical Biology, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Bryan VanSchouwen
- Department of Biochemistry and Biomedical Sciences and ‡Department of Chemistry and Chemical Biology, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Naeimeh Jafari
- Department of Biochemistry and Biomedical Sciences and ‡Department of Chemistry and Chemical Biology, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Xiaodan Ni
- Department of Biochemistry and Biomedical Sciences and ‡Department of Chemistry and Chemical Biology, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences and ‡Department of Chemistry and Chemical Biology, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences and ‡Department of Chemistry and Chemical Biology, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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21
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Oppong E, Stier G, Gaal M, Seeger R, Stoeck M, Delsuc MA, Cato ACB, Kieffer B. An Amyloidogenic Sequence at the N-Terminus of the Androgen Receptor Impacts Polyglutamine Aggregation. Biomolecules 2017. [PMID: 28629183 PMCID: PMC5485733 DOI: 10.3390/biom7020044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The human androgen receptor (AR) is a ligand inducible transcription factor that harbors an amino terminal domain (AR-NTD) with a ligand-independent activation function. AR-NTD is intrinsically disordered and displays aggregation properties conferred by the presence of a poly-glutamine (polyQ) sequence. The length of the polyQ sequence as well as its adjacent sequence motifs modulate this aggregation property. AR-NTD also contains a conserved KELCKAVSVSM sequence motif that displays an intrinsic property to form amyloid fibrils under mild oxidative conditions. As peptide sequences with intrinsic oligomerization properties are reported to have an impact on the aggregation of polyQ tracts, we determined the effect of the KELCKAVSVSM on the polyQ stretch in the context of the AR-NTD using atomic force microscopy (AFM). Here, we present evidence for a crosstalk between the amyloidogenic properties of the KELCKAVSVSM motif and the polyQ stretch at the AR-NTD.
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Affiliation(s)
- Emmanuel Oppong
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM, U964, CNRS, UMR-7104, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France.
| | - Gunter Stier
- Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany.
| | - Miriam Gaal
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Rebecca Seeger
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Melanie Stoeck
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Marc-André Delsuc
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM, U964, CNRS, UMR-7104, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France.
| | - Andrew C B Cato
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Bruno Kieffer
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM, U964, CNRS, UMR-7104, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden, France.
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22
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Kuiper EFE, de Mattos EP, Jardim LB, Kampinga HH, Bergink S. Chaperones in Polyglutamine Aggregation: Beyond the Q-Stretch. Front Neurosci 2017; 11:145. [PMID: 28386214 PMCID: PMC5362620 DOI: 10.3389/fnins.2017.00145] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/08/2017] [Indexed: 01/12/2023] Open
Abstract
Expanded polyglutamine (polyQ) stretches in at least nine unrelated proteins lead to inherited neuronal dysfunction and degeneration. The expansion size in all diseases correlates with age at onset (AO) of disease and with polyQ protein aggregation, indicating that the expanded polyQ stretch is the main driving force for the disease onset. Interestingly, there is marked interpatient variability in expansion thresholds for a given disease. Between different polyQ diseases the repeat length vs. AO also indicates the existence of modulatory effects on aggregation of the upstream and downstream amino acid sequences flanking the Q expansion. This can be either due to intrinsic modulation of aggregation by the flanking regions, or due to differential interaction with other proteins, such as the components of the cellular protein quality control network. Indeed, several lines of evidence suggest that molecular chaperones have impact on the handling of different polyQ proteins. Here, we review factors differentially influencing polyQ aggregation: the Q-stretch itself, modulatory flanking sequences, interaction partners, cleavage of polyQ-containing proteins, and post-translational modifications, with a special focus on the role of molecular chaperones. By discussing typical examples of how these factors influence aggregation, we provide more insight on the variability of AO between different diseases as well as within the same polyQ disorder, on the molecular level.
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Affiliation(s)
- E F E Kuiper
- Department of Cell Biology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Eduardo P de Mattos
- Department of Cell Biology, University Medical Center Groningen, University of GroningenGroningen, Netherlands; Programa de Pós-Graduação em Genética e Biologia Molecular, Department of Genetics, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil; Medical Genetics Service, Hospital de Clínicas de Porto AlegrePorto Alegre, Brazil
| | - Laura B Jardim
- Programa de Pós-Graduação em Genética e Biologia Molecular, Department of Genetics, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil; Medical Genetics Service, Hospital de Clínicas de Porto AlegrePorto Alegre, Brazil; Departamento de Medicina Interna, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Harm H Kampinga
- Department of Cell Biology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Steven Bergink
- Department of Cell Biology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
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23
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Lucato CM, Lupton CJ, Halls ML, Ellisdon AM. Amyloidogenicity at a Distance: How Distal Protein Regions Modulate Aggregation in Disease. J Mol Biol 2017; 429:1289-1304. [PMID: 28342736 DOI: 10.1016/j.jmb.2017.03.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/12/2017] [Accepted: 03/14/2017] [Indexed: 12/14/2022]
Abstract
The misfolding of proteins to form amyloid is a key pathological feature of several progressive, and currently incurable, diseases. A mechanistic understanding of the pathway from soluble, native protein to insoluble amyloid is crucial for therapeutic design, and recent efforts have helped to elucidate the key molecular events that trigger protein misfolding. Generally, either global or local structural perturbations occur early in amyloidogenesis to expose aggregation-prone regions of the protein that can then self-associate to form toxic oligomers. Surprisingly, these initiating structural changes are often caused or influenced by protein regions distal to the classically amyloidogenic sequences. Understanding the importance of these distal regions in the pathogenic process has highlighted many remaining knowledge gaps regarding the precise molecular events that occur in classic aggregation pathways. In this review, we discuss how these distal regions can influence aggregation in disease and the recent technical and conceptual advances that have allowed this insight.
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Affiliation(s)
- Christina M Lucato
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Christopher J Lupton
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Michelle L Halls
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Andrew M Ellisdon
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
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24
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Adegbuyiro A, Sedighi F, Pilkington AW, Groover S, Legleiter J. Proteins Containing Expanded Polyglutamine Tracts and Neurodegenerative Disease. Biochemistry 2017; 56:1199-1217. [PMID: 28170216 DOI: 10.1021/acs.biochem.6b00936] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Several hereditary neurological and neuromuscular diseases are caused by an abnormal expansion of trinucleotide repeats. To date, there have been 10 of these trinucleotide repeat disorders associated with an expansion of the codon CAG encoding glutamine (Q). For these polyglutamine (polyQ) diseases, there is a critical threshold length of the CAG repeat required for disease, and further expansion beyond this threshold is correlated with age of onset and symptom severity. PolyQ expansion in the translated proteins promotes their self-assembly into a variety of oligomeric and fibrillar aggregate species that accumulate into the hallmark proteinaceous inclusion bodies associated with each disease. Here, we review aggregation mechanisms of proteins with expanded polyQ-tracts, structural consequences of expanded polyQ ranging from monomers to fibrillar aggregates, the impact of protein context and post-translational modifications on aggregation, and a potential role for lipid membranes in aggregation. As the pathogenic mechanisms that underlie these disorders are often classified as either a gain of toxic function or loss of normal protein function, some toxic mechanisms associated with mutant polyQ tracts will also be discussed.
