1
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Dewison KM, Rowlinson B, Machin JM, Crossley JA, Thacker D, Wilkinson M, Ulamec SM, Khan GN, Ranson NA, van Oosten-Hawle P, Brockwell DJ, Radford SE. Residues 2 to 7 of α-synuclein regulate amyloid formation via lipid-dependent and lipid-independent pathways. Proc Natl Acad Sci U S A 2024; 121:e2315006121. [PMID: 39133842 PMCID: PMC11348338 DOI: 10.1073/pnas.2315006121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/09/2024] [Indexed: 08/29/2024] Open
Abstract
Amyloid formation by α-synuclein (αSyn) occurs in Parkinson's disease, multiple system atrophy, and dementia with Lewy bodies. Deciphering the residues that regulate αSyn amyloid fibril formation will not only provide mechanistic insight but may also reveal targets to prevent and treat disease. Previous investigations have identified several regions of αSyn to be important in the regulation of amyloid formation, including the non-amyloid-β component (NAC), P1 region (residues 36 to 42), and residues in the C-terminal domain. Recent studies have also indicated the importance of the N-terminal region of αSyn for both its physiological and pathological roles. Here, the role of residues 2 to 7 in the N-terminal region of αSyn is investigated in terms of their ability to regulate amyloid fibril formation in vitro and in vivo. Deletion of these residues (αSynΔN7) slows the rate of fibril formation in vitro and reduces the capacity of the protein to be recruited by wild-type (αSynWT) fibril seeds, despite cryo-EM showing a fibril structure consistent with those of full-length αSyn. Strikingly, fibril formation of αSynΔN7 is not induced by liposomes, despite the protein binding to liposomes with similar affinity to αSynWT. A Caenorhabditis elegans model also showed that αSynΔN7::YFP forms few puncta and lacks motility and lifespan defects typified by expression of αSynWT::YFP. Together, the results demonstrate the involvement of residues 2 to 7 of αSyn in amyloid formation, revealing a target for the design of amyloid inhibitors that may leave the functional role of the protein in membrane binding unperturbed.
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Affiliation(s)
- Katherine M. Dewison
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Benjamin Rowlinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Jonathan M. Machin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Joel A. Crossley
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Dev Thacker
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Sabine M. Ulamec
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - G. Nasir Khan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | | | - David J. Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
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2
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Reis PM, Holec SAM, Ezeiruaku C, Frost MP, Brown CK, Liu SL, Olson SH, Woerman AL. Structurally targeted mutagenesis identifies key residues supporting α -synuclein misfolding in multiple system atrophy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.04.602104. [PMID: 39026799 PMCID: PMC11257492 DOI: 10.1101/2024.07.04.602104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Multiple system atrophy (MSA) and Parkinson's disease (PD) are caused by misfolded α -synuclein spreading throughout the central nervous system. While familial PD is linked to several point mutations in α -synuclein, there are no known mutations associated with MSA. Our previous work investigating differences in α -synuclein misfolding between the two disorders showed that the familial PD mutation E46K inhibits replication of MSA prions both in vitro and in vivo, providing key evidence to support the hypothesis that α -synuclein adopts unique strains in patients. Here, to further interrogate α -synuclein misfolding, we engineered a panel of cell lines harboring both PD-linked and novel mutations designed to identify key residues that facilitate α -synuclein misfolding in MSA. These data were paired with in silico analyses using Maestro software to predict the effect of each mutation on the ability of α -synuclein to misfold into one of the reported MSA cryo-electron microscopy conformations. In many cases, our modeling accurately identified mutations that facilitated or inhibited MSA replication. However, Maestro was occasionally unable to predict the effect of a mutation on MSA propagation in vitro, demonstrating the challenge of using computational tools to investigate intrinsically disordered proteins. Finally, we used our cellular models to determine the mechanism underlying the E46K-driven inhibition of MSA replication, finding that the E46/K80 salt bridge is necessary to support α -synuclein misfolding. Overall, our studies use a structure-based approach to investigate α -synuclein misfolding, resulting in the creation of a powerful panel of cell lines that can be used to interrogate MSA strain biology.
