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Galvagnion C, Barclay A, Makasewicz K, Marlet FR, Moulin M, Devos JM, Linse S, Martel A, Porcar L, Sparr E, Pedersen MC, Roosen-Runge F, Arleth L, Buell AK. Structural characterisation of α-synuclein-membrane interactions and the resulting aggregation using small angle scattering. Phys Chem Chem Phys 2024; 26:10998-11013. [PMID: 38526443 DOI: 10.1039/d3cp05928f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
The presence of amyloid fibrils is a hallmark of several neurodegenerative diseases. Some amyloidogenic proteins, such as α-synuclein and amyloid β, interact with lipids, and this interaction can strongly favour the formation of amyloid fibrils. In particular the primary nucleation step, i.e. the de novo formation of amyloid fibrils, has been shown to be accelerated by lipids. However, the exact mechanism of this acceleration is still mostly unclear. Here we use a range of scattering methods, such as dynamic light scattering (DLS) and small angle X-ray and neutron scattering (SAXS and SANS) to obtain structural information on the binding of α-synuclein to model membranes formed from negatively charged lipids and their co-assembly into amyloid fibrils. We find that the model membranes take an active role in the reaction. The binding of α synuclein to the model membranes immediately induces a major structural change in the lipid assembly, which leads to a break-up into small and mostly disc- or rod-like lipid-protein particles. This transition can be reversed by temperature changes or proteolytic protein removal. Incubation of the small lipid-α-synuclein particles for several hours, however, leads to amyloid fibril formation, whereby the lipids are incorporated into the amyloid fibrils.
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Affiliation(s)
- Céline Galvagnion
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Abigail Barclay
- Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Katarzyna Makasewicz
- Division of Physical Chemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| | | | - Martine Moulin
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Juliette M Devos
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, SE22100 Lund, Sweden
| | - Anne Martel
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Lionel Porcar
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Emma Sparr
- Division of Physical Chemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| | | | - Felix Roosen-Runge
- Division of Physical Chemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
- Department of Biomedical Sciences and Biofilms Research Center for Biointerfaces, Malmö University, Malmö, Sweden
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
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2
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Ray S, Buell AK. Emerging experimental methods to study the thermodynamics of biomolecular condensate formation. J Chem Phys 2024; 160:091001. [PMID: 38445729 DOI: 10.1063/5.0190160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
The formation of biomolecular condensates in vivo is increasingly recognized to underlie a multitude of crucial cellular functions. Furthermore, the evolution of highly dynamic protein condensates into progressively less reversible assemblies is thought to be involved in a variety of disorders, from cancer over neurodegeneration to rare genetic disorders. There is an increasing need for efficient experimental methods to characterize the thermodynamics of condensate formation and that can be used in screening campaigns to identify and rationally design condensate modifying compounds. Theoretical advances in the field are also identifying the key parameters that need to be measured in order to obtain a comprehensive understanding of the underlying interactions and driving forces. Here, we review recent progress in the development of efficient and quantitative experimental methods to study the driving forces behind and the temporal evolution of biomolecular condensates.
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Affiliation(s)
- Soumik Ray
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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3
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Farzadfard A, Kunka A, Mason TO, Larsen JA, Norrild RK, Dominguez ET, Ray S, Buell AK. Thermodynamic characterization of amyloid polymorphism by microfluidic transient incomplete separation. Chem Sci 2024; 15:2528-2544. [PMID: 38362440 PMCID: PMC10866369 DOI: 10.1039/d3sc05371g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024] Open
Abstract
Amyloid fibrils of proteins such as α-synuclein are a hallmark of neurodegenerative diseases and much research has focused on their kinetics and mechanisms of formation. The question as to the thermodynamic stability of such structures has received much less attention. Here, we newly utilize the principle of transient incomplete separation of species in laminar flow in combination with chemical depolymerization for the quantification of amyloid fibril stability. The relative concentrations of fibrils and monomer at equilibrium are determined through an in situ separation of these species based on their different diffusivity inside a microfluidic capillary. The method is highly sample economical, using much less than a microliter of sample per data point and its only requirement is the presence of aromatic residues (W, Y) because of its label-free nature, which makes it widely applicable. Using this method, we investigate the differences in thermodynamic stability between different fibril polymorphs of α-synuclein and quantify these differences for the first time. Importantly, we show that fibril formation can be under kinetic or thermodynamic control and that a change in solution conditions can both stabilise and destabilise amyloid fibrils. Taken together, our results establish the thermodynamic stability as a well-defined and key parameter that can contribute towards a better understanding of the physiological roles of amyloid fibril polymorphism.
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Affiliation(s)
- Azad Farzadfard
- Protein Biophysics Group, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 227, Kgs. Lyngby 2800 Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Gustav Wieds Vej 14 8000 Aarhus C Denmark
| | - Antonin Kunka
- Protein Biophysics Group, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 227, Kgs. Lyngby 2800 Denmark
| | - Thomas Oliver Mason
- Protein Biophysics Group, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 227, Kgs. Lyngby 2800 Denmark
| | - Jacob Aunstrup Larsen
- Protein Biophysics Group, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 227, Kgs. Lyngby 2800 Denmark
| | - Rasmus Krogh Norrild
- Protein Biophysics Group, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 227, Kgs. Lyngby 2800 Denmark
| | - Elisa Torrescasana Dominguez
- Protein Biophysics Group, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 227, Kgs. Lyngby 2800 Denmark
| | - Soumik Ray
- Protein Biophysics Group, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 227, Kgs. Lyngby 2800 Denmark
| | - Alexander K Buell
- Protein Biophysics Group, Department of Biotechnology and Biomedicine, Technical University of Denmark Søltofts Plads, Building 227, Kgs. Lyngby 2800 Denmark
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Ray S, Mason TO, Boyens-Thiele L, Farzadfard A, Larsen JA, Norrild RK, Jahnke N, Buell AK. Mass photometric detection and quantification of nanoscale α-synuclein phase separation. Nat Chem 2023; 15:1306-1316. [PMID: 37337111 DOI: 10.1038/s41557-023-01244-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/19/2023] [Indexed: 06/21/2023]
Abstract
Protein liquid-liquid phase separation can lead to disease-related amyloid fibril formation. The mechanisms of conversion of monomeric protein into condensate droplets and of the latter into fibrils remain elusive. Here, using mass photometry, we demonstrate that the Parkinson's disease-related protein, α-synuclein, can form dynamic nanoscale clusters at physiologically relevant, sub-saturated concentrations. Nanoclusters nucleate in bulk solution and promote amyloid fibril formation of the dilute-phase monomers upon ageing. Their formation is instantaneous, even under conditions where macroscopic assemblies appear only after several days. The slow growth of the nanoclusters can be attributed to a kinetic barrier, probably due to an interfacial penalty from the charged C terminus of α-synuclein. Our findings reveal that α-synuclein phase separation occurs at much wider ranges of solution conditions than reported so far. Importantly, we establish mass photometry as a promising methodology to detect and quantify nanoscale precursors of phase separation. We also demonstrate its general applicability by probing the existence of nanoclusters of a non-amyloidogenic protein, Ddx4n1.
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Affiliation(s)
- Soumik Ray
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas O Mason
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lars Boyens-Thiele
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Azad Farzadfard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jacob Aunstrup Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Rasmus K Norrild
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Nadin Jahnke
- Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
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Abstract
The aggregation of the amyloid β (Aβ) peptide is a major hallmark of Alzheimer's disease. This peptide can aggregate into oligomers, proto-fibrils and mature fibrils, which eventually assemble into amyloid plaques in vivo. Several post-translational modifications lead to the presence of different forms of the Aβ peptide in the amyloid plaques with different biophysical and biochemical properties. While the canonical forms Aβ(1-40) and Aβ(1-42) have been found to be the major components of amyloid plaques, N-terminally pyroglutamate-modified variants, specifically pE-Aβ(3-42), amount to a significant fraction of the total Aβ plaque content of AD brains. With increased hydrophobicity, these variants display a more pronounced aggregation behaviour in vitro which, together with their higher stability against degradation in vivo is thought to make them crucial molecular players in the aetiology of AD. The peptide monomers are the smallest assembly units, and play an important role in most of the individual molecular processes involved in amyloid fibril formation, such as primary and secondary nucleation and elongation. Understanding the monomeric conformational ensembles of the isoforms is important in unraveling observed differences in their bio-physico-chemical properties. Here we use enhanced and extensive molecular dynamics simulations to study the structural flexibility of the N-terminally truncated Pyroglutamate modified isomer of Aβ, pE-Aβ(3-42) monomer, and compared it with simulations of the Aβ(1-42) peptide monomer under the same conditions. We find significant differences, especially in the secondary structure and hydrophobic exposure, which might be responsible for their different behaviour in biophysical experiments.
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Affiliation(s)
- Soumav Nath
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
- Institute of Biological Information Processing - Structural Biochemistry (IBI-7), Research Centre Jülich, Jülich, Germany
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Bogdan Barz
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
- Institute of Biological Information Processing - Structural Biochemistry (IBI-7), Research Centre Jülich, Jülich, Germany
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6
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Shenoy J, Lends A, Berbon M, Bilal M, El Mammeri N, Bertoni M, Saad A, Morvan E, Grélard A, Lecomte S, Theillet FX, Buell AK, Kauffmann B, Habenstein B, Loquet A. Structural polymorphism of the low-complexity C-terminal domain of TDP-43 amyloid aggregates revealed by solid-state NMR. Front Mol Biosci 2023; 10:1148302. [PMID: 37065450 PMCID: PMC10095165 DOI: 10.3389/fmolb.2023.1148302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Aberrant aggregation of the transactive response DNA-binding protein (TDP-43) is associated with several lethal neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia. Cytoplasmic neuronal inclusions of TDP-43 are enriched in various fragments of the low-complexity C-terminal domain and are associated with different neurotoxicity. Here we dissect the structural basis of TDP-43 polymorphism using magic-angle spinning solid-state NMR spectroscopy in combination with electron microscopy and Fourier-transform infrared spectroscopy. We demonstrate that various low-complexity C-terminal fragments, namely TDP-13 (TDP-43300–414), TDP-11 (TDP-43300–399), and TDP-10 (TDP-43314–414), adopt distinct polymorphic structures in their amyloid fibrillar state. Our work demonstrates that the removal of less than 10% of the low-complexity sequence at N- and C-termini generates amyloid fibrils with comparable macroscopic features but different local structural arrangement. It highlights that the assembly mechanism of TDP-43, in addition to the aggregation of the hydrophobic region, is also driven by complex interactions involving low-complexity aggregation-prone segments that are a potential source of structural polymorphism.