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Affiliation(s)
- Adewale Adegbuyiro
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Faezeh Sedighi
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Albert W Pilkington
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Sharon Groover
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, 217 Clark Hall, West Virginia University , Morgantown, West Virginia 26506, United States.,Blanchette Rockefeller Neurosciences Institute, Robert C. Byrd Health Sciences Center, P.O. Box 9304, West Virginia University , Morgantown, West Virginia 26506, United States.,NanoSAFE, P.O. Box 6223, West Virginia University , Morgantown, West Virginia 26506, United States
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25
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Grasso G, Tuszynski JA, Morbiducci U, Licandro G, Danani A, Deriu MA. Thermodynamic and kinetic stability of the Josephin Domain closed arrangement: evidences from replica exchange molecular dynamics. Biol Direct 2017; 12:2. [PMID: 28103906 PMCID: PMC5244572 DOI: 10.1186/s13062-016-0173-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/21/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Molecular phenomena driving pathological aggregation in neurodegenerative diseases are not completely understood yet. Peculiar is the case of Spinocerebellar Ataxia 3 (SCA3) where the conformational properties of the AT-3 N-terminal region, also called Josephin Domain (JD), play a key role in the first step of aggregation, having the JD an amyloidogenic propensity itself. For this reason, unraveling the intimate relationship between JD structural features and aggregation tendency may lead to a step forward in understanding the pathology and rationally design a cure. In this connection, computational modeling has demonstrated to be helpful in exploring the protein molecular dynamics and mechanism of action. RESULTS Conformational dynamics of the JD is here finely investigated by replica exchange molecular dynamics simulations able to sample the microsecond time scale and to provide both a thermodynamic and kinetic description of the protein conformational changes. Accessible structural conformations of the JD have been identified in: open, intermediate and closed like arrangement. Data indicated the closed JD arrangement as the most likely protein arrangement. The protein transition from closed toward intermediate/open states was characterized by a rate constant higher than 700 ns. This result also explains the inability of classical molecular dynamics to explore transitions from closed to open JD configuration on a time scale of hundreds of nanoseconds. CONCLUSION This work provides the first kinetic estimation of the JD transition pathway from open-like to closed-like arrangement and vice-versa, indicating the closed-like arrangement as the most likely configuration for a JD in water environment. More widely, the importance of our results is also underscored considering that the ability to provide a kinetic description of the protein conformational changes is a scientific challenge for both experimental and theoretical approaches to date. REVIEWERS This article was reviewed by Oliviero Carugo, Bojan Zagrovic.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928 Switzerland
| | - Jack A. Tuszynski
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy
| | | | - Ginevra Licandro
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928 Switzerland
| | - Andrea Danani
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928 Switzerland
| | - Marco A. Deriu
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928 Switzerland
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26
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Matos CA, Nóbrega C, Louros SR, Almeida B, Ferreiro E, Valero J, Pereira de Almeida L, Macedo-Ribeiro S, Carvalho AL. Ataxin-3 phosphorylation decreases neuronal defects in spinocerebellar ataxia type 3 models. J Cell Biol 2016; 212:465-80. [PMID: 26880203 PMCID: PMC4754714 DOI: 10.1083/jcb.201506025] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Ataxin-3, the protein involved in spinocerebellar ataxia type 3 or Machado-Joseph disease, causes dendritic and synapse loss in cultured neurons when expanded, and mutation of phosphorylation site S12 reduces aggregation, neuronal loss, and synapse loss. Different neurodegenerative diseases are caused by aberrant elongation of repeated glutamine sequences normally found in particular human proteins. Although the proteins involved are ubiquitously distributed in human tissues, toxicity targets only defined neuronal populations. Changes caused by an expanded polyglutamine protein are possibly influenced by endogenous cellular mechanisms, which may be harnessed to produce neuroprotection. Here, we show that ataxin-3, the protein involved in spinocerebellar ataxia type 3, also known as Machado-Joseph disease, causes dendritic and synapse loss in cultured neurons when expanded. We report that S12 of ataxin-3 is phosphorylated in neurons and that mutating this residue so as to mimic a constitutive phosphorylated state counters the neuromorphologic defects observed. In rats stereotaxically injected with expanded ataxin-3–encoding lentiviral vectors, mutation of serine 12 reduces aggregation, neuronal loss, and synapse loss. Our results suggest that S12 plays a role in the pathogenic pathways mediated by polyglutamine-expanded ataxin-3 and that phosphorylation of this residue protects against toxicity.
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Affiliation(s)
- Carlos A Matos
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Clévio Nóbrega
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Susana R Louros
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Bruno Almeida
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal
| | - Elisabete Ferreiro
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Jorge Valero
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal Ikerbasque Basque Foundation for Science and Achucarro Basque Center for Neuroscience, Bizkaia Science and Technology Park, E-48170 Zamudio, Spain
| | - Luís Pereira de Almeida
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal
| | - Ana Luísa Carvalho
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3004-517 Coimbra, Portugal
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27
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Inayathullah M, Tan A, Jeyaraj R, Lam J, Cho NJ, Liu CW, Manoukian MAC, Ashkan K, Mahmoudi M, Rajadas J. Self-assembly and sequence length dependence on nanofibrils of polyglutamine peptides. Neuropeptides 2016; 57:71-83. [PMID: 26874369 DOI: 10.1016/j.npep.2016.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/11/2016] [Accepted: 01/31/2016] [Indexed: 10/22/2022]
Abstract
Huntington's disease (HD) is recognized as a currently incurable, inherited neurodegenerative disorder caused by the accumulation of misfolded polyglutamine (polyQ) peptide aggregates in neuronal cells. Yet, the mechanism by which newly formed polyQ chains interact and assemble into toxic oligomeric structures remains a critical, unresolved issue. In order to shed further light on the matter, our group elected to investigate the folding of polyQ peptides - examining glutamine repeat lengths ranging from 3 to 44 residues. To characterize these aggregates we employed a diverse array of technologies, including: nuclear magnetic resonance; circular dichroism; Fourier transform infrared spectroscopy; fluorescence resonance energy transfer (FRET), and atomic force microscopy. The data we obtained suggest that an increase in the number of glutamine repeats above 14 residues results in disordered loop structures, with different repeat lengths demonstrating unique folding characteristics. This differential folding manifests in the formation of distinct nano-sized fibrils, and on this basis, we postulate the idea of 14 polyQ repeats representing a critical loop length for neurotoxicity - a property that we hope may prove amenable to future therapeutic intervention. Furthermore, FRET measurements on aged assemblages indicate an increase in the end-to-end distance of the peptide with time, most probably due to the intermixing of individual peptide strands within the nanofibril. Further insight into this apparent time-dependent reorganization of aggregated polyQ peptides may influence future disease modeling of polyQ-related proteinopathies, in addition to directing novel clinical innovations.