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Affiliation(s)
- Patricia M. Reis
- Department of Biology and Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, USA
- Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Sara A. M. Holec
- Department of Biology and Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, USA
- Department of Microbiology, Immunology, and Pathology, Prion Research Center, Colorado State University, Fort Collins, CO, USA
| | - Chimere Ezeiruaku
- Department of Biology and Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Matthew P. Frost
- Department of Biology and Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Christine K. Brown
- Department of Biology and Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Samantha L. Liu
- Department of Biology and Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Steven H. Olson
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Amanda L. Woerman
- Department of Biology and Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, USA
- Department of Microbiology, Immunology, and Pathology, Prion Research Center, Colorado State University, Fort Collins, CO, USA
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3
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Kochen NN, Seaney D, Vasandani V, Murray M, Braun AR, Sachs JN. Post-translational modification sites are present in hydrophilic cavities of alpha-synuclein, tau, FUS, and TDP-43 fibrils: A molecular dynamics study. Proteins 2024; 92:854-864. [PMID: 38458997 PMCID: PMC11147710 DOI: 10.1002/prot.26679] [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: 10/20/2023] [Revised: 02/09/2024] [Accepted: 02/28/2024] [Indexed: 03/10/2024]
Abstract
Hydration plays a crucial role in the refolding of intrinsically disordered proteins into amyloid fibrils; however, the specific interactions between water and protein that may contribute to this process are still unknown. In our previous studies of alpha-synuclein (aSyn), we have shown that waters confined in fibril cavities are stabilizing features of this pathological fold; and that amino acids that hydrogen bond with these confined waters modulate primary and seeded aggregation. Here, we extend our aSyn molecular dynamics (MD) simulations with three new polymorphs and correlate MD trajectory information with known post-translational modifications (PTMs) and experimental data. We show that cavity residues are more evolutionarily conserved than non-cavity residues and are enriched with PTM sites. As expected, the confinement within hydrophilic cavities results in more stably hydrated amino acids. Interestingly, cavity PTM sites display the longest protein-water hydrogen bond lifetimes, three-fold greater than non-PTM cavity sites. Utilizing the deep mutational screen dataset by Newberry et al. and the Thioflavin T aggregation review by Pancoe et al. parsed using a fibril cavity/non-cavity definition, we show that hydrophobic changes to amino acids in cavities have a larger effect on fitness and aggregation rate than residues outside cavities, supporting our hypothesis that these sites are involved in the inhibition of aSyn toxic fibrillization. Finally, we expand our study to include analysis of fibril structures of tau, FUS, TDP-43, prion, and hnRNPA1; all of which contained hydrated cavities, with tau, FUS, and TDP-43 recapitulating our PTM results in aSyn fibril cavities.
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Affiliation(s)
- Noah Nathan Kochen
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Darren Seaney
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Vivek Vasandani
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Marguerite Murray
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Anthony R Braun
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jonathan N Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
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4
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Burré J, Edwards RH, Halliday G, Lang AE, Lashuel HA, Melki R, Murayama S, Outeiro TF, Papa SM, Stefanis L, Woerman AL, Surmeier DJ, Kalia LV, Takahashi R. Research Priorities on the Role of α-Synuclein in Parkinson's Disease Pathogenesis. Mov Disord 2024. [PMID: 38946200 DOI: 10.1002/mds.29897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/16/2024] [Accepted: 06/03/2024] [Indexed: 07/02/2024] Open
Abstract
Various forms of Parkinson's disease, including its common sporadic form, are characterized by prominent α-synuclein (αSyn) aggregation in affected brain regions. However, the role of αSyn in the pathogenesis and evolution of the disease remains unclear, despite vast research efforts of more than a quarter century. A better understanding of the role of αSyn, either primary or secondary, is critical for developing disease-modifying therapies. Previous attempts to hone this research have been challenged by experimental limitations, but recent technological advances may facilitate progress. The Scientific Issues Committee of the International Parkinson and Movement Disorder Society (MDS) charged a panel of experts in the field to discuss current scientific priorities and identify research strategies with potential for a breakthrough. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Jacqueline Burré