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Affiliation(s)
- Jayakrishna Shenoy
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Alons Lends
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Mélanie Berbon
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Muhammed Bilal
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Nadia El Mammeri
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Mathilde Bertoni
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Ahmad Saad
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Estelle Morvan
- University Bordeaux, CNRS, INSERM, IECB, UAR 3033, Pessac, France
| | - Axelle Grélard
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Sophie Lecomte
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - François-Xavier Theillet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-surYvette Cedex, France
| | - Alexander K. Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Brice Kauffmann
- University Bordeaux, CNRS, INSERM, IECB, UAR 3033, Pessac, France
| | - Birgit Habenstein
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
- *Correspondence: Birgit Habenstein, ; Antoine Loquet,
| | - Antoine Loquet
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
- *Correspondence: Birgit Habenstein, ; Antoine Loquet,
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Sternke-Hoffmann R, Pauly T, Norrild RK, Hansen J, Tucholski F, Høie MH, Marcatili P, Dupré M, Duchateau M, Rey M, Malosse C, Metzger S, Boquoi A, Platten F, Egelhaaf SU, Chamot-Rooke J, Fenk R, Nagel-Steger L, Haas R, Buell AK. Widespread amyloidogenicity potential of multiple myeloma patient-derived immunoglobulin light chains. BMC Biol 2023; 21:21. [PMID: 36737754 PMCID: PMC9898917 DOI: 10.1186/s12915-022-01506-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/15/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND In a range of human disorders such as multiple myeloma (MM), immunoglobulin light chains (IgLCs) can be produced at very high concentrations. This can lead to pathological aggregation and deposition of IgLCs in different tissues, which in turn leads to severe and potentially fatal organ damage. However, IgLCs can also be highly soluble and non-toxic. It is generally thought that the cause for this differential solubility behaviour is solely found within the IgLC amino acid sequences, and a variety of individual sequence-related biophysical properties (e.g. thermal stability, dimerisation) have been proposed in different studies as major determinants of the aggregation in vivo. Here, we investigate biophysical properties underlying IgLC amyloidogenicity. RESULTS We introduce a novel and systematic workflow, Thermodynamic and Aggregation Fingerprinting (ThAgg-Fip), for detailed biophysical characterisation, and apply it to nine different MM patient-derived IgLCs. Our set of pathogenic IgLCs spans the entire range of values in those parameters previously proposed to define in vivo amyloidogenicity; however, none actually forms amyloid in patients. Even more surprisingly, we were able to show that all our IgLCs are able to form amyloid fibrils readily in vitro under the influence of proteolytic cleavage by co-purified cathepsins. CONCLUSIONS We show that (I) in vivo aggregation behaviour is unlikely to be mechanistically linked to any single biophysical or biochemical parameter and (II) amyloidogenic potential is widespread in IgLC sequences and is not confined to those sequences that form amyloid fibrils in patients. Our findings suggest that protein sequence, environmental conditions and presence and action of proteases all determine the ability of light chains to form amyloid fibrils in patients.
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Affiliation(s)
- Rebecca Sternke-Hoffmann
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.5991.40000 0001 1090 7501Department of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Thomas Pauly
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XForschungszentrum Jülich GmbH, IBI-7, Jülich, Germany
| | - Rasmus K. Norrild
- grid.5170.30000 0001 2181 8870Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jan Hansen
- grid.411327.20000 0001 2176 9917Condensed Matter Physics Laboratory, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Florian Tucholski
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Magnus Haraldson Høie
- grid.5170.30000 0001 2181 8870Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Paolo Marcatili
- grid.5170.30000 0001 2181 8870Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Mathieu Dupré
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Magalie Duchateau
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Martial Rey
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Christian Malosse
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Sabine Metzger
- grid.6190.e0000 0000 8580 3777Cologne Biocenter, Cluster of Excellence on Plant Sciences, Mass Spectrometry Platform, University of Cologne, Cologne, Germany
| | - Amelie Boquoi
- grid.411327.20000 0001 2176 9917Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Florian Platten
- grid.411327.20000 0001 2176 9917Condensed Matter Physics Laboratory, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XForschungszentrum Jülich GmbH, IBI-4, Jülich, Germany
| | - Stefan U. Egelhaaf
- grid.411327.20000 0001 2176 9917Condensed Matter Physics Laboratory, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Julia Chamot-Rooke
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Roland Fenk
- grid.411327.20000 0001 2176 9917Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Luitgard Nagel-Steger
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XForschungszentrum Jülich GmbH, IBI-7, Jülich, Germany
| | - Rainer Haas
- Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany.
| | - Alexander K. Buell
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.5170.30000 0001 2181 8870Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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8
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Madsen AV, Kristensen P, Buell AK, Goletz S. Generation of robust bispecific antibodies through fusion of single-domain antibodies on IgG scaffolds: a comprehensive comparison of formats. MAbs 2023; 15:2189432. [PMID: 36939220 PMCID: PMC10038023 DOI: 10.1080/19420862.2023.2189432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Bispecific antibodies (bsAbs) enable dual binding of different antigens with potential synergistic targeting effects and innovative therapeutic possibilities. The formation of bsAbs is, however, often dependent on complex engineering strategies with a high risk of antibody chain mispairing leading to contamination of the final product with incorrectly assembled antibody species. This study demonstrates formation of bsAbs in a generic and conceptually easy manner through fusion of single-domain antibodies (sdAbs) onto IgG scaffolds through flexible 10 amino acid linkers to form high-quality bsAbs with both binding functionalities intact and minimal product-related impurities. SdAbs are attractive fusion partners due to their small and monomeric nature combined with antigen-binding capabilities comparable to conventional human antibodies. By systematically comparing a comprehensive panel of symmetric αPD-L1×αHER2 antibodies, including reversely mirrored antigen specificities, we investigate how the molecular geometry affects production, stability, antigen binding and CD16a binding. SdAb fusion of the heavy chain was generally preferred over light chain fusion for promoting good expression and high biophysical stability as well as maintaining efficient binding to both antigens. We find that N-terminal sdAb fusion might sterically hinder antigen-binding to the Fv region of the IgG scaffold, whereas C-terminal fusion might disturb antigen-binding to the fused sdAb. Our work demonstrates a toolbox of complementary methods for in-depth analysis of key features, such as in-solution dual antigen binding, thermal stability, and aggregation propensity, to ensure high bsAb quality. These techniques can be executed at high-throughput and/or with very low material consumption and thus represent valuable tools for bsAb screening and development.
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Affiliation(s)
- Andreas V Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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9
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Mohammad-Beigi H, Wijaya W, Madsen M, Hayashi Y, Li R, Maria Rovers TA, Jæger TC, Buell AK, Hougaard AB, Kirkensgaard JJ, Westh P, Ipsen R, Svensson B. Association of caseins with β-lactoglobulin influenced by temperature and calcium ions: A multi-parameter analysis. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.108373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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10
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Abstract
Amyloid fibrils are supramolecular homopolymers of proteins that play important roles in biological functions and disease. These objects have received an exponential increase in attention during the last few decades, due to their role in the aetiology of a range of severe disorders, most notably some of a neurodegenerative nature. While an overwhelming number of experimental studies exist that investigate how, and how fast, amyloid fibrils form and how their formation can be inhibited, a much more limited body of experimental work attempts to answer the question as to why these types of structures form (i.e. the thermodynamic driving force) and how stable they actually are. In this review, I attempt to give an overview of the types of experiments that have been performed to-date to answer these questions, and to summarise our current understanding of amyloid thermodynamics.
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Affiliation(s)
- Alexander K Buell
- Technical University of Denmark, Department of Biotechnology and Biomedicine Søltofts Plads, Building 227 2800 Kgs. Lyngby Denmark
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11
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Leguizamon Herrera VL, Buell AK, Willbold D, Barz B. Interaction of Therapeutic d-Peptides with Aβ42 Monomers, Thermodynamics, and Binding Analysis. ACS Chem Neurosci 2022; 13:1638-1650. [PMID: 35580288 DOI: 10.1021/acschemneuro.2c00102] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The aggregation of the amyloid-β (Aβ) peptide is a major hallmark of Alzheimer's disease. This peptide can aggregate into oligomers, proto-fibrils, and mature fibrils, which eventually assemble into amyloid plaques. The peptide monomers are the smallest assembly units and play an important role in most of the individual processes involved in amyloid fibril formation, such as primary and secondary nucleation and elongation. Several d-peptides have been confirmed as promising candidates to inhibit the aggregation of Aβ into toxic oligomers and fibrils by specifically interacting with monomeric species. In this work, we elucidate the structural interaction and thermodynamics of binding between three d-peptides (D3, ANK6, and RD2) and Aβ42 monomers by means of enhanced molecular dynamics simulations. Our study derives thermodynamic energies in good agreement with experimental values and suggests that there is an enhanced binding for D3 and ANK6, which leads to more stable complexes than for RD2. The binding of D3 to Aβ42 is shown to be weakly exothermic and mainly entropically driven, whereas the complex formation between the ANK6 and RD2 with the Aβ42 free monomer is weakly endothermic. In addition, the changes in the solvent-accessible surface area and the radius of gyration support that the binding between Aβ42 and d-peptides is mainly driven by electrostatic and hydrophobic interactions and leads to more compact conformations.
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Affiliation(s)
| | - Alexander K. Buell
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Dieter Willbold
- Institute of Biological Information Processing-Structural Biochemistry (IBI-7), Research Centre Jülich, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Bogdan Barz
- Institute of Biological Information Processing-Structural Biochemistry (IBI-7), Research Centre Jülich, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
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12
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Norrild RK, Vettore N, Coden A, Xue WF, Buell AK. Corrigendum to “Thermodynamics of amyloid fibril formation from non-equilibrium experiments of growth and dissociation” [Biophysical Chemistry 271 (2021) 106549]. Biophys Chem 2022; 283:106764. [DOI: 10.1016/j.bpc.2022.106764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Mohammad-Beigi H, Zanganeh M, Scavenius C, Eskandari H, Farzadfard A, Shojaosadati SA, Enghild JJ, Otzen DE, Buell AK, Sutherland DS. A Protein Corona Modulates Interactions of α-Synuclein with Nanoparticles and Alters the Rates of the Microscopic Steps of Amyloid Formation. ACS Nano 2022; 16:1102-1118. [PMID: 34982538 DOI: 10.1021/acsnano.1c08825] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nanoparticles (NPs) can modulate protein aggregation and fibril formation in the context of amyloid diseases. Understanding the mechanism of this action remains a critical next step in developing nanomedicines for the treatment or prevention of Parkinson's disease. α-Synuclein (α-Syn) can undergo interactions of different strength with nanoparticles, and these interactions can be prevented by the presence of a protein corona (PC) acquired during the exposure of NPs to serum proteins. Here, we develop a method to attach the PC irreversibly to the NPs, which enables us to study in detail the interaction of α-Syn and polyethylenimine-coated carboxyl-modified polystyrene NPs (PsNPs-PEI) and the role of the dynamics of the interactions. Analysis of the kinetics of fibril formation reveals that the NPs surface promotes the primary nucleation step of amyloid fibril formation without significantly affecting the elongation and fragmentation steps or the final equilibrium. Furthermore, the results show that even though α-Syn can access the surface of NPs that are precoated with a PC, due to the dynamic nature of the PC proteins, the PC nevertheless reduces the acceleratoring effect of the NPs. This effect is likely to be caused by reducing the overall amount of weakly interacting α-Syn molecules on the NP surface and the access of further α-Syn required for fibril elongation. Our experimental approach provides microscopic insight into how serum proteins can modulate the complex interplay between NPs and amyloid proteins.