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Affiliation(s)
- Mohammed Inayathullah
- Biomaterials & Advanced Drug Delivery Laboratory (BioADD), Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA; Bioorganic and Neurochemistry Laboratory, Central Leather Research Institute, Adyar, Chennai, Tamilnadu, India; Cardiovascular Pharmacology Division, Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Aaron Tan
- Biomaterials & Advanced Drug Delivery Laboratory (BioADD), Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA; UCL Medical School, University College London (UCL), London, UK; University College London Hospitals NHS Foundation Trust, London, UK.
| | - Rebecca Jeyaraj
- UCL Medical School, University College London (UCL), London, UK
| | - James Lam
- UCL Medical School, University College London (UCL), London, UK
| | - Nam-Joon Cho
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA; School of Materials Science and Engineering, Nanyang Technological University, Singapore
| | - Corey W Liu
- Stanford Magnetic Resonance Laboratory, Stanford University, Palo Alto, CA, USA
| | - Martin A C Manoukian
- Department of Dermatology, Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Keyoumars Ashkan
- Department of Neurosurgery, King's College Hospital NHS Foundation Trust, King's College London, London, UK
| | - Morteza Mahmoudi
- Biomaterials & Advanced Drug Delivery Laboratory (BioADD), Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA; Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Cardiovascular Pharmacology Division, Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Jayakumar Rajadas
- Biomaterials & Advanced Drug Delivery Laboratory (BioADD), Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA; Cardiovascular Pharmacology Division, Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Palo Alto, CA, USA.
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28
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Characterization of the conformational fluctuations in the Josephin domain of ataxin-3. Biophys J 2016; 107:2932-2940. [PMID: 25517158 PMCID: PMC4269769 DOI: 10.1016/j.bpj.2014.10.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/10/2014] [Accepted: 10/10/2014] [Indexed: 11/24/2022] Open
Abstract
As for a variety of other molecular recognition processes, conformational fluctuations play an important role in the cleavage of polyubiquitin chains by the Josephin domain of ataxin-3. The interaction between Josephin and ubiquitin appears to be mediated by the motions of α-helical hairpin that is unusual among deubiquitinating enzymes. Here, we characterized the conformational fluctuations of the helical hairpin by incorporating NMR measurements as replica-averaged restraints in molecular dynamics simulations, and by validating the results by small-angle x-ray scattering measurements. This approach allowed us to define the extent of the helical hairpin motions and suggest a role of such motions in the recognition of ubiquitin.
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29
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Deriu MA, Grasso G, Tuszynski JA, Gallo D, Morbiducci U, Danani A. Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates. PLoS Comput Biol 2016; 12:e1004699. [PMID: 26745628 PMCID: PMC4706304 DOI: 10.1371/journal.pcbi.1004699] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 12/09/2015] [Indexed: 01/03/2023] Open
Abstract
The Josephin Domain (JD), i.e. the N-terminal domain of Ataxin 3 (At3) protein, is an interesting example of competition between physiological function and aggregation risk. In fact, the fibrillogenesis of Ataxin 3, responsible for the spinocerebbellar ataxia 3, is strictly related to the JD thermodynamic stability. Whereas recent NMR studies have demonstrated that different JD conformations exist, the likelihood of JD achievable conformational states in solution is still an open issue. Marked differences in the available NMR models are located in the hairpin region, supporting the idea that JD has a flexible hairpin in dynamic equilibrium between open and closed states. In this work we have carried out an investigation on the JD conformational arrangement by means of both classical molecular dynamics (MD) and Metadynamics employing essential coordinates as collective variables. We provide a representation of the free energy landscape characterizing the transition pathway from a JD open-like structure to a closed-like conformation. Findings of our in silico study strongly point to the closed-like conformation as the most likely for a Josephin Domain in water.
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Affiliation(s)
- Marco A. Deriu
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Manno, Switzerland
- * E-mail:
| | - Gianvito Grasso
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Manno, Switzerland
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Diego Gallo
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Andrea Danani
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Manno, Switzerland
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30
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Bonanomi M, Visentin C, Natalello A, Spinelli M, Vanoni M, Airoldi C, Regonesi ME, Tortora P. How Epigallocatechin-3-gallate and Tetracycline Interact with the Josephin Domain of Ataxin-3 and Alter Its Aggregation Mode. Chemistry 2015; 21:18383-93. [PMID: 26538519 DOI: 10.1002/chem.201503086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 12/17/2022]
Abstract
Epigallocatechin-3-gallate (EGCG) and tetracycline are two known inhibitors of amyloid aggregation able to counteract the fibrillation of most of the proteins involved in neurodegenerative diseases. We have recently investigated their effect on ataxin-3 (AT3), the polyglutamine-containing protein responsible for spinocerebellar ataxia type 3. We previously showed that EGCG and tetracycline can contrast the aggregation process and toxicity of expanded AT3, although by different mechanisms. Here, we have performed further experiments by using the sole Josephin domain (JD) to further elucidate the mechanism of action of the two compounds. By protein solubility assays and FTIR spectroscopy we have first observed that EGCG and tetracycline affect the JD aggregation essentially in the same way displayed when acting on the full-length expanded AT3. Then, by saturation transfer difference (STD) NMR experiments, we have shown that EGCG binds both the monomeric and the oligomeric JD form, whereas tetracycline can only interact with the oligomeric one. Surface plasmon resonance (SPR) analysis has confirmed the capability of the sole EGCG to bind monomeric JD, although with a KD value suggestive for a non-specific interaction. Our investigations provide new details on the JD interaction with EGCG and tetracycline, which could explain the different mechanisms by which the two compounds reduce the toxicity of AT3.
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Affiliation(s)
- Marcella Bonanomi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy)
| | - Cristina Visentin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy)
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR Milano-Bicocca, Milano (Italy).,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy)
| | - Michela Spinelli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,SysBio Centre for Systems Biology, Milano and Rome (Italy)
| | - Marco Vanoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy).,SysBio Centre for Systems Biology, Milano and Rome (Italy)
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy). .,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy). .,SysBio Centre for Systems Biology, Milano and Rome (Italy).
| | - Maria E Regonesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy). .,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy).
| | - Paolo Tortora
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy)
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31
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Lupton CJ, Steer DL, Wintrode PL, Bottomley SP, Hughes VA, Ellisdon AM. Enhanced molecular mobility of ordinarily structured regions drives polyglutamine disease. J Biol Chem 2015; 290:24190-200. [PMID: 26260925 DOI: 10.1074/jbc.m115.659532] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 01/09/2023] Open
Abstract
Polyglutamine expansion is a hallmark of nine neurodegenerative diseases, with protein aggregation intrinsically linked to disease progression. Although polyglutamine expansion accelerates protein aggregation, the misfolding process is frequently instigated by flanking domains. For example, polyglutamine expansion in ataxin-3 allosterically triggers the aggregation of the catalytic Josephin domain. The molecular mechanism that underpins this allosteric aggregation trigger remains to be determined. Here, we establish that polyglutamine expansion increases the molecular mobility of two juxtaposed helices critical to ataxin-3 deubiquitinase activity. Within one of these helices, we identified a highly amyloidogenic sequence motif that instigates aggregation and forms the core of the growing fibril. Critically, by mutating residues within this key region, we decrease local structural fluctuations to slow ataxin-3 aggregation. This provides significant insight, down to the molecular level, into how polyglutamine expansion drives aggregation and explains the positive correlation between polyglutamine tract length, protein aggregation, and disease severity.