- Appel Institute for Alzheimer's Disease Research and Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, USA
| | - Robert H Edwards
- Department of Physiology and Neurology, University of California, San Francisco School of Medicine, San Francisco, California, USA
| | - Glenda Halliday
- Brain and Mind Centre, School of Medical Sciences, The University of Sydney, Camperdown, New South Wales, Australia
| | - Anthony E Lang
- Edmond J. Safra Program in Parkinson's Disease, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Hilal A Lashuel
- Laboratory of Chemical Biology of Neurodegeneration, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ronald Melki
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-Aux-Roses, France
| | - Shigeo Murayama
- Department of Neuropathology, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
- The Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Osaka, Japan
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, University Medical Center, Göttingen, Germany
- Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Stella M Papa
- Department of Neurology, School of Medicine, and Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Leonidas Stefanis
- First Department of Neurology, Eginitio Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Amanda L Woerman
- Department of Biology, Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Microbiology, Immunology, and Pathology, Prion Research Center, Colorado State University, Fort Collins, Colorado, USA
| | - Dalton James Surmeier
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
| | - Lorraine V Kalia
- Edmond J. Safra Program in Parkinson's Disease, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ryosuke Takahashi
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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5
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Lázaro DF, Lee VMY. Navigating through the complexities of synucleinopathies: Insights into pathogenesis, heterogeneity, and future perspectives. Neuron 2024:S0896-6273(24)00364-7. [PMID: 38861985 DOI: 10.1016/j.neuron.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/22/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024]
Abstract
The aggregation of alpha-synuclein (aSyn) represents a neuropathological hallmark observed in a group of neurodegenerative disorders collectively known as synucleinopathies. Despite their shared characteristics, these disorders manifest diverse clinical and pathological phenotypes. The mechanism underlying this heterogeneity is thought to be due to the diversity in the aSyn strains present across the diseases. In this perspective, we will explore recent findings on aSyn strains and discuss recent discoveries about Lewy bodies' composition. We further discuss the current hypothesis for aSyn spreading and emphasize the emerging biomarker field demonstrating promising results. A comprehension of these mechanisms holds substantial promise for future clinical applications. This understanding can pave the way for the development of personalized medicine strategies, specifically targeting the unique underlying causes of each synucleinopathy. Such advancements can revolutionize therapeutic approaches and significantly contribute to more effective interventions in the intricate landscape of neurodegenerative disorders.
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Affiliation(s)
- Diana F Lázaro
- Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Medicine, University of Pennsylvania, Perelman School of Medicine at University of Pennsylvania, 3600 Spruce Street, 3 Maloney Building, Philadelphia, PA 19104, USA.
| | - Virginia M-Y Lee
- Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Medicine, University of Pennsylvania, Perelman School of Medicine at University of Pennsylvania, 3600 Spruce Street, 3 Maloney Building, Philadelphia, PA 19104, USA.
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6
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Avenali M, Cerri S, Palmieri I, Ongari G, Stiuso R, Buongarzone G, Tassorelli C, Biagini T, Valente M, Cereda C, Mazza T, Gana S, Pacchetti C, Valente EM. Functional Study of SNCA p.V15A Variant: Further Linking α-Synuclein and Glucocerebrosidase. Mov Disord 2024; 39:1060-1065. [PMID: 38436488 DOI: 10.1002/mds.29736] [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: 06/20/2023] [Revised: 12/16/2023] [Accepted: 01/22/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND SNCA p.V15A was reported in five families. In vitro models showed increased aggregation and seeding activity, mitochondrial damage, and apoptosis. Mutant flies had reduced flying ability and survival. OBJECTIVES To clinically and functionally evaluate SNCA p.V15A in a large Italian family with Parkinson's disease (PD). METHODS Genetic diagnosis was reached through next-generation sequencing. Pathogenicity was assessed by molecular dynamics simulation and biochemical studies on peripheral blood mononuclear cells (PBMCs). RESULTS Five siblings carried SNCA p.V15A; three developed bradykinetic-rigid PD in their 50s with rapid motor progression and variable cognitive impairment. A fourth sibling had isolated mood disturbance, whereas the fifth was still unaffected at age 47. The mutant protein showed decreased stability and an unstable folded structure. Proband's PBMCs showed elevated total and phosphorylated α-synuclein (α-syn) levels and significantly reduced glucocerebrosidase activity. CONCLUSION This study demonstrates accumulation of α-synV15A in PBMCs and strengthens the link between α-syn pathophysiology and glucocerebrosidase dysfunction. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Micol Avenali