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Affiliation(s)
- Hossein Mohammad-Beigi
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Masumeh Zanganeh
- Biotechnology Group, Faculty of Chemical Engineering, Tarbiat Modares University, 14115-143 Tehran, Iran
| | - Carsten Scavenius
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Hoda Eskandari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Azad Farzadfard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Seyed Abbas Shojaosadati
- Biotechnology Group, Faculty of Chemical Engineering, Tarbiat Modares University, 14115-143 Tehran, Iran
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Duncan S Sutherland
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark
- The Centre for Cellular Signal Patterns (CellPAT), Aarhus University, 8000 Aarhus C, Denmark
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14
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Zhang D, Sheng Y, Piano N, Jakuszeit T, Cozens E, Dong L, Buell AK, Pollet A, Lei IM, Wang W, Terentjev E, Huang YYS. Cancer cell migration on straight, wavy, loop and grid microfibre patterns. Biofabrication 2022; 14. [PMID: 34991078 DOI: 10.1088/1758-5090/ac48e6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/06/2022] [Indexed: 11/11/2022]
Abstract
Cell migration plays an important role in physiological and pathological processes where the fibrillar morphology of extracellular matrices (ECM) could regulate the migration dynamics. To mimic the morphological characteristics of fibrillar matrix structures, low-voltage continuous electrospinning was adapted to construct straight, wavy, looped and gridded fibre patterns made of polystyrene (of fibre diameter ca. 3 μm). Cells were free to explore their different shapes in response to the directly-adhered fibre, as well as to the neighbouring patterns. For all the patterns studied, analysing cellular migration dynamics of MDA-MB-231 (a highly migratory breast cancer cell line) demonstrated two interesting findings: first, although cells dynamically adjust their shapes and migration trajectories in response to different fibrillar environments, their average step speed is minimally affected by the fibre global pattern; secondly, a switch in behaviour was observed when the pattern features approach the upper limit of the cell body's minor axis, reflecting that cells' ability to divert from an existing fibre track is limited by the size along the cell body's minor axis. It is therefore concluded that the upper limit of cell body's minor axis might act as a guide for the design of microfibre patterns for different purposes of cell migration.
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Affiliation(s)
- Duo Zhang
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Yaqi Sheng
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Nicholas Piano
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Theresa Jakuszeit
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Edward Cozens
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Lingqing Dong
- School of Medicine, Zhejiang University, The Affiliated Stomatology Hospital., Hangzhou, Zhejiang, 310058, CHINA
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 227, 061 2800 Kgs. Lyngby, Lyngby, 2800, DENMARK
| | - Andreas Pollet
- Department of Mechanical Engineering, Eindhoven University of Technology, 5600MB Eindhoven, Eindhoven, Noord-Brabant, 5600 MB, NETHERLANDS
| | - Iek Man Lei
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Wenyu Wang
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Eugene Terentjev
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, CAMBRIDGE CB3 0HE, Cambridge, Cambridgeshire, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Yan Yan Shery Huang
- Department of Engineering, University of Cambridge, Trumpington Street, Cambridge, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
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15
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Nath S, Roy P, Mandal R, Roy R, Buell AK, Sengupta N, Tarafdar PK. Hydroxy-Porphyrin as an Effective, Endogenous Molecular Clamp during Early Stages of Amyloid Fibrillization. Chem Asian J 2021; 16:3931-3936. [PMID: 34570963 DOI: 10.1002/asia.202100965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Indexed: 11/08/2022]
Abstract
Amyloid fibril formation of proteins is of great concern in neurodegenerative disease and can be detrimental to the storage and stability of biologics. Recent evidence suggests that insulin fibril formation reduces the efficacy of type II diabetes management and may lead to several complications. To develop anti-amyloidogenic compounds of endogenous origin, we have utilized the hydrogen bond anchoring, π stacking ability of porphyrin, and investigated its role on the inhibition of insulin amyloid formation. We report that hydroxylation and metal removal from the heme moiety yields an excellent inhibitor of insulin fibril formation. Thioflavin T, tyrosine fluorescence, Circular Dichorism (CD) spectroscopy, Field emission scanning electron microscopy (FESEM) and molecular dynamics (MD) simulation studies suggest that hematoporphyrin (HP) having hydrogen bonding ability on both sides is a superior inhibitor compared to hemin and protoporphyrin (PP). Experiments with hen egg white lysozyme (HEWL) amyloid fibril formation also validated the efficacy of endogenous porphyrin based small molecules. Our results will help to decipher a general therapeutic strategy to counter amyloidogenesis.
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Affiliation(s)
- Soumav Nath
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, 741246, India
| | - Priti Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, 741246, India
| | - Raki Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, 741246, India
| | - Rajat Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, 741246, India
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark DTU, Søltofts Plads, 2800 Kgs., Lyngby, Denmark
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, 741246, India
| | - Pradip K Tarafdar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, 741246, India
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16
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Dupré M, Duchateau M, Sternke-Hoffmann R, Boquoi A, Malosse C, Fenk R, Haas R, Buell AK, Rey M, Chamot-Rooke J. De Novo Sequencing of Antibody Light Chain Proteoforms from Patients with Multiple Myeloma. Anal Chem 2021; 93:10627-10634. [PMID: 34292722 DOI: 10.1021/acs.analchem.1c01955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In multiple myeloma diseases, monoclonal immunoglobulin light chains (LCs) are abundantly produced, with, as a consequence in some cases, the formation of deposits affecting various organs, such as the kidney, while in other cases remaining soluble up to concentrations of several g·L-1 in plasma. The exact factors crucial for the solubility of LCs are poorly understood, but it can be hypothesized that their amino acid sequence plays an important role. Determining the precise sequences of patient-derived LCs is therefore highly desirable. We establish here a novel de novo sequencing workflow for patient-derived LCs, based on the combination of bottom-up and top-down proteomics without database search. PEAKS is used for the de novo sequencing of peptides that are further assembled into full length LC sequences using ALPS. Top-down proteomics provides the molecular masses of proteoforms and allows the exact determination of the amino acid sequence including all posttranslational modifications. This pipeline is then used for the complete de novo sequencing of LCs extracted from the urine of 10 patients with multiple myeloma. We show that for the bottom-up part, digestions with trypsin and Nepenthes digestive fluid are sufficient to produce overlapping peptides able to generate the best sequence candidates. Top-down proteomics is absolutely required to achieve 100% final sequence coverage and characterize clinical samples containing several LCs. Our work highlights an unexpected range of modifications.
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Affiliation(s)
- Mathieu Dupré
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, CNRS, 28 rue du Dr Roux, Paris 75015, France
| | - Magalie Duchateau
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, CNRS, 28 rue du Dr Roux, Paris 75015, France
| | - Rebecca Sternke-Hoffmann
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, Düsseldorf 40225, Germany
| | - Amelie Boquoi
- Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany, Moorenstr. 5, Düsseldorf 40225, Germany
| | - Christian Malosse
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, CNRS, 28 rue du Dr Roux, Paris 75015, France
| | - Roland Fenk
- Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany, Moorenstr. 5, Düsseldorf 40225, Germany
| | - Rainer Haas
- Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany, Moorenstr. 5, Düsseldorf 40225, Germany
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kgs. Lyngby 2800, Denmark
| | - Martial Rey
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, CNRS, 28 rue du Dr Roux, Paris 75015, France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, CNRS, 28 rue du Dr Roux, Paris 75015, France
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17
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López-Méndez B, Baron B, Brautigam CA, Jowitt TA, Knauer SH, Uebel S, Williams MA, Sedivy A, Abian O, Abreu C, Adamczyk M, Bal W, Berger S, Buell AK, Carolis C, Daviter T, Fish A, Garcia-Alai M, Guenther C, Hamacek J, Holková J, Houser J, Johnson C, Kelly S, Leech A, Mas C, Matulis D, McLaughlin SH, Montserret R, Nasreddine R, Nehmé R, Nguyen Q, Ortega-Alarcón D, Perez K, Pirc K, Piszczek G, Podobnik M, Rodrigo N, Rokov-Plavec J, Schaefer S, Sharpe T, Southall J, Staunton D, Tavares P, Vanek O, Weyand M, Wu D. Reproducibility and accuracy of microscale thermophoresis in the NanoTemper Monolith: a multi laboratory benchmark study. Eur Biophys J 2021; 50:411-427. [PMID: 33881594 PMCID: PMC8519905 DOI: 10.1007/s00249-021-01532-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 01/20/2023]
Abstract
Microscale thermophoresis (MST), and the closely related Temperature Related Intensity Change (TRIC), are synonyms for a recently developed measurement technique in the field of biophysics to quantify biomolecular interactions, using the (capillary-based) NanoTemper Monolith and (multiwell plate-based) Dianthus instruments. Although this technique has been extensively used within the scientific community due to its low sample consumption, ease of use, and ubiquitous applicability, MST/TRIC has not enjoyed the unambiguous acceptance from biophysicists afforded to other biophysical techniques like isothermal titration calorimetry (ITC) or surface plasmon resonance (SPR). This might be attributed to several facts, e.g., that various (not fully understood) effects are contributing to the signal, that the technique is licensed to only a single instrument developer, NanoTemper Technology, and that its reliability and reproducibility have never been tested independently and systematically. Thus, a working group of ARBRE-MOBIEU has set up a benchmark study on MST/TRIC to assess this technique as a method to characterize biomolecular interactions. Here we present the results of this study involving 32 scientific groups within Europe and two groups from the US, carrying out experiments on 40 Monolith instruments, employing a standard operation procedure and centrally prepared samples. A protein-small molecule interaction, a newly developed protein-protein interaction system and a pure dye were used as test systems. We characterized the instrument properties and evaluated instrument performance, reproducibility, the effect of different analysis tools, the influence of the experimenter during data analysis, and thus the overall reliability of this method.