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Affiliation(s)
- Christopher J Lupton
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
| | - David L Steer
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
| | - Patrick L Wintrode
- the Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201
| | - Stephen P Bottomley
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
| | - Victoria A Hughes
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia, 3800 and
| | - Andrew M Ellisdon
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia, 3800 and
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32
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Infrared nanospectroscopy characterization of oligomeric and fibrillar aggregates during amyloid formation. Nat Commun 2015. [PMID: 26215704 PMCID: PMC4525161 DOI: 10.1038/ncomms8831] [Citation(s) in RCA: 196] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Amyloids are insoluble protein fibrillar aggregates. The importance of characterizing their aggregation has steadily increased because of their link to human diseases and material science applications. In particular, misfolding and aggregation of the Josephin domain of ataxin-3 is implicated in spinocerebellar ataxia-3. Infrared nanospectroscopy, simultaneously exploiting atomic force microscopy and infrared spectroscopy, can characterize at the nanoscale the conformational rearrangements of proteins during their aggregation. Here we demonstrate that we can individually characterize the oligomeric and fibrillar species formed along the amyloid aggregation. We describe their secondary structure, monitoring at the nanoscale an α-to-β transition, and couple these studies with an independent measurement of the evolution of their intrinsic stiffness. These results suggest that the aggregation of Josephin proceeds from the monomer state to the formation of spheroidal intermediates with a native structure. Only successively, these intermediates evolve into misfolded aggregates and into the final fibrils. The onset of neurodegenerative disorders is associated at the molecular level with insoluble protein aggregates, named amyloids. Here, the authors characterize by infrared nanospectroscopy and nanomechanical studies, the amyloid aggregation at the individual species scale.
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33
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Li X, Liu H, Fischhaber PL, Tang TS. Toward therapeutic targets for SCA3: Insight into the role of Machado-Joseph disease protein ataxin-3 in misfolded proteins clearance. Prog Neurobiol 2015; 132:34-58. [PMID: 26123252 DOI: 10.1016/j.pneurobio.2015.06.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/30/2015] [Accepted: 06/16/2015] [Indexed: 01/09/2023]
Abstract
Machado-Joseph disease (MJD, also known as spinocerebellar ataxia type 3, SCA3), an autosomal dominant neurological disorder, is caused by an abnormal expanded polyglutamine (polyQ) repeat in the ataxin-3 protein. The length of the expanded polyQ stretch correlates positively with the severity of the disease and inversely with the age at onset. To date, we cannot fully explain the mechanism underlying neurobiological abnormalities of this disease. Yet, accumulating reports have demonstrated the functions of ataxin-3 protein in the chaperone system, ubiquitin-proteasome system, and aggregation-autophagy, all of which suggest a role of ataxin-3 in the clearance of misfolded proteins. Notably, the SCA3 pathogenic form of ataxin-3 (ataxin-3(exp)) impairs the misfolded protein clearance via mechanisms that are either dependent or independent of its deubiquitinase (DUB) activity, resulting in the accumulation of misfolded proteins and the progressive loss of neurons in SCA3. Some drugs, which have been used as activators/inducers in the chaperone system, ubiquitin-proteasome system, and aggregation-autophagy, have been demonstrated to be efficacious in the relief of neurodegeneration diseases like Huntington's disease (HD), Parkinson's (PD), Alzheimer's (AD) as well as SCA3 in animal models and clinical trials, putting misfolded protein clearance on the list of potential therapeutic targets. Here, we undertake a comprehensive review of the progress in understanding the physiological functions of ataxin-3 in misfolded protein clearance and how the polyQ expansion impairs misfolded protein clearance. We then detail the preclinical studies targeting the elimination of misfolded proteins for SCA3 treatment. We close with future considerations for translating these pre-clinical results into therapies for SCA3 patients.
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Affiliation(s)
- Xiaoling Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongmei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Paula L Fischhaber
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330-8262, USA.
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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34
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Almeida B, Abreu IA, Matos CA, Fraga JS, Fernandes S, Macedo MG, Gutiérrez-Gallego R, Pereira PJB, Carvalho AL, Macedo-Ribeiro S. SUMOylation of the brain-predominant Ataxin-3 isoform modulates its interaction with p97. Biochim Biophys Acta Mol Basis Dis 2015; 1852:1950-9. [PMID: 26073430 DOI: 10.1016/j.bbadis.2015.06.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 05/12/2015] [Accepted: 06/08/2015] [Indexed: 11/18/2022]
Abstract
BACKGROUND Machado-Joseph Disease (MJD), a form of dominantly inherited ataxia belonging to the group of polyQ expansion neurodegenerative disorders, occurs when a threshold value for the number of glutamines in Ataxin-3 (Atx3) polyglutamine region is exceeded. As a result of its modular multidomain architecture, Atx3 is known to engage in multiple macromolecular interactions, which might be unbalanced when the polyQ tract is expanded, culminating in the aggregation and formation of intracellular inclusions, a unifying fingerprint of this group of neurodegenerative disorders. Since aggregation is specific to certain brain regions, localization-dependent posttranslational modifications that differentially affect Atx3 might also contribute for MJD. METHODS We combined in vitro and cellular approaches to address SUMOylation in the brain-predominant Atx3 isoform and assessed the impact of this posttranslational modification on Atx3 self-assembly and interaction with its native partner, p97. RESULTS We demonstrate that Atx3 is SUMOylated at K356 both in vitro and in cells, which contributes for decreased formation of amyloid fibrils and for increased affinity towards p97. CONCLUSIONS AND GENERAL SIGNIFICANCE These findings highlight the role of SUMOylation as a regulator of Atx3 function, with implications on Atx3 protein interaction network and self-assembly, with potential impact for further understanding the molecular mechanisms underlying MJD pathogenesis.
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Affiliation(s)
- Bruno Almeida
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Isabel A Abreu
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Carlos A Matos
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; Department of Life Sciences, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Joana S Fraga
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Sara Fernandes
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Maria G Macedo
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Ricardo Gutiérrez-Gallego
- Bioanalysis Group, Neurosciences Research Program, Hospital del Mar Medical Research Institute (IMIM)-Parque de Salud Mar, 08003 Barcelona, Spain; Department of Experimental and Health Sciences, Pompeu Fabra University, 08003 Barcelona, Spain
| | - Pedro José Barbosa Pereira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Ana Luísa Carvalho
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; Department of Life Sciences, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-180 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.