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
- Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Silvia Cerri
- Cellular and Molecular Neurobiology Section, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Gerardo Ongari
- Cellular and Molecular Neurobiology Section, IRCCS Mondino Foundation, Pavia, Italy
| | - Rita Stiuso
- Cellular and Molecular Neurobiology Section, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Cristina Tassorelli
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
- Neurorehabilitation Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Tommaso Biagini
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Marialuisa Valente
- Clinical Pathology Unit, Medical Genetics Section, SS. Annunziata Hospital, ASL Taranto, Taranto, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Simone Gana
- Neurogenetics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Claudio Pacchetti
- Parkinson's Disease and Movement Disorders Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Enza Maria Valente
- Neurogenetics Unit, IRCCS Mondino Foundation, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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7
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Kishore A, Sturm M, Soman Pillai K, Hakkaart C, Kalikavil Puthanveedu D, Urulangodi M, Krishnan S, Ashok Kumar Sreelatha A, Rajan R, Pal PK, Yadav R, Sarma G, Casadei N, Gasser T, Bauer P, Riess O, Sharma M. Resequencing the complete SNCA locus in Indian patients with Parkinson's disease. NPJ Parkinsons Dis 2024; 10:85. [PMID: 38622158 PMCID: PMC11018851 DOI: 10.1038/s41531-024-00676-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 02/29/2024] [Indexed: 04/17/2024] Open
Abstract
The genetic loci implicated in familial Parkinson's disease (PD) have limited generalizability to the Indian PD population. We tested mutations and the frequency of known mutations in the SNCA gene in a PD cohort from India. We selected 298 PD cases and 301 age-matched controls for targeted resequencing (before QC), along with 363 PD genomes of Indian ancestry and 1029 publicly available whole genomes from India as healthy controls (IndiGenomes), to determine the frequency of monogenic SNCA mutations. The raw sequence reads were analyzed using an in-house analysis pipeline, allowing the detection of small variants and structural variants using Manta. The in-depth analysis of the SNCA locus did not identify missense or structural variants, including previously identified SNCA mutations, in the Indian population. The familial forms of SNCA gene variants do not play a major role in the Indian PD population and this warrants further research in the under-represented population.
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Affiliation(s)
- Asha Kishore
- Comprehensive Care Centre for Movement Disorders, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kochi, Kerala, India
- Parkinson and Movement Disorder Centre, Centre for Excellence in Neurosciences, Aster Medcity, Kochi, Kerala, India
| | - Marc Sturm
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Kanchana Soman Pillai
- Parkinson and Movement Disorder Centre, Centre for Excellence in Neurosciences, Aster Medcity, Kochi, Kerala, India
| | - Christopher Hakkaart
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Divya Kalikavil Puthanveedu
- Comprehensive Care Centre for Movement Disorders, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kochi, Kerala, India
| | - Madhusoodanan Urulangodi
- Comprehensive Care Centre for Movement Disorders, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kochi, Kerala, India
| | - Syam Krishnan
- Comprehensive Care Centre for Movement Disorders, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kochi, Kerala, India
| | - Ashwin Ashok Kumar Sreelatha
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tübingen, Tübingen, Germany
| | - Roopa Rajan
- Department of Neurology, All India Institute for Medical Sciences, New Delhi, India
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Ravi Yadav
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Gangadhara Sarma
- Comprehensive Care Centre for Movement Disorders, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Kochi, Kerala, India
| | - Nicolas Casadei
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Thomas Gasser
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Peter Bauer
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centogene GmbH, Rostock, Germany
- University Medicine Rostock, Internal Medicine III, Hematology, Rostock, Germany
| | - Olaf Riess
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Manu Sharma
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tübingen, Tübingen, Germany.