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Affiliation(s)
- Blanca López-Méndez
- Biophysics Platform, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Bruno Baron
- Molecular Biophysics, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Chad A Brautigam
- Departments of Biophysics and Microbiology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Thomas A Jowitt
- Biomolecular Analysis Core Facility, University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
| | - Stefan H Knauer
- Biochemistry IV-Biopolymers, University of Bayreuth, Universitaetsstr. 30, 95447, Bayreuth, Germany
| | - Stephan Uebel
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Planegg, Germany
| | - Mark A Williams
- Department of Biological Sciences, ISMB BiophysX Centre, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, WC1E 7HX, UK
| | - Arthur Sedivy
- ProteinTechnology, Vienna Biocenter Core Facilities GmbH, Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
| | - Olga Abian
- Departamento de Bioquímica y Biología Molecular y Celular-Institute of Biocomputation and Physics of Complex Systems (BIFI), Instituto Aragonés de Ciencias de la Salud (IACS), Instituto de Investigación Sanitaria Aragón (IIS Aragón), Universidad de Zaragoza, C/ Mariano Esquillor S/N, 50018, Zaragoza, Spain
| | - Celeste Abreu
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague, Czech Republic
| | - Malgorzata Adamczyk
- Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Warsaw University of Technology, ul. Noakowskiego 3, 00-664, Warsaw, Poland
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, PAS, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Sylvie Berger
- Institut de Recherches Servier, 125, Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kgs., 2800, Lyngby, Denmark
| | - Carlo Carolis
- BioMolecular Screening and Protein Technologies Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader St, 88, 08003, Barcelona, Spain
| | - Tina Daviter
- Department of Biological Sciences, BiophysX Centre, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK
- Shared Research Facilities, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Alexander Fish
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, Netherlands
| | | | | | - Josef Hamacek
- Center for Molecular Biophysics, UPR 4301 CNRS Orléans, Rue Charles Sadron, 45071, Orléans, France
| | - Jitka Holková
- Glycobiochemistry and Biomolecular Interaction and Crystallization Core Facility, CEITEC MU, Kamenice 5, 625 00, Brno, Czech Republic
| | - Josef Houser
- Glycobiochemistry and Biomolecular Interaction and Crystallization Core Facility, CEITEC MU, Kamenice 5, 625 00, Brno, Czech Republic
| | - Chris Johnson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Sharon Kelly
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, B4-13 Joseph Black Building, G12 8QQ, Glasgow, Scotland, UK
| | - Andrew Leech
- Department of Biology, Bioscience Technology Facility, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Caroline Mas
- Integrated Structural Biology Grenoble (ISBG), UMS 3518 (CNRS-CEA-UGA-EMBL), 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio StSaulėtekio 7, 10257, Vilnius, Lithuania
| | - Stephen H McLaughlin
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Roland Montserret
- Institut de Biologie et Chimie des protéines, CNRS, Université de Lyon, 7 passage du Vercors, 69367, cedex 07 Lyon, France
| | - Rouba Nasreddine
- Institut de Chimie Organique et Analytique (ICOA), CNRS FR 2708, UMR 7311, Université d'Orléans, Orléans, France
| | - Reine Nehmé
- Institut de Chimie Organique et Analytique (ICOA), CNRS FR 2708, UMR 7311, Université d'Orléans, Orléans, France
| | - Quyen Nguyen
- Institut de Recherches Servier, 125, Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - David Ortega-Alarcón
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, C/ Mariano Esquillor S/N, 50018, Zaragoza, Spain
| | - Kathryn Perez
- Biophysics Lab, Protein Expression and Purification Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Katja Pirc
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Grzegorz Piszczek
- NHLBI Biophysics Core Facility, NHLBI/NIH, 50 South Dr, Bethesda, MD, 20892, USA
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Natalia Rodrigo
- BioMolecular Screening and Protein Technologies Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader St, 88, 08003, Barcelona, Spain
| | - Jasmina Rokov-Plavec
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Susanne Schaefer
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Tim Sharpe
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - June Southall
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, B4-13 Joseph Black Building, G12 8QQ, Glasgow, Scotland, UK
| | - David Staunton
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford, OX13 5LA, UK
| | - Pedro Tavares
- Molecular Biophysics Research Laboratory, Departamento de Química, UCIBIO/Requimte, Faculdade de Ciências e Tecnologia, UNL, Campus Caparica, 2829-516, Costa da Caparica, Portugal
| | - Ondrej Vanek
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague, Czech Republic
| | - Michael Weyand
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Di Wu
- NHLBI Biophysics Core Facility, NHLBI/NIH, 50 South Dr, Bethesda, MD, 20892, USA
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Hadi Alijanvand S, Peduzzo A, Buell AK. Secondary Nucleation and the Conservation of Structural Characteristics of Amyloid Fibril Strains. Front Mol Biosci 2021; 8:669994. [PMID: 33937341 PMCID: PMC8085410 DOI: 10.3389/fmolb.2021.669994] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/30/2021] [Indexed: 12/17/2022] Open
Abstract
Amyloid fibrils are ordered protein aggregates and a hallmark of many severe neurodegenerative diseases. Amyloid fibrils form through primary nucleation from monomeric protein, grow through monomer addition and proliferate through fragmentation or through the nucleation of new fibrils on the surface of existing fibrils (secondary nucleation). It is currently still unclear how amyloid fibrils initially form in the brain of affected individuals and how they are amplified. A given amyloid protein can sometimes form fibrils of different structure under different solution conditions in vitro, but often fibrils found in patients are highly homogeneous. These findings suggest that the processes that amplify amyloid fibrils in vivo can in some cases preserve the structural characteristics of the initial seed fibrils. It has been known for many years that fibril growth by monomer addition maintains the structure of the seed fibril, as the latter acts as a template that imposes its fold on the newly added monomer. However, for fibrils that are formed through secondary nucleation it was, until recently, not clear whether the structure of the seed fibril is preserved. Here we review the experimental evidence on this question that has emerged over the last years. The overall picture is that the fibril strain that forms through secondary nucleation is mostly defined by the solution conditions and intrinsic structural preferences, and not by the seed fibril strain.
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Affiliation(s)
- Saeid Hadi Alijanvand
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Alessia Peduzzo
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Lyngby, Denmark
| | - Alexander K. Buell
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Lyngby, Denmark
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19
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Otzen DE, Buell AK, Jensen H. Microfluidics and the quantification of biomolecular interactions. Curr Opin Struct Biol 2021; 70:8-15. [PMID: 33831785 DOI: 10.1016/j.sbi.2021.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 10/21/2022]
Abstract
Microfluidic systems under laminar flow conditions provide in-solution information about species size and binding affinities at very modest sample costs. Flow-induced dispersion analysis directly measures the spread of the analyte profile using Taylor dispersion analysis, whereas microfluidic diffusional sizing quantifies the transfer of analyte from one phase to another. Species of sizes between 0.5 and 1000 nm can be analyzed, and different populations resolved. Both techniques also allow analysis in complex media and medium throughput analysis. These properties make them valuable complements to existing approaches to measure biomolecular interactions.
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Affiliation(s)
- Daniel E Otzen
- iNANO and Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK - 8000, Aarhus C, Denmark.
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltoft Plads, DK - 2800, Kgs. Lyngby, Denmark.
| | - Henrik Jensen
- Fida Biosystems Aps, Fruebjergvej 3, DK - 2100, Copenhagen, Denmark.
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20
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Affiliation(s)
- Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark.
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21
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Abstract
Amyloid β (Aβ) monomers are the smallest assembly units, and play an important role in most of the individual processes involved in amyloid fibril formation. An important question is whether the monomer can adopt transient fibril-like conformations in solution. Here we use enhanced sampling simulations to study the Aβ42 monomer structural flexibility. We show that the monomer frequently adopts conformations with the N-terminus region structured very similarly to the conformation it adopts inside the fibril. This intrinsic propensity of monomeric Aβ to adopt fibril-like conformations could explain the low free energy barrier for Aβ42 fibril elongation.
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Affiliation(s)
- Bogdan Barz
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany and Institute of Biological Information Processing - Structural Biochemistry (IBI-7), Research Centre Jülich, Jülich, Germany.
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Soumav Nath
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany and Institute of Biological Information Processing - Structural Biochemistry (IBI-7), Research Centre Jülich, Jülich, Germany.
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22
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Agerschou ED, Schützmann MP, Reppert N, Wördehoff MM, Shaykhalishahi H, Buell AK, Hoyer W. β-Turn exchanges in the α-synuclein segment 44-TKEG-47 reveal high sequence fidelity requirements of amyloid fibril elongation. Biophys Chem 2020; 269:106519. [PMID: 33333378 DOI: 10.1016/j.bpc.2020.106519] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 11/28/2022]
Abstract
The folding of turns and β-hairpins has been implicated in amyloid formation, with diverse potential consequences such as promotion or inhibition of fibril nucleation, fibril elongation, or off-pathway oligomer formation. In the Parkinson's disease-associated protein α-synuclein (αS), a β-hairpin comprised of residues 36-56 was detected in complex with an engineered binding protein, with a turn formed by the αS sequence segment 44-TKEG-47. Molecular dynamics simulations revealed extensive populations of transient β-hairpin conformations in this region in free, monomeric αS. Here, we investigated potential effects of turn formation on αS fibril formation by studying the aggregation kinetics of an extensive set of αS variants with between two and four amino acid exchanges in the 44-TKEG-47 segment. The exchanges were chosen to specifically promote formation of β1-, β1'-, or β2'-turns. All variants assembled into amyloid fibrils, with increased β1'- or β2'-turn propensity associated with faster aggregation and increased β1-turn propensity with slower aggregation compared to wild-type (WT) αS. Atomic force microscopy demonstrated that β-turn exchanges altered fibril morphology. In cross-elongation experiments, the turn variants showed a low ability to elongate WT fibril seeds, and, vice versa, WT monomer did not efficiently elongate turn variant fibril seeds. This demonstrates that sequence identity in the turn region is crucial for efficient αS fibril elongation. Elongation experiments of WT fibril seeds in the presence of both WT and turn variant monomers suggest that the turn variants can bind and block WT fibril ends to different degrees, but cannot efficiently convert into the WT fibril structure. Our results indicate that modifications in the 44-TKEG-47 segment strongly affect amyloid assembly by driving αS into alternative fibril morphologies, whose elongation requires high sequence fidelity.
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Affiliation(s)
- Emil Dandanell Agerschou
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Marie P Schützmann
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Nikolas Reppert
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Michael M Wördehoff
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Hamed Shaykhalishahi
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Alexander K Buell
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany; Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany.
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23
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Peduzzo A, Linse S, Buell AK. The Properties of α-Synuclein Secondary Nuclei Are Dominated by the Solution Conditions Rather than the Seed Fibril Strain. ACS Chem Neurosci 2020; 11:909-918. [PMID: 32069013 DOI: 10.1021/acschemneuro.9b00594] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Amyloid fibrils of α-synuclein (α-syn) are a component of Lewy bodies, the characteristic hallmark of Parkinson's disease. Amyloid fibrils arise through primary nucleation from monomers, which in the case of α-syn is often heterogeneous, followed by the growth of the nuclei by monomer addition. Secondary nucleation corresponds to the formation of new fibrils facilitated by pre-existing fibrils. While it is well-established that the newly added monomer in fibril elongation adopts the conformation of the monomers in the seed ("templating"), it is unclear whether fibrils formed through secondary nucleation of monomers on the surface of seed fibrils copy the structure of the "parent" fibril. Here we show by biochemical and microscopical methods that the secondary nucleation of α-syn, enabled at mildly acidic pH, leads to fibrils that structurally resemble more closely those formed de novo under the same conditions, rather than the seeds if these are formed under different solution conditions. This result has important implications for the mechanistic understanding of the secondary nucleation of amyloid fibrils and its role in the propagation of aggregate pathology in protein misfolding diseases.