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35
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Scarff CA, Almeida B, Fraga J, Macedo-Ribeiro S, Radford SE, Ashcroft AE. Examination of Ataxin-3 (atx-3) Aggregation by Structural Mass Spectrometry Techniques: A Rationale for Expedited Aggregation upon Polyglutamine (polyQ) Expansion. Mol Cell Proteomics 2015; 14:1241-53. [PMID: 25700012 PMCID: PMC4424396 DOI: 10.1074/mcp.m114.044610] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Indexed: 01/13/2023] Open
Abstract
Expansion of polyglutamine stretches leads to the formation of polyglutamine-containing neuronal aggregates and neuronal death in nine diseases for which there currently are no treatments or cures. This is largely due to a lack in understanding of the mechanisms by which expanded polyglutamine regions contribute to aggregation and disease. To complicate matters further, several of the polyglutamine-disease related proteins, including ataxin-3, have a multistage aggregation mechanism in which flanking domain self-assembly precedes polyglutamine aggregation yet is influenced by polyglutamine expansion. How polyglutamine expansion influences flanking domain aggregation is poorly understood. Here, we use a combination of mass spectrometry and biophysical approaches to investigate this issue for ataxin-3. We show that the conformational dynamics of the flanking Josephin domain in ataxin-3 with an expanded polyglutamine tract are altered in comparison to those exhibited by its nonexpanded counterpart, specifically within the aggregation-prone region of the Josephin domain (amino acid residues 73–96). Expansion thus exposes this region more frequently in ataxin-3 containing an expanded polyglutamine tract, providing a molecular explanation of why aggregation is accelerated upon polyglutamine expansion. Here, harnessing the power of ion mobility spectrometry-mass spectrometry, oligomeric species formed during aggregation are characterized and a model for oligomer growth proposed. The results suggest that a conformational change occurs at the dimer level that initiates self-assembly. New insights into ataxin-3 fibril architecture are also described, revealing the region of the Josephin domain involved in protofibril formation and demonstrating that polyglutamine aggregation proceeds as a distinct second step after protofibril formation without requiring structural rearrangement of the protofibril core. Overall, the results enable the effect of polyglutamine expansion on every stage of ataxin-3 self-assembly, from monomer through to fibril, to be described and a rationale for expedited aggregation upon polyglutamine expansion to be provided.
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Affiliation(s)
- Charlotte A Scarff
- From the ‡Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Bruno Almeida
- §IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-4180 Porto, Portugal
| | - Joana Fraga
- §IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-4180 Porto, Portugal
| | - Sandra Macedo-Ribeiro
- §IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4150-4180 Porto, Portugal
| | - Sheena E Radford
- From the ‡Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK;
| | - Alison E Ashcroft
- From the ‡Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK;
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36
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Gershenson A, Gierasch LM, Pastore A, Radford SE. Energy landscapes of functional proteins are inherently risky. Nat Chem Biol 2014; 10:884-91. [PMID: 25325699 PMCID: PMC4416114 DOI: 10.1038/nchembio.1670] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 09/19/2014] [Indexed: 01/08/2023]
Abstract
Evolutionary pressure for protein function leads to unavoidable sampling of conformational states that are at risk of misfolding and aggregation. The resulting tension between functional requirements and the risk of misfolding and/or aggregation in the evolution of proteins is becoming more and more apparent. One outcome of this tension is sensitivity to mutation, in which only subtle changes in sequence that may be functionally advantageous can tip the delicate balance toward protein aggregation. Similarly, increasing the concentration of aggregation-prone species by reducing the ability to control protein levels or compromising protein folding capacity engenders increased risk of aggregation and disease. In this Perspective, we describe examples that epitomize the tension between protein functional energy landscapes and aggregation risk. Each case illustrates how the energy landscapes for the at-risk proteins are sculpted to enable them to perform their functions and how the risks of aggregation are minimized under cellular conditions using a variety of compensatory mechanisms.
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Affiliation(s)
- Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Annalisa Pastore
- Department of Clinical Neurosciences, King’s College London, Denmark Hill Campus, London, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
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Deriu MA, Grasso G, Licandro G, Danani A, Gallo D, Tuszynski JA, Morbiducci U. Investigation of the Josephin Domain protein-protein interaction by molecular dynamics. PLoS One 2014; 9:e108677. [PMID: 25268243 PMCID: PMC4182536 DOI: 10.1371/journal.pone.0108677] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/23/2014] [Indexed: 11/18/2022] Open
Abstract
Spinocerebellar ataxia (SCA) 3, the most common form of SCA, is a neurodegenerative rare disease characterized by polyglutamine tract expansion and self-assembly of Ataxin3 (At3) misfolded proteins into highly organized fibrillar aggregates. The At3 N-terminal Josephin Domain (JD) has been suggested as being responsible for mediating the initial phase of the At3 double-step fibrillogenesis. Several issues concerning the residues involved in the JD's aggregation and, more generally, the JD clumping mechanism have not been clarified yet. In this paper we present an investigation focusing on the JD protein-protein interaction by means of molecular modeling. Our results suggest possible aminoacids involved in JD contact together with local and non-local effects following JD dimerization. Surprisingly, JD conformational changes following the binding may involve ubiquitin binding sites and hairpin region even though they do not pertain to the JD interaction surfaces. Moreover, the JD binding event has been found to alter the hairpin open-like conformation toward a closed-like arrangement over the simulated timescale. Finally, our results suggest that the JD aggregation might be a multi-step process, with an initial fast JD-JD binding mainly driven by Arg101, followed by slower structural global rearrangements involving the exposure to the solvent of Leu84-Trp87, which might play a role in a second step of JD aggregation.
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Affiliation(s)
- Marco A. Deriu
- Institute of Computer Integrated Manufacturing for Sustainable Innovation, Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
- * E-mail:
| | - Gianvito Grasso
- Institute of Computer Integrated Manufacturing for Sustainable Innovation, Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
| | - Ginevra Licandro
- Institute of Computer Integrated Manufacturing for Sustainable Innovation, Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
| | - Andrea Danani
- Institute of Computer Integrated Manufacturing for Sustainable Innovation, Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Manno, Switzerland
| | - Diego Gallo
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
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Sironi E, Colombo L, Lompo A, Messa M, Bonanomi M, Regonesi ME, Salmona M, Airoldi C. Natural Compounds against Neurodegenerative Diseases: Molecular Characterization of the Interaction of Catechins from Green Tea with Aβ1–42, PrP106–126, and Ataxin‐3 Oligomers. Chemistry 2014; 20:13793-800. [DOI: 10.1002/chem.201403188] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Erika Sironi
- Department of Biotechnology and Biosciences University of Milano‐Bicocca, P.zza della Scienza, 2, 20126, Milano (Italy), Fax: (+39) 02‐6448‐3565
| | - Laura Colombo
- Department Biochemistry and Molecular Pharmacology, IRCCS‐Istituto di Ricerche Farmacologiche “Mario Negri”, Via Giuseppe La Masa, 19 20156 Milano (Italy)
| | - Angela Lompo
- Department of Biotechnology and Biosciences University of Milano‐Bicocca, P.zza della Scienza, 2, 20126, Milano (Italy), Fax: (+39) 02‐6448‐3565
| | - Massimo Messa
- Department Biochemistry and Molecular Pharmacology, IRCCS‐Istituto di Ricerche Farmacologiche “Mario Negri”, Via Giuseppe La Masa, 19 20156 Milano (Italy)
| | - Marcella Bonanomi
- Department of Biotechnology and Biosciences University of Milano‐Bicocca, P.zza della Scienza, 2, 20126, Milano (Italy), Fax: (+39) 02‐6448‐3565
| | - Maria Elena Regonesi
- Department of Statistics and Quantitative Methods, University of Milano‐Bicocca, Via Bicocca degli Arcimboldi, 8, 20126, Milano (Italy)
| | - Mario Salmona
- Department Biochemistry and Molecular Pharmacology, IRCCS‐Istituto di Ricerche Farmacologiche “Mario Negri”, Via Giuseppe La Masa, 19 20156 Milano (Italy)
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences University of Milano‐Bicocca, P.zza della Scienza, 2, 20126, Milano (Italy), Fax: (+39) 02‐6448‐3565
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Evers MM, Toonen LJA, van Roon-Mom WMC. Ataxin-3 protein and RNA toxicity in spinocerebellar ataxia type 3: current insights and emerging therapeutic strategies. Mol Neurobiol 2014; 49:1513-31. [PMID: 24293103 PMCID: PMC4012159 DOI: 10.1007/s12035-013-8596-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/14/2013] [Indexed: 01/10/2023]
Abstract
Ataxin-3 is a ubiquitously expressed deubiqutinating enzyme with important functions in the proteasomal protein degradation pathway and regulation of transcription. The C-terminus of the ataxin-3 protein contains a polyglutamine (PolyQ) region that, when mutationally expanded to over 52 glutamines, causes the neurodegenerative disease spinocerebellar ataxia 3 (SCA3). In spite of extensive research, the molecular mechanisms underlying the cellular toxicity resulting from mutant ataxin-3 remain elusive and no preventive treatment is currently available. It has become clear over the last decade that the hallmark intracellular ataxin-3 aggregates are likely not the main toxic entity in SCA3. Instead, the soluble PolyQ containing fragments arising from proteolytic cleavage of ataxin-3 by caspases and calpains are now regarded to be of greater influence in pathogenesis. In addition, recent evidence suggests potential involvement of a RNA toxicity component in SCA3 and other PolyQ expansion disorders, increasing the pathogenic complexity. Herein, we review the functioning of ataxin-3 and the involvement of known protein and RNA toxicity mechanisms of mutant ataxin-3 that have been discovered, as well as future opportunities for therapeutic intervention.