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Tarutani A, Hasegawa M. Ultrastructures of α-Synuclein Filaments in Synucleinopathy Brains and Experimental Models. J Mov Disord 2024; 17:15-29. [PMID: 37990381 PMCID: PMC10846975 DOI: 10.14802/jmd.23213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/11/2023] [Accepted: 11/22/2023] [Indexed: 11/23/2023] Open
Abstract
Intracellular α-synuclein (α-syn) inclusions are a neuropathological hallmark of Lewy body disease (LBD) and multiple system atrophy (MSA), both of which are termed synucleinopathies. LBD is defined by Lewy bodies and Lewy neurites in neurons, while MSA displays glial cytoplasmic inclusions in oligodendrocytes. Pathological α-syn adopts an ordered filamentous structure with a 5-10 nm filament diameter, and this conformational change has been suggested to be involved in the disease onset and progression. Synucleinopathies also exhibit characteristic ultrastructural and biochemical properties of α-syn filaments, and α-syn strains with distinct conformations have been identified. Numerous experimental studies have supported the idea that pathological α-syn self-amplifies and spreads throughout the brain, during which processes the conformation of α-syn filaments may drive the disease specificity. In this review, we summarize the ultrastructural features and heterogeneity of α-syn filaments in the brains of patients with synucleinopathy and in experimental models of seeded α-syn aggregation.
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Affiliation(s)
- Airi Tarutani
- Department of Brain and Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Masato Hasegawa
- Department of Brain and Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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9
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Livesey BJ, Marsh JA. Updated benchmarking of variant effect predictors using deep mutational scanning. Mol Syst Biol 2023; 19:e11474. [PMID: 37310135 PMCID: PMC10407742 DOI: 10.15252/msb.202211474] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/14/2023] Open
Abstract
The assessment of variant effect predictor (VEP) performance is fraught with biases introduced by benchmarking against clinical observations. In this study, building on our previous work, we use independently generated measurements of protein function from deep mutational scanning (DMS) experiments for 26 human proteins to benchmark 55 different VEPs, while introducing minimal data circularity. Many top-performing VEPs are unsupervised methods including EVE, DeepSequence and ESM-1v, a protein language model that ranked first overall. However, the strong performance of recent supervised VEPs, in particular VARITY, shows that developers are taking data circularity and bias issues seriously. We also assess the performance of DMS and unsupervised VEPs for discriminating between known pathogenic and putatively benign missense variants. Our findings are mixed, demonstrating that some DMS datasets perform exceptionally at variant classification, while others are poor. Notably, we observe a striking correlation between VEP agreement with DMS data and performance in identifying clinically relevant variants, strongly supporting the validity of our rankings and the utility of DMS for independent benchmarking.
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Affiliation(s)
- Benjamin J Livesey
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
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10
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Sharma M, Burré J. α-Synuclein in synaptic function and dysfunction. Trends Neurosci 2023; 46:153-166. [PMID: 36567199 PMCID: PMC9877183 DOI: 10.1016/j.tins.2022.11.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/07/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
α-Synuclein is a neuronal protein that is enriched in presynaptic terminals. Under physiological conditions, it binds to synaptic vesicle membranes and functions in neurotransmitter release, although the molecular details remain unclear, and it is controversial whether α-synuclein inhibits or facilitates neurotransmitter release. Pathologically, in synucleinopathies including Parkinson's disease (PD), α-synuclein forms aggregates that recruit monomeric α-synuclein and spread throughout the brain, which triggers neuronal dysfunction at molecular, cellular, and organ levels. Here, we present an overview of the effects of α-synuclein on SNARE-complex assembly, neurotransmitter release, and synaptic vesicle pool homeostasis, and discuss how the observed divergent effects of α-synuclein on neurotransmitter release can be reconciled. We also discuss how gain-of-function versus loss-of-function of α-synuclein may contribute to pathogenesis in synucleinopathies.
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Affiliation(s)
- Manu Sharma
- Appel Alzheimer's Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
| | - Jacqueline Burré
- Appel Alzheimer's Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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Liquid-liquid Phase Separation of α-Synuclein: A New Mechanistic Insight for α-Synuclein Aggregation Associated with Parkinson's Disease Pathogenesis. J Mol Biol 2023; 435:167713. [PMID: 35787838 DOI: 10.1016/j.jmb.2022.167713] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023]
Abstract
Aberrant aggregation of the misfolded presynaptic protein, α-Synuclein (α-Syn) into Lewy body (LB) and Lewy neuritis (LN) is a major pathological hallmark of Parkinson's disease (PD) and other synucleinopathies. Numerous studies have suggested that prefibrillar and fibrillar species of the misfolded α-Syn aggregates are responsible for cell death in PD pathogenesis. However, the precise molecular events during α-Syn aggregation, especially in the early stages, remain elusive. Emerging evidence has demonstrated that liquid-liquid phase separation (LLPS) of α-Syn occurs in the nucleation step of α-Syn aggregation, which offers an alternate non-canonical aggregation pathway in the crowded microenvironment. The liquid-like α-Syn droplets gradually undergo an irreversible liquid-to-solid phase transition into amyloid-like hydrogel entrapping oligomers and fibrils. This new mechanism of α-Syn LLPS and gel formation might represent the molecular basis of cellular toxicity associated with PD. This review aims to demonstrate the recent development of α-Syn LLPS, the underlying mechanism along with the microscopic events of aberrant phase transition. This review further discusses how several intrinsic and extrinsic factors regulate the thermodynamics and kinetics of α-Syn LLPS and co-LLPS with other proteins, which might explain the pathophysiology of α-Syn in various neurodegenerative diseases.