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Affiliation(s)
- Alessia Peduzzo
- Institute of Physical Biology, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, SE-221 00 Lund, Sweden
| | - Alexander K. Buell
- Institute of Physical Biology, Heinrich-Heine University, 40225 Düsseldorf, Germany
- Technical University of Denmark, Department of Biotechnology and Biomedicine, 2800 Lyngby, Denmark
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24
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Sternke-Hoffmann R, Boquoi A, Lopez Y Niedenhoff D, Platten F, Fenk R, Haas R, Buell AK. Biochemical and biophysical characterisation of immunoglobulin free light chains derived from an initially unbiased population of patients with light chain disease. PeerJ 2020; 8:e8771. [PMID: 32211238 PMCID: PMC7083161 DOI: 10.7717/peerj.8771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/19/2020] [Indexed: 11/20/2022] Open
Abstract
In light chain (LC) diseases, monoclonal immunoglobulin LCs are abundantly produced with the consequence in some cases to form deposits of a fibrillar or amorphous nature affecting various organs, such as heart and kidney. The factors that determine the solubility of any given LC in vivo are still not well understood. We hypothesize that some of the biochemical properties of the LCs that have been shown to correlate with amyloid fibril formation in patients also can be used as predictors for the degree of kidney damage in a patient group that is only biased by protein availability. We performed detailed biochemical and biophysical investigations of light chains extracted and purified from the urine of a group of 20 patients with light chain disease. For all samples that contained a sufficiently high concentration of LC, we quantified the unfolding temperature of the LCs, the monomer-dimer distribution, the digestibility by trypsin and the formation of amyloid fibrils under various conditions of pH and reducing agent. We correlated the results of our biophysical and biochemical experiments with the degree of kidney damage in the patient group and found that most of these parameters do not correlate with kidney damage as defined by clinical parameters. However, the patients with the greatest impairment of kidney function have light chains which display very poor digestibility by trypsin. Most of the LC properties reported before to be predictors of amyloid formation cannot be used to assess the degree of kidney damage. Our finding that poor trypsin digestibility correlates with kidney damage warrants further investigation in order to probe a putative mechanistic link between these factors.
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Affiliation(s)
| | - Amelie Boquoi
- Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - David Lopez Y Niedenhoff
- Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Florian Platten
- Condensed Matter Physics Laboratory, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Roland Fenk
- Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Rainer Haas
- Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Alexander K Buell
- Institute of Physical Biology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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25
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Galvagnion C, Topgaard D, Makasewicz K, Buell AK, Linse S, Sparr E, Dobson CM. Lipid Dynamics and Phase Transition within α-Synuclein Amyloid Fibrils. J Phys Chem Lett 2019; 10:7872-7877. [PMID: 31790267 PMCID: PMC6937551 DOI: 10.1021/acs.jpclett.9b03005] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/02/2019] [Indexed: 05/23/2023]
Abstract
The deposition of coassemblies made of the small presynaptic protein, α-synuclein, and lipids in the brains of patients is the hallmark of Parkinson's disease. In this study, we used natural abundance 13C and 31P magic-angle spinning nuclear magnetic resonance spectroscopy together with cryo-electron microscopy and differential scanning calorimetry to characterize the fibrils formed by α-synuclein in the presence of vesicles made of 1,2-dimyristoyl-sn-glycero-3-phospho-L-serine or 1,2-dilauroyl-sn-glycero-3-phospho-L-serine. Our results show that these lipids coassemble with α-synuclein molecules to give thin and curly amyloid fibrils. The coassembly leads to slower and more isotropic reorientation of lipid molecular segments and a decrease in both the temperature and enthalpy of the lipid chain-melting compared with those in the protein-free lipid lamellar phase. These findings provide new insights into the properties of lipids within protein-lipid assemblies that can be associated with Parkinson's disease.
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Affiliation(s)
- Céline Galvagnion
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- German
Center for Neurodegenerative Diseases, Sigmund-Freud-Str. 27, 53127 Bonn,Germany
| | - Daniel Topgaard
- Division
of Physical Chemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Katarzyna Makasewicz
- Division
of Physical Chemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Alexander K. Buell
- Department
of Biotechnology and Biomedicine, DTU Bioengineering, Technical University of Denmark, Soltofts Plads 227, DK-2800 Kgs. Lyngby, Denmark
| | - Sara Linse
- Department
of Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
| | - Emma Sparr
- Division
of Physical Chemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Christopher M. Dobson
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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26
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Abstract
Amyloid fibrils are homo-molecular protein polymers that play an important role in disease and biological function. While much is known about their kinetics and mechanisms of formation, the origin and magnitude of their thermodynamic stability has received significantly less attention. This is despite the fact that the thermodynamic stability of amyloid fibrils is an important determinant of their lifetimes and processing in vivo. Here we use depolymerization by chemical denaturants of amyloid fibrils of two different proteins (PI3K-SH3 and glucagon) at different concentrations and show that the previously applied isodesmic linear polymerization model is an oversimplification that does not capture the concentration dependence of chemical depolymerization of amyloid fibrils. We show that cooperative polymerization, which is compatible with the picture of amyloid formation as a nucleated polymerization process, is able to quantitatively describe the thermodynamic data. We use this combined experimental and conceptual framework in order to probe the ionic strength dependence of amyloid fibril stability. In combination with previously published data on the ionic strength dependence of amyloid fibril growth kinetics, our results provide strong evidence for the product-like nature of the transition state of amyloid fibril growth.
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Affiliation(s)
- Nicola Vettore
- Institut for Physical Biology, Heinrich-Heine-Universitaet Duesseldorf, Universitaetstrasse 1, Duesseldorf, Germany
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27
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Agerschou ED, Flagmeier P, Saridaki T, Galvagnion C, Komnig D, Heid L, Prasad V, Shaykhalishahi H, Willbold D, Dobson CM, Voigt A, Falkenburger B, Hoyer W, Buell AK. An engineered monomer binding-protein for α-synuclein efficiently inhibits the proliferation of amyloid fibrils. eLife 2019; 8:46112. [PMID: 31389332 PMCID: PMC6721797 DOI: 10.7554/elife.46112] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/04/2019] [Indexed: 12/14/2022] Open
Abstract
Removing or preventing the formation of α-synuclein aggregates is a plausible strategy against Parkinson’s disease. To this end, we have engineered the β-wrapin AS69 to bind monomeric α-synuclein with high affinity. In cultured cells, AS69 reduced the self-interaction of α-synuclein and formation of visible α-synuclein aggregates. In flies, AS69 reduced α-synuclein aggregates and the locomotor deficit resulting from α-synuclein expression in neuronal cells. In biophysical experiments in vitro, AS69 highly sub-stoichiometrically inhibited both primary and autocatalytic secondary nucleation processes, even in the presence of a large excess of monomer. We present evidence that the AS69-α-synuclein complex, rather than the free AS69, is the inhibitory species responsible for sub-stoichiometric inhibition of secondary nucleation. These results represent a new paradigm that high affinity monomer binders can lead to strongly sub-stoichiometric inhibition of nucleation processes.
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Affiliation(s)
| | - Patrick Flagmeier
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.,Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | | | - Céline Galvagnion
- RG Mechanisms of Neuroprotection, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Pharmacology and Drug Design, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Komnig
- Department of Neurology, RWTH Aachen University, Aachen, Germany
| | - Laetitia Heid
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Vibha Prasad
- Department of Neurology, RWTH Aachen University, Aachen, Germany
| | - Hamed Shaykhalishahi
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.,Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Aaron Voigt
- Department of Neurology, RWTH Aachen University, Aachen, Germany
| | - Bjoern Falkenburger
- Department of Neurology, RWTH Aachen University, Aachen, Germany.,Department of Neurology, Dresden University Medical Center, Dresden, Germany.,JARA BRAIN Institute II, Julich and Aachen, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Alexander K Buell
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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28
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Falke M, Victor J, Wördehoff MM, Peduzzo A, Zhang T, Schröder GF, Buell AK, Hoyer W, Etzkorn M. α-Synuclein-derived lipoparticles in the study of α-Synuclein amyloid fibril formation. Chem Phys Lipids 2019; 220:57-65. [PMID: 30826264 PMCID: PMC6451039 DOI: 10.1016/j.chemphyslip.2019.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 12/23/2022]
Abstract
Aggregation of the protein α-Synuclein (αSyn) is of great interest due to its involvement in the pathology of Parkinson’s disease. However, under in vitro conditions αSyn is very soluble and kinetically stable for extended time periods. As a result, most αSyn aggregation assays rely on conditions that artificially induce or enhance aggregation, often by introducing rather non-native conditions. It has been shown that αSyn interacts with membranes and conditions have been identified in which membranes can promote as well as inhibit αSyn aggregation. It has also been shown that αSyn has the intrinsic capability to assemble lipid-protein-particles, in a similar way as apolipoproteins can form lipid-bilayer nanodiscs. Here we show that these αSyn-lipid particles (αSyn-LiPs) can also effectively induce, accelerate or inhibit αSyn aggregation, depending on the applied conditions. αSyn-LiPs therefore provide a general platform and additional tool, complementary to other setups, to study various aspects of αSyn amyloid fibril formation.
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Affiliation(s)
- Marcel Falke
- Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf, Germany
| | - Julian Victor
- Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf, Germany
| | - Michael M Wördehoff
- Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf, Germany
| | - Alessia Peduzzo
- Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf, Germany
| | - Tao Zhang
- Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf, Germany
| | - Gunnar F Schröder
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, Germany
| | - Alexander K Buell
- Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf, Germany
| | - Manuel Etzkorn
- Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, Germany.
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29
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Abstract
The self-assembly of short aromatic peptides and peptide derivatives into a variety of different nano- and microstructures (fibrillar gels, crystals, spheres, plates) is a promising route toward the creation of bio-compatible materials with often unexpected and useful properties. Furthermore, such simple self-assembling systems have been proposed as model systems for the self-assembly of longer peptides, a process that can be linked to biological function and malfunction. Much effort has been made in the last 15 years to explore the space of peptide sequences, chemical modifications and solvent conditions in order to maximise the diversity of assembly morphologies and properties. However, quantitative studies of the corresponding mechanisms of, and driving forces for, peptide self-assembly have remained relatively scarce until recently. In this chapter we review the current state of understanding of the thermodynamic driving forces and self-assembly mechanisms of short aromatic peptides into supramolecular structures. We will focus on experimental studies of the assembly process and our perspective will be centered around diphenylalanine (FF), a key motif of the amyloid β sequence and a paradigmatic self-assembly building block. Our main focus is the basic physical chemistry and key structural aspects of such systems, and we will also compare the mechanism of dipeptide aggregation with that of longer peptide sequences into amyloid fibrils, with discussion on how these mechanisms may be revealed through detailed analysis of growth kinetics, thermodynamics and other fundamental properties of the aggregation process.
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Affiliation(s)
- Thomas O Mason
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DTU, Lyngby, Denmark.