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Affiliation(s)
- Melvin M. Evers
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Lodewijk J. A. Toonen
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Willeke M. C. van Roon-Mom
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
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40
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Matilla-Dueñas A, Ashizawa T, Brice A, Magri S, McFarland KN, Pandolfo M, Pulst SM, Riess O, Rubinsztein DC, Schmidt J, Schmidt T, Scoles DR, Stevanin G, Taroni F, Underwood BR, Sánchez I. Consensus paper: pathological mechanisms underlying neurodegeneration in spinocerebellar ataxias. CEREBELLUM (LONDON, ENGLAND) 2014; 13:269-302. [PMID: 24307138 PMCID: PMC3943639 DOI: 10.1007/s12311-013-0539-y] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intensive scientific research devoted in the recent years to understand the molecular mechanisms or neurodegeneration in spinocerebellar ataxias (SCAs) are identifying new pathways and targets providing new insights and a better understanding of the molecular pathogenesis in these diseases. In this consensus manuscript, the authors discuss their current views on the identified molecular processes causing or modulating the neurodegenerative phenotype in spinocerebellar ataxias with the common opinion of translating the new knowledge acquired into candidate targets for therapy. The following topics are discussed: transcription dysregulation, protein aggregation, autophagy, ion channels, the role of mitochondria, RNA toxicity, modulators of neurodegeneration and current therapeutic approaches. Overall point of consensus includes the common vision of neurodegeneration in SCAs as a multifactorial, progressive and reversible process, at least in early stages. Specific points of consensus include the role of the dysregulation of protein folding, transcription, bioenergetics, calcium handling and eventual cell death with apoptotic features of neurons during SCA disease progression. Unresolved questions include how the dysregulation of these pathways triggers the onset of symptoms and mediates disease progression since this understanding may allow effective treatments of SCAs within the window of reversibility to prevent early neuronal damage. Common opinions also include the need for clinical detection of early neuronal dysfunction, for more basic research to decipher the early neurodegenerative process in SCAs in order to give rise to new concepts for treatment strategies and for the translation of the results to preclinical studies and, thereafter, in clinical practice.
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Affiliation(s)
- A Matilla-Dueñas
- Health Sciences Research Institute Germans Trias i Pujol (IGTP), Ctra. de Can Ruti, Camí de les Escoles s/n, Badalona, Barcelona, Spain,
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41
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Menon RP, Soong D, de Chiara C, Holt M, McCormick JE, Anilkumar N, Pastore A. Mapping the self-association domains of ataxin-1: identification of novel non overlapping motifs. PeerJ 2014; 2:e323. [PMID: 24711972 PMCID: PMC3970802 DOI: 10.7717/peerj.323] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/07/2014] [Indexed: 12/13/2022] Open
Abstract
The neurodegenerative disease spinocerebellar ataxia type 1 (SCA1) is caused by aggregation and misfolding of the ataxin-1 protein. While the pathology correlates with mutations that lead to expansion of a polyglutamine tract in the protein, other regions contribute to the aggregation process as also non-expanded ataxin-1 is intrinsically aggregation-prone and forms nuclear foci in cell. Here, we have used a combined approach based on FRET analysis, confocal microscopy and in vitro techniques to map aggregation-prone regions other than polyglutamine and to establish the importance of dimerization in self-association/foci formation. Identification of aggregation-prone regions other than polyglutamine could greatly help the development of SCA1 treatment more specific than that based on targeting the low complexity polyglutamine region.
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Affiliation(s)
- Rajesh P Menon
- MRC National Institute for Medical Research, The Ridgeway , London , UK
| | - Daniel Soong
- Randall Division for Cell and Molecular Biophysics, New Hunt's House, King's College London , Guy's Campus, London , UK ; British Heart Foundation Centre of Research Excellence, King's College London , Denmark Hill Campus, London , UK
| | - Cesira de Chiara
- MRC National Institute for Medical Research, The Ridgeway , London , UK
| | - Mark Holt
- Randall Division for Cell and Molecular Biophysics, New Hunt's House, King's College London , Guy's Campus, London , UK
| | - John E McCormick
- MRC National Institute for Medical Research, The Ridgeway , London , UK
| | - Narayana Anilkumar
- British Heart Foundation Centre of Research Excellence, King's College London , Denmark Hill Campus, London , UK
| | - Annalisa Pastore
- MRC National Institute for Medical Research, The Ridgeway , London , UK ; Department of Molecular Neuroscience, Institute of Psychiatry, King's College London , Denmark Hill Campus, London , UK
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42
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Modeling the polyglutamine aggregation pathway in Huntington's disease: from basic studies to clinical applications. Subcell Biochem 2014; 65:353-88. [PMID: 23225011 DOI: 10.1007/978-94-007-5416-4_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Huntington's disease (HD) is among the polyglutamine (polyQ) disorders, which are caused by expansion of CAG-trinucleotide repeats. These disorders share common characteristics, and have thus long been thought to have a unifying pathogenic mechanism resulting from polyQ expansion. However, this scenario has recently become more complex, as studies have found multiple pathways for the assembly of disease-related polyQ protein aggregates that differ in both structure and toxicity. There are fascinating disease-specific aspects of the polyQ disorders, including the repeat-length dependence of both clinical features and the propensity of the expanded polyQ protein to aggregate. Such aggregation kinetics have proven useful in explaining the disease process. This chapter describes two risk-based stochastic kinetic models, the cumulative-damage and one-hit models, that describe genotype-phenotype correlations in patients with polyQ diseases and reflect alternative pathways of polyQ aggregation. Using repeat-length as an index, several models explore the quantitative connection between aggregation kinetics and clinical data from HD patients. The correlations between CAG repeat-length and age-of-onset are re-evaluated, and the rate of disease progression (as assessed by clinical measures and longitudinal imaging studies of brain structure) are surveyed. Finally, I present a mathematical model by which the time course of neurodegeneration in HD can be precisely predicted, and discuss the association of the models with the major controversies about HD pathogenesis.