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12
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Gao V, Briano JA, Komer LE, Burré J. Functional and Pathological Effects of α-Synuclein on Synaptic SNARE Complexes. J Mol Biol 2023; 435:167714. [PMID: 35787839 PMCID: PMC10472340 DOI: 10.1016/j.jmb.2022.167714] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 02/07/2023]
Abstract
α-Synuclein is an abundant protein at the neuronal synapse that has been implicated in Parkinson's disease for over 25 years and characterizes the hallmark pathology of a group of neurodegenerative diseases now known as the synucleinopathies. Physiologically, α-synuclein exists in an equilibrium between a synaptic vesicle membrane-bound α-helical multimer and a cytosolic largely unstructured monomer. Through its membrane-bound state, α-synuclein functions in neurotransmitter release by modulating several steps in the synaptic vesicle cycle, including synaptic vesicle clustering and docking, SNARE complex assembly, and homeostasis of synaptic vesicle pools. These functions have been ascribed to α-synuclein's interactions with the synaptic vesicle SNARE protein VAMP2/synaptobrevin-2, the synaptic vesicle-attached synapsins, and the synaptic vesicle membrane itself. How α-synuclein affects these processes, and whether disease is due to loss-of-function or gain-of-toxic-function of α-synuclein remains unclear. In this review, we provide an in-depth summary of the existing literature, discuss possible reasons for the discrepancies in the field, and propose a working model that reconciles the findings in the literature.
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Affiliation(s)
- Virginia Gao
- Appel Alzheimer's Disease Research Institute & Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA; Department of Neurology, New York Presbyterian/Weill Cornell Medicine, New York, NY, USA.
| | - Juan A Briano
- Appel Alzheimer's Disease Research Institute & Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Lauren E Komer
- Appel Alzheimer's Disease Research Institute & Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA. https://www.twitter.com/lauren_komer
| | - Jacqueline Burré
- Appel Alzheimer's Disease Research Institute & Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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Holec SAM, Lee J, Oehler A, Batia L, Wiggins-Gamble A, Lau J, Ooi FK, Merz GE, Wang M, Mordes DA, Olson SH, Woerman AL. The E46K mutation modulates α-synuclein prion replication in transgenic mice. PLoS Pathog 2022; 18:e1010956. [PMID: 36454879 PMCID: PMC9714912 DOI: 10.1371/journal.ppat.1010956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/28/2022] [Indexed: 12/03/2022] Open
Abstract
In multiple system atrophy (MSA), the α-synuclein protein misfolds into a self-templating prion conformation that spreads throughout the brain, leading to progressive neurodegeneration. While the E46K mutation in α-synuclein causes familial Parkinson's disease (PD), we previously discovered that this mutation blocks in vitro propagation of MSA prions. Recent studies by others indicate that α-synuclein adopts a misfolded conformation in MSA in which a Greek key motif is stabilized by an intramolecular salt bridge between residues E46 and K80. Hypothesizing that the E46K mutation impedes salt bridge formation and, therefore, exerts a selective pressure that can modulate α-synuclein strain propagation, we asked whether three distinct α-synuclein prion strains could propagate in TgM47+/- mice, which express human α-synuclein with the E46K mutation. Following intracranial injection of these strains, TgM47+/- mice were resistant to MSA prion transmission, whereas recombinant E46K preformed fibrils (PFFs) transmitted neurological disease to mice and induced the formation of phosphorylated α-synuclein neuropathology. In contrast, heterotypic seeding following wild-type (WT) PFF-inoculation resulted in preclinical α-synuclein prion propagation. Moreover, when we inoculated TgM20+/- mice, which express WT human α-synuclein, with E46K PFFs, we observed delayed transmission kinetics with an incomplete attack rate. These findings suggest that the E46K mutation constrains the number of α-synuclein prion conformations that can propagate in TgM47+/- mice, expanding our understanding of the selective pressures that impact α-synuclein prion replication.