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30
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Ziehm T, Buell AK, Willbold D. Role of Hydrophobicity and Charge of Amyloid-Beta Oligomer Eliminating d-Peptides in the Interaction with Amyloid-Beta Monomers. ACS Chem Neurosci 2018; 9:2679-2688. [PMID: 29893543 DOI: 10.1021/acschemneuro.8b00132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Inhibition of the self-assembly process of amyloid-beta and even more the removal of already existing toxic amyloid-beta assemblies represent promising therapeutic strategies against Alzheimer's disease. To approach this aim, we selected a d-enantiomeric peptide by phage-display based on the interaction with amyloid-beta monomers. This lead compound was successfully optimized by peptide microarrays with respect to its affinity and specificity to the target resulting in d-peptides with both increased hydrophobicity and net charge. Here, we present a detailed biophysical characterization of the interactions between these optimized d-peptides and amyloid-beta monomers in comparison to the original lead compound in order to obtain a more thorough understanding of the physicochemical determinants of the interactions. Kinetics and apparent stoichiometry of complex formation were studied using surface plasmon resonance. Potential modes of binding to amyloid-beta were identified, and the influences of ionic strength on complex stability, as well as on the inhibitory effect on amyloid-beta aggregation were investigated. The results reveal a very different mode of interaction of the optimized d-peptides based on a combination of electrostatic and hydrophobic interactions as compared to the mostly electrostatically driven interaction of the lead compound. These conclusions were supported by the thermodynamic profiles of the interaction between optimized d-peptides and Aβ monomers, which indicate an increase in binding entropy with respect to the lead compound.
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Affiliation(s)
- Tamar Ziehm
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Alexander K. Buell
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
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31
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van der Wateren IM, Knowles TPJ, Buell AK, Dobson CM, Galvagnion C. C-terminal truncation of α-synuclein promotes amyloid fibril amplification at physiological pH. Chem Sci 2018; 9:5506-5516. [PMID: 30061982 PMCID: PMC6048717 DOI: 10.1039/c8sc01109e] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/22/2018] [Indexed: 11/21/2022] Open
Abstract
Parkinson's disease is one of the major neurodegenerative disorders affecting the ageing populations of the modern world. One of the hallmarks of this disease is the deposition of aggregates, mainly of the small pre-synaptic protein α-synuclein (AS), in the brains of patients. Several very significantly modified forms of AS have been found in these deposits including those resulting from truncations of the protein at its C-terminus. Here, we report how two physiologically relevant C-terminal truncations of AS, AS(1-119) and AS(1-103), where either half or virtually all of the C-terminal domain, respectively, has been truncated, affect the mechanism of AS aggregation and the properties of the fibrils formed. In particular, we have found that the deletion of these C-terminal residues induces a shift of the pH region where autocatalytic secondary processes dominate the kinetics of AS aggregation towards higher pH values, from AS wild-type (pH 3.6-5.6) to AS(1-119) (pH 4.2-7.0) and AS(1-103) (pH 5.6-8.0). In addition, we found that both truncated variants formed protofibrils in the presence of lipid vesicles, but only those formed by AS(1-103) had the capacity to convert readily into mature fibrils. These results suggest that electrostatics play an important role in secondary nucleation, a key factor in aggregate proliferation, and in the conversion of AS fibrils from protofibrils to mature fibrils. In particular, our results demonstrate that sequence truncations of AS can shift the pH range where autocatalytic proliferation of fibrils is possible into the neutral, physiological regime, thus providing an explanation of the increased propensity of the C-truncated variants to aggregate in vivo.
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Affiliation(s)
- Ingrid M van der Wateren
- Centre for Misfolding Diseases , Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases , Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
- Cavendish Laboratory , Department of Physics , University of Cambridge , J J Thomson Avenue , Cambridge , CB3 1HE , UK
| | - Alexander K Buell
- Institute of Physical Biology , Heinrich Heine Universität , Universitätsstr. 1 , 40225 , Düsseldorf , Germany .
| | - Christopher M Dobson
- Centre for Misfolding Diseases , Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
| | - Céline Galvagnion
- Centre for Misfolding Diseases , Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
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32
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Viennet T, Wördehoff MM, Uluca B, Poojari C, Shaykhalishahi H, Willbold D, Strodel B, Heise H, Buell AK, Hoyer W, Etzkorn M. Structural insights from lipid-bilayer nanodiscs link α-Synuclein membrane-binding modes to amyloid fibril formation. Commun Biol 2018; 1:44. [PMID: 30271927 PMCID: PMC6123806 DOI: 10.1038/s42003-018-0049-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/23/2018] [Indexed: 01/24/2023] Open
Abstract
The protein α-Synuclein (αS) is linked to Parkinson’s disease through its abnormal aggregation, which is thought to involve cytosolic and membrane-bound forms of αS. Following previous studies using micelles and vesicles, we present a comprehensive study of αS interaction with phospholipid bilayer nanodiscs. Using a combination of NMR-spectroscopic, biophysical, and computational methods, we structurally and kinetically characterize αS interaction with different membrane discs in a quantitative and site-resolved way. We obtain global and residue-specific αS membrane affinities, and determine modulations of αS membrane binding due to αS acetylation, membrane plasticity, lipid charge density, and accessible membrane surface area, as well as the consequences of the different binding modes for αS amyloid fibril formation. Our results establish a structural and kinetic link between the observed dissimilar binding modes and either aggregation-inhibiting properties, largely unperturbed aggregation, or accelerated aggregation due to membrane-assisted fibril nucleation. Thibault Viennet and colleagues gain structural insight into amyloid fibril formation from their innovative use of lipid bilayer nanodiscs. This study connects α-Synuclein membrane binding modes to its aggregation properties, furthering our understanding of the cause of neurodegerative diseases.
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Affiliation(s)
- Thibault Viennet
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany.,Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Michael M Wördehoff
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Boran Uluca
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany.,Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Chetan Poojari
- Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany.,Department of Physics, Tampere University of Technology, Korkeakoulunkatu 10, 33720, Tampere, Finland.,Department of Physics, University of Helsinki, Gustaf Hällströmin katu 2a, 00560, Helsinki, Finland
| | - Hamed Shaykhalishahi
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany.,Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Birgit Strodel
- Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Henrike Heise
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany.,Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Alexander K Buell
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany.,Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Manuel Etzkorn
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany. .,Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany.
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33
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Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M, Dobson CM, Buell AK, Knowles TPJ, Linse S. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nat Chem 2018; 10:523-531. [PMID: 29581486 PMCID: PMC5911155 DOI: 10.1038/s41557-018-0023-x] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/06/2018] [Indexed: 12/23/2022]
Abstract
Mapping energy landscapes has proved to be a powerful tool for studying reaction mechanisms. Many complex biomolecular assembly processes, however, have remained challenging to access using this approach, including the aggregation of peptides and proteins into amyloid fibrils implicated in various disorders. Here we generalize the strategy used to probe energy landscapes in protein folding to determine the activation energies and entropies that characterise each of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which is associated with Alzheimer’s disease. Our results reveal that interactions between monomeric Aβ and amyloid fibrils during fibril-dependent nucleation fundamentally reverse the thermodynamic signature of this process relative to primary nucleation, even though both processes generate aggregates from soluble peptides. By mapping the energetic and entropic contributions along the reactive trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results from the enthalpic stabilisation of adsorbing peptides in conformations amenable to nucleation, driving a dramatic lowering of the activation energy barrier for nucleation.
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Affiliation(s)
- Samuel I A Cohen
- Department of Chemistry and Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Risto Cukalevski
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Lund, Sweden
| | - Thomas C T Michaels
- Department of Chemistry and Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK.,Paulson School of Engineering and Applied Science, Harvard University, Cambridge, MA, USA
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK
| | - Mattias Törnquist
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Lund, Sweden
| | - Michele Vendruscolo
- Department of Chemistry and Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Christopher M Dobson
- Department of Chemistry and Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Alexander K Buell
- Institute of Physical Biology, University of Duesseldorf, Duesseldorf, Germany
| | - Tuomas P J Knowles
- Department of Chemistry and Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK. .,Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Lund, Sweden.
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34
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Gang H, Galvagnion C, Meisl G, Müller T, Pfammatter M, Buell AK, Levin A, Dobson CM, Mu B, Knowles TPJ. Microfluidic Diffusion Platform for Characterizing the Sizes of Lipid Vesicles and the Thermodynamics of Protein–Lipid Interactions. Anal Chem 2018; 90:3284-3290. [DOI: 10.1021/acs.analchem.7b04820] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hongze Gang
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 People’s Republic of China
| | - Céline Galvagnion
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Georg Meisl
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Thomas Müller
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
- Fluidic
Analytics
Ltd, Unit 5 Chesterton Mill, French’s Road, Cambridge, CB4 3NP, United Kingdom
| | - Manuela Pfammatter
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Alexander K. Buell
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Aviad Levin
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Christopher M. Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Bozhong Mu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 People’s Republic of China
| | - Tuomas P. J. Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 1HE, United Kingdom
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35
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Brown JWP, Meisl G, Knowles TPJ, Buell AK, Dobson CM, Galvagnion C. Kinetic barriers to α-synuclein protofilament formation and conversion into mature fibrils. Chem Commun (Camb) 2018; 54:7854-7857. [DOI: 10.1039/c8cc03002b] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An increase in temperature allows the conversion of α-synuclein lipid-induced proto-fibrils to mature fibrils by overcoming the associated energy barrier.
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Affiliation(s)
- James W. P. Brown
- Centre for Misfolding Diseases
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| | - Georg Meisl
- Centre for Misfolding Diseases
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| | - Tuomas P. J. Knowles
- Centre for Misfolding Diseases
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| | | | - Christopher M. Dobson
- Centre for Misfolding Diseases
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
| | - Céline Galvagnion
- Centre for Misfolding Diseases
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
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36
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Mason TO, Michaels TCT, Levin A, Dobson CM, Gazit E, Knowles TPJ, Buell AK. Thermodynamics of Polypeptide Supramolecular Assembly in the Short-Chain Limit. J Am Chem Soc 2017; 139:16134-16142. [DOI: 10.1021/jacs.7b00229] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas O. Mason
- Department of Chemistry, University of Cambridge, Cambridge CB2 1TN, United Kingdom
| | - Thomas C. T. Michaels
- Department of Chemistry, University of Cambridge, Cambridge CB2 1TN, United Kingdom
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Aviad Levin
- Department of Chemistry, University of Cambridge, Cambridge CB2 1TN, United Kingdom
| | | | - Ehud Gazit
- Department for Molecular Microbiology and Biotechnology, University of Tel Aviv, Tel Aviv 6997801, Israel
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Cambridge CB2 1TN, United Kingdom
| | - Alexander K. Buell
- Institute of Physical Biology, University of Düsseldorf, Düsseldorf 40225, Germany
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37
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Meisl G, Rajah L, Cohen SAI, Pfammatter M, Šarić A, Hellstrand E, Buell AK, Aguzzi A, Linse S, Vendruscolo M, Dobson CM, Knowles TPJ. Scaling behaviour and rate-determining steps in filamentous self-assembly. Chem Sci 2017; 8:7087-7097. [PMID: 29147538 PMCID: PMC5637470 DOI: 10.1039/c7sc01965c] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/31/2017] [Indexed: 12/30/2022] Open
Abstract
The formation of filaments from naturally occurring protein molecules is a process at the core of a range of functional and aberrant biological phenomena, such as the assembly of the cytoskeleton or the appearance of aggregates in Alzheimer's disease. The macroscopic behaviour associated with such processes is remarkably diverse, ranging from simple nucleated growth to highly cooperative processes with a well-defined lagtime. Thus, conventionally, different molecular mechanisms have been used to explain the self-assembly of different proteins. Here we show that this range of behaviour can be quantitatively captured by a single unifying Petri net that describes filamentous growth in terms of aggregate number and aggregate mass concentrations. By considering general features associated with a particular network connectivity, we are able to establish directly the rate-determining steps of the overall aggregation reaction from the system's scaling behaviour. We illustrate the power of this framework on a range of different experimental and simulated aggregating systems. The approach is general and will be applicable to any future extensions of the reaction network of filamentous self-assembly.
