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Lau D, Tang Y, Kenche V, Copie T, Kempe D, Jary E, Graves NJ, Biro M, Masters CL, Dzamko N, Gambin Y, Sierecki E. Single-Molecule Fingerprinting Reveals Different Growth Mechanisms in Seed Amplification Assays for Different Polymorphs of α-Synuclein Fibrils. ACS Chem Neurosci 2024; 15:3270-3285. [PMID: 39197832 PMCID: PMC11413846 DOI: 10.1021/acschemneuro.4c00185] [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: 03/28/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 09/01/2024] Open
Abstract
α-Synuclein (αSyn) aggregates, detected in the biofluids of patients with Parkinson's disease (PD), have the ability to catalyze their own aggregation, leading to an increase in the number and size of aggregates. This self-templated amplification is used by newly developed assays to diagnose Parkinson's disease and turns the presence of αSyn aggregates into a biomarker of the disease. It has become evident that αSyn can form fibrils with slightly different structures, called "strains" or polymorphs, but little is known about their differential reactivity in diagnostic assays. Here, we compared the properties of two well-described αSyn polymorphs. Using single-molecule techniques, we observed that one of the polymorphs had an increased tendency to undergo secondary nucleation and we showed that this could explain the differences in reactivity observed in in vitro seed amplification assay and cellular assays. Simulations and high-resolution microscopy suggest that a 100-fold difference in the apparent rate of growth can be generated by a surprisingly low number of secondary nucleation "points" (1 every 2000 monomers added by elongation). When both strains are present in the same seeded reaction, secondary nucleation displaces proportions dramatically and causes a single strain to dominate the reaction as the major end product.
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Affiliation(s)
- Derrick Lau
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Yuan Tang
- Brain
and Mind Centre and Faculty of Medicine and Health, School of Medical
Sciences, University of Sydney, Camperdown, NSW 2050, Australia
| | - Vijaya Kenche
- Florey
Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Thomas Copie
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Daryan Kempe
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Eve Jary
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Noah J. Graves
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Maté Biro
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Colin L. Masters
- Florey
Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nicolas Dzamko
- Brain
and Mind Centre and Faculty of Medicine and Health, School of Medical
Sciences, University of Sydney, Camperdown, NSW 2050, Australia
| | - Yann Gambin
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Emma Sierecki
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
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Frey L, Ghosh D, Qureshi BM, Rhyner D, Guerrero-Ferreira R, Pokharna A, Kwiatkowski W, Serdiuk T, Picotti P, Riek R, Greenwald J. On the pH-dependence of α-synuclein amyloid polymorphism and the role of secondary nucleation in seed-based amyloid propagation. eLife 2024; 12:RP93562. [PMID: 39196271 DOI: 10.7554/elife.93562] [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] [Indexed: 08/29/2024] Open
Abstract
The aggregation of the protein α-synuclein is closely associated with several neurodegenerative disorders and as such the structures of the amyloid fibril aggregates have high scientific and medical significance. However, there are dozens of unique atomic-resolution structures of these aggregates, and such a highly polymorphic nature of the α-synuclein fibrils hampers efforts in disease-relevant in vitro studies on α-synuclein amyloid aggregation. In order to better understand the factors that affect polymorph selection, we studied the structures of α-synuclein fibrils in vitro as a function of pH and buffer using cryo-EM helical reconstruction. We find that in the physiological range of pH 5.8-7.4, a pH-dependent selection between Type 1, 2, and 3 polymorphs occurs. Our results indicate that even in the presence of seeds, the polymorph selection during aggregation is highly dependent on the buffer conditions, attributed to the non-polymorph-specific nature of secondary nucleation. We also uncovered two new polymorphs that occur at pH 7.0 in phosphate-buffered saline. The first is a monofilament Type 1 fibril that highly resembles the structure of the juvenile-onset synucleinopathy polymorph found in patient-derived material. The second is a new Type 5 polymorph that resembles a polymorph that has been recently reported in a study that used diseased tissues to seed aggregation. Taken together, our results highlight the shallow amyloid energy hypersurface that can be altered by subtle changes in the environment, including the pH which is shown to play a major role in polymorph selection and in many cases appears to be the determining factor in seeded aggregation. The results also suggest the possibility of producing disease-relevant structure in vitro.
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Affiliation(s)
- Lukas Frey
- Institute of Molecular Physical Science, Zürich, Switzerland
| | - Dhiman Ghosh
- Institute of Molecular Physical Science, Zürich, Switzerland
| | - Bilal M Qureshi
- Scientific Center for Optical and Electron Microscopy, Zürich, Switzerland
| | - David Rhyner
- Institute of Molecular Physical Science, Zürich, Switzerland
| | | | - Aditya Pokharna
- Institute of Molecular Physical Science, Zürich, Switzerland
| | | | - Tetiana Serdiuk
- Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Roland Riek
- Institute of Molecular Physical Science, Zürich, Switzerland
| | - Jason Greenwald
- Institute of Molecular Physical Science, Zürich, Switzerland
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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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Makasewicz K, Linse S, Sparr E. Interplay of α-synuclein with Lipid Membranes: Cooperative Adsorption, Membrane Remodeling and Coaggregation. JACS AU 2024; 4:1250-1262. [PMID: 38665673 PMCID: PMC11040681 DOI: 10.1021/jacsau.3c00579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 04/28/2024]
Abstract
α-Synuclein is a small neuronal protein enriched at presynaptic termini. It is hypothesized to play a role in neurotransmitter release and synaptic vesicle cycling, while the formation of α-synuclein amyloid fibrils is associated with several neurodegenerative diseases, most notably Parkinson's Disease. The molecular mechanisms of both the physiological and pathological functions of α-synuclein remain to be fully understood, but in both cases, interactions with membranes play an important role. In this Perspective, we discuss several aspects of α-synuclein interactions with lipid membranes including cooperative adsorption, membrane remodeling and α-synuclein amyloid fibril formation in the presence of lipid membranes. We highlight the coupling between the different phenomena and their interplay in the context of physiological and pathological functions of α-synuclein.
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Affiliation(s)
- Katarzyna Makasewicz
- Division
of Physical Chemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Sara Linse
- Biochemistry
and Structural Biology, Lund University, SE-22100 Lund, Sweden
| | - Emma Sparr
- Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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Lindberg M, Axell E, Sparr E, Linse S. A label-free high-throughput protein solubility assay and its application to Aβ40. Biophys Chem 2024; 307:107165. [PMID: 38309218 DOI: 10.1016/j.bpc.2023.107165] [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: 10/02/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 02/05/2024]
Abstract
A major hallmark of Alzheimer's disease is the accumulation of aggregated amyloid β peptide (Aβ) in the brain. Here we develop a solubility assay for proteins and measure the solubility of Aβ40. In brief, the method utilizes 96-well filter plates to separate monomeric Aβ from aggregated Aβ, and the small species are quantified with the amine reactive dye o-phthalaldehyde (OPA). This procedure ensures that solubility is measured for unlabeled species, and makes the assay high-throughput and inexpensive. We demonstrate that the filter plates successfully separate fibrils from monomer, with negligible monomer adsorption, and that OPA can quantify Aβ peptides in a concentration range from 40 nM to 20 μM. We also show that adding a methionine residue to the N-terminus of Aβ1-40 decreases the solubility by <3-fold. The method will facilitate further solubility studies, and contribute to the understanding of the thermodynamics of amyloid fibril formation.
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Affiliation(s)
- Max Lindberg
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Emil Axell
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Emma Sparr
- Division of Physical Chemistry, Department of Chemistry, Lund University, Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Lund University, Lund, Sweden.
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