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Affiliation(s)
- Sara A. M. Holec
- Department of Biology and Institute for Applied Life Sciences, University of Massachusetts Amherst; Amherst, Massachusetts, United States of America
| | - Jisoo Lee
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco; San Francisco, California, United States of America
| | - Abby Oehler
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco; San Francisco, California, United States of America
| | - Lyn Batia
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco; San Francisco, California, United States of America
| | - Aryanna Wiggins-Gamble
- Department of Biology and Institute for Applied Life Sciences, University of Massachusetts Amherst; Amherst, Massachusetts, United States of America
| | - Jeffrey Lau
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco; San Francisco, California, United States of America
| | - Felicia K. Ooi
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco; San Francisco, California, United States of America
| | - Gregory E. Merz
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco; San Francisco, California, United States of America
- Department of Neurology, University of California, San Francisco; San Francisco, California, United States of America
| | - Man Wang
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco; San Francisco, California, United States of America
| | - Daniel A. Mordes
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco; San Francisco, California, United States of America
- Department of Pathology, University of California, San Francisco; San Francisco, California, United States of America
| | - Steven H. Olson
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco; San Francisco, California, United States of America
- Department of Neurology, University of California, San Francisco; San Francisco, California, United States of America
| | - Amanda L. Woerman
- Department of Biology and Institute for Applied Life Sciences, University of Massachusetts Amherst; Amherst, Massachusetts, United States of America
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco; San Francisco, California, United States of America
- Department of Neurology, University of California, San Francisco; San Francisco, California, United States of America
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14
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Daida K, Shimonaka S, Shiba‐Fukushima K, Ogata J, Yoshino H, Okuzumi A, Hatano T, Motoi Y, Hirunagi T, Katsuno M, Shindou H, Funayama M, Nishioka K, Hattori N, Imai Y. α-Synuclein V15A Variant in Familial Parkinson's Disease Exhibits a Weaker Lipid-Binding Property. Mov Disord 2022; 37:2075-2085. [PMID: 35894540 PMCID: PMC9796804 DOI: 10.1002/mds.29162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/03/2022] [Accepted: 07/05/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The α-Synuclein (α-Syn) V15A variant has been found in two Caucasian families with Parkinson's disease (PD). However, the significance of this missense variant remained unclear. OBJECTIVE We sought to elucidate whether V15A could increase aggregation or change phospholipid affinity. METHODS A sequencing analysis for the SNCA encoding α-Syn from 875 patients with PD and 324 control subjects was performed. Comparing with known pathogenic missense variants of α-Syn, A30P, and A53T, we analyzed the effects of V15A on binding to phospholipid membrane, self-aggregation, and seed-dependent aggregation in cultured cells. RESULTS Genetic screening identified SNCA c.44 T>C (p.V15A) from two Japanese PD families. The missense variant V15A was extremely rare in several public databases and predicted as pathogenic using in silico tools. The amplification activity of α-Syn V15A fibrils was stronger than that of wild-type α-Syn fibrils. CONCLUSIONS The discovery of the V15A variant from Japanese families reinforces the possibility that the V15A variant may be a causative variant for developing PD. V15A had a reduced affinity for phospholipids and increased propagation activity compared with wild-type. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Kensuke Daida
- Department of NeurologyJuntendo University School of MedicineTokyoJapan
| | - Shotaro Shimonaka
- Department of Diagnosis, Prevention, and Treatment of DementiaJuntendo University Graduate School of MedicineTokyoJapan,Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Kahori Shiba‐Fukushima
- Department of Drug Development for Parkinson's DiseaseJuntendo University Graduate School of MedicineTokyoJapan
| | - Jun Ogata
- Department of Research for Parkinson's DiseaseJuntendo University Graduate School of MedicineTokyoJapan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Ayami Okuzumi
- Department of NeurologyJuntendo University School of MedicineTokyoJapan