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Affiliation(s)
- Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
| | - Luke Rajah
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
| | - Samuel A I Cohen
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
| | - Manuela Pfammatter
- Institute of Neuropathology , University Hospital of Zurich , Schmelzbergstrasse 12 , 8091 Zurich , Switzerland
| | - Anđela Šarić
- Department of Physics and Astronomy , Institute for the Physics of Living Systems , University College London , London WC1E 6BT , UK
| | - Erik Hellstrand
- Chemistry Department and Molecular Protein Science , Lund University , P. O. Box 124 , SE221 00 Lund , Sweden
| | - Alexander K Buell
- Institute of Physical Biology , University of Duesseldorf , Universitaetsstr. 1 , 40225 Duesseldorf , Germany
| | - Adriano Aguzzi
- Institute of Neuropathology , University Hospital of Zurich , Schmelzbergstrasse 12 , 8091 Zurich , Switzerland
| | - Sara Linse
- Chemistry Department and Molecular Protein Science , Lund University , P. O. Box 124 , SE221 00 Lund , Sweden
| | - Michele Vendruscolo
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
| | - Christopher M Dobson
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
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38
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Fisher E, Zhao Y, Richardson R, Janik M, Buell AK, Aigbirhio FI, Tóth G. Detection and Characterization of Small Molecule Interactions with Fibrillar Protein Aggregates Using Microscale Thermophoresis. ACS Chem Neurosci 2017. [PMID: 28640595 DOI: 10.1021/acschemneuro.7b00228] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Neurodegenerative diseases such as Parkinson's and Alzheimer's disease share the pathological hallmark of fibrillar protein aggregates. The specific detection of these protein aggregates by positron emission tomography (PET) in the patient brain can yield valuable information for diagnosis and disease progression. However, the identification of novel small compounds that bind fibrillar protein aggregates has been a challenge. In this study, microscale thermophoresis (MST) was applied to assess the binding affinity of known small molecule ligands of α-synuclein fibrils, which were also tested in parallel in a thioflavin T fluorescence competition assay for further validation. In addition, a MST assay was also developed for the detection of the interaction between a variety of small molecules and tau fibrils. The results of this study demonstrate that MST is a powerful and practical methodology to quantify interactions between small molecules and protein fibrillar aggregates, which suggests that it can be applied for the identification and development of PET radioligands and potentially of therapeutic candidates for protein misfolding diseases.
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Affiliation(s)
- Emily Fisher
- Molecular Imaging
Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of
Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, U.K
| | - Yanyan Zhao
- Molecular Imaging
Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of
Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, U.K
| | - Robert Richardson
- Molecular Imaging
Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of
Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, U.K
| | - Malgorzata Janik
- MTA-TTK-NAP
B, Drug Discovery Research Group, Neurodegenerative Diseases, Institute
of Organic Chemistry, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1051, Hungary
| | - Alexander K. Buell
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Franklin I. Aigbirhio
- Molecular Imaging
Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of
Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, U.K
| | - Gergely Tóth
- Molecular Imaging
Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of
Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, U.K
- MTA-TTK-NAP
B, Drug Discovery Research Group, Neurodegenerative Diseases, Institute
of Organic Chemistry, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1051, Hungary
- Cantabio Pharmaceuticals Inc., Sunnyvale, California 94085, United States
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39
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Wördehoff MM, Shaykhalishahi H, Groß L, Gremer L, Stoldt M, Buell AK, Willbold D, Hoyer W. Opposed Effects of Dityrosine Formation in Soluble and Aggregated α-Synuclein on Fibril Growth. J Mol Biol 2017; 429:3018-3030. [PMID: 28918091 PMCID: PMC5637163 DOI: 10.1016/j.jmb.2017.09.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/03/2017] [Accepted: 09/06/2017] [Indexed: 12/20/2022]
Abstract
Parkinson's disease is the second most common neurodegenerative disease. It is characterized by aggregation of the protein α-synuclein (α-syn) in Lewy bodies, mitochondrial dysfunction, and increased oxidative stress in the substantia nigra. Oxidative stress leads to several modifications of biomolecules including dityrosine (DiY) crosslinking in proteins, which has recently been detected in α-syn in Lewy bodies from Parkinson's disease patients. Here we report that α-syn is highly susceptible to ultraviolet-induced DiY formation. We investigated DiY formation of α-syn and nine tyrosine-to-alanine mutants and monitored its effect on α-syn fibril formation in vitro. Ultraviolet irradiation of intrinsically disordered α-syn generates DiY-modified monomers and dimers, which inhibit fibril formation of unmodified α-syn by interfering with fibril elongation. The inhibition depends on both the DiY group and its integration into α-syn. When preformed α-syn fibrils are crosslinked by DiY formation, they gain increased resistance to denaturation. DiY-stabilized α-syn fibrils retain their high seeding efficiency even after being exposed to denaturant concentrations that completely depolymerize non-crosslinked seeds. Oxidative stress-associated DiY crosslinking of α-syn therefore entails two opposing effects: (i) inhibition of aggregation by DiY-modified monomers and dimers, and (ii) stabilization of fibrillar aggregates against potential degradation mechanisms, which can lead to promotion of aggregation, especially in the presence of secondary nucleation. Oxidative stress can lead to dityrosine (DiY) crosslinks in α-synuclein (α-syn). α-Syn is highly susceptible to DiY formation by UV light irradiation. DiY-crosslinked soluble α-syn inhibits aggregation of unmodified α-syn. DiY crosslinking of α-syn fibrils stabilizes on-pathway aggregation seeds. DiY formation in α-syn has opposed effects on the pathogenic aggregation process.
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Affiliation(s)
- Michael M Wördehoff
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Hamed Shaykhalishahi
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Luca Groß
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Lothar Gremer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - Matthias Stoldt
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - Alexander K Buell
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.
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40
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Iljina M, Hong L, Horrocks MH, Ludtmann MH, Choi ML, Hughes CD, Ruggeri FS, Guilliams T, Buell AK, Lee JE, Gandhi S, Lee SF, Bryant CE, Vendruscolo M, Knowles TPJ, Dobson CM, De Genst E, Klenerman D. Nanobodies raised against monomeric ɑ-synuclein inhibit fibril formation and destabilize toxic oligomeric species. BMC Biol 2017; 15:57. [PMID: 28673288 PMCID: PMC5496350 DOI: 10.1186/s12915-017-0390-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/06/2017] [Indexed: 11/16/2022] Open
Abstract
Background The aggregation of the protein ɑ-synuclein (ɑS) underlies a range of increasingly common neurodegenerative disorders including Parkinson’s disease. One widely explored therapeutic strategy for these conditions is the use of antibodies to target aggregated ɑS, although a detailed molecular-level mechanism of the action of such species remains elusive. Here, we characterize ɑS aggregation in vitro in the presence of two ɑS-specific single-domain antibodies (nanobodies), NbSyn2 and NbSyn87, which bind to the highly accessible C-terminal region of ɑS. Results We show that both nanobodies inhibit the formation of ɑS fibrils. Furthermore, using single-molecule fluorescence techniques, we demonstrate that nanobody binding promotes a rapid conformational conversion from more stable oligomers to less stable oligomers of ɑS, leading to a dramatic reduction in oligomer-induced cellular toxicity. Conclusions The results indicate a novel mechanism by which diseases associated with protein aggregation can be inhibited, and suggest that NbSyn2 and NbSyn87 could have significant therapeutic potential. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0390-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marija Iljina
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Liu Hong
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing, 100084, China
| | - Mathew H Horrocks
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Marthe H Ludtmann
- Department of Molecular Neuroscience, University College London, Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Minee L Choi
- Department of Molecular Neuroscience, University College London, Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Craig D Hughes
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Francesco S Ruggeri
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tim Guilliams
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Present address: Healx Ltd., St John's Innovation Centre, Cowley Road, Cambridge, CB4 0WS, UK
| | - Alexander K Buell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Present address: Institute of Physical Biology, University of Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Ji-Eun Lee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sonia Gandhi
- Department of Molecular Neuroscience, University College London, Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Clare E Bryant
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Erwin De Genst
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. .,Present address: Astra Zeneca, Innovative Medicines Discovery Sciences Unit 310, Darwin Building, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK.
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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41
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Dammers C, Schwarten M, Buell AK, Willbold D. Pyroglutamate-modified Aβ(3-42) affects aggregation kinetics of Aβ(1-42) by accelerating primary and secondary pathways. Chem Sci 2017; 8:4996-5004. [PMID: 28970886 PMCID: PMC5612032 DOI: 10.1039/c6sc04797a] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 05/03/2017] [Indexed: 12/14/2022] Open
Abstract
The aggregation into amyloid fibrils of amyloid-β (Aβ) peptides is a hallmark of Alzheimer's disease. A variety of Aβ peptides have been discovered in vivo, with pyroglutamate-modified Aβ (pEAβ) forming a significant proportion. pEAβ is mainly localized in the core of plaques, suggesting a possible role in inducing and facilitating Aβ oligomerization and accumulation. Despite this potential importance, the aggregation mechanism of pEAβ and its influence on the aggregation kinetics of other Aβ variants have not yet been elucidated. Here we show that pEAβ(3-42) forms fibrils much faster than Aβ(1-42) and the critical concentration above which aggregation was observed was drastically decreased by one order of magnitude compared to Aβ(1-42). We elucidated the co-aggregation mechanism of Aβ(1-42) with pEAβ(3-42). At concentrations at which both species do not aggregate as homofibrils, mixtures of pEAβ(3-42) and Aβ(1-42) aggregate, suggesting the formation of mixed nuclei. We show that the presence of pEAβ(3-42) monomers increases the rate of primary nucleation of Aβ(1-42) and that fibrils of pEAβ(3-42) serve as highly efficient templates for elongation and catalytic surfaces for secondary nucleation of Aβ(1-42). On the other hand, the addition of Aβ(1-42) monomers drastically decelerates the primary and secondary nucleation of pEAβ(3-42) while not altering the pEAβ(3-42) elongation rate. In addition, even moderate concentrations of fibrillar Aβ(1-42) prevent pEAβ(3-42) aggregation, likely due to non-reactive binding of pEAβ(3-42) monomers to the surfaces of Aβ(1-42) fibrils. Thus, pEAβ(3-42) accelerates aggregation of Aβ(1-42) by affecting all individual reaction steps of the aggregation process while Aβ(1-42) dramatically slows down the primary and secondary nucleation of pEAβ(3-42).