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43
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The conformational ensemble of the disordered and aggregation-protective 182–291 region of ataxin-3. Biochim Biophys Acta Gen Subj 2013; 1830:5236-47. [DOI: 10.1016/j.bbagen.2013.07.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 06/10/2013] [Accepted: 07/10/2013] [Indexed: 12/23/2022]
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44
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Faggiano S, Menon RP, Kelly GP, McCormick J, Todi SV, Scaglione KM, Paulson HL, Pastore A. Enzymatic production of mono-ubiquitinated proteins for structural studies: The example of the Josephin domain of ataxin-3. FEBS Open Bio 2013; 3:453-8. [PMID: 24251111 PMCID: PMC3829987 DOI: 10.1016/j.fob.2013.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/07/2013] [Accepted: 10/07/2013] [Indexed: 12/03/2022] Open
Abstract
Protein ubiquitination occurs through formation of an isopeptide bond between the C-terminal glycine of ubiquitin (Ub) and the ɛ-amino group of a substrate lysine residue. This post-translational modification, which occurs through the attachment of single and/or multiple copies of mono-ubiquitin and poly-ubiquitin chains, is involved in crucial cellular events such as protein degradation, cell-cycle regulation and DNA repair. The abnormal functioning of ubiquitin pathways is also implicated in the pathogenesis of several human diseases ranging from cancer to neurodegeneration. However, despite the undoubted biological importance, understanding the molecular basis of how ubiquitination regulates different pathways has up to now been strongly limited by the difficulty of producing the amounts of highly homogeneous samples that are needed for a structural characterization by X-ray crystallography and/or NMR. Here, we report on the production of milligrams of highly pure Josephin mono-ubiquitinated on lysine 117 through large scale in vitro enzymatic ubiquitination. Josephin is the catalytic domain of ataxin-3, a protein responsible for spinocerebellar ataxia type 3. Ataxin-3 is the first deubiquitinating enzyme (DUB) reported to be activated by mono-ubiquitination. We demonstrate that the samples produced with the described method are correctly folded and suitable for structural studies. The protocol allows facile selective labelling of the components. Our results provide an important proof-of-concept that may pave the way to new approaches to the in vitro study of ubiquitinated proteins. We set up a protocol for large-scale in vitro enzymatic ubiqitination. This produced milligrams of highly pure mono-ubiquitinated Josephin domain of ataxin-3. We applied an alternative labelling scheme for the structural characterization of the sample by NMR. Ubiquitin covalently linked on lysine 117 directly interacts with Josephin but does not alter the overall fold of the protein.
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Key Words
- ATP, adenosine triphosphate
- DTT, dithiothreitol
- DUB, deubiquitinating enzyme
- Deubiquitinating enzyme
- GST, glutathione-S-transferase
- HSQC, heteronuclear single quantum coherence
- IAA, iodoacetamide
- Isopeptide bond
- JosK117-only, Josephin mutant in which all lysines but K117 are mutated
- Josephin
- MS/MS tandem, mass spectrometry
- Machado–Joseph disease
- NMR, nuclear magnetic resonance
- PDB, Protein Data Bank
- Post-translational modification
- SDS–PAGE, sodium dodecyl sulfate–polyacrylamide gel electrophoresis
- Spinocerebellar ataxia type 3
- Tris–HCl, 2-amino-2-(hydroxymethyl)-1,3-propanediol hydrochloride
- Ubiquitin
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Affiliation(s)
- Serena Faggiano
- National Institute for Medical Research, MRC, The Ridgeway, London, United Kingdom
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Different ataxin-3 amyloid aggregates induce intracellular Ca(2+) deregulation by different mechanisms in cerebellar granule cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:3155-3165. [PMID: 24035922 DOI: 10.1016/j.bbamcr.2013.08.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 11/23/2022]
Abstract
This work aims at elucidating the relation between morphological and physicochemical properties of different ataxin-3 (ATX3) aggregates and their cytotoxicity. We investigated a non-pathological ATX3 form (ATX3Q24), a pathological expanded form (ATX3Q55), and an ATX3 variant truncated at residue 291 lacking the polyQ expansion (ATX3/291Δ). Solubility, morphology and hydrophobic exposure of oligomeric aggregates were characterized. Then we monitored the changes in the intracellular Ca(2+) levels and the abnormal Ca(2+) signaling resulting from aggregate interaction with cultured rat cerebellar granule cells. ATX3Q55, ATX3/291Δ and, to a lesser extent, ATX3Q24 oligomers displayed similar morphological and physicochemical features and induced qualitatively comparable time-dependent intracellular Ca(2+) responses. However, only the pre-fibrillar aggregates of expanded ATX3 (the only variant which forms bundles of mature fibrils) triggered a characteristic Ca(2+) response at a later stage that correlated with a larger hydrophobic exposure relative to the two other variants. Cell interaction with early oligomers involved glutamatergic receptors, voltage-gated channels and monosialotetrahexosylganglioside (GM1)-rich membrane domains, whereas cell interaction with more aged ATX3Q55 pre-fibrillar aggregates resulted in membrane disassembly by a mechanism involving only GM1-rich areas. Exposure to ATX3Q55 and ATX3/291Δ aggregates resulted in cell apoptosis, while ATX3Q24 was substantially innocuous. Our findings provide insight into the mechanisms of ATX3 aggregation, aggregate cytotoxicity and calcium level modifications in exposed cerebellar cells.
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Cushman-Nick M, Bonini NM, Shorter J. Hsp104 suppresses polyglutamine-induced degeneration post onset in a drosophila MJD/SCA3 model. PLoS Genet 2013; 9:e1003781. [PMID: 24039611 PMCID: PMC3764203 DOI: 10.1371/journal.pgen.1003781] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 07/25/2013] [Indexed: 11/22/2022] Open
Abstract
There are no effective therapeutics that antagonize or reverse the protein-misfolding events underpinning polyglutamine (PolyQ) disorders, including Spinocerebellar Ataxia Type-3 (SCA3). Here, we augment the proteostasis network of Drosophila SCA3 models with Hsp104, a powerful protein disaggregase from yeast, which is bafflingly absent from metazoa. Hsp104 suppressed eye degeneration caused by a C-terminal ataxin-3 (MJD) fragment containing the pathogenic expanded PolyQ tract, but unexpectedly enhanced aggregation and toxicity of full-length pathogenic MJD. Hsp104 suppressed toxicity of MJD variants lacking a portion of the N-terminal deubiquitylase domain and full-length MJD variants unable to engage polyubiquitin, indicating that MJD-ubiquitin interactions hinder protective Hsp104 modalities. Importantly, in staging experiments, Hsp104 suppressed toxicity of a C-terminal MJD fragment when expressed after the onset of PolyQ-induced degeneration, whereas Hsp70 was ineffective. Thus, we establish the first disaggregase or chaperone treatment administered after the onset of pathogenic protein-induced degeneration that mitigates disease progression.