| | - Taku Hatano
- Department of NeurologyJuntendo University School of MedicineTokyoJapan
| | - Yumiko Motoi
- Department of NeurologyJuntendo University School of MedicineTokyoJapan,Department of Diagnosis, Prevention, and Treatment of DementiaJuntendo University Graduate School of MedicineTokyoJapan
| | - Tomoki Hirunagi
- Department of NeurologyNagoya University Graduate School of MedicineNagoyaJapan
| | - Masahisa Katsuno
- Department of NeurologyNagoya University Graduate School of MedicineNagoyaJapan
| | - Hideo Shindou
- Department of Lipid SignalingNational Center for Global Health and MedicineTokyoJapan,Department of Lipid Medical ScienceGraduate School of Medicine, University of TokyoTokyoJapan
| | - Manabu Funayama
- Department of NeurologyJuntendo University School of MedicineTokyoJapan,Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Kenya Nishioka
- Department of NeurologyJuntendo University School of MedicineTokyoJapan
| | - Nobutaka Hattori
- Department of NeurologyJuntendo University School of MedicineTokyoJapan,Department of Diagnosis, Prevention, and Treatment of DementiaJuntendo University Graduate School of MedicineTokyoJapan,Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan,Department of Drug Development for Parkinson's DiseaseJuntendo University Graduate School of MedicineTokyoJapan,Department of Research for Parkinson's DiseaseJuntendo University Graduate School of MedicineTokyoJapan
| | - Yuzuru Imai
- Department of NeurologyJuntendo University School of MedicineTokyoJapan,Department of Research for Parkinson's DiseaseJuntendo University Graduate School of MedicineTokyoJapan
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Single residue modulators of amyloid formation in the N-terminal P1-region of α-synuclein. Nat Commun 2022; 13:4986. [PMID: 36008493 PMCID: PMC9411612 DOI: 10.1038/s41467-022-32687-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 08/10/2022] [Indexed: 11/09/2022] Open
Abstract
Alpha-synuclein (αSyn) is a protein involved in neurodegenerative disorders including Parkinson’s disease. Amyloid formation of αSyn can be modulated by the ‘P1 region’ (residues 36-42). Here, mutational studies of P1 reveal that Y39A and S42A extend the lag-phase of αSyn amyloid formation in vitro and rescue amyloid-associated cytotoxicity in C. elegans. Additionally, L38I αSyn forms amyloid fibrils more rapidly than WT, L38A has no effect, but L38M does not form amyloid fibrils in vitro and protects from proteotoxicity. Swapping the sequence of the two residues that differ in the P1 region of the paralogue γSyn to those of αSyn did not enhance fibril formation for γSyn. Peptide binding experiments using NMR showed that P1 synergises with residues in the NAC and C-terminal regions to initiate aggregation. The remarkable specificity of the interactions that control αSyn amyloid formation, identifies this region as a potential target for therapeutics, despite their weak and transient nature. The authors of this work characterize the effect of amino acid substitution on α-synuclein (α-Syn) aggregation. Residues 38 and 42 (in addition to 39) within the P1 region of α-Syn affect amyloid formation. The effect of substitution at position 38 is dependent on the amino-acid introduced, suggesting that specific interactions control α -Syn aggregation.
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Holec SAM, Liu SL, Woerman AL. Consequences of variability in α-synuclein fibril structure on strain biology. Acta Neuropathol 2022; 143:311-330. [PMID: 35122113 DOI: 10.1007/s00401-022-02403-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/15/2022]
Abstract
Synucleinopathies are a group of clinically and neuropathologically distinct protein misfolding diseases caused by unique α-synuclein conformations, or strains. While multiple atomic resolution cryo-electron microscopy structures of α-synuclein fibrils are now deposited in Protein Data Bank, significant gaps in the biological consequences arising from each conformation have yet to be unraveled. Mutations in the α-synuclein gene (SNCA), cofactors, and the solvation environment contribute to the formation and maintenance of each disease-causing strain. This review highlights the impact of each of these factors on α-synuclein misfolding and discusses the implications of the resulting structural variability on therapeutic development.
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Affiliation(s)
- Sara A M Holec
- Department of Biology, Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Samantha L Liu
- Department of Biology, Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Program, Dartmouth College, Hanover, NH, USA
| | - Amanda L Woerman
- Department of Biology, Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, USA.
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