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Affiliation(s)
- C Dammers
- Institute of Complex Systems (ICS-6) Structural Biochemistry , Forschungszentrum Jülich , 52425 Jülich , Germany .
| | - M Schwarten
- Institute of Complex Systems (ICS-6) Structural Biochemistry , Forschungszentrum Jülich , 52425 Jülich , Germany .
| | - A K Buell
- Institut für Physikalische Biologie , Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf , Germany
| | - D Willbold
- Institute of Complex Systems (ICS-6) Structural Biochemistry , Forschungszentrum Jülich , 52425 Jülich , Germany .
- Institut für Physikalische Biologie , Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf , Germany
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Affiliation(s)
- Ricardo Gaspar
- a Department of Physical-Chemistry and.,b Department of Biochemistry and Structural Biology , Lund University , Sweden
| | - Georg Meisl
- c Department of Chemistry , University of Cambridge , Cambridge , UK
| | - Alexander K Buell
- c Department of Chemistry , University of Cambridge , Cambridge , UK.,d Institute of Physical Biology, University of Düsseldorf , Düsseldorf , Germany , and
| | - Laurence Young
- e Department of Chemical Engineering and Biotechnology , University of Cambridge , Cambridge , UK
| | - Clemens F Kaminski
- e Department of Chemical Engineering and Biotechnology , University of Cambridge , Cambridge , UK
| | | | | | - Sara Linse
- b Department of Biochemistry and Structural Biology , Lund University , Sweden
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Buell AK. The Nucleation of Protein Aggregates - From Crystals to Amyloid Fibrils. International Review of Cell and Molecular Biology 2017; 329:187-226. [DOI: 10.1016/bs.ircmb.2016.08.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Šarić A, Buell AK, Meisl G, Michaels TCT, Dobson CM, Linse S, Knowles TPJ, Frenkel D. Physical determinants of the self-replication of protein fibrils. Nat Phys 2016; 12:874-880. [PMID: 31031819 PMCID: PMC6485595 DOI: 10.1038/nphys3828] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The ability of biological molecules to replicate themselves, achieved with the aid of a complex cellular machinery, is the foundation of life. However, a range of aberrant processes involve the self-replication of pathological protein structures without any additional factors. A dramatic example is the autocatalytic replication of pathological protein aggregates, including amyloid fibrils and prions, involved in neurodegenerative disorders. Here, we use computer simulations to identify the necessary requirements for the self-replication of fibrillar assemblies of proteins. We establish that a key physical determinant for this process is the affinity of proteins for the surfaces of fibrils. We find that self-replication can only take place in a very narrow regime of inter-protein interactions, implying a high level of sensitivity to system parameters and experimental conditions. We then compare our theoretical predictions with kinetic and biosensor measurements of fibrils formed from the Aβ peptide associated with Alzheimer's disease. Our results show a quantitative connection between the kinetics of self-replication and the surface coverage of fibrils by monomeric proteins. These findings reveal the fundamental physical requirements for the formation of supra-molecular structures able to replicate themselves, and shed light on mechanisms in play in the proliferation of protein aggregates in nature.
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Affiliation(s)
- Anđela Šarić
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK
| | - Alexander K Buell
- Institute of Physical Biology, University of Duesseldorf, Duesseldorf Germany
| | - Georg Meisl
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | | | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | | | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Cambridge, UK
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Zhang Y, Buell AK, Müller T, De Genst E, Benesch J, Dobson CM, Knowles TPJ. Protein Aggregate-Ligand Binding Assays Based on Microfluidic Diffusional Separation. Chembiochem 2016; 17:1920-1924. [DOI: 10.1002/cbic.201600384] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Yingbo Zhang
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Alexander K. Buell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Institute of Physical Biology; University of Düsseldorf; Universitätsstrasse 1 40225 Düsseldorf Germany
| | - Thomas Müller
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Fluidic Analytics Ltd; Unit 5 Chesterton Mill; French's Road Cambridge CB4 3NP UK
| | - Erwin De Genst
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- AstraZeneca; Innovative Medicines, Discovery Sciences; Cambridge Science Park Milton Road Cambridge CB4 0WG UK
| | - Justin Benesch
- Department of Chemistry; Physical and Theoretical Chemistry Laboratory; University of Oxford; South Parks Road Oxford OX3 1QZ UK
| | - Christopher M. Dobson
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Tuomas P. J. Knowles
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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Mason TO, Michaels TCT, Levin A, Gazit E, Dobson CM, Buell AK, Knowles TPJ. Synthesis of Nonequilibrium Supramolecular Peptide Polymers on a Microfluidic Platform. J Am Chem Soc 2016; 138:9589-96. [PMID: 27387359 DOI: 10.1021/jacs.6b04136] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The self-assembly of peptides and peptide mimetics into supramolecular polymers has been established in recent years as a route to biocompatible nanomaterials with novel mechanical, optical, and electronic properties. The morphologies of the resulting polymers are usually dictated by the strengths as well as lifetimes of the noncovalent bonds that lead to the formation of the structures. Together with an often incomplete understanding of the assembly mechanisms, these factors limit the control over the formation of polymers with tailored structures. Here, we have developed a microfluidic flow reactor to measure growth rates directly and accurately on the axial and radial faces of crystalline peptide supramolecular polymers. We show that the structures grow through two-dimensional nucleation mechanisms, with rates that depend exponentially on the concentration of soluble peptide. Using these mechanistic insights into the growth behavior of the axial and radial faces, we have been able to tune the aspect ratio of populations of dipeptide assemblies. These results demonstrate a general strategy to control kinetically self-assembly beyond thermodynamic products governed by the intrinsic properties of the building blocks in order to attain the required morphology and function.
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Affiliation(s)
- Thomas O Mason
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Thomas C T Michaels
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Aviad Levin
- Department for Molecular Microbiology and Biotechnology, University of Tel Aviv , Tel Aviv 6997801, Israel
| | - Ehud Gazit
- Department for Molecular Microbiology and Biotechnology, University of Tel Aviv , Tel Aviv 6997801, Israel.,Department of Materials Science and Engineering, Tel Aviv University , Tel Aviv 6997801, Israel
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Alexander K Buell
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom.,Institute of Physical Biology, Heinrich-Heine-University Düsseldorf , Düsseldorf 40225, Germany
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
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Wolff M, Mittag JJ, Herling TW, Genst ED, Dobson CM, Knowles TPJ, Braun D, Buell AK. Quantitative thermophoretic study of disease-related protein aggregates. Sci Rep 2016; 6:22829. [PMID: 26984748 PMCID: PMC4794802 DOI: 10.1038/srep22829] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/22/2016] [Indexed: 01/03/2023] Open
Abstract
Amyloid fibrils are a hallmark of a range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. A detailed understanding of the physico-chemical properties of the different aggregated forms of proteins, and of their interactions with other compounds of diagnostic or therapeutic interest, is crucial for devising effective strategies against such diseases. Protein aggregates are situated at the boundary between soluble and insoluble structures, and are challenging to study because classical biophysical techniques, such as scattering, spectroscopic and calorimetric methods, are not well adapted for their study. Here we present a detailed characterization of the thermophoretic behavior of different forms of the protein α-synuclein, whose aggregation is associated with Parkinson's disease. Thermophoresis is the directed net diffusional flux of molecules and colloidal particles in a temperature gradient. Because of their low volume requirements and rapidity, analytical methods based on this effect have considerable potential for high throughput screening for drug discovery. In this paper we rationalize and describe in quantitative terms the thermophoretic behavior of monomeric, oligomeric and fibrillar forms of α-synuclein. Furthermore, we demonstrate that microscale thermophoresis (MST) is a valuable method for screening for ligands and binding partners of even such highly challenging samples as supramolecular protein aggregates.
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Affiliation(s)
- Manuel Wolff
- Systems Biophysics, Physics Department, Nanosystems Initiative Munich and Center for NanoScience, Ludwig-Maximilians-Universität München, Amalienstr. 54, 80799 München, Germany
| | - Judith J Mittag
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig Maximilians University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Therese W Herling
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Erwin De Genst
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Dieter Braun
- Systems Biophysics, Physics Department, Nanosystems Initiative Munich and Center for NanoScience, Ludwig-Maximilians-Universität München, Amalienstr. 54, 80799 München, Germany
| | - Alexander K Buell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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Michaels TCT, Yde P, Willis JCW, Jensen MH, Otzen D, Dobson CM, Buell AK, Knowles TPJ. The length distribution of frangible biofilaments. J Chem Phys 2015; 143:164901. [DOI: 10.1063/1.4933230] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Thomas C. T. Michaels
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Pernille Yde
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Julian C. W. Willis
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Mogens H. Jensen
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Daniel Otzen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Center for Insoluble Protein Structures, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Alexander K. Buell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Galvagnion C, Buell AK. [Fundamental mechanisms of amyloid fibril formation by alpha-synuclein in Parkinson's disease: quantitative modelling]. Med Sci (Paris) 2015; 31:597-600. [PMID: 26152159 DOI: 10.1051/medsci/20153106008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Céline Galvagnion
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, Royaume-Uni
| | - Alexander K Buell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, Royaume-Uni
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Galvagnion C, Buell AK, Meisl G, Michaels TCT, Vendruscolo M, Knowles TPJ, Dobson CM. Lipid vesicles trigger α-synuclein aggregation by stimulating primary nucleation. Nat Chem Biol 2015; 11:229-34. [PMID: 25643172 DOI: 10.1038/nchembio.1750] [Citation(s) in RCA: 439] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 12/17/2014] [Indexed: 12/24/2022]
Abstract
α-Synuclein (α-syn) is a 140-residue intrinsically disordered protein that is involved in neuronal and synaptic vesicle plasticity, but its aggregation to form amyloid fibrils is the hallmark of Parkinson's disease (PD). The interaction between α-syn and lipid surfaces is believed to be a key feature for mediation of its normal function, but under other circumstances it is able to modulate amyloid fibril formation. Using a combination of experimental and theoretical approaches, we identify the mechanism through which facile aggregation of α-syn is induced under conditions where it binds a lipid bilayer, and we show that the rate of primary nucleation can be enhanced by three orders of magnitude or more under such conditions. These results reveal the key role that membrane interactions can have in triggering conversion of α-syn from its soluble state to the aggregated state that is associated with neurodegeneration and to its associated disease states.
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Affiliation(s)
| | | | - Georg Meisl
- Department of Chemistry, University of Cambridge, Cambridge, UK
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