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Affiliation(s)
- Mimi Cushman-Nick
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nancy M. Bonini
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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47
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Saunders HM, Hughes VA, Cappai R, Bottomley SP. Conformational behavior and aggregation of ataxin-3 in SDS. PLoS One 2013; 8:e69416. [PMID: 23894474 PMCID: PMC3718759 DOI: 10.1371/journal.pone.0069416] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 06/11/2013] [Indexed: 01/08/2023] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3) is one of nine polyglutamine (polyQ) diseases all characterized by the presence of intraneuronal inclusions that contain aggregated protein. Aggregation of ataxin-3, the causative protein of SCA3, has been well characterized in vitro, with both pathogenic and non-pathogenic length ataxin-3 undergoing fibrillogenesis. However, only ataxin-3 containing an expanded polyQ tract leads to SCA3. Therefore other cellular factors, not present in previous in vitro studies, may modulate aggregation during disease. The interactions between fibrillar species and cell membranes have been characterized in a number of amyloid diseases, including Huntington’s Disease, and these interactions affect aggregation and toxicity. We have characterized the effects of the membrane mimetic sodium dodecyl sulfate (SDS) on ataxin-3 structure and aggregation, to show that both micellar and non-micellar SDS have differing effects on the two stages of ataxin-3 aggregation. We also demonstrate that fibrillar ataxin-3 binds phospholipids, in particular phosphorylated phosphotidylinositols. These results highlight the effect of intracellular factors on the ataxin-3 misfolding landscape and their implications in SCA3 and polyQ diseases in general are discussed.
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Affiliation(s)
- Helen M. Saunders
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Victoria A. Hughes
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Roberto Cappai
- Department of Pathology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Stephen P. Bottomley
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- * E-mail:
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48
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Scarff CA, Sicorello A, Tomé RJ, Macedo-Ribeiro S, Ashcroft AE, Radford SE. A tale of a tail: Structural insights into the conformational properties of the polyglutamine protein ataxin-3. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2013; 345-347:63-70. [PMID: 25844046 PMCID: PMC4375668 DOI: 10.1016/j.ijms.2012.08.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 05/24/2023]
Abstract
Ataxin-3 is the protein responsible for the neurodegenerative polyglutamine disease Spinocerebellar ataxia type 3. Full structural characterisation of ataxin-3 is required to aid in understanding the mechanism of disease. Despite extensive study, little is known about the conformational properties of the full-length protein, in either its non-expanded healthy or expanded pathogenic forms, particularly since its polyglutamine-containing region has denied structural elucidation. In this work, travelling-wave ion mobility spectrometry-mass spectrometry and limited proteolysis have been used to compare the conformational properties of full-length non-expanded ataxin-3 (14Q) and its isolated N-terminal Josephin domain (JD). Limited proteolysis experiments have confirmed that the JD is stable, being extremely resistant to trypsin digestion, with the exception of the α2/α3 hairpin which is flexible and exposed to protease cleavage in solution. The C-terminal region of ataxin-3 which contains the glutamine-rich sequences is largely unstructured, showing little resistance to limited proteolysis. Using ion mobility spectrometry-mass spectrometry we show that ataxin-3 (14Q) adopts a wide range of conformational states in vitro conferred by the flexibility of its C-terminal tail and the α2/α3 hairpin of the N-terminal JD. This study highlights how the power of MS-based approaches to protein structural characterisation can be particularly useful when the target protein is aggregation-prone and has intrinsically unordered regions.
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Affiliation(s)
- Charlotte A. Scarff
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Alessandro Sicorello
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Ricardo J.L. Tomé
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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Almeida B, Fernandes S, Abreu IA, Macedo-Ribeiro S. Trinucleotide repeats: a structural perspective. Front Neurol 2013; 4:76. [PMID: 23801983 PMCID: PMC3687200 DOI: 10.3389/fneur.2013.00076] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/04/2013] [Indexed: 11/29/2022] Open
Abstract
Trinucleotide repeat (TNR) expansions are present in a wide range of genes involved in several neurological disorders, being directly involved in the molecular mechanisms underlying pathogenesis through modulation of gene expression and/or the function of the RNA or protein it encodes. Structural and functional information on the role of TNR sequences in RNA and protein is crucial to understand the effect of TNR expansions in neurodegeneration. Therefore, this review intends to provide to the reader a structural and functional view of TNR and encoded homopeptide expansions, with a particular emphasis on polyQ expansions and its role at inducing the self-assembly, aggregation and functional alterations of the carrier protein, which culminates in neuronal toxicity and cell death. Detail will be given to the Machado-Joseph Disease-causative and polyQ-containing protein, ataxin-3, providing clues for the impact of polyQ expansion and its flanking regions in the modulation of ataxin-3 molecular interactions, function, and aggregation.
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Affiliation(s)
- Bruno Almeida
- Instituto de Biologia Molecular e Celular, Universidade do Porto , Porto , Portugal
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Carra S, Rusmini P, Crippa V, Giorgetti E, Boncoraglio A, Cristofani R, Naujock M, Meister M, Minoia M, Kampinga HH, Poletti A. Different anti-aggregation and pro-degradative functions of the members of the mammalian sHSP family in neurological disorders. Philos Trans R Soc Lond B Biol Sci 2013; 368:20110409. [PMID: 23530259 DOI: 10.1098/rstb.2011.0409] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The family of the mammalian small heat-shock proteins consists of 10 members (sHSPs/HSPBs: HSPB1-HSPB10) that all share a highly conserved C-terminal alpha-crystallin domain, important for the modulation of both their structural and functional properties. HSPB proteins are biochemically classified as molecular chaperones and participate in protein quality control, preventing the aggregation of unfolded or misfolded proteins and/or assisting in their degradation. Thus, several members of the HSPB family have been suggested to be protective in a number of neurodegenerative and neuromuscular diseases that are characterized by protein misfolding. However, the pro-refolding, anti-aggregation or pro-degradative properties of the various members of the HSPB family differ largely, thereby influencing their efficacy and protective functions. Such diversity depends on several factors, including biochemical and physical properties of the unfolded/misfolded client, the expression levels and the subcellular localization of both the chaperone and the client proteins. Furthermore, although some HSPB members are inefficient at inhibiting protein aggregation, they can still exert neuroprotective effects by other, as yet unidentified, manners; e.g. by maintaining the proper cellular redox state or/and by preventing the activation of the apoptotic cascade. Here, we will focus our attention on how the differences in the activities of the HSPB proteins can influence neurodegenerative and neuromuscular disorders characterized by accumulation of aggregate-prone proteins. Understanding their mechanism of action may allow us to target a specific member in a specific cell type/disease for therapeutic purposes.
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Affiliation(s)
- Serena Carra
- Dipartimento di Scienze Biomediche, Universita' degli Studi di Modena e Reggio Emilia, , via G. Campi 287, Modena 41125, Italy
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